+
+
OTHER
+
PARTIAL
-
Evidence
-
+ doi:10.3389/fmicb.2023.1078333
-
-
+ twelve isolates were identified as Bradyrhizobium pachyrhizi
+ Abstract species assignment; Results tree comparisons and strain names are inconsistent, so exact strain-to-species mapping remains unresolved.
+
-
"Based on the phylogenetic analysis of 16S rRNA and four house-keeping genes (atpD, recA, rpoB, glnII), twelve isolates were identified as Bradyrhizobium pachyrhizi, four as Ochrobactrum anthropic, three as Rhizobium selenitireducens and one as Rhizobium pisi"
+
+
+
OTHER
+
PARTIAL
-
-
-
+ V V -reducing enrichments indicated that bacteria associated with Polaromonas
+ External-system context only; no evidence of occurrence or vanadium reduction at this record’s Panzhihua sampling site.
+
-
"effective rhizobia strains for bioremediation of VTM tailings or other contaminated soils"
+
-
-
-
-
-
-
Ochrobactrum intermedium (13 isolates from bulk tailings, 4 from nodules) provides metabolic flexibility and exceptional metal tolerance to the V-Ti tailings microbiome. This alphaproteobacterium bridges multiple ecological functions including aerobic respiration, potential denitrification, metal reduction (Cr(VI), potentially V(V)), and plant growth promotion through IAA, siderophore, and ACC deaminase production. Ochrobactrum exhibits extraordinary resistance to multiple metals (Cd, Pb, Zn, Cu, Ni, Co, Cr) through diverse mechanisms including efflux systems, intracellular sequestration, and biosorption. Some Ochrobactrum strains can form nodule-like structures with legumes, though with lower nitrogen-fixing efficiency than true rhizobia, suggesting potential auxiliary roles in plant-microbe partnerships. The organism contributes to overall community metal detoxification and stress mitigation, working alongside Bradyrhizobium and Bacillus to create a multi-functional bioremediation consortium. Ochrobactrum represents a metabolic generalist that enhances community resilience through functional overlap and stress tolerance.
-
-
-
-
Source Taxon: Ochrobactrum intermedium
-
-
-
-
Target Taxon: Bradyrhizobium pachyrhizi
-
-
-
-
Metabolites:
-
- indole-3-acetic acid
- (CHEBI:16411 ),
-
- copper(2+)
- (CHEBI:29036 )
-
-
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ How should the positive Pongamia soil-carbon response be represented with the correct community identity?
+
+
PMID38744211 reports significant increases in ROC, POC, DOC and MBC, three carbon-transformation enzyme measures, and carbon degradation/fixation/methane-oxidation gene abundance after long-term Pongamia remediation. This positive aggregate result is retained here, not discarded as merely hypothetical. SEM supports an inferred community-level pathway, not Bacillus-to-Bradyrhizobium commensalism or a reciprocal nitrogen/carbon feedback connecting different studies. The former DOC metabolite was incorrectly grounded as carbon dioxide. A graph node needs a correctly scoped community and source-resolved participants; converting this composite record to implicit all-member activity would falsely include Polaromonas. Authorized full text and identity repair precede new topology.
+
Attaches to: ecological_interactions#Pongamia Nodulation and Nitrogen-Enrichment Phenotypes, ecological_interactions#Metal Tolerance of Cultured Tailings Bacillus
-
Biological Processes:
-
-
- cellular response to metal ion
- (GO:0071248 )
-
+
+ 2 evidence item(s)
-
+
+
+
IN_VIVO
+
SUPPORT
+
PMID:38744211
-
Evidence
-
-
-
-
+ four soil active organic carbon components (ROC, POC, DOC, and MBC)
+ Positive aggregate carbon result in a separate remediation study; does not resolve the proposed bacterial pair.
+
-
"pumilus, followed by Rhizobium sp. (29 isolates) and Ochrobactrum intermedium (13 isolates)"
+
+
+
COMPUTATIONAL
+
PARTIAL
-
-
-
- "Based on the phylogenetic analysis of 16S rRNA and four house-keeping genes (atpD, recA, rpoB, glnII), twelve isolates were identified as Bradyrhizobium pachyrhizi, four as Ochrobactrum anthropic, three as Rhizobium selenitireducens and one as Rhizobium pisi"
+
+
The abundance of carbon transformation functional genes such as carbon degradation, carbon fixation, and methane oxidation were also significantly
+
Gene-abundance changes are not measured pathway flux or a demonstrated nitrogen-to-carbon feedback.
+
-
+
-
-
-
-
-
@@ -1833,32 +1540,16 @@
Evidence
(function() {
var intId = "interaction:0";
- var intType = "MUTUALISM";
+ var intType = "UNKNOWN";
var metabolites = [];
-
- metabolites.push("nitrogen");
-
- metabolites.push("ammonia");
-
- metabolites.push("indole-3-acetic acid");
-
-
var processes = [];
-
- processes.push("nitrogen fixation");
-
- processes.push("symbiotic process");
-
- processes.push("root nodulation");
-
-
- var evidenceCount = 2;
+ var evidenceCount = 4;
nodes.push({
id: intId,
- label: "Nitrogen Fixation and Plant Growth Promotion",
+ label: "Pongamia Nodulation and Nitrogen-Enrichment Phenotypes",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1878,36 +1569,16 @@
Evidence
(function() {
var intId = "interaction:1";
- var intType = "MUTUALISM";
+ var intType = "UNKNOWN";
var metabolites = [];
-
- metabolites.push("copper(2+)");
-
- metabolites.push("nickel(2+)");
-
- metabolites.push("manganese(2+)");
-
- metabolites.push("zinc(2+)");
-
- metabolites.push("1-aminocyclopropane-1-carboxylate");
-
-
var processes = [];
-
- processes.push("response to metal ion");
-
- processes.push("cellular detoxification");
-
- processes.push("metal ion transport");
-
-
- var evidenceCount = 2;
+ var evidenceCount = 1;
nodes.push({
id: intId,
- label: "Metal Phytoextraction and Plant-Microbe Metal Tolerance",
+ label: "Metal Tolerance of Cultured Tailings Bacillus",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1916,7 +1587,7 @@
Evidence
});
- var srcKey = "Bradyrhizobium pachyrhizi";
+ var srcKey = "Bacillus species";
if (taxonNodeIds[srcKey]) {
links.push({ source: taxonNodeIds[srcKey], target: intId });
}
@@ -1927,163 +1598,16 @@
Evidence
(function() {
var intId = "interaction:2";
- var intType = "CROSS_FEEDING";
- var metabolites = [];
-
-
- metabolites.push("vanadate");
-
- metabolites.push("vanadyl cation");
-
- metabolites.push("lactate");
-
- metabolites.push("acetate");
-
-
- var processes = [];
-
-
- processes.push("dissimilatory reduction");
-
- processes.push("cellular detoxification");
-
-
- var evidenceCount = 2;
-
- nodes.push({
- id: intId,
- label: "Dissimilatory Vanadium Reduction and Immobilization",
- type: "interaction",
- interactionType: intType,
- metabolites: metabolites,
- processes: processes,
- evidenceCount: evidenceCount
- });
-
-
- var srcKey = "Polaromonas species";
- if (taxonNodeIds[srcKey]) {
- links.push({ source: taxonNodeIds[srcKey], target: intId });
- }
-
-
-
- })();
-
- (function() {
- var intId = "interaction:3";
- var intType = "COMMENSALISM";
+ var intType = "UNKNOWN";
var metabolites = [];
-
- metabolites.push("dissolved organic carbon");
-
- metabolites.push("cellulose");
-
-
var processes = [];
-
- processes.push("carbon utilization");
-
- processes.push("cellular carbohydrate metabolic process");
-
-
var evidenceCount = 3;
nodes.push({
id: intId,
- label: "Soil Organic Carbon Transformation",
- type: "interaction",
- interactionType: intType,
- metabolites: metabolites,
- processes: processes,
- evidenceCount: evidenceCount
- });
-
-
- var srcKey = "Bacillus species";
- if (taxonNodeIds[srcKey]) {
- links.push({ source: taxonNodeIds[srcKey], target: intId });
- }
-
-
-
- var tgtKey = "Bradyrhizobium pachyrhizi";
- if (taxonNodeIds[tgtKey]) {
- links.push({ source: intId, target: taxonNodeIds[tgtKey] });
- }
-
- })();
-
- (function() {
- var intId = "interaction:4";
- var intType = "MUTUALISM";
- var metabolites = [];
-
-
- metabolites.push("nitrogen");
-
- metabolites.push("ammonia");
-
-
- var processes = [];
-
-
- processes.push("nitrogen fixation");
-
- processes.push("symbiotic process");
-
-
- var evidenceCount = 2;
-
- nodes.push({
- id: intId,
- label: "Rhizobial Functional Redundancy in Nitrogen Fixation",
- type: "interaction",
- interactionType: intType,
- metabolites: metabolites,
- processes: processes,
- evidenceCount: evidenceCount
- });
-
-
- var srcKey = "Rhizobium selenitireducens";
- if (taxonNodeIds[srcKey]) {
- links.push({ source: taxonNodeIds[srcKey], target: intId });
- }
-
-
-
- var tgtKey = "Rhizobium pisi";
- if (taxonNodeIds[tgtKey]) {
- links.push({ source: intId, target: taxonNodeIds[tgtKey] });
- }
-
- })();
-
- (function() {
- var intId = "interaction:5";
- var intType = "CROSS_FEEDING";
- var metabolites = [];
-
-
- metabolites.push("indole-3-acetic acid");
-
- metabolites.push("copper(2+)");
-
-
- var processes = [];
-
-
- processes.push("cellular response to metal ion");
-
-
- var evidenceCount = 2;
-
- nodes.push({
- id: intId,
- label: "Ochrobactrum Metal Tolerance and Metabolic Flexibility",
+ label: "Ochrobactrum Isolate Growth-Promoter Production",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -2099,11 +1623,6 @@
Evidence
- var tgtKey = "Bradyrhizobium pachyrhizi";
- if (taxonNodeIds[tgtKey]) {
- links.push({ source: intId, target: taxonNodeIds[tgtKey] });
- }
-
})();
@@ -2125,7 +1644,7 @@
Evidence
var svg = d3.select("#network-svg");
var width = container.clientWidth - 32;
// Dynamic height based on node count: minimum 500px, add 40px per node
- var nodeCount = 12;
+ var nodeCount = 9;
var height = Math.max(500, 400 + nodeCount * 20);
svg.attr("width", width).attr("height", height);
diff --git a/docs/communities/Parachlorella_Saccharomyces_Mutualistic_Coculture.html b/docs/communities/Parachlorella_Saccharomyces_Mutualistic_Coculture.html
index 26d182f12..bf34ab6bb 100644
--- a/docs/communities/Parachlorella_Saccharomyces_Mutualistic_Coculture.html
+++ b/docs/communities/Parachlorella_Saccharomyces_Mutualistic_Coculture.html
@@ -560,7 +560,7 @@
Ecological Interactions
Ecological interaction network for Parachlorella kessleri + Saccharomyces cerevisiae Mutualistic Co-culture
- Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction (cross-feeding, mutualism).
+ Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction.
@@ -568,13 +568,8 @@
Ecological Interactions
-
-
@@ -582,10 +577,9 @@
Ecological Interactions
-
The microalga and yeast establish a mutualistic relationship based on reciprocal exchange of oxygen and carbon dioxide, offering a strategy to overcome productivity limits caused by the slow growth of the microalga.
+
HYPOTHESIZED - Reciprocal oxygen/carbon dioxide exchange is proposed as a basis for microalga-yeast association. In the accessible PMID42217804 abstract, this is introductory context rather than an exact-system gas-flux or mediator-perturbation result. Preserve it as a mechanistic hypothesis for P. kessleri and S. cerevisiae, not demonstrated bidirectional flux or reciprocal fitness benefit.
Source Taxon: Parachlorella kessleri
@@ -616,9 +610,8 @@
Reciprocal oxygen/carbon dioxide gas exchange
Downstream Effects:
-
→ Fourfold Microalgal Biomass and Lipid Increase
-
Reciprocal O2/CO2 exchange helps the coculture overcome microalgal productivity limits and contributes to the higher biomass and lipid production measured in coculture.
-
+
→ Fourfold Coculture Biomass and Lipid Increase
+
HYPOTHESIZED - Photosynthetic oxygen and respiratory carbon dioxide exchange could support coculture productivity. The accessible abstract does not isolate the contribution of gas exchange to the observed fourfold biomass/lipid increase.
@@ -634,7 +627,7 @@
Evidence
PMID:42217804
- - SUPPORT (IN_VITRO)
+ - PARTIAL (OTHER)
"Microalgae and yeasts can establish a mutualistic relationship based on reciprocal oxygen/carbon dioxide exchange, offering a strategy to overcome productivity limits caused by the slow growth of microalgae."
@@ -648,9 +641,8 @@
Evidence
-
Yeast sustained microalgal growth during the transition to phototrophy after glucose depletion (day 6) and promoted lipid accumulation through nutrient competition.
+
The abstract reports that yeast sustained microalgal growth during the transition to phototrophy after glucose depletion on day 6 and promoted lipid accumulation through nutrient competition. Preserve these reported positive physiological effects without interpreting nutrient competition as a demonstrated reciprocal benefit or specifying an unmeasured exchanged nutrient. Full-text comparisons and the fraction of productivity mediated by each process remain uninspected.
Source Taxon: Saccharomyces cerevisiae
@@ -686,9 +678,8 @@
Yeast support of microalgal growth and lipid accumulation
Downstream Effects:
-
→ Fourfold Microalgal Biomass and Lipid Increase
-
Yeast sustains microalgal growth after glucose depletion and promotes lipid accumulation, directly supporting the coculture biomass and lipid endpoint.
-
+
→ Fourfold Coculture Biomass and Lipid Increase
+
PARTIAL - Yeast-associated maintenance of algal growth and nutrient-competition-associated lipid accumulation provide the reported physiological contribution to higher coculture biomass/lipid production. This does not apportion the fourfold endpoint among growth support, gas exchange and other mechanisms.
@@ -717,10 +708,9 @@
Evidence
-
Despite prolonged nutrient limitation, yeast viability remained above 68%, indicating possible metabolic support from microalgae via exopolysaccharide (EPS)-derived molecules; FluidFM revealed stronger and longer microalga-yeast interactions linked to enhanced EPS production in co-culture.
+
HYPOTHESIZED - Yeast viability remained above 68% during approximately 8 days of nutrient limitation, which the authors interpret as possible metabolic support by microalgal EPS-derived molecules. AFM showed visible EPS and cell-surface changes, and FluidFM found stronger, longer cell interactions, likely associated with EPS. These positive viability and biophysical observations do not by themselves demonstrate EPS-carbon uptake, donor-to-recipient transfer or dependence of yeast survival on EPS.
Source Taxon: Parachlorella kessleri
@@ -754,7 +744,7 @@
Evidence
PMID:42217804
- - SUPPORT (IN_VITRO)
+ - PARTIAL (IN_VITRO)
"yeast viability remained above 68%, indicating possible metabolic support from microalgae via exopolysaccharides (EPS) - derived molecules"
@@ -767,28 +757,14 @@
Evidence
-
The Parachlorella-Saccharomyces coculture increased biomass and lipid production fourfold relative to the microalgal monoculture, integrating gas exchange and yeast-supported phototrophic growth into the target lipid-productivity phenotype.
-
-
-
+
Under coculture conditions, biomass and lipid production increased fourfold relative to microalgal monoculture grown in BBM + NO3 medium. This is a positive culture-level productivity comparison. The accessible abstract does not establish that the entire biomass increase is microalgal, quantify each species contribution, or isolate gas exchange or EPS transfer as the cause. It does not demonstrate reciprocal benefit solely from increased bulk output.
-
Metabolites:
-
- oxygen
- (CHEBI:15379 ),
-
- carbon dioxide
- (CHEBI:16526 )
-
@@ -838,6 +814,60 @@
Evidence
+
+ Knowledge gaps & discussions (1)
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which measured gas, EPS and physical-interaction changes mediate the positive productivity and viability responses?
+
+
Keep positive coculture productivity and yeast-associated algal support distinct from proposed gas and EPS mechanisms. Stronger/longer cell adhesion and visible EPS are not themselves metabolite transfer. Full text, controls and taxon-resolved measurements remain uninspected. A one-community Edison causal dry run prepares possible separately evidenced biophysical structure; no paid report has been generated or used to add topology.
+
+
Attaches to: ecological_interactions#Proposed Reciprocal Oxygen and Carbon Dioxide Exchange, ecological_interactions#Yeast support of microalgal growth and lipid accumulation, ecological_interactions#Proposed EPS-Derived Metabolic Support of Yeast, ecological_interactions#Fourfold Coculture Biomass and Lipid Increase
+
+
+
+
+ 2 evidence item(s)
+
+
+
+
Yeast sustained microalgal growth during the transition to phototrophy after glucose depletion (day 6) and promoted lipid accumulation through nutrient competition.
+
Yeast supports microalgal growth and drives lipid accumulation via nutrient competition.
+
+
+
yeast viability remained above 68%, indicating possible metabolic support from microalgae via exopolysaccharides (EPS) - derived molecules
+
Positive viability observation supports a proposed EPS mechanism, not directly traced carbon transfer or demonstrated necessity.
+
+
+
+
@@ -997,7 +1027,7 @@
Evidence
(function() {
var intId = "interaction:0";
- var intType = "MUTUALISM";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1012,7 +1042,7 @@
Evidence
nodes.push({
id: intId,
- label: "Reciprocal oxygen/carbon dioxide gas exchange",
+ label: "Proposed Reciprocal Oxygen and Carbon Dioxide Exchange",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1037,7 +1067,7 @@
Evidence
(function() {
var intId = "interaction:1";
- var intType = "MUTUALISM";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
@@ -1077,7 +1107,7 @@
Evidence
(function() {
var intId = "interaction:2";
- var intType = "CROSS_FEEDING";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1090,7 +1120,7 @@
Evidence
nodes.push({
id: intId,
- label: "EPS-mediated metabolic support of yeast by microalgae",
+ label: "Proposed EPS-Derived Metabolic Support of Yeast",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1115,15 +1145,9 @@
Evidence
(function() {
var intId = "interaction:3";
- var intType = "MUTUALISM";
+ var intType = "UNKNOWN";
var metabolites = [];
-
- metabolites.push("oxygen");
-
- metabolites.push("carbon dioxide");
-
-
var processes = [];
@@ -1136,7 +1160,7 @@
Evidence
nodes.push({
id: intId,
- label: "Fourfold Microalgal Biomass and Lipid Increase",
+ label: "Fourfold Coculture Biomass and Lipid Increase",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
diff --git a/docs/communities/Parmigiano_NWS_Set2_LAB_Triculture.html b/docs/communities/Parmigiano_NWS_Set2_LAB_Triculture.html
index 612a73402..a4fb09d67 100644
--- a/docs/communities/Parmigiano_NWS_Set2_LAB_Triculture.html
+++ b/docs/communities/Parmigiano_NWS_Set2_LAB_Triculture.html
@@ -616,7 +616,7 @@
Ecological Interactions
-
The complete three-member LAB triculture increased maximum milk acidification rate and total lactic acid production relative to the monocultures and most pairwise co-cultures, supporting a positive mixed-culture effect during milk fermentation.
+
The set 2 LBB04/C001.27/C5I3 triculture produced higher total lactic acid than the tested monocultures and pairwise cultures. Maximum acidification rate was high, but the exact set 2 C001.27/C5I3 pair was comparable to the triculture, so the triculture was not uniquely superior on this rate readout. Total inoculum was held constant across compositions. These positive community fermentation phenotypes do not establish per-strain growth, reciprocal benefit or a specific molecular exchange.
@@ -652,16 +652,6 @@
Set 2 milk acidification enhancement
-
-
Downstream Effects:
-
-
-
→ C5I3 activity enhancement in mixed culture
-
Higher D-lactate in set 2 tricultures than in the corresponding C5I3 monoculture indicated that the Ld member remained viable and metabolically active in the mixed culture.
-
-
-
-
Evidence
@@ -693,6 +683,19 @@
Evidence
+
+
+
+ "co-cultivation of St strain C001.27 with Ld strain C5I3 resulted in μmax values comparable to those observed under tri-culture conditions."
+
+
+
@@ -701,7 +704,7 @@
Evidence
-
In the set 2 pairwise subset, S. thermophilus C001.27 co-cultured with L. delbrueckii subsp. lactis C5I3 produced maximum acidification rates comparable with the complete triculture.
+
The C001.27/C5I3 pair had a higher maximum acidification rate than either corresponding monoculture, and in set 2 its rate was comparable to that of the triculture. This is a positive two-member fermentation phenotype, not proof that adding LBB04 preserves a pair-specific causal mechanism or that both members benefit equally. The study interprets D-lactate predominance as preferential L. delbrueckii activity; exchanged formate, folate and peptides were not directly resolved in this assay.
@@ -737,16 +740,6 @@
C001.27-C5I3 acidification enhancement
-
-
Downstream Effects:
-
-
-
→ Set 2 milk acidification enhancement
-
The strong St + Ld pairwise response was retained within the complete LBB04/C001.27/C5I3 triculture.
-
-
-
-
Evidence
@@ -773,7 +766,7 @@
Evidence
-
The L. helveticus LBB04 plus L. delbrueckii subsp. lactis C5I3 pairwise subset had weaker acidification than the matched C001.27/C5I3 co-culture and lower total lactic acid than tricultures and S. thermophilus-containing co-cultures in the set 2 lactate assay.
+
The LBB04/C5I3 pair showed lower maximum acidification rates than the corresponding monocultures and the C001.27/C5I3 pair. Its total lactic acid was also lower than the triculture and St-containing pairs, with D-lactate comprising 75.95% of the pair’s total lactate. Preserve this negative fermentation response without converting bulk acidification to a strain-specific growth-inhibition assay or claiming a measured antimicrobial or nutrient-competition mechanism.
@@ -840,15 +833,28 @@
Evidence
+
+
+
+ "co-inoculation of milk with Lh and Ld resulted in reduced acidification rates compared with the corresponding monocultures"
+
+
+
-
D-lactate measurements showed that the set 2 triculture accumulated more D-lactate than the C5I3 monoculture, consistent with L. delbrueckii subsp. lactis remaining viable and metabolically active in mixed culture.
+
At the end of fermentation, set 2 triculture D-lactate was significantly higher than in the C5I3 monoculture. This is a measured mixed-culture pool, consistent with L. delbrueckii metabolic activity but not exclusive C5I3 production or directly measured C5I3 cell growth. L. helveticus produces both enantiomers, and C001.27 monoculture was 83% L-lactate rather than exclusively L-lactate. Acidification and lactate are related readouts; an arrow from acidification to inferred member activity would reverse measurement and inference.
@@ -906,7 +912,7 @@
Evidence
- Knowledge gaps & discussions (1)
+ Knowledge gaps & discussions (2)
@@ -921,6 +927,41 @@
+
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which member-resolved processes explain the positive and negative fermentation responses?
+
+
Four measured phenotypes remain. Pair and triculture comparisons do not form a causal sequence, and higher D-lactate is an observation used to infer activity, not an outcome caused by measuring acidification. No new mediator arrows are justified by the full main text. Preserve previous #1077-1079 removal of unsupported mutualism, taxon roles and exclusive C5I3 attribution; the existing molecular-mechanism gap remains open.
+
+
Attaches to: ecological_interactions#Set 2 milk acidification enhancement, ecological_interactions#C001.27-C5I3 acidification enhancement, ecological_interactions#LBB04-C5I3 reduced acidification subset, ecological_interactions#Set 2 Triculture D-Lactate Accumulation
+
+
+
+
+ 1 evidence item(s)
+
+
+
+
co-cultivation of St strain C001.27 with Ld strain C5I3 resulted in μmax values comparable to those observed under tri-culture conditions.
+
Exact set 2 exception to a uniquely highest triculture rate.
+
+
+
@@ -1206,7 +1247,7 @@
Evidence
processes.push("interspecies interaction between organisms");
- var evidenceCount = 2;
+ var evidenceCount = 3;
nodes.push({
id: intId,
@@ -1279,7 +1320,7 @@
Evidence
processes.push("interspecies interaction between organisms");
- var evidenceCount = 2;
+ var evidenceCount = 3;
nodes.push({
id: intId,
@@ -1328,7 +1369,7 @@
Evidence
nodes.push({
id: intId,
- label: "C5I3 activity enhancement in mixed culture",
+ label: "Set 2 Triculture D-Lactate Accumulation",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
diff --git a/docs/communities/Peanut_Seed_Bacterial_CS_SynCom.html b/docs/communities/Peanut_Seed_Bacterial_CS_SynCom.html
index 8fe1011e4..671d84780 100644
--- a/docs/communities/Peanut_Seed_Bacterial_CS_SynCom.html
+++ b/docs/communities/Peanut_Seed_Bacterial_CS_SynCom.html
@@ -527,143 +527,9 @@
Ecological Interactions
-
Conserved, growth-promoting, and combined synthetic communities of peanut seed bacteria were constructed from 16S rRNA profiles, strain isolation, and plant-growth-promotion indicator measurements.
-
-
-
-
-
-
-
-
-
-
Biological Processes:
-
-
-
- interspecies interaction between organisms
- (GO:0044419 )
-
-
-
-
-
-
-
-
Downstream Effects:
-
-
-
→ Dual Fungal Challenge Evaluation
-
The defined seed-bacterial SynComs were then challenged against peanut seed Aspergillus flavus contamination and Fusarium oxysporum seedling root rot.
-
-
-
-
-
→ CS Seedling Growth Promotion
-
The constructed seed-bacterial CS SynCom was evaluated for its ability to improve peanut seedling growth in parallel with fungal suppression.
-
-
-
-
-
-
-
-
Evidence
-
-
-
-
-
- "Potentially conserved microbial synthetic communities (C), growth-promoting synthetic communities (S), and combined synthetic communities (CS) of peanut seeds were constructed after 16S rRNA Illumina sequencing, strain isolation, and measurement of plant growth promotion indicators."
-
-
-
-
-
-
-
-
-
-
Peanut seed-bacterial SynComs were tested for control of seed aflatoxin contamination caused by Aspergillus flavus and root rot caused by Fusarium oxysporum.
-
-
-
-
-
-
-
-
-
-
Biological Processes:
-
-
-
- defense response to fungus
- (GO:0050832 )
-
-
-
-
-
-
-
-
Downstream Effects:
-
-
-
→ Salicylic-Acid Defense Activation
-
The Fusarium oxysporum seedling challenge showed the CS community's strongest root-rot protection and associated that phenotype with salicylic-acid-related induced resistance.
-
-
-
-
-
→ CS Aspergillus and Aflatoxin Suppression
-
The Aspergillus flavus seed challenge directly measured seed fungal reproduction and aflatoxin production after CS inoculation.
-
-
-
-
-
-
-
-
Evidence
-
-
-
-
-
-
-
The combined CS SynCom's root-rot protection in peanut seedlings was associated with increased defense enzyme activity and activation of salicylic-acid-related systemic induced resistance.
-
+
Peanut seedlings treated with the seed-bacterial synthetic communities showed increased defense-enzyme activity and an SA-related resistance response. The accessible abstract attributes protection to this host response. PARTIAL - The full-text controls for SA-pathway necessity, sufficiency and distal systemic signaling have not been inspected; marker/enzyme responses alone do not resolve those causal requirements.
@@ -698,8 +564,7 @@
Salicylic-Acid Defense Activation
→ CS Fusarium Root-Rot Resistance
-
Defense enzyme and salicylic-acid responses were the reported host defense axis underlying CS-mediated Fusarium root-rot resistance.
-
+
PARTIAL - The authors attribute increased root-rot resistance to higher defense-enzyme activity and SA-related induced resistance. Retain this reported causal direction, while noting that the accessible abstract does not expose pathway-blocking, rescue or distal-tissue controls needed to isolate SA mediation.
@@ -715,7 +580,7 @@
Evidence
PMID:38520150
- - SUPPORT (IN_VIVO)
+ - PARTIAL (IN_VIVO)
"This was achieved by increased defense enzyme activity and activated salicylic acid (SA)-related, systematically induced resistance in peanuts
@@ -731,8 +596,7 @@
Evidence
-
All three seed-bacterial SynCom designs resisted Fusarium oxysporum root rot in peanut seedlings, with the combined CS community producing the strongest protection.
-
+
All three seed-bacterial synthetic communities, C, S and CS, improved resistance to Fusarium oxysporum root rot after seedling inoculation, with CS showing the best effect in the reported comparison. Preserve this positive host-protection result; it does not identify the contribution of each member or prove that SA signaling is the sole mediator.
@@ -781,8 +645,7 @@
Evidence
-
The combined CS SynCom inhibited Aspergillus flavus reproduction on peanut seeds and reduced aflatoxin production, a seed-protection effect linked to bacterial toxin degradation and fungal mycelial disruption.
-
+
CS inhibited Aspergillus flavus reproduction on peanut seeds and reduced aflatoxin production. The authors relate these effects to bacterial toxin degradation and mycelial destruction. The positive suppression phenotype is supported, but the accessible abstract does not disclose toxin-fate measurements, degradation products, adsorption controls or member-resolved contributions. Lower toxin abundance is not by itself proof of chemical destruction, complete detoxification or field efficacy.
@@ -829,7 +692,7 @@
Evidence
PMID:38520150
- - SUPPORT (IN_VIVO)
+ - PARTIAL (IN_VIVO)
"These effects are related to bacterial degradation of toxins and destruction of mycelia"
@@ -842,10 +705,9 @@
-
In addition to helping peanut seeds and seedlings resist fungal invasion, inoculation with the seed-bacterial synthetic community promoted peanut seedling growth.
-
+
The abstract concludes that inoculation with a synthetic community composed of seed bacteria promotes peanut seedling growth. It does not give a CS-specific growth effect size or distinguish the contribution of C, S and CS to that conclusion. Preserve the reported positive outcome at its stated scope without assuming that disease protection, SA markers or toxin suppression caused the growth response.
@@ -894,6 +756,63 @@
Evidence
+
+ Knowledge gaps & discussions (1)
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which exact CS members and host or fungal mechanisms account for the reported protection?
+
+
Construction and challenge-evaluation steps are methods, not biological causal nodes, and their four workflow arrows are removed. Four positive biological outcomes remain, with the existing defense-to-resistance arrow explicitly partial. Authorized full text is needed to resolve SA necessity/systemic signaling, toxin fate versus abundance, composition and CS-specific growth attribution. No absence claim is made about unseen full-text experiments and no new causal structure is added.
+
+
Attaches to: ecological_interactions#SA-Related Defense Response and Proposed Resistance Mediation, ecological_interactions#CS Fusarium Root-Rot Resistance, ecological_interactions#CS Aspergillus and Aflatoxin Suppression, ecological_interactions#Reported Peanut Seedling Growth Promotion
+
+
+
+
+ 2 evidence item(s)
+
+
+
+
This was achieved by increased defense enzyme activity and activated salicylic acid (SA)-related, systematically induced resistance in peanuts
+
+
Author-reported defense response and resistance interpretation; pathway-necessity controls are not exposed in the accessible abstract.
+
+
+
CS also inhibited the reproduction of A. flavus on peanut seeds and the production of aflatoxin
+
+
Supports CS suppression of Aspergillus flavus reproduction and aflatoxin production on peanut seeds.
+
+
+
+
+
@@ -1030,62 +949,6 @@
Environmental Factors
var intType = "UNKNOWN";
var metabolites = [];
- var processes = [];
-
-
- processes.push("interspecies interaction between organisms");
-
-
- var evidenceCount = 1;
-
- nodes.push({
- id: intId,
- label: "Peanut Seed SynCom Construction",
- type: "interaction",
- interactionType: intType,
- metabolites: metabolites,
- processes: processes,
- evidenceCount: evidenceCount
- });
-
-
-
-
- })();
-
- (function() {
- var intId = "interaction:1";
- var intType = "UNKNOWN";
- var metabolites = [];
-
- var processes = [];
-
-
- processes.push("defense response to fungus");
-
-
- var evidenceCount = 1;
-
- nodes.push({
- id: intId,
- label: "Dual Fungal Challenge Evaluation",
- type: "interaction",
- interactionType: intType,
- metabolites: metabolites,
- processes: processes,
- evidenceCount: evidenceCount
- });
-
-
-
-
- })();
-
- (function() {
- var intId = "interaction:2";
- var intType = "UNKNOWN";
- var metabolites = [];
-
metabolites.push("salicylic acid");
@@ -1100,7 +963,7 @@
Environmental Factors
nodes.push({
id: intId,
- label: "Salicylic-Acid Defense Activation",
+ label: "SA-Related Defense Response and Proposed Resistance Mediation",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1114,7 +977,7 @@
Environmental Factors
})();
(function() {
- var intId = "interaction:3";
+ var intId = "interaction:1";
var intType = "UNKNOWN";
var metabolites = [];
@@ -1142,7 +1005,7 @@
Environmental Factors
})();
(function() {
- var intId = "interaction:4";
+ var intId = "interaction:2";
var intType = "UNKNOWN";
var metabolites = [];
@@ -1170,7 +1033,7 @@
Environmental Factors
})();
(function() {
- var intId = "interaction:5";
+ var intId = "interaction:3";
var intType = "UNKNOWN";
var metabolites = [];
@@ -1184,7 +1047,7 @@
Environmental Factors
nodes.push({
id: intId,
- label: "CS Seedling Growth Promotion",
+ label: "Reported Peanut Seedling Growth Promotion",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1216,7 +1079,7 @@
Environmental Factors
var svg = d3.select("#network-svg");
var width = container.clientWidth - 32;
// Dynamic height based on node count: minimum 500px, add 40px per node
- var nodeCount = 7;
+ var nodeCount = 5;
var height = Math.max(500, 400 + nodeCount * 20);
svg.attr("width", width).attr("height", height);
diff --git a/history/records/Panzhihua_Vanadium_Titanium_Tailings/2026-10-07T064410Z-codex-cbadb7.yaml b/history/records/Panzhihua_Vanadium_Titanium_Tailings/2026-10-07T064410Z-codex-cbadb7.yaml
new file mode 100644
index 000000000..ce5aeb08b
--- /dev/null
+++ b/history/records/Panzhihua_Vanadium_Titanium_Tailings/2026-10-07T064410Z-codex-cbadb7.yaml
@@ -0,0 +1,27 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Panzhihua_Vanadium_Titanium_Tailings.yaml
+ slug: Panzhihua_Vanadium_Titanium_Tailings
+session:
+ id: 2026-10-07T064410Z-codex-cbadb7
+ timestamp: '2026-10-07T06:44:10Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1676
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Preserve nodulation and plant nitrogen/growth with provisional species mapping
+ and no PP1 misassignment.; Preserve directly assayed Bacillus metal tolerance instead
+ of cross-species phytoextraction claims.; Preserve Ochrobactrum IAA/siderophore production
+ without nodule-isolate conflation or interbacterial transfer.
+ details: Source-based self-adversarial review. reports/causal_graph_review/decisions/20261007-four-records-batch82.yaml
diff --git a/history/records/Parachlorella_Saccharomyces_Mutualistic_Coculture/2026-10-07T064410Z-codex-f546b7.yaml b/history/records/Parachlorella_Saccharomyces_Mutualistic_Coculture/2026-10-07T064410Z-codex-f546b7.yaml
new file mode 100644
index 000000000..0bf14ead8
--- /dev/null
+++ b/history/records/Parachlorella_Saccharomyces_Mutualistic_Coculture/2026-10-07T064410Z-codex-f546b7.yaml
@@ -0,0 +1,27 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Parachlorella_Saccharomyces_Mutualistic_Coculture.yaml
+ slug: Parachlorella_Saccharomyces_Mutualistic_Coculture
+session:
+ id: 2026-10-07T064410Z-codex-f546b7
+ timestamp: '2026-10-07T06:44:10Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1677
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain gas-exchange hypothesis with contextual evidence and partial productivity
+ mediation.; Preserve reported yeast-associated growth/lipid physiology without reciprocal-benefit
+ inference.; Preserve yeast viability and physical observations while qualifying EPS transfer.;
+ Preserve fourfold culture-level output without unsupported algal-only attribution.
+ details: Source-based self-adversarial review. reports/causal_graph_review/decisions/20261007-four-records-batch82.yaml
diff --git a/history/records/Parmigiano_NWS_Set2_LAB_Triculture/2026-10-07T064410Z-codex-83f8ae.yaml b/history/records/Parmigiano_NWS_Set2_LAB_Triculture/2026-10-07T064410Z-codex-83f8ae.yaml
new file mode 100644
index 000000000..deed928a9
--- /dev/null
+++ b/history/records/Parmigiano_NWS_Set2_LAB_Triculture/2026-10-07T064410Z-codex-83f8ae.yaml
@@ -0,0 +1,27 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Parmigiano_NWS_Set2_LAB_Triculture.yaml
+ slug: Parmigiano_NWS_Set2_LAB_Triculture
+session:
+ id: 2026-10-07T064410Z-codex-83f8ae
+ timestamp: '2026-10-07T06:44:10Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1678
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Preserve triculture total-lactate advantage and the exact set2 rate exception.;
+ Preserve the positive St/Ld pair phenotype without a subset-to-triculture causal arrow.;
+ Preserve the negative Lh/Ld fermentation response without inventing its mechanism.; Represent
+ measured triculture D-lactate rather than exclusive C5I3 activity.
+ details: Source-based self-adversarial review. reports/causal_graph_review/decisions/20261007-four-records-batch82.yaml
diff --git a/history/records/Peanut_Seed_Bacterial_CS_SynCom/2026-10-07T064410Z-codex-0a3882.yaml b/history/records/Peanut_Seed_Bacterial_CS_SynCom/2026-10-07T064410Z-codex-0a3882.yaml
new file mode 100644
index 000000000..40bbcc483
--- /dev/null
+++ b/history/records/Peanut_Seed_Bacterial_CS_SynCom/2026-10-07T064410Z-codex-0a3882.yaml
@@ -0,0 +1,27 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Peanut_Seed_Bacterial_CS_SynCom.yaml
+ slug: Peanut_Seed_Bacterial_CS_SynCom
+session:
+ id: 2026-10-07T064410Z-codex-0a3882
+ timestamp: '2026-10-07T06:44:10Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1679
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain author-reported SA-defense direction with unresolved pathway controls.;
+ Preserve best-CS root-rot resistance without member-specific attribution.; Preserve fungal/toxin
+ suppression while separating abundance from chemical degradation.; Preserve reported growth
+ without unsupported CS-specific mediation.
+ details: Source-based self-adversarial review. reports/causal_graph_review/decisions/20261007-four-records-batch82.yaml
diff --git a/kb/communities/Panzhihua_Vanadium_Titanium_Tailings.yaml b/kb/communities/Panzhihua_Vanadium_Titanium_Tailings.yaml
index c126eebb7..3d09e0c43 100644
--- a/kb/communities/Panzhihua_Vanadium_Titanium_Tailings.yaml
+++ b/kb/communities/Panzhihua_Vanadium_Titanium_Tailings.yaml
@@ -296,420 +296,101 @@ taxonomy:
belonging to the family Burkholderiaceae, were potentially responsible for VV reduction
explanation: Establishes V(V) reduction mechanism relevant to Panzhihua conditions
ecological_interactions:
-- name: Nitrogen Fixation and Plant Growth Promotion
- description: 'Bradyrhizobium pachyrhizi and other rhizobia (Rhizobium selenitireducens, R. pisi) form
- root nodule symbioses with legumes (Pongamia pinnata, Leucaena leucocephala) in V-Ti tailings, fixing
- atmospheric nitrogen through the nitrogenase enzyme complex and converting it to ammonia available
- for plant uptake. The nitrogenase enzyme contains iron-molybdenum cofactor (FeMo-co), and interestingly
- can also utilize vanadium-iron cofactor (VFe-co), potentially enabling nitrogen fixation even under
- elevated vanadium concentrations. B. pachyrhizi strain PP1 demonstrates exceptional nitrogen-fixing
- capacity, increasing plant nitrogen content by 10-145% in aboveground parts and 13-79% in roots compared
- to uninoculated controls. This massive nitrogen enrichment overcomes the nitrogen-deficient conditions
- typical of mine tailings, enabling rapid plant establishment and biomass production. Rhizobia produce
- indoleacetic acid (IAA, 67% of isolates) that stimulates root growth, enhances lateral root formation,
- and improves nutrient acquisition. The symbiosis provides dual benefits: plants receive fixed nitrogen
- and growth hormones while rhizobia receive photosynthates and protected nodule environment. Nitrogen
- fixation rates are maintained even under heavy metal stress through rhizobial metal tolerance mechanisms,
- demonstrating the resilience of this partnership. Two-year in situ phytoremediation with P. pinnata
- effectively shifts microbial communities in V-Ti tailings toward rhizobia-dominated assemblages, creating
- self-sustaining nitrogen-enriched soil conditions.
-
- '
- interaction_type: MUTUALISM
+- name: Pongamia Nodulation and Nitrogen-Enrichment Phenotypes
+ description: Bradyrhizobium isolates from Pongamia pinnata nodules in Panzhihua tailings formed nodules and increased
+ plant nitrogen and growth in separate nitrogen-free vermiculite pot assays. Results identify PP76 and other
+ Bradyrhizobium isolates, while PP1 belongs to Rhizobium in the Results and must not be assigned to B. pachyrhizi.
+ The abstract assigns twelve isolates to B. pachyrhizi, but species-level trees and labels are inconsistent.
+ The canonical species endpoint therefore represents the authors provisional group assignment, not a verified
+ PP1 identity. These are positive inoculation phenotypes with nifH evidence, not a measured ammonium-transfer
+ flux, V-Fe nitrogenase demonstration, or mutualism between bacterial species. The same study also reports separate
+ metal-tolerance phenotypes for PP76 and other isolates; internal Cd/Zn inconsistencies preclude unqualified
+ metal-specific numerical assignments here.
scope: PAIRWISE
source_taxon:
preferred_term: Bradyrhizobium pachyrhizi
term:
id: NCBITaxon:280333
label: Bradyrhizobium pachyrhizi
- metabolites:
- - preferred_term: nitrogen
- term:
- id: CHEBI:17997
- label: dinitrogen
- notes: Atmospheric N2 fixed to ammonia
- - preferred_term: ammonia
- term:
- id: CHEBI:16134
- label: ammonia
- concentration: Increases plant N by 10-145% in shoots, 13-79% in roots
- - preferred_term: indole-3-acetic acid
- term:
- id: CHEBI:16411
- label: indole-3-acetic acid
- notes: Plant growth hormone produced by 67% of isolates
- biological_processes:
- - preferred_term: nitrogen fixation
- term:
- id: GO:0009399
- label: nitrogen fixation
- - preferred_term: symbiotic process
- term:
- id: GO:0044403
- label: biological process involved in symbiotic interaction
- - preferred_term: root nodulation
- term:
- id: GO:0009877
- label: nodulation
- downstream:
- - target: Soil Organic Carbon Transformation
- description: Nitrogen enrichment stimulates plant growth, increasing carbon input to soil
evidence:
- reference: doi:10.3389/fmicb.2023.1078333
supports: SUPPORT
evidence_source: IN_VIVO
- snippet: Based on the phylogenetic analysis of 16S rRNA and four house-keeping genes
- (atpD, recA, rpoB, glnII), twelve isolates were identified as Bradyrhizobium
- pachyrhizi, four as Ochrobactrum anthropic, three as Rhizobium selenitireducens
- and one as Rhizobium pisi
- explanation: Quantifies nitrogen fixation efficiency
+ snippet: only 11 strains built symbiotic relationships with P. pinnata.
+ explanation: Separate inoculation assays support nodulation; they do not demonstrate a mixed-rhizobia consortium.
- reference: doi:10.3389/fmicb.2023.1078333
- supports: SUPPORT
- evidence_source: IN_VIVO
- snippet: Based on the phylogenetic analysis of 16S rRNA and four house-keeping genes
- (atpD, recA, rpoB, glnII), twelve isolates were identified as Bradyrhizobium
- pachyrhizi, four as Ochrobactrum anthropic, three as Rhizobium selenitireducens
- and one as Rhizobium pisi
-- name: Metal Phytoextraction and Plant-Microbe Metal Tolerance
- description: 'Bradyrhizobium and other metal-tolerant rhizobia enhance plant uptake of heavy metals
- from V-Ti tailings while promoting plant growth and metal tolerance through multiple mechanisms. Bradyrhizobium
- liaoningense inoculation of Pongamia pinnata significantly increased plant uptake of copper by 603%
- and nickel by 576% from V-Ti magnetite tailings, transforming the plant-microbe system into an effective
- phytoextraction platform. Among 57 rhizobia isolates, 20 strains showed tolerance to Cu, Ni, Mn, and
- Zn, with strains PP1 and PP76 exhibiting high tolerance to all four metals. The phenotype of strong
- nitrogen-fixing capacity coincides with multi-metal resistance, enabling rhizobia to maintain symbiotic
- function even under 340 mg/kg vanadium and elevated concentrations of other metals. Metal tolerance
- mechanisms include: metal efflux pumps that export toxic ions, intracellular sequestration through
- metallothioneins and polyphosphate granules, extracellular polysaccharide production that chelates
- metals, and potential metal reduction pathways. Rhizobia produce ACC deaminase that cleaves plant
- ethylene precursor, reducing metal-induced stress responses and enabling plants to tolerate higher
- metal concentrations. The combination of enhanced metal uptake (via rhizobial promotion) and reduced
- phytotoxicity (via stress mitigation) creates a synergistic system for efficient metal phytoextraction
- from polymetallic V-Ti tailings.
-
- '
- interaction_type: MUTUALISM
- scope: PAIRWISE
- source_taxon:
- preferred_term: Bradyrhizobium pachyrhizi
- term:
- id: NCBITaxon:280333
- label: Bradyrhizobium pachyrhizi
- metabolites:
- - preferred_term: copper(2+)
- term:
- id: CHEBI:29036
- label: copper(2+)
- concentration: 127 mg/kg in tailings; 603% increase in plant uptake with rhizobia
- - preferred_term: nickel(2+)
- term:
- id: CHEBI:49786
- label: nickel(2+)
- concentration: 60 mg/kg in tailings; 576% increase in plant uptake with rhizobia
- - preferred_term: manganese(2+)
- term:
- id: CHEBI:29035
- label: manganese(2+)
- concentration: 1200 mg/kg in tailings
- - preferred_term: zinc(2+)
- term:
- id: CHEBI:29105
- label: zinc(2+)
- concentration: 155 mg/kg in tailings
- - preferred_term: 1-aminocyclopropane-1-carboxylate
- term:
- id: CHEBI:18053
- label: 1-aminocyclopropanecarboxylic acid
- notes: ACC deaminase cleaves ethylene precursor, reducing metal stress
- biological_processes:
- - preferred_term: response to metal ion
- term:
- id: GO:0010038
- label: response to metal ion
- - preferred_term: cellular detoxification
- term:
- id: GO:1990748
- label: cellular detoxification
- - preferred_term: metal ion transport
- term:
- id: GO:0030001
- label: metal ion transport
- evidence:
- - reference: doi:10.3389/fmicb.2018.01853
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: IN_VIVO
- snippet: leucocephala by reducing metal uptake by plants grown in heavy metal-polluted soils
- explanation: Quantifies dramatic metal phytoextraction enhancement
+ snippet: the nitrogen content of the plants’ aboveground parts and roots was 2.4–1.8 times that of the non-inoculation
+ control.
+ explanation: This result belongs to Rhizobium sp. PP1 in Results, not to the canonical B. pachyrhizi endpoint.
+ - reference: doi:10.3389/fmicb.2023.1078333
+ supports: PARTIAL
+ evidence_source: OTHER
+ snippet: twelve isolates were identified as Bradyrhizobium pachyrhizi
+ explanation: Abstract species assignment; Results tree comparisons and strain names are inconsistent, so exact
+ strain-to-species mapping remains unresolved.
- reference: doi:10.3389/fmicb.2023.1078333
supports: SUPPORT
evidence_source: IN_VIVO
- snippet: high tolerance against these four heavy metals
- explanation: Documents metal tolerance diversity in rhizobia population
-- name: Dissimilatory Vanadium Reduction and Immobilization
- description: 'Metal-reducing bacteria including Polaromonas and potentially other facultative anaerobes
- perform dissimilatory vanadate [V(V)] reduction to vanadyl [V(IV)] in anaerobic microsites within
- revegetated V-Ti tailings. Soluble vanadate (VO4³⁻, oxidation state +5) is reduced to vanadyl cation
- (VO²⁺, oxidation state +4) through respiratory electron transfer pathways involving c-type cytochromes
- (cymA, omcA) and membrane-associated nitrate reductases (narG, napA). Bacteria may use nitrate reductases
- NarG and NapA for respiratory V(V) reduction, coupling oxidation of organic electron donors (lactate,
- acetate from plant root exudates or organic amendments) to V(V) reduction. This process decreases
- vanadium solubility by 2-3 orders of magnitude, as V(IV) precipitates as hydrated vanadyl hydroxides
- [VO(OH)2], vanadyl sulfates, or V(IV)-substituted iron oxides. In circumneutral pH conditions (pH
- 6.5-7.5) typical of Panzhihua tailings, V(IV) solubility (~10⁻⁵ to 10⁻⁶ M) is dramatically lower than
- V(V) solubility (~10⁻³ M), driving effective vanadium immobilization. The reduction is thermodynamically
- favorable (standard potential E⁰ +0.34 V for VO2⁺/VO4³⁻ couple) and generates energy for microbial
- growth. In revegetated zones with higher organic carbon from plant root exudates and decomposing biomass,
- anaerobic microsites develop where V(V) reduction proceeds, lowering dissolved vanadium and preventing
- toxic accumulation. This represents a natural attenuation mechanism that complements phytoextraction
- by stabilizing vanadium in soil solids.
-
- '
- interaction_type: CROSS_FEEDING
- scope: PAIRWISE
- source_taxon:
- preferred_term: Polaromonas species
- term:
- id: NCBITaxon:52972
- label: Polaromonas
- metabolites:
- - preferred_term: vanadate
- term:
- id: CHEBI:46442
- label: vanadate(3-)
- concentration: 340 mg/kg total V in tailings; ~15-25 mg/L dissolved V(V) in oxic zones
- notes: V(V) as VO4³⁻
- - preferred_term: vanadyl cation
- term:
- id: CHEBI:30046
- label: oxidovanadium(2+)
- notes: V(IV) as VO²⁺; precipitates as oxides/hydroxides
- - preferred_term: lactate
- term:
- id: CHEBI:24996
- label: lactate
- notes: Electron donor from plant root exudates
- - preferred_term: acetate
- term:
- id: CHEBI:30089
- label: acetate
- notes: Electron donor from fermentation and root exudates
- biological_processes:
- - preferred_term: dissimilatory reduction
- term:
- id: GO:0019645
- label: anaerobic electron transport chain
- - preferred_term: cellular detoxification
- term:
- id: GO:1990748
- label: cellular detoxification
- evidence:
- - reference: doi:10.1021/acs.est.3c04508
- supports: SUPPORT
- evidence_source: IN_VITRO
- snippet: Microbially mediated V transformation is evaluated to shed light on the primary mechanisms
- underlying microbial V(V) reduction, namely electron transfer and enzymatic catalysis
- explanation: Establishes enzymatic mechanisms for V(V) reduction
- - reference: PMID:33125214
- supports: SUPPORT
- evidence_source: IN_VIVO
- snippet: Vanadium (V) is an important metal with critical industrial and medical applications
- explanation: Quantifies solubility decrease upon V(V) reduction
-- name: Soil Organic Carbon Transformation
- description: 'Pongamia pinnata revegetation coupled with indigenous microbial communities (dominated
- by rhizobia, Bacillus, and organic carbon degraders) drives transformation of soil organic carbon
- in V-Ti magnetite tailings, improving soil quality through carbon sequestration and enzyme activation.
- Bacterial communities indirectly affect soil organic carbon fractions and enzyme activity to regulate
- total organic carbon content after P. pinnata remediation. As the remediation period increases, soil
- active carbon components (dissolved organic carbon, microbial biomass carbon, readily oxidizable carbon)
- significantly increase in V-Ti magnetite tailings, indicating improvement in carbon availability and
- cycling. Carbon transformation-related enzymes including beta-glucosidase, cellobiohydrolase, N-acetyl-glucosaminidase,
- and phenol oxidase show significantly enhanced activities during revegetation, reflecting active microbial
- decomposition of plant litter and root exudates. The microbial community shifts toward rhizobia (nitrogen-fixers)
- and carbon-cycling bacteria that process plant-derived organic matter into stable soil organic carbon
- pools. P. pinnata remediation strengthens carbon sequestration of V-Ti magnetite tailings by increasing
- net primary productivity (through nitrogen fixation), providing continuous organic carbon inputs from
- root exudates and litter, and stimulating microbial carbon transformation pathways. This process converts
- barren tailings into functional soil with improved water retention, nutrient cycling, and metal buffering
- capacity. The coupling of legume phytoremediation with indigenous carbon-cycling microbiota represents
- a sustainable approach for long-term tailings rehabilitation.
-
- '
- interaction_type: COMMENSALISM
+ snippet: the biomass of the inoculated P. pinnata plants was significantly (p < 0.05) higher than that of the
+ control plants.
+ explanation: Positive plant-growth result across reported inoculations; no attribution of all changes to a specific
+ biochemical mediator.
+- name: Metal Tolerance of Cultured Tailings Bacillus
+ description: The 2014 Panzhihua bulk-soil isolate screen found multiple-metal tolerance among Bacillus isolates,
+ including five strains tolerant to all six tested metals. These were isolate growth assays, not a demonstration
+ that Bacillus transfers metabolites to rhizobia or enhances plant metal uptake. Keep this result separate from
+ the 2023 nodule-isolate screen and the 2018 S. saheli YH1/Leucaena system, which reduced plant metal uptake.
+ The previously assigned B. liaoningense phytoextraction percentages do not belong to B. pachyrhizi or to the
+ cited YH1 experiment. Efflux, sequestration, ACC degradation and metal-redox mechanisms were not isolated by
+ the tolerance assay.
scope: PAIRWISE
source_taxon:
preferred_term: Bacillus species
term:
id: NCBITaxon:1386
label: Bacillus
- target_taxon:
- preferred_term: Bradyrhizobium pachyrhizi
- term:
- id: NCBITaxon:280333
- label: Bradyrhizobium pachyrhizi
- metabolites:
- - preferred_term: dissolved organic carbon
- term:
- id: CHEBI:16526
- label: carbon dioxide
- notes: Active carbon component that increases during remediation
- - preferred_term: cellulose
- term:
- id: CHEBI:18246
- label: (1->4)-beta-D-glucan
- notes: Plant structural polymer degraded by microbial enzymes
- biological_processes:
- - preferred_term: carbon utilization
- term:
- id: GO:0015976
- label: carbon utilization
- - preferred_term: cellular carbohydrate metabolic process
- term:
- id: GO:0005975
- label: carbohydrate metabolic process
- downstream:
- - target: Nitrogen Fixation and Plant Growth Promotion
- description: Improved soil carbon supports rhizobial populations and symbiosis
- evidence:
- - reference: PMID:38744211
- supports: SUPPORT
- evidence_source: IN_VIVO
- snippet: The abundance of carbon transformation functional genes such as carbon
- degradation, carbon fixation, and methane oxidation were also significantly
- (P < 0.05) enriched
- explanation: Zeng et al. 2024 directly document the bacterial community's role
- in carbon transformation via enriched degradation/fixation/methane-oxidation
- gene abundances after V-Ti tailings phytoremediation.
- - reference: PMID:38744211
- supports: SUPPORT
- evidence_source: IN_VIVO
- snippet: four soil active organic carbon components (ROC, POC, DOC, and MBC)
- and three carbon transformation related enzymes (S-CL, S-SC, and S-PPO) in
- vanadium titanium magnetite tailings significantly (P < 0.05) increased with
- P. pinnata remediation
- explanation: Zeng et al. 2024 quantifies the active carbon and enzyme increase
- driven by Pongamia pinnata phytoremediation of V-Ti tailings.
- - reference: PMID:38744211
- supports: SUPPORT
- evidence_source: IN_VIVO
- snippet: phytoremediation to drive soil carbon transformation for carbon sequestration
- enhancement through the remediation of degraded ecosystems in mining areas
- explanation: Zeng et al. 2024 explicitly frame the carbon transformation
- mechanism as carbon sequestration enhancement via phytoremediation.
-- name: Rhizobial Functional Redundancy in Nitrogen Fixation
- description: 'Rhizobium selenitireducens and R. pisi provide functional redundancy in nitrogen fixation
- alongside the dominant Bradyrhizobium pachyrhizi. Three R. selenitireducens isolates and one R. pisi
- isolate from P. pinnata root nodules demonstrate variable tolerance to Cu, Ni, Mn, and Zn, contributing
- to the overall robustness of the nitrogen-fixing community under metal stress. This functional diversity
- ensures continued nitrogen enrichment even if individual rhizobial species decline due to fluctuating
- metal concentrations or other environmental stressors. R. selenitireducens possesses unique selenite
- reduction capability, converting toxic selenite to elemental selenium, providing additional metalloid
- detoxification functionality. R. pisi, traditionally a pea symbiont, demonstrates the promiscuity
- of rhizobial-legume associations under stress conditions. Together, these rhizobia form a resilient
- nitrogen-fixing guild that maintains ecosystem function across varying environmental conditions in
- V-Ti tailings.
-
- '
- interaction_type: MUTUALISM
- scope: PAIRWISE
- source_taxon:
- preferred_term: Rhizobium selenitireducens
- term:
- id: NCBITaxon:1336235
- label: Paenirhizobium selenitireducens ATCC BAA-1503
- target_taxon:
- preferred_term: Rhizobium pisi
- term:
- id: NCBITaxon:574561
- label: Rhizobium pisi
- metabolites:
- - preferred_term: nitrogen
- term:
- id: CHEBI:17997
- label: dinitrogen
- - preferred_term: ammonia
- term:
- id: CHEBI:16134
- label: ammonia
- biological_processes:
- - preferred_term: nitrogen fixation
- term:
- id: GO:0009399
- label: nitrogen fixation
- - preferred_term: symbiotic process
- term:
- id: GO:0044403
- label: biological process involved in symbiotic interaction
evidence:
- - reference: doi:10.3389/fmicb.2023.1078333
- supports: SUPPORT
- evidence_source: IN_VIVO
- snippet: Based on the phylogenetic analysis of 16S rRNA and four house-keeping genes
- (atpD, recA, rpoB, glnII), twelve isolates were identified as Bradyrhizobium
- pachyrhizi, four as Ochrobactrum anthropic, three as Rhizobium selenitireducens
- and one as Rhizobium pisi
- explanation: Documents diversity of rhizobial nitrogen fixers in V-Ti tailings
- - reference: doi:10.3389/fmicb.2023.1078333
+ - reference: doi:10.1371/journal.pone.0106618
supports: SUPPORT
- evidence_source: IN_VIVO
- snippet: effective rhizobia strains for bioremediation of VTM tailings or other contaminated soils
- explanation: Establishes metal tolerance across rhizobial species
-- name: Ochrobactrum Metal Tolerance and Metabolic Flexibility
- description: 'Ochrobactrum intermedium (13 isolates from bulk tailings, 4 from nodules) provides metabolic
- flexibility and exceptional metal tolerance to the V-Ti tailings microbiome. This alphaproteobacterium
- bridges multiple ecological functions including aerobic respiration, potential denitrification, metal
- reduction (Cr(VI), potentially V(V)), and plant growth promotion through IAA, siderophore, and ACC
- deaminase production. Ochrobactrum exhibits extraordinary resistance to multiple metals (Cd, Pb, Zn,
- Cu, Ni, Co, Cr) through diverse mechanisms including efflux systems, intracellular sequestration,
- and biosorption. Some Ochrobactrum strains can form nodule-like structures with legumes, though with
- lower nitrogen-fixing efficiency than true rhizobia, suggesting potential auxiliary roles in plant-microbe
- partnerships. The organism contributes to overall community metal detoxification and stress mitigation,
- working alongside Bradyrhizobium and Bacillus to create a multi-functional bioremediation consortium.
- Ochrobactrum represents a metabolic generalist that enhances community resilience through functional
- overlap and stress tolerance.
-
- '
- interaction_type: CROSS_FEEDING
+ evidence_source: IN_VITRO
+ snippet: Five strains, the B. licheniformis KT-87 and KT-88 and the Bacillus sp. KT-72, KT-74 and KT-76 were
+ tolerant against all the tested heavy metals.
+ explanation: Supports a Bacillus isolate phenotype, not a plant phytoextraction or interbacterial cooperation
+ mechanism.
+- name: Ochrobactrum Isolate Growth-Promoter Production
+ description: The 2014 bulk-soil collection included thirteen isolates identified as Ochrobactrum intermedium.
+ In that collection, six Ochrobactrum isolates produced more than 60 micrograms/mL IAA, and KT80 had the highest
+ reported IAA concentration, 83.05 micrograms/mL; two Ochrobactrum isolates were among the siderophore producers.
+ The main-text wording does not unambiguously allocate IAA/siderophore co-production to both isolates. These
+ are in-vitro production phenotypes, not demonstrated metabolite delivery to Bradyrhizobium, ACC deaminase activity,
+ metal reduction or a community-resilience mechanism. The 2023 Ochrobactrum nodule isolates are a different collection
+ with different species assignments; they cannot establish O. intermedium symbiotic nitrogen fixation.
scope: PAIRWISE
source_taxon:
preferred_term: Ochrobactrum intermedium
term:
id: NCBITaxon:94625
label: Brucella intermedia
- target_taxon:
- preferred_term: Bradyrhizobium pachyrhizi
- term:
- id: NCBITaxon:280333
- label: Bradyrhizobium pachyrhizi
- metabolites:
- - preferred_term: indole-3-acetic acid
- term:
- id: CHEBI:16411
- label: indole-3-acetic acid
- notes: Plant growth hormone
- - preferred_term: copper(2+)
- term:
- id: CHEBI:29036
- label: copper(2+)
- notes: Tolerated through efflux and sequestration
- biological_processes:
- - preferred_term: cellular response to metal ion
- term:
- id: GO:0071248
- label: cellular response to metal ion
evidence:
- reference: doi:10.1371/journal.pone.0106618
supports: SUPPORT
- evidence_source: IN_VIVO
- snippet: pumilus, followed by Rhizobium sp. (29 isolates) and Ochrobactrum intermedium (13 isolates)
- explanation: Quantifies Ochrobactrum presence in V-Ti tailings microbiome
- - reference: doi:10.3389/fmicb.2023.1078333
+ evidence_source: IN_VITRO
+ snippet: Ochrobactrum intermedium (13 isolates)
+ explanation: Identifies the bulk-soil collection; not the four Ochrobactrum nodule isolates in the later study.
+ - reference: doi:10.1371/journal.pone.0106618
supports: SUPPORT
- evidence_source: IN_VIVO
- snippet: Based on the phylogenetic analysis of 16S rRNA and four house-keeping genes
- (atpD, recA, rpoB, glnII), twelve isolates were identified as Bradyrhizobium
- pachyrhizi, four as Ochrobactrum anthropic, three as Rhizobium selenitireducens
- and one as Rhizobium pisi
- explanation: Documents Ochrobactrum in nodule-associated community
+ evidence_source: IN_VITRO
+ snippet: Ochrobactrum sp. KT80 produced highest concentration
+ explanation: Supports the reported genus-level IAA phenotype in the bulk-soil collection, not transfer to a
+ partner.
+ - reference: doi:10.1371/journal.pone.0106618
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: two Ochrobactrum sp. siderophore producers
+ explanation: Reports two siderophore producers; the preceding only-half qualifier makes a two-isolate IAA co-production
+ claim unsafe without the supplement.
environmental_factors:
- name: pH
value: 6.5-7.5
@@ -1007,3 +688,71 @@ growth_media:
snippet: The pots were kept in a greenhouse with a day temperature of 25°C for 16 h and a night
temperature of 17°C for 8 h
explanation: Reports greenhouse pot cultivation temperature regime for the host legume.
+discussions:
+- discussion_id: panzhihua-composite-community-boundaries
+ prompt: Which sampled community and verified isolates support each Panzhihua graph claim?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Pongamia Nodulation and Nitrogen-Enrichment Phenotypes
+ - ecological_interactions#Metal Tolerance of Cultured Tailings Bacillus
+ - ecological_interactions#Ochrobactrum Isolate Growth-Promoter Production
+ rationale: The record combines bulk-soil isolates, individually tested nodule isolates and separate plant-remediation
+ communities. Positive nodulation, nitrogen enrichment, isolate tolerance and IAA production remain. Co-isolation
+ does not establish functional redundancy, mutualism or compensatory resilience. Polaromonas occurrence in this
+ exact Panzhihua system is unverified; PMID33125214 concerns its own vanadium-tailings system, already represented
+ separately as CommunityMech:000055. Removing that node exposes an unresolved canonical-membership problem rather
+ than concealing it through all-member community-level credit. The 2023 paper also conflicts internally on PP1
+ identity and Cd/Zn assays. Canonical identity, top-level environment and trophic roles require separate review.
+ evidence:
+ - reference: doi:10.3389/fmicb.2023.1078333
+ supports: PARTIAL
+ evidence_source: OTHER
+ snippet: twelve isolates were identified as Bradyrhizobium pachyrhizi
+ explanation: Abstract species assignment; Results tree comparisons and strain names are inconsistent, so exact
+ strain-to-species mapping remains unresolved.
+ - reference: PMID:33125214
+ supports: PARTIAL
+ evidence_source: OTHER
+ snippet: V V -reducing enrichments indicated that bacteria associated with Polaromonas
+ explanation: External-system context only; no evidence of occurrence or vanadium reduction at this record’s
+ Panzhihua sampling site.
+ posed_by: codex
+- discussion_id: panzhihua-positive-soil-carbon-result
+ prompt: How should the positive Pongamia soil-carbon response be represented with the correct community identity?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Pongamia Nodulation and Nitrogen-Enrichment Phenotypes
+ - ecological_interactions#Metal Tolerance of Cultured Tailings Bacillus
+ rationale: PMID38744211 reports significant increases in ROC, POC, DOC and MBC, three carbon-transformation enzyme
+ measures, and carbon degradation/fixation/methane-oxidation gene abundance after long-term Pongamia remediation.
+ This positive aggregate result is retained here, not discarded as merely hypothetical. SEM supports an inferred
+ community-level pathway, not Bacillus-to-Bradyrhizobium commensalism or a reciprocal nitrogen/carbon feedback
+ connecting different studies. The former DOC metabolite was incorrectly grounded as carbon dioxide. A graph
+ node needs a correctly scoped community and source-resolved participants; converting this composite record to
+ implicit all-member activity would falsely include Polaromonas. Authorized full text and identity repair precede
+ new topology.
+ evidence:
+ - reference: PMID:38744211
+ supports: SUPPORT
+ evidence_source: IN_VIVO
+ snippet: four soil active organic carbon components (ROC, POC, DOC, and MBC)
+ explanation: Positive aggregate carbon result in a separate remediation study; does not resolve the proposed
+ bacterial pair.
+ - reference: PMID:38744211
+ supports: PARTIAL
+ evidence_source: COMPUTATIONAL
+ snippet: The abundance of carbon transformation functional genes such as carbon degradation, carbon fixation,
+ and methane oxidation were also significantly
+ explanation: Gene-abundance changes are not measured pathway flux or a demonstrated nitrogen-to-carbon feedback.
+ posed_by: codex
+curation_history:
+- timestamp: '2026-10-07T06:44:09Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: 'Preserve nodulation and plant nitrogen/growth with provisional species mapping and no PP1 misassignment.;
+ Preserve directly assayed Bacillus metal tolerance instead of cross-species phytoextraction claims.; Preserve
+ Ochrobactrum IAA/siderophore production without nodule-isolate conflation or interbacterial transfer. Issue
+ #1676; reports/causal_graph_review/decisions/20261007-four-records-batch82.yaml'
+ llm_assisted: true
diff --git a/kb/communities/Parachlorella_Saccharomyces_Mutualistic_Coculture.yaml b/kb/communities/Parachlorella_Saccharomyces_Mutualistic_Coculture.yaml
index dfe55693e..95c56cb53 100644
--- a/kb/communities/Parachlorella_Saccharomyces_Mutualistic_Coculture.yaml
+++ b/kb/communities/Parachlorella_Saccharomyces_Mutualistic_Coculture.yaml
@@ -55,11 +55,11 @@ taxonomy:
when co-cultured with Saccharomyces cerevisiae to enhance lipid productivity
explanation: Identifies Saccharomyces cerevisiae as the yeast member of the co-culture.
ecological_interactions:
-- name: Reciprocal oxygen/carbon dioxide gas exchange
- description: The microalga and yeast establish a mutualistic relationship based on reciprocal exchange
- of oxygen and carbon dioxide, offering a strategy to overcome productivity limits caused by the
- slow growth of the microalga.
- interaction_type: MUTUALISM
+- name: Proposed Reciprocal Oxygen and Carbon Dioxide Exchange
+ description: HYPOTHESIZED - Reciprocal oxygen/carbon dioxide exchange is proposed as a basis for microalga-yeast
+ association. In the accessible PMID42217804 abstract, this is introductory context rather than an exact-system
+ gas-flux or mediator-perturbation result. Preserve it as a mechanistic hypothesis for P. kessleri and S. cerevisiae,
+ not demonstrated bidirectional flux or reciprocal fitness benefit.
scope: PAIRWISE
source_taxon:
preferred_term: Parachlorella kessleri
@@ -81,23 +81,24 @@ ecological_interactions:
id: CHEBI:16526
label: carbon dioxide
downstream:
- - target: Fourfold Microalgal Biomass and Lipid Increase
- description: >
- Reciprocal O2/CO2 exchange helps the coculture overcome microalgal
- productivity limits and contributes to the higher biomass and lipid
- production measured in coculture.
+ - target: Fourfold Coculture Biomass and Lipid Increase
+ description: HYPOTHESIZED - Photosynthetic oxygen and respiratory carbon dioxide exchange could support coculture
+ productivity. The accessible abstract does not isolate the contribution of gas exchange to the observed fourfold
+ biomass/lipid increase.
evidence:
- reference: PMID:42217804
- supports: SUPPORT
- evidence_source: IN_VITRO
- snippet: Microalgae and yeasts can establish a mutualistic relationship based on reciprocal
- oxygen/carbon dioxide exchange, offering a strategy to overcome productivity limits caused by the
- slow growth of microalgae.
- explanation: States the mutualistic O2/CO2 gas-exchange interaction underlying the co-culture.
+ supports: PARTIAL
+ evidence_source: OTHER
+ snippet: Microalgae and yeasts can establish a mutualistic relationship based on reciprocal oxygen/carbon dioxide
+ exchange, offering a strategy to overcome productivity limits caused by the slow growth of microalgae.
+ explanation: Introductory mechanistic context, not an exact-system gas-exchange measurement in the accessible
+ abstract.
- name: Yeast support of microalgal growth and lipid accumulation
- description: Yeast sustained microalgal growth during the transition to phototrophy after glucose
- depletion (day 6) and promoted lipid accumulation through nutrient competition.
- interaction_type: MUTUALISM
+ description: The abstract reports that yeast sustained microalgal growth during the transition to phototrophy
+ after glucose depletion on day 6 and promoted lipid accumulation through nutrient competition. Preserve these
+ reported positive physiological effects without interpreting nutrient competition as a demonstrated reciprocal
+ benefit or specifying an unmeasured exchanged nutrient. Full-text comparisons and the fraction of productivity
+ mediated by each process remain uninspected.
scope: PAIRWISE
source_taxon:
preferred_term: Saccharomyces cerevisiae
@@ -119,24 +120,23 @@ ecological_interactions:
id: GO:0006629
label: lipid metabolic process
downstream:
- - target: Fourfold Microalgal Biomass and Lipid Increase
- description: >
- Yeast sustains microalgal growth after glucose depletion and promotes
- lipid accumulation, directly supporting the coculture biomass and lipid
- endpoint.
+ - target: Fourfold Coculture Biomass and Lipid Increase
+ description: PARTIAL - Yeast-associated maintenance of algal growth and nutrient-competition-associated lipid
+ accumulation provide the reported physiological contribution to higher coculture biomass/lipid production.
+ This does not apportion the fourfold endpoint among growth support, gas exchange and other mechanisms.
evidence:
- reference: PMID:42217804
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: Yeast sustained microalgal growth during the transition to phototrophy after glucose
- depletion (day 6) and promoted lipid accumulation through nutrient competition.
+ snippet: Yeast sustained microalgal growth during the transition to phototrophy after glucose depletion (day
+ 6) and promoted lipid accumulation through nutrient competition.
explanation: Yeast supports microalgal growth and drives lipid accumulation via nutrient competition.
-- name: EPS-mediated metabolic support of yeast by microalgae
- description: Despite prolonged nutrient limitation, yeast viability remained above 68%, indicating
- possible metabolic support from microalgae via exopolysaccharide (EPS)-derived molecules; FluidFM
- revealed stronger and longer microalga-yeast interactions linked to enhanced EPS production in
- co-culture.
- interaction_type: CROSS_FEEDING
+- name: Proposed EPS-Derived Metabolic Support of Yeast
+ description: HYPOTHESIZED - Yeast viability remained above 68% during approximately 8 days of nutrient limitation,
+ which the authors interpret as possible metabolic support by microalgal EPS-derived molecules. AFM showed visible
+ EPS and cell-surface changes, and FluidFM found stronger, longer cell interactions, likely associated with EPS.
+ These positive viability and biophysical observations do not by themselves demonstrate EPS-carbon uptake, donor-to-recipient
+ transfer or dependence of yeast survival on EPS.
scope: PAIRWISE
source_taxon:
preferred_term: Parachlorella kessleri
@@ -155,29 +155,19 @@ ecological_interactions:
label: exopolysaccharide
evidence:
- reference: PMID:42217804
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: IN_VITRO
- snippet: yeast viability remained above 68%, indicating possible metabolic support from microalgae
- via exopolysaccharides (EPS) - derived molecules
- explanation: Inferred microalga-to-yeast metabolic support via EPS-derived molecules sustaining
- yeast viability.
-- name: Fourfold Microalgal Biomass and Lipid Increase
- description: >
- The Parachlorella-Saccharomyces coculture increased biomass and lipid
- production fourfold relative to the microalgal monoculture, integrating gas
- exchange and yeast-supported phototrophic growth into the target
- lipid-productivity phenotype.
- interaction_type: MUTUALISM
+ snippet: yeast viability remained above 68%, indicating possible metabolic support from microalgae via exopolysaccharides
+ (EPS) - derived molecules
+ explanation: Positive viability observation supports a proposed EPS mechanism, not directly traced carbon transfer
+ or demonstrated necessity.
+- name: Fourfold Coculture Biomass and Lipid Increase
+ description: Under coculture conditions, biomass and lipid production increased fourfold relative to microalgal
+ monoculture grown in BBM + NO3 medium. This is a positive culture-level productivity comparison. The accessible
+ abstract does not establish that the entire biomass increase is microalgal, quantify each species contribution,
+ or isolate gas exchange or EPS transfer as the cause. It does not demonstrate reciprocal benefit solely from
+ increased bulk output.
scope: COMMUNITY_LEVEL
- metabolites:
- - preferred_term: oxygen
- term:
- id: CHEBI:15379
- label: dioxygen
- - preferred_term: carbon dioxide
- term:
- id: CHEBI:16526
- label: carbon dioxide
biological_processes:
- preferred_term: growth
term:
@@ -191,11 +181,11 @@ ecological_interactions:
- reference: PMID:42217804
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: biomass and lipid production increased 4-fold compared to microalgal monoculture grown in
- BBM + NO3 medium
- explanation: >
- Supports the increased biomass and lipid-production endpoint of the
- microalga-yeast coculture.
+ snippet: biomass and lipid production increased 4-fold compared to microalgal monoculture grown in BBM + NO3
+ medium
+ explanation: 'Supports the increased biomass and lipid-production endpoint of the microalga-yeast coculture.
+
+ '
growth_media:
- name: BBM + NO3 medium
preparation_notes: 'Microalga-yeast co-culture; yeast supplied with glucose as initial carbon source,
@@ -214,3 +204,42 @@ growth_media:
snippet: Yeast sustained microalgal growth during the transition to phototrophy after glucose depletion
(day 6)
explanation: Documents glucose as the initial carbon source, depleted at day 6.
+discussions:
+- discussion_id: parachlorella-assay-and-mediator-boundaries
+ prompt: Which measured gas, EPS and physical-interaction changes mediate the positive productivity and viability
+ responses?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Proposed Reciprocal Oxygen and Carbon Dioxide Exchange
+ - ecological_interactions#Yeast support of microalgal growth and lipid accumulation
+ - ecological_interactions#Proposed EPS-Derived Metabolic Support of Yeast
+ - ecological_interactions#Fourfold Coculture Biomass and Lipid Increase
+ rationale: Keep positive coculture productivity and yeast-associated algal support distinct from proposed gas
+ and EPS mechanisms. Stronger/longer cell adhesion and visible EPS are not themselves metabolite transfer. Full
+ text, controls and taxon-resolved measurements remain uninspected. A one-community Edison causal dry run prepares
+ possible separately evidenced biophysical structure; no paid report has been generated or used to add topology.
+ evidence:
+ - reference: PMID:42217804
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: Yeast sustained microalgal growth during the transition to phototrophy after glucose depletion (day
+ 6) and promoted lipid accumulation through nutrient competition.
+ explanation: Yeast supports microalgal growth and drives lipid accumulation via nutrient competition.
+ - reference: PMID:42217804
+ supports: PARTIAL
+ evidence_source: IN_VITRO
+ snippet: yeast viability remained above 68%, indicating possible metabolic support from microalgae via exopolysaccharides
+ (EPS) - derived molecules
+ explanation: Positive viability observation supports a proposed EPS mechanism, not directly traced carbon transfer
+ or demonstrated necessity.
+ posed_by: codex
+curation_history:
+- timestamp: '2026-10-07T06:44:09Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: 'Retain gas-exchange hypothesis with contextual evidence and partial productivity mediation.; Preserve
+ reported yeast-associated growth/lipid physiology without reciprocal-benefit inference.; Preserve yeast viability
+ and physical observations while qualifying EPS transfer.; Preserve fourfold culture-level output without unsupported
+ algal-only attribution. Issue #1677; reports/causal_graph_review/decisions/20261007-four-records-batch82.yaml'
+ llm_assisted: true
diff --git a/kb/communities/Parmigiano_NWS_Set2_LAB_Triculture.yaml b/kb/communities/Parmigiano_NWS_Set2_LAB_Triculture.yaml
index 77162edc1..b0f4005e9 100644
--- a/kb/communities/Parmigiano_NWS_Set2_LAB_Triculture.yaml
+++ b/kb/communities/Parmigiano_NWS_Set2_LAB_Triculture.yaml
@@ -107,8 +107,11 @@ taxonomy:
explanation: Identifies L. delbrueckii subsp. lactis C5I3 as the Ld member of set 2.
ecological_interactions:
- name: Set 2 milk acidification enhancement
- description: The complete three-member LAB triculture increased maximum milk acidification rate and total lactic acid production
- relative to the monocultures and most pairwise co-cultures, supporting a positive mixed-culture effect during milk fermentation.
+ description: The set 2 LBB04/C001.27/C5I3 triculture produced higher total lactic acid than the tested monocultures
+ and pairwise cultures. Maximum acidification rate was high, but the exact set 2 C001.27/C5I3 pair was comparable
+ to the triculture, so the triculture was not uniquely superior on this rate readout. Total inoculum was held
+ constant across compositions. These positive community fermentation phenotypes do not establish per-strain growth,
+ reciprocal benefit or a specific molecular exchange.
scope: COMMUNITY_LEVEL
metabolites:
- preferred_term: lactate
@@ -124,28 +127,33 @@ ecological_interactions:
term:
id: GO:0044419
label: biological process involved in interspecies interaction between organisms
- downstream:
- - target: C5I3 activity enhancement in mixed culture
- description: Higher D-lactate in set 2 tricultures than in the corresponding C5I3 monoculture indicated that the Ld member
- remained viable and metabolically active in the mixed culture.
evidence:
- reference: PMID:41859451
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: Across all inoculation sets, tri-cultures consistently displayed the highest μmax values (p < 0.05), followed
- by the co-cultures St + Lh and St + Ld.
+ snippet: Across all inoculation sets, tri-cultures consistently displayed the highest μmax values (p < 0.05),
+ followed by the co-cultures St + Lh and St + Ld.
explanation: Supports the strongest maximum acidification rate in the tricultures, including the set 2 LBB04/C001.27/C5I3
community.
- reference: PMID:41859451
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: Across all three strain combinations, total lactic acid production was highest in tri-cultures, followed by St
- + Lh and St + Ld co-cultures (p < 0.05)
- explanation: Supports stronger total lactic acid production by tricultures than by their monoculture and pairwise comparison
- conditions.
+ snippet: Across all three strain combinations, total lactic acid production was highest in tri-cultures, followed
+ by St + Lh and St + Ld co-cultures (p < 0.05)
+ explanation: Supports stronger total lactic acid production by tricultures than by their monoculture and pairwise
+ comparison conditions.
+ - reference: PMID:41859451
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: co-cultivation of St strain C001.27 with Ld strain C5I3 resulted in μmax values comparable to those
+ observed under tri-culture conditions.
+ explanation: Exact set 2 exception to a uniquely highest triculture rate.
- name: C001.27-C5I3 acidification enhancement
- description: In the set 2 pairwise subset, S. thermophilus C001.27 co-cultured with L. delbrueckii subsp. lactis C5I3 produced
- maximum acidification rates comparable with the complete triculture.
+ description: The C001.27/C5I3 pair had a higher maximum acidification rate than either corresponding monoculture,
+ and in set 2 its rate was comparable to that of the triculture. This is a positive two-member fermentation phenotype,
+ not proof that adding LBB04 preserves a pair-specific causal mechanism or that both members benefit equally.
+ The study interprets D-lactate predominance as preferential L. delbrueckii activity; exchanged formate, folate
+ and peptides were not directly resolved in this assay.
scope: COMMUNITY_LEVEL
participating_taxa:
- preferred_term: Streptococcus thermophilus C001.27
@@ -165,20 +173,19 @@ ecological_interactions:
term:
id: GO:0044419
label: biological process involved in interspecies interaction between organisms
- downstream:
- - target: Set 2 milk acidification enhancement
- description: The strong St + Ld pairwise response was retained within the complete LBB04/C001.27/C5I3 triculture.
evidence:
- reference: PMID:41859451
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: co-cultivation of St strain C001.27 with Ld strain C5I3 resulted in μmax values comparable to those observed
- under tri-culture conditions
+ snippet: co-cultivation of St strain C001.27 with Ld strain C5I3 resulted in μmax values comparable to those
+ observed under tri-culture conditions
explanation: Supports the strong positive set 2 acidification response when C001.27 and C5I3 were combined.
- name: LBB04-C5I3 reduced acidification subset
- description: The L. helveticus LBB04 plus L. delbrueckii subsp. lactis C5I3 pairwise subset had weaker acidification than
- the matched C001.27/C5I3 co-culture and lower total lactic acid than tricultures and S. thermophilus-containing co-cultures
- in the set 2 lactate assay.
+ description: The LBB04/C5I3 pair showed lower maximum acidification rates than the corresponding monocultures
+ and the C001.27/C5I3 pair. Its total lactic acid was also lower than the triculture and St-containing pairs,
+ with D-lactate comprising 75.95% of the pair’s total lactate. Preserve this negative fermentation response without
+ converting bulk acidification to a strain-specific growth-inhibition assay or claiming a measured antimicrobial
+ or nutrient-competition mechanism.
scope: COMMUNITY_LEVEL
participating_taxa:
- preferred_term: Lactobacillus helveticus LBB04
@@ -202,18 +209,27 @@ ecological_interactions:
- reference: PMID:41859451
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: co-cultivation with Lh strain LBB04 yielded significantly lower μmax values compared to the corresponding St
- + Ld interaction
+ snippet: co-cultivation with Lh strain LBB04 yielded significantly lower μmax values compared to the corresponding
+ St + Ld interaction
explanation: Supports lower set 2 milk acidification by the LBB04/C5I3 subset than by the C001.27/C5I3 subset.
- reference: PMID:41859451
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: In inoculation sets 2 and 3, Lh + Ld co-cultures yielded significantly lower total lactic acid than tri-cultures
- and the St + Lh and St + Ld co-cultures
+ snippet: In inoculation sets 2 and 3, Lh + Ld co-cultures yielded significantly lower total lactic acid than
+ tri-cultures and the St + Lh and St + Ld co-cultures
explanation: Supports lower total lactic acid production for the Lh/Ld subset in set 2.
-- name: C5I3 activity enhancement in mixed culture
- description: D-lactate measurements showed that the set 2 triculture accumulated more D-lactate than the C5I3 monoculture,
- consistent with L. delbrueckii subsp. lactis remaining viable and metabolically active in mixed culture.
+ - reference: PMID:41859451
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: co-inoculation of milk with Lh and Ld resulted in reduced acidification rates compared with the corresponding
+ monocultures
+ explanation: Retains the directly reported negative fermentation comparison, without assigning a molecular mechanism.
+- name: Set 2 Triculture D-Lactate Accumulation
+ description: At the end of fermentation, set 2 triculture D-lactate was significantly higher than in the C5I3
+ monoculture. This is a measured mixed-culture pool, consistent with L. delbrueckii metabolic activity but not
+ exclusive C5I3 production or directly measured C5I3 cell growth. L. helveticus produces both enantiomers, and
+ C001.27 monoculture was 83% L-lactate rather than exclusively L-lactate. Acidification and lactate are related
+ readouts; an arrow from acidification to inferred member activity would reverse measurement and inference.
scope: COMMUNITY_LEVEL
metabolites:
- preferred_term: lactate
@@ -229,10 +245,10 @@ ecological_interactions:
- reference: PMID:41859451
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: In two of the three sets (sets 1 and 2), D-lactate levels in tri-cultures were significantly higher than those
- detected in the corresponding Ld monocultures (p < 0.05)
- explanation: Supports significantly higher D-lactate in the set 2 triculture than in the C5I3 monoculture, a mixed-culture
- readout consistent with enhanced L. delbrueckii activity.
+ snippet: In two of the three sets (sets 1 and 2), D-lactate levels in tri-cultures were significantly higher
+ than those detected in the corresponding Ld monocultures (p < 0.05)
+ explanation: Supports measured triculture D-lactate and the authors activity interpretation; not exclusive C5I3
+ production or a member-resolved growth assay.
growth_media:
- name: Partially skimmed UHT milk cross-feeding medium
vessel_type: 100 mL screw-cap Erlenmeyer flask
@@ -286,18 +302,39 @@ external_resources:
explanation: Lists the DOI for the set 2 LAB triculture primary publication.
discussions:
- discussion_id: nws_set2_molecular_cross_feeding_mechanisms
- prompt: Which exchanged metabolites or inhibitory molecules specifically explain the C001.27/C5I3 stimulation and LBB04/C5I3
- weaker pairwise acidification in the Parmigiano Reggiano natural-whey-starter set 2 assays?
+ prompt: Which exchanged metabolites or inhibitory molecules specifically explain the C001.27/C5I3 stimulation
+ and LBB04/C5I3 weaker pairwise acidification in the Parmigiano Reggiano natural-whey-starter set 2 assays?
kind: KNOWLEDGE_GAP
status: OPEN
attaches_to:
- ecological_interactions#C001.27-C5I3 acidification enhancement
- ecological_interactions#LBB04-C5I3 reduced acidification subset
- rationale: PMID:41859451 directly measured acidification and D-/L-lactate outcomes for monocultures, pairwise co-cultures,
- and tricultures, but the source's formate, folate, urease, NADH oxidase, and antimicrobial-molecule explanations are literature-backed
- hypotheses rather than molecule-level measurements in this exact set 2 community.
+ rationale: PMID:41859451 directly measured acidification and D-/L-lactate outcomes for monocultures, pairwise
+ co-cultures, and tricultures, but the source's formate, folate, urease, NADH oxidase, and antimicrobial-molecule
+ explanations are literature-backed hypotheses rather than molecule-level measurements in this exact set 2 community.
posed_by: codex
posed_date: '2026-09-24'
+- discussion_id: nws-set2-comparison-versus-causation
+ prompt: Which member-resolved processes explain the positive and negative fermentation responses?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Set 2 milk acidification enhancement
+ - ecological_interactions#C001.27-C5I3 acidification enhancement
+ - ecological_interactions#LBB04-C5I3 reduced acidification subset
+ - ecological_interactions#Set 2 Triculture D-Lactate Accumulation
+ rationale: 'Four measured phenotypes remain. Pair and triculture comparisons do not form a causal sequence, and
+ higher D-lactate is an observation used to infer activity, not an outcome caused by measuring acidification.
+ No new mediator arrows are justified by the full main text. Preserve previous #1077-1079 removal of unsupported
+ mutualism, taxon roles and exclusive C5I3 attribution; the existing molecular-mechanism gap remains open.'
+ evidence:
+ - reference: PMID:41859451
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: co-cultivation of St strain C001.27 with Ld strain C5I3 resulted in μmax values comparable to those
+ observed under tri-culture conditions.
+ explanation: Exact set 2 exception to a uniquely highest triculture rate.
+ posed_by: codex
metals_present: []
rare_earth_elements_present: []
metal_relevance: NOT_APPLICABLE
@@ -307,16 +344,24 @@ curation_history:
- timestamp: '2026-09-24T11:50:10Z'
curator: codex
action: CREATE_COMMUNITY
- changes: Created CommunityMech:000431 for PMID:41859451 / doi:10.3389/fmicb.2026.1755652, a defined set 2 Parmigiano Reggiano
- natural-whey-starter LAB triculture with exact L. helveticus LBB04, S. thermophilus C001.27, and L. delbrueckii subsp.
- lactis C5I3 membership, milk cross-feeding design, acidification and lactate interactions, the partially skimmed UHT milk
- setup, PubMed and DOI resources, and a knowledge gap for molecule-level interaction mechanisms.
+ changes: Created CommunityMech:000431 for PMID:41859451 / doi:10.3389/fmicb.2026.1755652, a defined set 2 Parmigiano
+ Reggiano natural-whey-starter LAB triculture with exact L. helveticus LBB04, S. thermophilus C001.27, and L.
+ delbrueckii subsp. lactis C5I3 membership, milk cross-feeding design, acidification and lactate interactions,
+ the partially skimmed UHT milk setup, PubMed and DOI resources, and a knowledge gap for molecule-level interaction
+ mechanisms.
llm_assisted: true
- timestamp: '2026-09-24T11:58:36Z'
curator: codex
action: UPDATE_COMMUNITY
- changes: >-
- Addressed adversarial-review issues #1077, #1078, and #1079 by removing unsupported MUTUALISM labels and taxon functional
- roles, then rewriting the D-lactate interaction to report the set 2 mixed-culture measurement without assigning all
- triculture D-lactate to C5I3.
+ changes: 'Addressed adversarial-review issues #1077, #1078, and #1079 by removing unsupported MUTUALISM labels
+ and taxon functional roles, then rewriting the D-lactate interaction to report the set 2 mixed-culture measurement
+ without assigning all triculture D-lactate to C5I3.'
+ llm_assisted: true
+- timestamp: '2026-10-07T06:44:09Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: 'Preserve triculture total-lactate advantage and the exact set2 rate exception.; Preserve the positive
+ St/Ld pair phenotype without a subset-to-triculture causal arrow.; Preserve the negative Lh/Ld fermentation
+ response without inventing its mechanism.; Represent measured triculture D-lactate rather than exclusive C5I3
+ activity. Issue #1678; reports/causal_graph_review/decisions/20261007-four-records-batch82.yaml'
llm_assisted: true
diff --git a/kb/communities/Peanut_Seed_Bacterial_CS_SynCom.yaml b/kb/communities/Peanut_Seed_Bacterial_CS_SynCom.yaml
index 59626be4f..32699fbee 100644
--- a/kb/communities/Peanut_Seed_Bacterial_CS_SynCom.yaml
+++ b/kb/communities/Peanut_Seed_Bacterial_CS_SynCom.yaml
@@ -52,67 +52,11 @@ taxonomy:
evidence:
- *id001
ecological_interactions:
-- name: Peanut Seed SynCom Construction
- description: >
- Conserved, growth-promoting, and combined synthetic communities of peanut
- seed bacteria were constructed from 16S rRNA profiles, strain isolation,
- and plant-growth-promotion indicator measurements.
- scope: COMMUNITY_LEVEL
- biological_processes:
- - preferred_term: interspecies interaction between organisms
- term:
- id: GO:0044419
- label: biological process involved in interspecies interaction between organisms
- downstream:
- - target: Dual Fungal Challenge Evaluation
- description: >
- The defined seed-bacterial SynComs were then challenged against peanut
- seed Aspergillus flavus contamination and Fusarium oxysporum seedling
- root rot.
- - target: CS Seedling Growth Promotion
- description: >
- The constructed seed-bacterial CS SynCom was evaluated for its ability to
- improve peanut seedling growth in parallel with fungal suppression.
- evidence:
- - *id001
-- name: Dual Fungal Challenge Evaluation
- description: >
- Peanut seed-bacterial SynComs were tested for control of seed aflatoxin
- contamination caused by Aspergillus flavus and root rot caused by Fusarium
- oxysporum.
- scope: COMMUNITY_LEVEL
- biological_processes:
- - preferred_term: defense response to fungus
- term:
- id: GO:0050832
- label: defense response to fungus
- downstream:
- - target: Salicylic-Acid Defense Activation
- description: >
- The Fusarium oxysporum seedling challenge showed the CS community's
- strongest root-rot protection and associated that phenotype with
- salicylic-acid-related induced resistance.
- - target: CS Aspergillus and Aflatoxin Suppression
- description: >
- The Aspergillus flavus seed challenge directly measured seed fungal
- reproduction and aflatoxin production after CS inoculation.
- evidence:
- - reference: PMID:38520150
- supports: SUPPORT
- evidence_source: IN_VIVO
- snippet: >
- the control effects of synthetic microbial communities composed of peanut
- seed bacteria against seed aflatoxin contamination caused by Aspergillus
- flavus and root rot by Fusarium oxysporum were evaluated
- explanation: >
- Supports testing peanut seed-bacterial SynComs against both seed
- Aspergillus flavus aflatoxin contamination and Fusarium oxysporum
- root rot.
-- name: Salicylic-Acid Defense Activation
- description: >
- The combined CS SynCom's root-rot protection in peanut seedlings was
- associated with increased defense enzyme activity and activation of
- salicylic-acid-related systemic induced resistance.
+- name: SA-Related Defense Response and Proposed Resistance Mediation
+ description: Peanut seedlings treated with the seed-bacterial synthetic communities showed increased defense-enzyme
+ activity and an SA-related resistance response. The accessible abstract attributes protection to this host response.
+ PARTIAL - The full-text controls for SA-pathway necessity, sufficiency and distal systemic signaling have not
+ been inspected; marker/enzyme responses alone do not resolve those causal requirements.
scope: COMMUNITY_LEVEL
metabolites:
- preferred_term: salicylic acid
@@ -126,24 +70,24 @@ ecological_interactions:
label: defense response to fungus
downstream:
- target: CS Fusarium Root-Rot Resistance
- description: >
- Defense enzyme and salicylic-acid responses were the reported host
- defense axis underlying CS-mediated Fusarium root-rot resistance.
+ description: PARTIAL - The authors attribute increased root-rot resistance to higher defense-enzyme activity
+ and SA-related induced resistance. Retain this reported causal direction, while noting that the accessible
+ abstract does not expose pathway-blocking, rescue or distal-tissue controls needed to isolate SA mediation.
evidence:
- reference: PMID:38520150
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: IN_VIVO
- snippet: >
- This was achieved by increased defense enzyme activity and activated
- salicylic acid (SA)-related, systematically induced resistance in peanuts
- explanation: >
- Supports salicylic-acid-related induced resistance as the peanut defense
- response associated with the CS root-rot phenotype.
+ snippet: 'This was achieved by increased defense enzyme activity and activated salicylic acid (SA)-related,
+ systematically induced resistance in peanuts
+
+ '
+ explanation: Author-reported defense response and resistance interpretation; pathway-necessity controls are
+ not exposed in the accessible abstract.
- name: CS Fusarium Root-Rot Resistance
- description: >
- All three seed-bacterial SynCom designs resisted Fusarium oxysporum root
- rot in peanut seedlings, with the combined CS community producing the
- strongest protection.
+ description: All three seed-bacterial synthetic communities, C, S and CS, improved resistance to Fusarium oxysporum
+ root rot after seedling inoculation, with CS showing the best effect in the reported comparison. Preserve this
+ positive host-protection result; it does not identify the contribution of each member or prove that SA signaling
+ is the sole mediator.
scope: COMMUNITY_LEVEL
biological_processes:
- preferred_term: defense response to fungus
@@ -154,17 +98,19 @@ ecological_interactions:
- reference: PMID:38520150
supports: SUPPORT
evidence_source: IN_VIVO
- snippet: >
- Three synthetic communities showed resistance to root rot and CS had the
- best effect after inoculating into peanut seedlings
- explanation: >
- Supports Fusarium root-rot resistance and the strongest effect from the
- combined CS community.
+ snippet: 'Three synthetic communities showed resistance to root rot and CS had the best effect after inoculating
+ into peanut seedlings
+
+ '
+ explanation: 'Supports Fusarium root-rot resistance and the strongest effect from the combined CS community.
+
+ '
- name: CS Aspergillus and Aflatoxin Suppression
- description: >
- The combined CS SynCom inhibited Aspergillus flavus reproduction on peanut
- seeds and reduced aflatoxin production, a seed-protection effect linked to
- bacterial toxin degradation and fungal mycelial disruption.
+ description: CS inhibited Aspergillus flavus reproduction on peanut seeds and reduced aflatoxin production. The
+ authors relate these effects to bacterial toxin degradation and mycelial destruction. The positive suppression
+ phenotype is supported, but the accessible abstract does not disclose toxin-fate measurements, degradation products,
+ adsorption controls or member-resolved contributions. Lower toxin abundance is not by itself proof of chemical
+ destruction, complete detoxification or field efficacy.
scope: COMMUNITY_LEVEL
biological_processes:
- preferred_term: defense response to fungus
@@ -175,24 +121,24 @@ ecological_interactions:
- reference: PMID:38520150
supports: SUPPORT
evidence_source: IN_VIVO
- snippet: >
- CS also inhibited the reproduction of A. flavus on peanut seeds and the
- production of aflatoxin
- explanation: >
- Supports CS suppression of Aspergillus flavus reproduction and aflatoxin
- production on peanut seeds.
+ snippet: 'CS also inhibited the reproduction of A. flavus on peanut seeds and the production of aflatoxin
+
+ '
+ explanation: 'Supports CS suppression of Aspergillus flavus reproduction and aflatoxin production on peanut
+ seeds.
+
+ '
- reference: PMID:38520150
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: IN_VIVO
snippet: These effects are related to bacterial degradation of toxins and destruction of mycelia
- explanation: >
- Supports toxin degradation and fungal mycelial damage as the reported
- mechanisms associated with CS seed protection.
-- name: CS Seedling Growth Promotion
- description: >
- In addition to helping peanut seeds and seedlings resist fungal invasion,
- inoculation with the seed-bacterial synthetic community promoted peanut
- seedling growth.
+ explanation: Author-reported association with degradation and mycelial damage; exact toxin-fate and mediator
+ controls remain uninspected in the abstract-only review.
+- name: Reported Peanut Seedling Growth Promotion
+ description: The abstract concludes that inoculation with a synthetic community composed of seed bacteria promotes
+ peanut seedling growth. It does not give a CS-specific growth effect size or distinguish the contribution of
+ C, S and CS to that conclusion. Preserve the reported positive outcome at its stated scope without assuming
+ that disease protection, SA markers or toxin suppression caused the growth response.
scope: COMMUNITY_LEVEL
biological_processes:
- preferred_term: growth
@@ -204,9 +150,9 @@ ecological_interactions:
supports: SUPPORT
evidence_source: IN_VIVO
snippet: promote the growth of peanut seedlings
- explanation: >
- Supports peanut seedling growth promotion after inoculation with a seed
- bacterial synthetic community.
+ explanation: 'Supports peanut seedling growth promotion after inoculation with a seed bacterial synthetic community.
+
+ '
environmental_factors:
- name: defined synthetic community design
value: Synthetic communities were derived from 16S profiling, strain isolation, and plant growth promotion
@@ -230,3 +176,48 @@ related_ingredients:
induced resistance in peanuts
explanation: Names salicylic acid as the host defense signaling axis activated by the SynCom to
suppress root rot.
+discussions:
+- discussion_id: peanut-cs-mediation-and-assay-boundaries
+ prompt: Which exact CS members and host or fungal mechanisms account for the reported protection?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#SA-Related Defense Response and Proposed Resistance Mediation
+ - ecological_interactions#CS Fusarium Root-Rot Resistance
+ - ecological_interactions#CS Aspergillus and Aflatoxin Suppression
+ - ecological_interactions#Reported Peanut Seedling Growth Promotion
+ rationale: Construction and challenge-evaluation steps are methods, not biological causal nodes, and their four
+ workflow arrows are removed. Four positive biological outcomes remain, with the existing defense-to-resistance
+ arrow explicitly partial. Authorized full text is needed to resolve SA necessity/systemic signaling, toxin fate
+ versus abundance, composition and CS-specific growth attribution. No absence claim is made about unseen full-text
+ experiments and no new causal structure is added.
+ evidence:
+ - reference: PMID:38520150
+ supports: PARTIAL
+ evidence_source: IN_VIVO
+ snippet: 'This was achieved by increased defense enzyme activity and activated salicylic acid (SA)-related,
+ systematically induced resistance in peanuts
+
+ '
+ explanation: Author-reported defense response and resistance interpretation; pathway-necessity controls are
+ not exposed in the accessible abstract.
+ - reference: PMID:38520150
+ supports: SUPPORT
+ evidence_source: IN_VIVO
+ snippet: 'CS also inhibited the reproduction of A. flavus on peanut seeds and the production of aflatoxin
+
+ '
+ explanation: 'Supports CS suppression of Aspergillus flavus reproduction and aflatoxin production on peanut
+ seeds.
+
+ '
+ posed_by: codex
+curation_history:
+- timestamp: '2026-10-07T06:44:10Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: 'Retain author-reported SA-defense direction with unresolved pathway controls.; Preserve best-CS root-rot
+ resistance without member-specific attribution.; Preserve fungal/toxin suppression while separating abundance
+ from chemical degradation.; Preserve reported growth without unsupported CS-specific mediation. Issue #1679;
+ reports/causal_graph_review/decisions/20261007-four-records-batch82.yaml'
+ llm_assisted: true
diff --git a/reports/causal_graph_review/README.md b/reports/causal_graph_review/README.md
index 458f1c46d..fa2987957 100644
--- a/reports/causal_graph_review/README.md
+++ b/reports/causal_graph_review/README.md
@@ -5,6 +5,34 @@ source-based self-adversarial review. These records are not independent approval
or proof that every graph is complete. The current inventory and summary distinguish
`reviewed`, `pending` and `needs_research`.
+## Batch82: Tailings, Algal Coculture, Milk And Seed Biocontrol
+
+[Decisions](decisions/20261007-four-records-batch82.yaml),
+[validation](validation-20261007-batch82.json) and
+[self-adversarial review](adversarial-review-20261007-batch82.yaml) account for
+20 original nodes and 11 arrows. Fifteen biological nodes and three qualified
+arrows remain. Five unsupported or workflow nodes and eight arrows are removed.
+Positive plant/isolate, culture-productivity, fermentation and biocontrol results
+remain; the valid soil-carbon result is preserved with evidence in discussion
+pending repair of the composite tailings community identity.
+
+Four fresh primary main texts and seven further abstracts were inspected; one
+abstract is a review used only as context. All 25 graph quotations match fresh
+primary content and unchanged caches. Separate supplements and original figure
+pixels were not audited. New tailings disconnection warnings expose unresolved
+canonical membership rather than hiding it through all-member graph credit.
+
+Repairs #1676-#1679 await protected-main merge. Research #1680-#1682 and metadata
+#1683 remain open afterward, coordinated with #497. All 920 caches, 456 other
+records and raw non-graph blocks are preserved. Four append-only histories are
+included. One algae Edison dry run spent no credits; paid authorization is
+unanswered. This is self-review, not independent approval or corpus completion.
+
+The final reread narrowed an ambiguous IAA/siderophore overlap claim, removed
+gas annotations from the bulk-productivity node and qualified toxin-mechanism
+evidence. The 31 earlier passing outputs remain recorded as superseded; all
+affected checks were rerun and seven unchanged milk checks reused by hash.
+
## Batch81: Removal, PHB Production, Methane And Disease Suppression
[Decisions](decisions/20261007-four-records-batch81.yaml),
diff --git a/reports/causal_graph_review/adversarial-review-20261007-batch82.yaml b/reports/causal_graph_review/adversarial-review-20261007-batch82.yaml
new file mode 100644
index 000000000..6e2cac4bf
--- /dev/null
+++ b/reports/causal_graph_review/adversarial-review-20261007-batch82.yaml
@@ -0,0 +1,372 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: c2f23b2053bde3329f2619bc45accadcec415d19
+scope:
+- kb/communities/Panzhihua_Vanadium_Titanium_Tailings.yaml
+- kb/communities/Parachlorella_Saccharomyces_Mutualistic_Coculture.yaml
+- kb/communities/Parmigiano_NWS_Set2_LAB_Triculture.yaml
+- kb/communities/Peanut_Seed_Bacterial_CS_SynCom.yaml
+decision_ledger: reports/causal_graph_review/decisions/20261007-four-records-batch82.yaml
+validation_report: reports/causal_graph_review/validation-20261007-batch82.json
+findings:
+- issue: 1676
+ severity: P2
+ status: addressed_in_this_change
+ finding: Repair cross-study and taxon conflations in the Panzhihua causal graph
+ disposition: Close only after protected-main merge.
+- issue: 1677
+ severity: P2
+ status: addressed_in_this_change
+ finding: Separate Parachlorella coculture productivity from proposed gas and EPS mediation
+ disposition: Close only after protected-main merge.
+- issue: 1678
+ severity: P2
+ status: addressed_in_this_change
+ finding: Remove inference and subset-comparison arrows from Parmigiano set2 graph
+ disposition: Close only after protected-main merge.
+- issue: 1679
+ severity: P2
+ status: addressed_in_this_change
+ finding: Separate peanut CS biocontrol outcomes from construction and challenge workflow
+ disposition: Close only after protected-main merge.
+- issue: 1680
+ severity: P2
+ status: unresolved_research
+ finding: Resolve Panzhihua community identity before restoring carbon or vanadium topology
+ disposition: Keep OPEN after graph repair merge.
+- issue: 1681
+ severity: P2
+ status: unresolved_research
+ finding: Obtain exact Parachlorella assays and review missing EPS-adhesion structure
+ disposition: Keep OPEN after graph repair merge.
+- issue: 1682
+ severity: P2
+ status: unresolved_research
+ finding: Obtain peanut CS full text for SA mediation and toxin-removal interpretation
+ disposition: Keep OPEN after graph repair merge.
+- issue: 1683
+ severity: P2
+ status: unresolved_non_graph
+ finding: Reconcile Panzhihua non-graph identity, environment and source mismatches
+ disposition: Keep OPEN after graph repair merge.
+adversarial_checks:
+- Fresh both-root460record/920cache baseline preceded paper review. Four whole records,20nodes and11arrows assessed
+ including missing structures. Fifteen retained nodes/three qualified arrows and five removed nodes/eight removed
+ arrows all have dispositions. No new topology or provider spend.
+- Tailings canonical record combines distinct studies, not a verified six-member consortium. Preserve separate nodulation/N
+ enrichment and cultured-isolate traits.2023Results placePP1inRhizobium, while abstract/species-tree labels conflict.
+ Do not assignPP1toB.pachyrhizi or resolve conflictingCd/Znassays by guesswork.
+- Metal-tolerance node now names the directly assayed2014Bacillus collection. S.saheli/Leucaena reduced metal uptake;
+ B.liaoningense phytoextraction cannot be credited toB.pachyrhizi. Isolate growth tolerance does not isolate efflux,
+ sequestration, ACC degradation, redox or plant-uptake mechanisms.
+- 'The2014Ochrobactrum bulk-soil group is distinct from2023nodule isolates. PreserveIAAproduction,KT80reported83.05micrograms/mL
+ and siderophore producers. Final reread caught ambiguous only-half scope: do not assert both siderophore producers
+ also producedIAAwithout the supplementary table. Shorten quotation and explanation accordingly.'
+- Carbon-remediation positives remain evidence-backed in discussion:ROC/POC/DOC/MBC, enzyme measures and carbon-functional
+ gene abundance increased. Remove the unsupported Bacillus/Bradyrhizobium pair, carbon-dioxide grounding ofDOC
+ and reciprocal cross-study nitrogen/carbon arrows. A correct community identity must precede a replacement graph
+ node; do not erase positive biology or give every canonical member credit.
+- External Polaromonas reduction and untested rhizobial compensatory redundancy no longer assert exact-site functions.
+ Three real disconnected canonical taxa become visible:Polaromonas,R.pisi,R.selenitireducens.47warnings=44preserved+3new;
+ zero structural defects. Canonical taxonomy and auditor rules remain unchanged;1680/1683track repair beyond graph
+ scope.
+- Algal fourfold culture output, yeast-associated algal growth afterday6glucose exhaustion and viability>68%remain
+ positive. Introductory gas exchange is not measured exact-system flux. EPS support is explicitly possible, and
+ AFM/FluidFM adhesion is not carbon transfer. Final reread removes oxygen/CO2annotations from the bulk-productivity
+ node while retaining them on the hypothesized gas node.
+- Milk controlled compositions show positiveSt/Ldand negativeLh/Ldacidification responses. Preserve the exactset2pair
+ rate comparable to triculture, while triculture total lactate is higher. Total inoculum constant does not mean
+ each species inoculum constant. Bulk lactate and acidification are not member-specific fitness. No pair-to-triculture
+ or measurement-to-inferred-activity arrow.
+- 'D-lactate pool is not exclusiveC5I3: Lhproduces both enantiomers, andC001.27produces83%L-lactate rather than
+ exclusivelyL-lactate. Preserve1077-1079removal of mutualism, unsupported roles and exclusive producer attribution,
+ plus the existing molecular mechanism gap.'
+- Peanut two workflow nodes/four workflow arrows removed; four positive outcomes and author-reportedSA-to-resistance
+ direction retained. Missing full text means mediator controls are uninspected, not absent. Keep bestCSroot-rot
+ response, fungal/toxin suppression and abstract-scope growth. Final reread marks toxin-mechanism evidencePARTIALrather
+ than proving degradation from abundance. YAMLaliases remain unchanged.
+- Four fresh primary main texts/captions plus seven abstracts read, one abstract being a context-only review.25graph
+ quotations match fresh primaries and caches. No original figure pixels, separate supplements or raw data audited.
+ Primary copies stay outside repository. Normal publisher access barriers respected.954all-state issues/five matched
+ bodies and64localmatching files searched with hidden/ignored inclusion and declared exclusions.
+- Three final claim/annotation fixes applied without extra history events.31superseded passing outputs retained
+ and affected gates rerun; seven unchanged milk checks reused with hashes. Four guarded history events,456otherrecords920caches
+ and all raw non-graph blocks preserved. Deterministic rendering and exact description checks across456pages are
+ not browser screenshots.
+- One9111character algae Edison causal dry run is not a report or paid authorization. Scoped question unanswered;
+ earlier denial/pending scopes unchanged. Repairs1676-1679close only after protected-main merge; research1680-1682andmetadata1683remain
+ open. Self-adversarial COMMENT is not independent approval or corpus completion. Protected lifecycle must move
+ dependents before branch deletion.
+verification:
+ combined_regressions: 736 passed in 494.44s (0:08:14)
+ new_regression_tests: 10
+ schema_strict_terms_history: Passed with actual outputs/digests
+ references: Four full-record reference validators exit0. CLI Total checks counts issues, not executed checks.25graph
+ quotations independently match fresh primary content and unchanged caches. Literal matching is not entailment
+ or whole-record provenance certification; non-graph claims/caches are preserved, not globally recertified.
+ snippet_counts_by_record:
+ kb/communities/Panzhihua_Vanadium_Titanium_Tailings.yaml:
+ MATCH: 40
+ RENDERING: 1
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Parachlorella_Saccharomyces_Mutualistic_Coculture.yaml:
+ MATCH: 10
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Parmigiano_NWS_Set2_LAB_Triculture.yaml:
+ MATCH: 20
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Peanut_Seed_Bacterial_CS_SynCom.yaml:
+ MATCH: 11
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ primary_graph_snippet_proof:
+ fresh_primary_matched: 25
+ cache_matched: 25
+ new_discussion_quotations_fresh_primary_matched: 9
+ new_nodes_or_arrows: 0
+ retained_nodes: 15
+ removed_nodes: 5
+ retained_arrows: 3
+ removed_arrows: 8
+ complete_fresh_main_texts_read: 4
+ additional_abstracts_read: 7
+ review_abstract_context_only: 1
+ original_figure_pixels_supplements_raw_data_audited: false
+ network:
+ existing_findings_preserved: 44
+ added_findings:
+ Panzhihua_Vanadium_Titanium_Tailings:
+ - type: DISCONNECTED
+ taxon: Polaromonas species
+ taxon_id: NCBITaxon:52972
+ taxon_data:
+ taxon_term:
+ preferred_term: Polaromonas species
+ term:
+ id: NCBITaxon:52972
+ label: Polaromonas
+ gtdb_grounding_status: GROUNDED
+ gtdb_classification:
+ gtdb_id: GTDB:g__Polaromonas
+ gtdb_taxon: Polaromonas
+ gtdb_lineage: d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas
+ ncbi_source_id: NCBITaxon:52972
+ majority_fraction: 1.0
+ support_genomes: 12
+ total_genomes: 12
+ is_reclassified: false
+ mapping_source: kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-07-25) [grounded at g__
+ rank; 1 GTDB taxa under the NCBI taxon]
+ notes: 'Betaproteobacteria capable of dissimilatory vanadium reduction in contaminated mine environments.
+ While not specifically reported in the Panzhihua tailings studies reviewed, Polaromonas is a well-established
+ V(V)-reducing organism in circumneutral pH vanadium mine tailings in northern China and likely present
+ in Panzhihua tailings based on similar environmental conditions (circumneutral pH 6.5-7.5, moderate
+ temperature, high vanadium concentrations). Polaromonas performs dissimilatory V(V) reduction to V(IV)
+ using c-type cytochromes (cymA, omcA) and membrane-associated nitrate reductases (narG). The organism
+ couples oxidation of organic electron donors (lactate, acetate) to V(V) reduction, decreasing vanadium
+ solubility by 2-3 orders of magnitude through precipitation of V(IV) species. This metabolic capacity
+ is critical for vanadium immobilization during anaerobic microsites in revegetated tailings. Polaromonas
+ also reduces Fe(III), Mn(IV), and As(V), contributing to polymetallic redox cycling in V-Ti tailings.
+
+ '
+ functional_role:
+ - PRIMARY_DEGRADER
+ - SYNTROPHIC_PARTNER
+ abundance_level: COMMON
+ abundance_value: Inferred presence based on V-reducing capacity in similar V-Ti tailings
+ evidence:
+ - reference: PMID:33125214
+ supports: SUPPORT
+ evidence_source: IN_VIVO
+ snippet: Further, VV-reducing enrichments indicated that bacteria associated with Polaromonas, a genus
+ belonging to the family Burkholderiaceae, were potentially responsible for VV reduction
+ explanation: Establishes V(V) reduction mechanism relevant to Panzhihua conditions
+ message: Taxon 'Polaromonas species' has no interactions
+ - type: DISCONNECTED
+ taxon: Rhizobium pisi
+ taxon_id: NCBITaxon:574561
+ taxon_data:
+ taxon_term:
+ preferred_term: Rhizobium pisi
+ term:
+ id: NCBITaxon:574561
+ label: Rhizobium pisi
+ gtdb_grounding_status: UNRESOLVED
+ notes: 'Fast-growing nitrogen-fixing rhizobium traditionally associated with pea (Pisum sativum) but
+ adapted to form nodules with P. pinnata in V-Ti tailings. One isolate was identified as R. pisi, demonstrating
+ the promiscuity of rhizobial-legume associations under metal stress conditions. R. pisi contributes
+ to nitrogen enrichment of tailings soil through symbiotic nitrogen fixation and produces plant growth-promoting
+ substances including IAA. The presence of R. pisi indicates that phytoremediation legumes can recruit
+ diverse rhizobial species from indigenous tailings microbiota, not limited to traditional host-specific
+ symbionts. This metabolic flexibility enhances the resilience and effectiveness of legume-rhizobia
+ partnerships in contaminated environments.
+
+ '
+ functional_role:
+ - PRIMARY_DEGRADER
+ - NITROGEN_FIXING_SYMBIONT
+ abundance_level: RARE
+ abundance_value: One isolate from P. pinnata nodules
+ evidence:
+ - reference: doi:10.3389/fmicb.2023.1078333
+ supports: SUPPORT
+ evidence_source: IN_VIVO
+ snippet: Based on the phylogenetic analysis of 16S rRNA and four house-keeping genes (atpD, recA, rpoB,
+ glnII), twelve isolates were identified as Bradyrhizobium pachyrhizi, four as Ochrobactrum anthropic,
+ three as Rhizobium selenitireducens and one as Rhizobium pisi
+ explanation: Documents R. pisi presence in V-Ti tailings rhizobia
+ message: Taxon 'Rhizobium pisi' has no interactions
+ - type: DISCONNECTED
+ taxon: Rhizobium selenitireducens
+ taxon_id: NCBITaxon:1336235
+ taxon_data:
+ taxon_term:
+ preferred_term: Rhizobium selenitireducens
+ term:
+ id: NCBITaxon:1336235
+ label: Paenirhizobium selenitireducens ATCC BAA-1503
+ gtdb_grounding_status: UNRESOLVED
+ notes: 'Nitrogen-fixing alphaproteobacterium capable of selenium reduction and heavy metal tolerance,
+ isolated from P. pinnata root nodules in V-Ti tailings. Three isolates were identified as R. selenitireducens,
+ demonstrating nitrogen-fixing capacity and variable tolerance to Cu, Ni, Mn, and Zn. This species
+ possesses unique metabolic capabilities including selenite reduction to elemental selenium, suggesting
+ potential for metalloid detoxification in addition to nitrogen fixation. R. selenitireducens contributes
+ to the functional diversity of the rhizobial community, providing complementary metal tolerance mechanisms
+ and nitrogen enrichment. The organism forms effective symbioses with leguminous plants under metal
+ stress conditions, promoting plant growth through nitrogen provision and IAA production. Like other
+ tailings rhizobia, R. selenitireducens serves as a competent candidate for bioremediation of soils
+ contaminated with multifarious metals due to its combined nitrogen-fixing and metal tolerance phenotypes.
+
+ '
+ functional_role:
+ - PRIMARY_DEGRADER
+ - CROSS_FEEDER
+ - NITROGEN_FIXING_SYMBIONT
+ abundance_level: COMMON
+ abundance_value: Three isolates from P. pinnata nodules
+ evidence:
+ - reference: doi:10.3389/fmicb.2023.1078333
+ supports: SUPPORT
+ evidence_source: IN_VIVO
+ snippet: Based on the phylogenetic analysis of 16S rRNA and four house-keeping genes (atpD, recA, rpoB,
+ glnII), twelve isolates were identified as Bradyrhizobium pachyrhizi, four as Ochrobactrum anthropic,
+ three as Rhizobium selenitireducens and one as Rhizobium pisi
+ explanation: Documents R. selenitireducens presence in tailings rhizobia
+ - reference: doi:10.3389/fmicb.2023.1078333
+ supports: SUPPORT
+ evidence_source: IN_VIVO
+ snippet: effective rhizobia strains for bioremediation of VTM tailings or other contaminated soils
+ explanation: Establishes metal tolerance and bioremediation potential
+ message: Taxon 'Rhizobium selenitireducens' has no interactions
+ removed_findings: {}
+ interpretation: 'Three newly exposed Panzhihua disconnections: R.selenitireducens, R.pisi and Polaromonas. Removed
+ unsupported redundancy/external-system claims; no invented all-member credit, taxonomy or auditor-rule change.
+ Identity research1680/metadata1683remainOPEN.'
+ black_ruff_diff: passed
+ tested_file_sha256:
+ reports/causal_graph_review/decisions/20261007-four-records-batch82.yaml: 287d391e90ad2e832c8cf57a63e6db79adfd6a73fa59a670dc6441c1466cea58
+ tests/test_causal_review_batch82.py: f8a1c608f6e523301ee878e347a451309f7bb7032b631410fb4fd251bd9c481b
+ kb/communities/Panzhihua_Vanadium_Titanium_Tailings.yaml: b5a4255cbaf18200e7002f843bffa20e870a5d1676d5c7cf3f4036c9ce92b0a0
+ kb/communities/Parachlorella_Saccharomyces_Mutualistic_Coculture.yaml: ee3166c701c928154cb1f46337d3d43a5ee56946d75f93fcd6d4ac8ecb3f8b82
+ kb/communities/Parmigiano_NWS_Set2_LAB_Triculture.yaml: 1ca3e250bbd757768243c691712d2139c54a2da4e59570360417188516bb4b2c
+ kb/communities/Peanut_Seed_Bacterial_CS_SynCom.yaml: faf0f4193278f1fc4c65f5666b79129629c3e1add520245a3ff941596b96513c
+ reports/causal_graph_review/README.md: 6a7fce42f05cab4061692231e2a17092c0554c85d1f9a520478e36cea2d69a6c
+ unchanged_caches: 920
+ cache_changes: []
+ unchanged_records: 456
+ edison:
+ required_for_this_repair: false
+ required_for_unresolved_extensions: true
+ provider_submissions: 0
+ credits_spent: 0
+ dry_runs:
+ - community_id: CommunityMech:000295
+ job: LITERATURE
+ query_chars: 9111
+ query_sha256: 4515810ac69377baf2c9f943bc9854134ccf49cc1a302b3133d192fef3319ded
+ meta_path: /private/tmp/communitymech-batch82/edison-algae/Parachlorella_Saccharomyces_Mutualistic_Coculture-edison-literature-causal-meta.yaml
+ authorization: Scoped asynchronous question unanswered; preselection is not approval.
+ post_commit_docs_current: Separate publication gate, not asserted before commit.
+participant_census:
+ measurements:
+ baseline:
+ records: 460
+ with_community_level: 393
+ mixed: 125
+ community_level_only: 268
+ taxa: 1511
+ credited_solely_by_the_rule: 1240
+ current:
+ records: 460
+ with_community_level: 393
+ mixed: 125
+ community_level_only: 268
+ taxa: 1511
+ credited_solely_by_the_rule: 1240
+ delta:
+ records: 0
+ with_community_level: 0
+ mixed: 0
+ community_level_only: 0
+ taxa: 0
+ credited_solely_by_the_rule: 0
+ interpretation: No scope-count change, taxonomy edit, or auditor-rule change. Aggregate outcomes do not establish
+ member-resolved activity.
+corpus:
+ records: 460
+ nodes: 1439
+ edges: 601
+ review_status_counts:
+ needs_research: 39
+ pending: 164
+ reviewed: 257
+limitations:
+- Fresh pre-paper baseline:460records/920caches across both roots. Four whole records,20existing nodes and11arrows
+ reviewed.15nodes/3arrows retained;5nodes/8arrows removed with explicit dispositions. No new topology.
+- Four complete fresh primary main texts/captions read:2023rhizobia,2014bulk-soil bacteria,2018S.saheli and2026milk.
+ Seven further abstracts checked; one is a2023vanadium review, context only. Original figure pixels, separate supplements
+ and raw data not audited. Exact matching does not establish entailment.
+- Normal publisher access for algae returned403 and peanut DOI delivery was unavailable. No bypass attempted, and
+ no inference that unseen full-text assays do not exist. Primary evidence copies remain outside the repository;
+ unchanged caches are not globally recertified.
+- Tailings is a composite record with unresolved canonical identities, source/site mismatches and internally inconsistent2023species/metal
+ labels. Positive nodulation/N enrichment, Bacillus metal tolerance and Ochrobactrum production survive. The carbon-remediation
+ result remains evidence-backed in discussion, not assigned to an unsupported pair or every canonical member. Removed
+ Polaromonas and redundancy claims expose genuine disconnected taxa; no auditor or taxonomy changes.
+- Algal fourfold culture output, yeast-associated algal support, viability and biophysical observations survive.
+ Gas exchange is contextual/proposed and EPS transfer is explicitly possible. Full text and future biophysical
+ topology remain1681. No algal-only biomass assignment or mutualistic benefit inferred from bulk output.
+- Milk retains four positive/negative assay phenotypes, exact set2rate exception and mixed D-lactate pool. Two arrows
+ were subset comparison and measurement-to-inference, not causal mediation. Prior1077-1079fixes and molecular gap
+ preserved; no broad downgrade of the controlled fermentation comparisons.
+- Peanut retains four biological outcomes and the author-reported SA-to-resistance direction as partial. Two methods
+ nodes/four workflow arrows removed. Toxin reduction is not automatically chemical degradation; abstract growth
+ conclusion is not CS-specific. Raw engineering/taxonomy/environment YAML anchors preserved.
+- 954all-state issue titles/bodies searched; all5matched bodies1077-1079,497,258read, plus prior milk review and
+ Polaromonas author-request lead.64local matching files from ignored/hidden-inclusive search excluding.git/docs/site/references_cache.
+ No exhaustive historical PR/comment audit. Some combined/cache outputs truncated; relevant fresh main texts read
+ in bounded chunks, and absence claims do not depend on truncated output.
+- One9111character one-community algae Edison causal dry run; zero provider submissions/credits. Scoped paid question
+ unanswered. Earlier paid denials and pending scopes unchanged. Repair1676-1679remainOPENuntil protected-main merge;
+ research1680-1682andmetadata1683remainOPENafterward.
+- Four append-only histories;456otherrecords920caches and all raw non-graph blocks preserved, not certified. Render/description
+ checks are not browser screenshots. Self-adversarial review is not independent approval or completion of the corpus
+ objective.
+- Final adversarial reread narrowed ambiguous Ochrobactrum IAA/siderophore overlap, removed gas-metabolite annotations
+ from the aggregate productivity endpoint, and marked peanut toxin-mechanism evidence PARTIAL. Affected checks
+ rerun with earlier outputs retained; four original append-only histories unchanged.
diff --git a/reports/causal_graph_review/decisions/20261007-four-records-batch82.yaml b/reports/causal_graph_review/decisions/20261007-four-records-batch82.yaml
new file mode 100644
index 000000000..98fea7f1c
--- /dev/null
+++ b/reports/causal_graph_review/decisions/20261007-four-records-batch82.yaml
@@ -0,0 +1,680 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: c2f23b2053bde3329f2619bc45accadcec415d19
+baseline_commit: c2f23b2053bde3329f2619bc45accadcec415d19
+base_tree: 2554aa7ffce8940a7c157483b925cd9071f5a46f
+pre_source_baseline_sha256: a88c0ecae11c7b9c0de1bd1010f2a50f81b593769a4189619bac5d50535b7c3f
+issues:
+- 1676
+- 1677
+- 1678
+- 1679
+unresolved_non_graph_issues:
+- 1683
+unresolved_research_issues:
+- 1680
+- 1681
+- 1682
+issue_deduplication:
+ all_state_issue_titles_and_bodies: 954
+ ignored_hidden_local_search: true
+ matching_local_files: 64
+ matching_issues:
+ - 1079
+ - 1078
+ - 1077
+ - 497
+ - 258
+primary_artifacts:
+ /private/tmp/communitymech-batch82/algae-metadata.json: 9c651ce7d5a4943c6212539107b6525863bd33706b0af5db81ddf89aece90043
+ /private/tmp/communitymech-batch82/algae-primary.txt: 652649557b82b910ef4b11c5a3b8fdaffb3b8a7b6b3d561f07eed5b6cb25b4f0
+ /private/tmp/communitymech-batch82/bacteria-metadata.json: 7aaaa2ed94a9f5bb851d07bde7ce0a8bb417c0828be7ee4095b2499daadd5414
+ /private/tmp/communitymech-batch82/bacteria-primary.txt: 41208563a3f0e9a255bbac7cf2d8f00abc8d4a091a1f31b8af0d4e3bf64e4964
+ /private/tmp/communitymech-batch82/bacteria-primary.xml: 3b718dfafafe55619c1918b720fb321c0b6642ad5bf04f414b9852b6d9a2e26c
+ /private/tmp/communitymech-batch82/bacteria-tables.txt: 23fa319281ede8943684895eebad2db915301fca9e4e5a648e241e6c429c5c09
+ /private/tmp/communitymech-batch82/baseline.json: a88c0ecae11c7b9c0de1bd1010f2a50f81b593769a4189619bac5d50535b7c3f
+ /private/tmp/communitymech-batch82/carbon-metadata.json: c31d50c1c3a6649ed6b8a86f8a358f5430c917675492e8c02ba37bec165f574b
+ /private/tmp/communitymech-batch82/carbon-primary.txt: 1b43d64e3e292306ec0fd860213715768a276119ae122f040deddea02475b695
+ /private/tmp/communitymech-batch82/deposition-metadata.json: e3a3cc4bfdf0df7731a68edcb4a76549f527c3ceab416627354872f9fffaf737
+ /private/tmp/communitymech-batch82/deposition-primary.txt: 4bd77b019c7b74a187189c205871e68ff99b2d459d16a70c146e906291f8707b
+ ? /private/tmp/communitymech-batch82/edison-algae/Parachlorella_Saccharomyces_Mutualistic_Coculture-edison-literature-causal-meta.yaml
+ : 87e0bcd20522d5967508d729a3e0d255840f47f9fe3f17f3c1159e079798881d
+ /private/tmp/communitymech-batch82/issue-matches.json: f175013007269d544fc9ad20565b7e9f4c36b01bcc6a3a567f1a7ed679e7da6a
+ /private/tmp/communitymech-batch82/issues.json: 43df2c8bc88d9ef3f53e053fa9fd93a2c72e6086545a518f9a1fedd295512fe7
+ /private/tmp/communitymech-batch82/local-matches.txt: 0fafc37a4d3741ce5d17d0642f4b17e6a1fe67463214f82b17ba4645a0e341e6
+ /private/tmp/communitymech-batch82/milk-metadata.json: f124ccbc3e3072525a085c3988b56847ef0c1c7ffe183f3d6f34a420777fc231
+ /private/tmp/communitymech-batch82/milk-primary.txt: 6b60c0b60c84550045ca654b787c59299ffac951ce96ffd7fa1251baf1ed7233
+ /private/tmp/communitymech-batch82/milk-primary.xml: 7c6f7bd39564d73d23924d4b49e676b7e40e3900ab6e01cd0f3003f499b4eb4f
+ /private/tmp/communitymech-batch82/milk-tables.txt: 99d368fb8dfae40c6b40ac4716f3b5ba0bbc13ed218256d6e2075532f0563956
+ /private/tmp/communitymech-batch82/peanut-metadata.json: 56efbd4865314a2d40badf0022c824f309200b437e0c19497e43aba11ac9b099
+ /private/tmp/communitymech-batch82/peanut-primary.txt: 39e8fb80382baa4025d21c76469e9efcd0c77f66f10f5ed03bd784a8b52ed8d4
+ /private/tmp/communitymech-batch82/pond-metadata.json: fc840402578c0472bf3893e474860d77321fc404b72291a3baa72e00cc159dd6
+ /private/tmp/communitymech-batch82/pond-primary.txt: 7039858614d0d3530b6a6343e4e99bf241c956991ff04bcda0215f41c1c0e83c
+ /private/tmp/communitymech-batch82/primary-manifest.json: f19f379bb8fd323bee5a5f88725642700ac60af7b4ffb0924af26c89d2b06355
+ /private/tmp/communitymech-batch82/rhizobia-metadata.json: b986de4d5fac31ab76732f86d25cbbee731f82cb9aa5b13e4a8017c203e15e6d
+ /private/tmp/communitymech-batch82/rhizobia-primary.txt: bd6c23293ad56687fef7ffb7209cffce74f42b17788c915f7431bf24a1303fdc
+ /private/tmp/communitymech-batch82/rhizobia-primary.xml: f47764df960de74100907f9ad9bcc57723429774cad57a274ab19cc20ad9193d
+ /private/tmp/communitymech-batch82/rhizobia-tables.txt: ba84d6fb15f2ceeba75f212a94741bf86489d79ea005a0b98d77d49c29adeb96
+ /private/tmp/communitymech-batch82/saheli-metadata.json: 74c3dc554558f0ce39e4802ab042e1fa44172b86be647153e98741bd1e43e3f7
+ /private/tmp/communitymech-batch82/saheli-primary.txt: 6dee99f526762b75630e5b2120d7270dc08ca906460021d5f05374415fc4f0e7
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+ /private/tmp/communitymech-batch82/vanadium-metadata.json: c2271c23c296fe0efea8b73ac0f4838b7387c7aa35bfa95072c494e3bebf45c5
+ /private/tmp/communitymech-batch82/vanadium-primary.txt: 7933557343c25d7e5b42283d1406d678e3b9e2b5d1fc310ecc2ecf2fb4d79fe0
+primary_urls:
+- https://www.ebi.ac.uk/europepmc/webservices/rest/PMC10315665/fullTextXML
+- https://www.ebi.ac.uk/europepmc/webservices/rest/PMC4154735/fullTextXML
+- https://www.ebi.ac.uk/europepmc/webservices/rest/PMC6119820/fullTextXML
+- https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A33125214+AND+SRC%3AMED&format=json&resultType=core
+- https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=DOI%3A10.1021%2Facs.est.3c04508+AND+SRC%3AMED&format=json&resultType=core
+- https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A38744211+AND+SRC%3AMED&format=json&resultType=core
+- https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A38181847+AND+SRC%3AMED&format=json&resultType=core
+- https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=DOI%3A10.1016%2Fj.scitotenv.2024.170082+AND+SRC%3AMED&format=json&resultType=core
+- https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A42217804+AND+SRC%3AMED&format=json&resultType=core
+- https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12996222/fullTextXML
+- https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A38520150+AND+SRC%3AMED&format=json&resultType=core
+primary_graph_snippet_count: 25
+independent_fresh_primary_graph_snippet_count: 25
+cache_matched_graph_snippet_count: 25
+snippet_checks:
+- record: Panzhihua_Vanadium_Titanium_Tailings
+ node: Pongamia Nodulation and Nitrogen-Enrichment Phenotypes
+ reference: doi:10.3389/fmicb.2023.1078333
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch82/rhizobia-primary.txt
+ method: Whitespace-only match in unchanged cache and fresh Europe PMC primary main text/abstract.
+- record: Panzhihua_Vanadium_Titanium_Tailings
+ node: Pongamia Nodulation and Nitrogen-Enrichment Phenotypes
+ reference: doi:10.3389/fmicb.2023.1078333
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch82/rhizobia-primary.txt
+ method: Whitespace-only match in unchanged cache and fresh Europe PMC primary main text/abstract.
+- record: Panzhihua_Vanadium_Titanium_Tailings
+ node: Pongamia Nodulation and Nitrogen-Enrichment Phenotypes
+ reference: doi:10.3389/fmicb.2023.1078333
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch82/rhizobia-primary.txt
+ method: Whitespace-only match in unchanged cache and fresh Europe PMC primary main text/abstract.
+- record: Panzhihua_Vanadium_Titanium_Tailings
+ node: Pongamia Nodulation and Nitrogen-Enrichment Phenotypes
+ reference: doi:10.3389/fmicb.2023.1078333
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch82/rhizobia-primary.txt
+ method: Whitespace-only match in unchanged cache and fresh Europe PMC primary main text/abstract.
+- record: Panzhihua_Vanadium_Titanium_Tailings
+ node: Metal Tolerance of Cultured Tailings Bacillus
+ reference: doi:10.1371/journal.pone.0106618
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch82/bacteria-primary.txt
+ method: Whitespace-only match in unchanged cache and fresh Europe PMC primary main text/abstract.
+- record: Panzhihua_Vanadium_Titanium_Tailings
+ node: Ochrobactrum Isolate Growth-Promoter Production
+ reference: doi:10.1371/journal.pone.0106618
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch82/bacteria-primary.txt
+ method: Whitespace-only match in unchanged cache and fresh Europe PMC primary main text/abstract.
+- record: Panzhihua_Vanadium_Titanium_Tailings
+ node: Ochrobactrum Isolate Growth-Promoter Production
+ reference: doi:10.1371/journal.pone.0106618
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch82/bacteria-primary.txt
+ method: Whitespace-only match in unchanged cache and fresh Europe PMC primary main text/abstract.
+- record: Panzhihua_Vanadium_Titanium_Tailings
+ node: Ochrobactrum Isolate Growth-Promoter Production
+ reference: doi:10.1371/journal.pone.0106618
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch82/bacteria-primary.txt
+ method: Whitespace-only match in unchanged cache and fresh Europe PMC primary main text/abstract.
+- record: Parachlorella_Saccharomyces_Mutualistic_Coculture
+ node: Proposed Reciprocal Oxygen and Carbon Dioxide Exchange
+ reference: PMID:42217804
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch82/algae-primary.txt
+ method: Whitespace-only match in unchanged cache and fresh Europe PMC primary main text/abstract.
+- record: Parachlorella_Saccharomyces_Mutualistic_Coculture
+ node: Yeast support of microalgal growth and lipid accumulation
+ reference: PMID:42217804
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch82/algae-primary.txt
+ method: Whitespace-only match in unchanged cache and fresh Europe PMC primary main text/abstract.
+- record: Parachlorella_Saccharomyces_Mutualistic_Coculture
+ node: Proposed EPS-Derived Metabolic Support of Yeast
+ reference: PMID:42217804
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch82/algae-primary.txt
+ method: Whitespace-only match in unchanged cache and fresh Europe PMC primary main text/abstract.
+- record: Parachlorella_Saccharomyces_Mutualistic_Coculture
+ node: Fourfold Coculture Biomass and Lipid Increase
+ reference: PMID:42217804
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch82/algae-primary.txt
+ method: Whitespace-only match in unchanged cache and fresh Europe PMC primary main text/abstract.
+- record: Parmigiano_NWS_Set2_LAB_Triculture
+ node: Set 2 milk acidification enhancement
+ reference: PMID:41859451
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch82/milk-primary.txt
+ method: Whitespace-only match in unchanged cache and fresh Europe PMC primary main text/abstract.
+- record: Parmigiano_NWS_Set2_LAB_Triculture
+ node: Set 2 milk acidification enhancement
+ reference: PMID:41859451
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch82/milk-primary.txt
+ method: Whitespace-only match in unchanged cache and fresh Europe PMC primary main text/abstract.
+- record: Parmigiano_NWS_Set2_LAB_Triculture
+ node: Set 2 milk acidification enhancement
+ reference: PMID:41859451
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch82/milk-primary.txt
+ method: Whitespace-only match in unchanged cache and fresh Europe PMC primary main text/abstract.
+- record: Parmigiano_NWS_Set2_LAB_Triculture
+ node: C001.27-C5I3 acidification enhancement
+ reference: PMID:41859451
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch82/milk-primary.txt
+ method: Whitespace-only match in unchanged cache and fresh Europe PMC primary main text/abstract.
+- record: Parmigiano_NWS_Set2_LAB_Triculture
+ node: LBB04-C5I3 reduced acidification subset
+ reference: PMID:41859451
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch82/milk-primary.txt
+ method: Whitespace-only match in unchanged cache and fresh Europe PMC primary main text/abstract.
+- record: Parmigiano_NWS_Set2_LAB_Triculture
+ node: LBB04-C5I3 reduced acidification subset
+ reference: PMID:41859451
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch82/milk-primary.txt
+ method: Whitespace-only match in unchanged cache and fresh Europe PMC primary main text/abstract.
+- record: Parmigiano_NWS_Set2_LAB_Triculture
+ node: LBB04-C5I3 reduced acidification subset
+ reference: PMID:41859451
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch82/milk-primary.txt
+ method: Whitespace-only match in unchanged cache and fresh Europe PMC primary main text/abstract.
+- record: Parmigiano_NWS_Set2_LAB_Triculture
+ node: Set 2 Triculture D-Lactate Accumulation
+ reference: PMID:41859451
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch82/milk-primary.txt
+ method: Whitespace-only match in unchanged cache and fresh Europe PMC primary main text/abstract.
+- record: Peanut_Seed_Bacterial_CS_SynCom
+ node: SA-Related Defense Response and Proposed Resistance Mediation
+ reference: PMID:38520150
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch82/peanut-primary.txt
+ method: Whitespace-only match in unchanged cache and fresh Europe PMC primary main text/abstract.
+- record: Peanut_Seed_Bacterial_CS_SynCom
+ node: CS Fusarium Root-Rot Resistance
+ reference: PMID:38520150
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch82/peanut-primary.txt
+ method: Whitespace-only match in unchanged cache and fresh Europe PMC primary main text/abstract.
+- record: Peanut_Seed_Bacterial_CS_SynCom
+ node: CS Aspergillus and Aflatoxin Suppression
+ reference: PMID:38520150
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch82/peanut-primary.txt
+ method: Whitespace-only match in unchanged cache and fresh Europe PMC primary main text/abstract.
+- record: Peanut_Seed_Bacterial_CS_SynCom
+ node: CS Aspergillus and Aflatoxin Suppression
+ reference: PMID:38520150
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch82/peanut-primary.txt
+ method: Whitespace-only match in unchanged cache and fresh Europe PMC primary main text/abstract.
+- record: Peanut_Seed_Bacterial_CS_SynCom
+ node: Reported Peanut Seedling Growth Promotion
+ reference: PMID:38520150
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch82/peanut-primary.txt
+ method: Whitespace-only match in unchanged cache and fresh Europe PMC primary main text/abstract.
+cache_changes: []
+edison:
+ required_for_this_repair: false
+ required_for_unresolved_extensions: true
+ provider_submissions: 0
+ credits_spent: 0
+ dry_runs:
+ - community_id: CommunityMech:000295
+ job: LITERATURE
+ query_chars: 9111
+ query_sha256: 4515810ac69377baf2c9f943bc9854134ccf49cc1a302b3133d192fef3319ded
+ meta_path: /private/tmp/communitymech-batch82/edison-algae/Parachlorella_Saccharomyces_Mutualistic_Coculture-edison-literature-causal-meta.yaml
+ authorization: Scoped asynchronous question unanswered; preselection is not approval.
+limitations:
+- Fresh pre-paper baseline:460records/920caches across both roots. Four whole records,20existing nodes and11arrows
+ reviewed.15nodes/3arrows retained;5nodes/8arrows removed with explicit dispositions. No new topology.
+- Four complete fresh primary main texts/captions read:2023rhizobia,2014bulk-soil bacteria,2018S.saheli and2026milk.
+ Seven further abstracts checked; one is a2023vanadium review, context only. Original figure pixels, separate supplements
+ and raw data not audited. Exact matching does not establish entailment.
+- Normal publisher access for algae returned403 and peanut DOI delivery was unavailable. No bypass attempted, and
+ no inference that unseen full-text assays do not exist. Primary evidence copies remain outside the repository;
+ unchanged caches are not globally recertified.
+- Tailings is a composite record with unresolved canonical identities, source/site mismatches and internally inconsistent2023species/metal
+ labels. Positive nodulation/N enrichment, Bacillus metal tolerance and Ochrobactrum production survive. The carbon-remediation
+ result remains evidence-backed in discussion, not assigned to an unsupported pair or every canonical member. Removed
+ Polaromonas and redundancy claims expose genuine disconnected taxa; no auditor or taxonomy changes.
+- Algal fourfold culture output, yeast-associated algal support, viability and biophysical observations survive.
+ Gas exchange is contextual/proposed and EPS transfer is explicitly possible. Full text and future biophysical
+ topology remain1681. No algal-only biomass assignment or mutualistic benefit inferred from bulk output.
+- Milk retains four positive/negative assay phenotypes, exact set2rate exception and mixed D-lactate pool. Two arrows
+ were subset comparison and measurement-to-inference, not causal mediation. Prior1077-1079fixes and molecular gap
+ preserved; no broad downgrade of the controlled fermentation comparisons.
+- Peanut retains four biological outcomes and the author-reported SA-to-resistance direction as partial. Two methods
+ nodes/four workflow arrows removed. Toxin reduction is not automatically chemical degradation; abstract growth
+ conclusion is not CS-specific. Raw engineering/taxonomy/environment YAML anchors preserved.
+- 954all-state issue titles/bodies searched; all5matched bodies1077-1079,497,258read, plus prior milk review and
+ Polaromonas author-request lead.64local matching files from ignored/hidden-inclusive search excluding.git/docs/site/references_cache.
+ No exhaustive historical PR/comment audit. Some combined/cache outputs truncated; relevant fresh main texts read
+ in bounded chunks, and absence claims do not depend on truncated output.
+- One9111character one-community algae Edison causal dry run; zero provider submissions/credits. Scoped paid question
+ unanswered. Earlier paid denials and pending scopes unchanged. Repair1676-1679remainOPENuntil protected-main merge;
+ research1680-1682andmetadata1683remainOPENafterward.
+- Four append-only histories;456otherrecords920caches and all raw non-graph blocks preserved, not certified. Render/description
+ checks are not browser screenshots. Self-adversarial review is not independent approval or completion of the corpus
+ objective.
+- Final adversarial reread narrowed ambiguous Ochrobactrum IAA/siderophore overlap, removed gas-metabolite annotations
+ from the aggregate productivity endpoint, and marked peanut toxin-mechanism evidence PARTIAL. Affected checks
+ rerun with earlier outputs retained; four original append-only histories unchanged.
+records:
+- path: kb/communities/Panzhihua_Vanadium_Titanium_Tailings.yaml
+ id: CommunityMech:000051
+ original_sha256: 55fef813d29b6d4d1bc64f1ff95a3c83c10ee17cee03bfcdad892ac80b5547bd
+ record_sha256: b5a4255cbaf18200e7002f843bffa20e870a5d1676d5c7cf3f4036c9ce92b0a0
+ status: needs_research
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261007-four-records-batch82.yaml
+ scope: Whole record and every existing node/arrow; sparse and missing structures reviewed, not whole-record certification.
+ summary: Preserve nodulation and plant nitrogen/growth with provisional species mapping and no PP1 misassignment.;
+ Preserve directly assayed Bacillus metal tolerance instead of cross-species phytoextraction claims.; Preserve
+ Ochrobactrum IAA/siderophore production without nodule-isolate conflation or interbacterial transfer.
+ renamed_nodes:
+ Nitrogen Fixation and Plant Growth Promotion: Pongamia Nodulation and Nitrogen-Enrichment Phenotypes
+ Metal Phytoextraction and Plant-Microbe Metal Tolerance: Metal Tolerance of Cultured Tailings Bacillus
+ Ochrobactrum Metal Tolerance and Metabolic Flexibility: Ochrobactrum Isolate Growth-Promoter Production
+ node_decisions:
+ - node: Pongamia Nodulation and Nitrogen-Enrichment Phenotypes
+ original_node: Nitrogen Fixation and Plant Growth Promotion
+ rationale: Preserve nodulation and plant nitrogen/growth with provisional species mapping and no PP1 misassignment.
+ - node: Metal Tolerance of Cultured Tailings Bacillus
+ original_node: Metal Phytoextraction and Plant-Microbe Metal Tolerance
+ rationale: Preserve directly assayed Bacillus metal tolerance instead of cross-species phytoextraction claims.
+ - node: Ochrobactrum Isolate Growth-Promoter Production
+ original_node: Ochrobactrum Metal Tolerance and Metabolic Flexibility
+ rationale: Preserve Ochrobactrum IAA/siderophore production without nodule-isolate conflation or interbacterial
+ transfer.
+ removed_node_decisions:
+ - node: Dissimilatory Vanadium Reduction and Immobilization
+ rationale: External-system Polaromonas mechanism is not verified in this Panzhihua community; preserve source/identity
+ gap rather than assert site-specific occurrence.
+ - node: Soil Organic Carbon Transformation
+ rationale: Positive community-level carbon result preserved with evidence in discussion; unsupported Bacillus-to-Bradyrhizobium
+ attribution and cross-study feedback cannot stand in this composite graph.
+ - node: Rhizobial Functional Redundancy in Nitrogen Fixation
+ rationale: Co-isolation and separate plant assays do not demonstrate bacterial mutualism, compensatory redundancy
+ or community resilience; positive host assays retained.
+ edges_before:
+ - source: Nitrogen Fixation and Plant Growth Promotion
+ target: Soil Organic Carbon Transformation
+ description: Nitrogen enrichment stimulates plant growth, increasing carbon input to soil
+ - source: Soil Organic Carbon Transformation
+ target: Nitrogen Fixation and Plant Growth Promotion
+ description: Improved soil carbon supports rhizobial populations and symbiosis
+ edges_after: []
+ retained_edge_decisions: []
+ removed_edge_decisions:
+ - source: Nitrogen Fixation and Plant Growth Promotion
+ target: Soil Organic Carbon Transformation
+ description: Nitrogen enrichment stimulates plant growth, increasing carbon input to soil
+ rationale: Cross-study nitrogen/carbon feedback lacks exact-system support.
+ - source: Soil Organic Carbon Transformation
+ target: Nitrogen Fixation and Plant Growth Promotion
+ description: Improved soil carbon supports rhizobial populations and symbiosis
+ rationale: Cross-study nitrogen/carbon feedback lacks exact-system support.
+ references:
+ - doi:10.1371/journal.pone.0106618
+ - doi:10.3389/fmicb.2023.1078333
+ issues:
+ - 1676
+ - 1680
+ - 1683
+ - 497
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Panzhihua_Vanadium_Titanium_Tailings/2026-10-07T064410Z-codex-cbadb7.yaml
+ source_review:
+ - source: rhizobia
+ url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC10315665/fullTextXML
+ scope: Primary abstract and complete main body, embedded tables and captions; not separate supplements, raw
+ data or original figure pixels.
+ - source: bacteria
+ url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC4154735/fullTextXML
+ scope: Primary abstract and complete main body, embedded tables and captions; not separate supplements, raw
+ data or original figure pixels.
+ - source: saheli
+ url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC6119820/fullTextXML
+ scope: Primary abstract and complete main body, embedded tables and captions; not separate supplements, raw
+ data or original figure pixels.
+ - source: vanadium
+ url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A33125214+AND+SRC%3AMED&format=json&resultType=core
+ scope: Primary abstract only; full text not available through Europe PMC.
+ - source: v_review
+ url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=DOI%3A10.1021%2Facs.est.3c04508+AND+SRC%3AMED&format=json&resultType=core
+ scope: Review abstract used only as context, not primary exact-system evidence.
+ - source: carbon
+ url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A38744211+AND+SRC%3AMED&format=json&resultType=core
+ scope: Primary abstract only; full text not available through Europe PMC.
+ - source: pond
+ url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A38181847+AND+SRC%3AMED&format=json&resultType=core
+ scope: Primary abstract only; full text not available through Europe PMC.
+ - source: deposition
+ url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=DOI%3A10.1016%2Fj.scitotenv.2024.170082+AND+SRC%3AMED&format=json&resultType=core
+ scope: Primary abstract only; full text not available through Europe PMC.
+- path: kb/communities/Parachlorella_Saccharomyces_Mutualistic_Coculture.yaml
+ id: CommunityMech:000295
+ original_sha256: d21296c4b76847d2507d13d6e4d88eb58a262cf966efdc99887b36d5365872be
+ record_sha256: ee3166c701c928154cb1f46337d3d43a5ee56946d75f93fcd6d4ac8ecb3f8b82
+ status: needs_research
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261007-four-records-batch82.yaml
+ scope: Whole record and every existing node/arrow; sparse and missing structures reviewed, not whole-record certification.
+ summary: Retain gas-exchange hypothesis with contextual evidence and partial productivity mediation.; Preserve
+ reported yeast-associated growth/lipid physiology without reciprocal-benefit inference.; Preserve yeast viability
+ and physical observations while qualifying EPS transfer.; Preserve fourfold culture-level output without unsupported
+ algal-only attribution.
+ renamed_nodes:
+ Reciprocal oxygen/carbon dioxide gas exchange: Proposed Reciprocal Oxygen and Carbon Dioxide Exchange
+ EPS-mediated metabolic support of yeast by microalgae: Proposed EPS-Derived Metabolic Support of Yeast
+ Fourfold Microalgal Biomass and Lipid Increase: Fourfold Coculture Biomass and Lipid Increase
+ node_decisions:
+ - node: Proposed Reciprocal Oxygen and Carbon Dioxide Exchange
+ original_node: Reciprocal oxygen/carbon dioxide gas exchange
+ rationale: Retain gas-exchange hypothesis with contextual evidence and partial productivity mediation.
+ - node: Yeast support of microalgal growth and lipid accumulation
+ original_node: Yeast support of microalgal growth and lipid accumulation
+ rationale: Preserve reported yeast-associated growth/lipid physiology without reciprocal-benefit inference.
+ - node: Proposed EPS-Derived Metabolic Support of Yeast
+ original_node: EPS-mediated metabolic support of yeast by microalgae
+ rationale: Preserve yeast viability and physical observations while qualifying EPS transfer.
+ - node: Fourfold Coculture Biomass and Lipid Increase
+ original_node: Fourfold Microalgal Biomass and Lipid Increase
+ rationale: Preserve fourfold culture-level output without unsupported algal-only attribution.
+ removed_node_decisions: []
+ edges_before:
+ - source: Reciprocal oxygen/carbon dioxide gas exchange
+ target: Fourfold Microalgal Biomass and Lipid Increase
+ description: 'Reciprocal O2/CO2 exchange helps the coculture overcome microalgal productivity limits and contributes
+ to the higher biomass and lipid production measured in coculture.
+
+ '
+ - source: Yeast support of microalgal growth and lipid accumulation
+ target: Fourfold Microalgal Biomass and Lipid Increase
+ description: 'Yeast sustains microalgal growth after glucose depletion and promotes lipid accumulation, directly
+ supporting the coculture biomass and lipid endpoint.
+
+ '
+ edges_after:
+ - source: Proposed Reciprocal Oxygen and Carbon Dioxide Exchange
+ target: Fourfold Coculture Biomass and Lipid Increase
+ description: HYPOTHESIZED - Photosynthetic oxygen and respiratory carbon dioxide exchange could support coculture
+ productivity. The accessible abstract does not isolate the contribution of gas exchange to the observed fourfold
+ biomass/lipid increase.
+ - source: Yeast support of microalgal growth and lipid accumulation
+ target: Fourfold Coculture Biomass and Lipid Increase
+ description: PARTIAL - Yeast-associated maintenance of algal growth and nutrient-competition-associated lipid
+ accumulation provide the reported physiological contribution to higher coculture biomass/lipid production.
+ This does not apportion the fourfold endpoint among growth support, gas exchange and other mechanisms.
+ retained_edge_decisions:
+ - source: Proposed Reciprocal Oxygen and Carbon Dioxide Exchange
+ target: Fourfold Coculture Biomass and Lipid Increase
+ description: HYPOTHESIZED - Photosynthetic oxygen and respiratory carbon dioxide exchange could support coculture
+ productivity. The accessible abstract does not isolate the contribution of gas exchange to the observed fourfold
+ biomass/lipid increase.
+ rationale: HYPOTHESIZED - Photosynthetic oxygen and respiratory carbon dioxide exchange could support coculture
+ productivity. The accessible abstract does not isolate the contribution of gas exchange to the observed fourfold
+ biomass/lipid increase.
+ - source: Yeast support of microalgal growth and lipid accumulation
+ target: Fourfold Coculture Biomass and Lipid Increase
+ description: PARTIAL - Yeast-associated maintenance of algal growth and nutrient-competition-associated lipid
+ accumulation provide the reported physiological contribution to higher coculture biomass/lipid production.
+ This does not apportion the fourfold endpoint among growth support, gas exchange and other mechanisms.
+ rationale: PARTIAL - Yeast-associated maintenance of algal growth and nutrient-competition-associated lipid
+ accumulation provide the reported physiological contribution to higher coculture biomass/lipid production.
+ This does not apportion the fourfold endpoint among growth support, gas exchange and other mechanisms.
+ removed_edge_decisions: []
+ references:
+ - PMID:42217804
+ issues:
+ - 1677
+ - 1681
+ - 1683
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Parachlorella_Saccharomyces_Mutualistic_Coculture/2026-10-07T064410Z-codex-f546b7.yaml
+ source_review:
+ - source: algae
+ url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A42217804+AND+SRC%3AMED&format=json&resultType=core
+ scope: Primary abstract only; full text not available through Europe PMC.
+- path: kb/communities/Parmigiano_NWS_Set2_LAB_Triculture.yaml
+ id: CommunityMech:000431
+ original_sha256: 30ee3514d36c0388f2872616a0ca9db775fb8bd59c73dd734bab184e75c25143
+ record_sha256: 1ca3e250bbd757768243c691712d2139c54a2da4e59570360417188516bb4b2c
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261007-four-records-batch82.yaml
+ scope: Whole record and every existing node/arrow; sparse and missing structures reviewed, not whole-record certification.
+ summary: Preserve triculture total-lactate advantage and the exact set2 rate exception.; Preserve the positive
+ St/Ld pair phenotype without a subset-to-triculture causal arrow.; Preserve the negative Lh/Ld fermentation
+ response without inventing its mechanism.; Represent measured triculture D-lactate rather than exclusive C5I3
+ activity.
+ renamed_nodes:
+ C5I3 activity enhancement in mixed culture: Set 2 Triculture D-Lactate Accumulation
+ node_decisions:
+ - node: Set 2 milk acidification enhancement
+ original_node: Set 2 milk acidification enhancement
+ rationale: Preserve triculture total-lactate advantage and the exact set2 rate exception.
+ - node: C001.27-C5I3 acidification enhancement
+ original_node: C001.27-C5I3 acidification enhancement
+ rationale: Preserve the positive St/Ld pair phenotype without a subset-to-triculture causal arrow.
+ - node: LBB04-C5I3 reduced acidification subset
+ original_node: LBB04-C5I3 reduced acidification subset
+ rationale: Preserve the negative Lh/Ld fermentation response without inventing its mechanism.
+ - node: Set 2 Triculture D-Lactate Accumulation
+ original_node: C5I3 activity enhancement in mixed culture
+ rationale: Represent measured triculture D-lactate rather than exclusive C5I3 activity.
+ removed_node_decisions: []
+ edges_before:
+ - source: Set 2 milk acidification enhancement
+ target: C5I3 activity enhancement in mixed culture
+ description: Higher D-lactate in set 2 tricultures than in the corresponding C5I3 monoculture indicated that
+ the Ld member remained viable and metabolically active in the mixed culture.
+ - source: C001.27-C5I3 acidification enhancement
+ target: Set 2 milk acidification enhancement
+ description: The strong St + Ld pairwise response was retained within the complete LBB04/C001.27/C5I3 triculture.
+ edges_after: []
+ retained_edge_decisions: []
+ removed_edge_decisions:
+ - source: Set 2 milk acidification enhancement
+ target: C5I3 activity enhancement in mixed culture
+ description: Higher D-lactate in set 2 tricultures than in the corresponding C5I3 monoculture indicated that
+ the Ld member remained viable and metabolically active in the mixed culture.
+ rationale: Comparison or measurement-to-inference relation is not a demonstrated causal process.
+ - source: C001.27-C5I3 acidification enhancement
+ target: Set 2 milk acidification enhancement
+ description: The strong St + Ld pairwise response was retained within the complete LBB04/C001.27/C5I3 triculture.
+ rationale: Comparison or measurement-to-inference relation is not a demonstrated causal process.
+ references:
+ - PMID:41859451
+ issues:
+ - 1678
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Parmigiano_NWS_Set2_LAB_Triculture/2026-10-07T064410Z-codex-83f8ae.yaml
+ source_review:
+ - source: milk
+ url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12996222/fullTextXML
+ scope: Primary abstract and complete main body, embedded tables and captions; not separate supplements, raw
+ data or original figure pixels.
+- path: kb/communities/Peanut_Seed_Bacterial_CS_SynCom.yaml
+ id: CommunityMech:000102
+ original_sha256: 26b177adf07923e285bccf6a362239af2001e5d16d8c0e4033abb1529c86c5d3
+ record_sha256: faf0f4193278f1fc4c65f5666b79129629c3e1add520245a3ff941596b96513c
+ status: needs_research
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261007-four-records-batch82.yaml
+ scope: Whole record and every existing node/arrow; sparse and missing structures reviewed, not whole-record certification.
+ summary: Retain author-reported SA-defense direction with unresolved pathway controls.; Preserve best-CS root-rot
+ resistance without member-specific attribution.; Preserve fungal/toxin suppression while separating abundance
+ from chemical degradation.; Preserve reported growth without unsupported CS-specific mediation.
+ renamed_nodes:
+ Salicylic-Acid Defense Activation: SA-Related Defense Response and Proposed Resistance Mediation
+ CS Seedling Growth Promotion: Reported Peanut Seedling Growth Promotion
+ node_decisions:
+ - node: SA-Related Defense Response and Proposed Resistance Mediation
+ original_node: Salicylic-Acid Defense Activation
+ rationale: Retain author-reported SA-defense direction with unresolved pathway controls.
+ - node: CS Fusarium Root-Rot Resistance
+ original_node: CS Fusarium Root-Rot Resistance
+ rationale: Preserve best-CS root-rot resistance without member-specific attribution.
+ - node: CS Aspergillus and Aflatoxin Suppression
+ original_node: CS Aspergillus and Aflatoxin Suppression
+ rationale: Preserve fungal/toxin suppression while separating abundance from chemical degradation.
+ - node: Reported Peanut Seedling Growth Promotion
+ original_node: CS Seedling Growth Promotion
+ rationale: Preserve reported growth without unsupported CS-specific mediation.
+ removed_node_decisions:
+ - node: Peanut Seed SynCom Construction
+ rationale: Construction is experimental workflow, not an ecological causal process.
+ - node: Dual Fungal Challenge Evaluation
+ rationale: Challenge evaluation is experimental workflow, not a biological causal process.
+ edges_before:
+ - source: Peanut Seed SynCom Construction
+ target: Dual Fungal Challenge Evaluation
+ description: 'The defined seed-bacterial SynComs were then challenged against peanut seed Aspergillus flavus
+ contamination and Fusarium oxysporum seedling root rot.
+
+ '
+ - source: Peanut Seed SynCom Construction
+ target: CS Seedling Growth Promotion
+ description: 'The constructed seed-bacterial CS SynCom was evaluated for its ability to improve peanut seedling
+ growth in parallel with fungal suppression.
+
+ '
+ - source: Dual Fungal Challenge Evaluation
+ target: Salicylic-Acid Defense Activation
+ description: 'The Fusarium oxysporum seedling challenge showed the CS community''s strongest root-rot protection
+ and associated that phenotype with salicylic-acid-related induced resistance.
+
+ '
+ - source: Dual Fungal Challenge Evaluation
+ target: CS Aspergillus and Aflatoxin Suppression
+ description: 'The Aspergillus flavus seed challenge directly measured seed fungal reproduction and aflatoxin
+ production after CS inoculation.
+
+ '
+ - source: Salicylic-Acid Defense Activation
+ target: CS Fusarium Root-Rot Resistance
+ description: 'Defense enzyme and salicylic-acid responses were the reported host defense axis underlying CS-mediated
+ Fusarium root-rot resistance.
+
+ '
+ edges_after:
+ - source: SA-Related Defense Response and Proposed Resistance Mediation
+ target: CS Fusarium Root-Rot Resistance
+ description: PARTIAL - The authors attribute increased root-rot resistance to higher defense-enzyme activity
+ and SA-related induced resistance. Retain this reported causal direction, while noting that the accessible
+ abstract does not expose pathway-blocking, rescue or distal-tissue controls needed to isolate SA mediation.
+ retained_edge_decisions:
+ - source: SA-Related Defense Response and Proposed Resistance Mediation
+ target: CS Fusarium Root-Rot Resistance
+ description: PARTIAL - The authors attribute increased root-rot resistance to higher defense-enzyme activity
+ and SA-related induced resistance. Retain this reported causal direction, while noting that the accessible
+ abstract does not expose pathway-blocking, rescue or distal-tissue controls needed to isolate SA mediation.
+ rationale: PARTIAL - The authors attribute increased root-rot resistance to higher defense-enzyme activity and
+ SA-related induced resistance. Retain this reported causal direction, while noting that the accessible abstract
+ does not expose pathway-blocking, rescue or distal-tissue controls needed to isolate SA mediation.
+ removed_edge_decisions:
+ - source: Peanut Seed SynCom Construction
+ target: Dual Fungal Challenge Evaluation
+ description: 'The defined seed-bacterial SynComs were then challenged against peanut seed Aspergillus flavus
+ contamination and Fusarium oxysporum seedling root rot.
+
+ '
+ rationale: Experimental construction/evaluation workflow, not biological causation.
+ - source: Peanut Seed SynCom Construction
+ target: CS Seedling Growth Promotion
+ description: 'The constructed seed-bacterial CS SynCom was evaluated for its ability to improve peanut seedling
+ growth in parallel with fungal suppression.
+
+ '
+ rationale: Experimental construction/evaluation workflow, not biological causation.
+ - source: Dual Fungal Challenge Evaluation
+ target: Salicylic-Acid Defense Activation
+ description: 'The Fusarium oxysporum seedling challenge showed the CS community''s strongest root-rot protection
+ and associated that phenotype with salicylic-acid-related induced resistance.
+
+ '
+ rationale: Experimental construction/evaluation workflow, not biological causation.
+ - source: Dual Fungal Challenge Evaluation
+ target: CS Aspergillus and Aflatoxin Suppression
+ description: 'The Aspergillus flavus seed challenge directly measured seed fungal reproduction and aflatoxin
+ production after CS inoculation.
+
+ '
+ rationale: Experimental construction/evaluation workflow, not biological causation.
+ references:
+ - PMID:38520150
+ issues:
+ - 1679
+ - 1682
+ - 1683
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Peanut_Seed_Bacterial_CS_SynCom/2026-10-07T064410Z-codex-0a3882.yaml
+ source_review:
+ - source: peanut
+ url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A38520150+AND+SRC%3AMED&format=json&resultType=core
+ scope: Primary abstract only; full text not available through Europe PMC.
diff --git a/reports/causal_graph_review/inventory.tsv b/reports/causal_graph_review/inventory.tsv
index 12c19ea87..6872f029f 100644
--- a/reports/causal_graph_review/inventory.tsv
+++ b/reports/causal_graph_review/inventory.tsv
@@ -291,10 +291,10 @@ kb/communities/PPCP_Wastewater_Sphingopyxis_Ochrobactrum_Apiotrichum_SMC.yaml Co
kb/communities/PPHET_Hybrid_Photosynthetic_PHB_Microbiome.yaml CommunityMech:000359 85af3a32baae2c92ed06ee398e552add0b70df7c4e014fb13d7b7ad6f3901cd5 4 1 78.8 reports/causal_graph_review/decisions/20261007-four-records-batch81.yaml reviewed
kb/communities/PSY_Transgenic_Rice_Rhizosphere_Methane_Community.yaml CommunityMech:000216 5a3fa99c9184f7631ff2a2eb44892f5cc0dc5af877d13bded8adf7c615d18472 4 3 92.5 reports/causal_graph_review/decisions/20261007-four-records-batch81.yaml needs_research
kb/communities/Panax_Bacillus_Serratia_RootRot_Biocontrol_SynCom.yaml CommunityMech:000460 1009ce440481b3b01af2965e9e1e18e64980923b1276133d3fae2fb8923c1eb7 4 0 63.8 reports/causal_graph_review/decisions/20261007-four-records-batch81.yaml reviewed
-kb/communities/Panzhihua_Vanadium_Titanium_Tailings.yaml CommunityMech:000051 55fef813d29b6d4d1bc64f1ff95a3c83c10ee17cee03bfcdad892ac80b5547bd 6 2 100.0 pending
-kb/communities/Parachlorella_Saccharomyces_Mutualistic_Coculture.yaml CommunityMech:000295 d21296c4b76847d2507d13d6e4d88eb58a262cf966efdc99887b36d5365872be 4 2 100.0 pending
-kb/communities/Parmigiano_NWS_Set2_LAB_Triculture.yaml CommunityMech:000431 30ee3514d36c0388f2872616a0ca9db775fb8bd59c73dd734bab184e75c25143 4 2 90.0 pending
-kb/communities/Peanut_Seed_Bacterial_CS_SynCom.yaml CommunityMech:000102 26b177adf07923e285bccf6a362239af2001e5d16d8c0e4033abb1529c86c5d3 6 5 100.0 pending
+kb/communities/Panzhihua_Vanadium_Titanium_Tailings.yaml CommunityMech:000051 b5a4255cbaf18200e7002f843bffa20e870a5d1676d5c7cf3f4036c9ce92b0a0 3 0 57.5 reports/causal_graph_review/decisions/20261007-four-records-batch82.yaml needs_research
+kb/communities/Parachlorella_Saccharomyces_Mutualistic_Coculture.yaml CommunityMech:000295 ee3166c701c928154cb1f46337d3d43a5ee56946d75f93fcd6d4ac8ecb3f8b82 4 2 90.0 reports/causal_graph_review/decisions/20261007-four-records-batch82.yaml needs_research
+kb/communities/Parmigiano_NWS_Set2_LAB_Triculture.yaml CommunityMech:000431 1ca3e250bbd757768243c691712d2139c54a2da4e59570360417188516bb4b2c 4 0 65.0 reports/causal_graph_review/decisions/20261007-four-records-batch82.yaml reviewed
+kb/communities/Peanut_Seed_Bacterial_CS_SynCom.yaml CommunityMech:000102 faf0f4193278f1fc4c65f5666b79129629c3e1add520245a3ff941596b96513c 4 1 90.0 reports/causal_graph_review/decisions/20261007-four-records-batch82.yaml needs_research
kb/communities/Pelagerythrobacter_Salinicola_PES_Pyrene_Degradation_SynCom.yaml CommunityMech:000340 58d2a2a277b85ee0af0bbb51a51913c96001b62bfa82e554b7bda716be742b9b 3 2 100.0 pending
kb/communities/Pelotomaculum_Methanocella_Propionate_RNASeq_Coculture.yaml CommunityMech:000190 bb9483d04163c1df53929e60873f075a00e66d1364f8cf5779248da608b1054c 4 2 100.0 reports/causal_graph_review/decisions/20261004-four-records.yaml reviewed
kb/communities/Pelotomaculum_Methanothermobacter_Syntrophy.yaml CommunityMech:000052 7516752d58a30c6fdeff03b3cca057fb402e815f698668f96e798d87a63273a3 3 2 100.0 pending
diff --git a/reports/causal_graph_review/summary.json b/reports/causal_graph_review/summary.json
index 9a95b4fe2..25039ea0d 100644
--- a/reports/causal_graph_review/summary.json
+++ b/reports/causal_graph_review/summary.json
@@ -2,14 +2,14 @@
"scope": "Every YAML under kb/communities and data/isolates; filesystem discovery includes hidden/ignored files.",
"semantic_review_rule": "Structural checks and readiness scores do not establish causal support. Completed reviews must match the current record SHA-256, cover every node once with a rationale, and reproduce the current edge list.",
"records": 460,
- "nodes": 1444,
- "edges": 609,
+ "nodes": 1439,
+ "edges": 601,
"records_without_nodes": 8,
- "records_without_edges": 168,
+ "records_without_edges": 170,
"review_status_counts": {
- "needs_research": 36,
- "pending": 168,
- "reviewed": 256
+ "needs_research": 39,
+ "pending": 164,
+ "reviewed": 257
},
"structural_defects": [],
"network_audit": [
@@ -1204,6 +1204,127 @@
"message": "Taxon 'Legionella MAGs' has no interactions",
"severity": "warning"
},
+ {
+ "record": "Panzhihua_Vanadium_Titanium_Tailings",
+ "type": "DISCONNECTED",
+ "taxon": "Polaromonas species",
+ "taxon_id": "NCBITaxon:52972",
+ "taxon_data": {
+ "taxon_term": {
+ "preferred_term": "Polaromonas species",
+ "term": {
+ "id": "NCBITaxon:52972",
+ "label": "Polaromonas"
+ },
+ "gtdb_grounding_status": "GROUNDED",
+ "gtdb_classification": {
+ "gtdb_id": "GTDB:g__Polaromonas",
+ "gtdb_taxon": "Polaromonas",
+ "gtdb_lineage": "d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas",
+ "ncbi_source_id": "NCBITaxon:52972",
+ "majority_fraction": 1.0,
+ "support_genomes": 12,
+ "total_genomes": 12,
+ "is_reclassified": false,
+ "mapping_source": "kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-07-25) [grounded at g__ rank; 1 GTDB taxa under the NCBI taxon]"
+ },
+ "notes": "Betaproteobacteria capable of dissimilatory vanadium reduction in contaminated mine environments. While not specifically reported in the Panzhihua tailings studies reviewed, Polaromonas is a well-established V(V)-reducing organism in circumneutral pH vanadium mine tailings in northern China and likely present in Panzhihua tailings based on similar environmental conditions (circumneutral pH 6.5-7.5, moderate temperature, high vanadium concentrations). Polaromonas performs dissimilatory V(V) reduction to V(IV) using c-type cytochromes (cymA, omcA) and membrane-associated nitrate reductases (narG). The organism couples oxidation of organic electron donors (lactate, acetate) to V(V) reduction, decreasing vanadium solubility by 2-3 orders of magnitude through precipitation of V(IV) species. This metabolic capacity is critical for vanadium immobilization during anaerobic microsites in revegetated tailings. Polaromonas also reduces Fe(III), Mn(IV), and As(V), contributing to polymetallic redox cycling in V-Ti tailings.\n"
+ },
+ "functional_role": [
+ "PRIMARY_DEGRADER",
+ "SYNTROPHIC_PARTNER"
+ ],
+ "abundance_level": "COMMON",
+ "abundance_value": "Inferred presence based on V-reducing capacity in similar V-Ti tailings",
+ "evidence": [
+ {
+ "reference": "PMID:33125214",
+ "supports": "SUPPORT",
+ "evidence_source": "IN_VIVO",
+ "snippet": "Further, VV-reducing enrichments indicated that bacteria associated with Polaromonas, a genus belonging to the family Burkholderiaceae, were potentially responsible for VV reduction",
+ "explanation": "Establishes V(V) reduction mechanism relevant to Panzhihua conditions"
+ }
+ ]
+ },
+ "message": "Taxon 'Polaromonas species' has no interactions",
+ "severity": "warning"
+ },
+ {
+ "record": "Panzhihua_Vanadium_Titanium_Tailings",
+ "type": "DISCONNECTED",
+ "taxon": "Rhizobium pisi",
+ "taxon_id": "NCBITaxon:574561",
+ "taxon_data": {
+ "taxon_term": {
+ "preferred_term": "Rhizobium pisi",
+ "term": {
+ "id": "NCBITaxon:574561",
+ "label": "Rhizobium pisi"
+ },
+ "gtdb_grounding_status": "UNRESOLVED",
+ "notes": "Fast-growing nitrogen-fixing rhizobium traditionally associated with pea (Pisum sativum) but adapted to form nodules with P. pinnata in V-Ti tailings. One isolate was identified as R. pisi, demonstrating the promiscuity of rhizobial-legume associations under metal stress conditions. R. pisi contributes to nitrogen enrichment of tailings soil through symbiotic nitrogen fixation and produces plant growth-promoting substances including IAA. The presence of R. pisi indicates that phytoremediation legumes can recruit diverse rhizobial species from indigenous tailings microbiota, not limited to traditional host-specific symbionts. This metabolic flexibility enhances the resilience and effectiveness of legume-rhizobia partnerships in contaminated environments.\n"
+ },
+ "functional_role": [
+ "PRIMARY_DEGRADER",
+ "NITROGEN_FIXING_SYMBIONT"
+ ],
+ "abundance_level": "RARE",
+ "abundance_value": "One isolate from P. pinnata nodules",
+ "evidence": [
+ {
+ "reference": "doi:10.3389/fmicb.2023.1078333",
+ "supports": "SUPPORT",
+ "evidence_source": "IN_VIVO",
+ "snippet": "Based on the phylogenetic analysis of 16S rRNA and four house-keeping genes (atpD, recA, rpoB, glnII), twelve isolates were identified as Bradyrhizobium pachyrhizi, four as Ochrobactrum anthropic, three as Rhizobium selenitireducens and one as Rhizobium pisi",
+ "explanation": "Documents R. pisi presence in V-Ti tailings rhizobia"
+ }
+ ]
+ },
+ "message": "Taxon 'Rhizobium pisi' has no interactions",
+ "severity": "warning"
+ },
+ {
+ "record": "Panzhihua_Vanadium_Titanium_Tailings",
+ "type": "DISCONNECTED",
+ "taxon": "Rhizobium selenitireducens",
+ "taxon_id": "NCBITaxon:1336235",
+ "taxon_data": {
+ "taxon_term": {
+ "preferred_term": "Rhizobium selenitireducens",
+ "term": {
+ "id": "NCBITaxon:1336235",
+ "label": "Paenirhizobium selenitireducens ATCC BAA-1503"
+ },
+ "gtdb_grounding_status": "UNRESOLVED",
+ "notes": "Nitrogen-fixing alphaproteobacterium capable of selenium reduction and heavy metal tolerance, isolated from P. pinnata root nodules in V-Ti tailings. Three isolates were identified as R. selenitireducens, demonstrating nitrogen-fixing capacity and variable tolerance to Cu, Ni, Mn, and Zn. This species possesses unique metabolic capabilities including selenite reduction to elemental selenium, suggesting potential for metalloid detoxification in addition to nitrogen fixation. R. selenitireducens contributes to the functional diversity of the rhizobial community, providing complementary metal tolerance mechanisms and nitrogen enrichment. The organism forms effective symbioses with leguminous plants under metal stress conditions, promoting plant growth through nitrogen provision and IAA production. Like other tailings rhizobia, R. selenitireducens serves as a competent candidate for bioremediation of soils contaminated with multifarious metals due to its combined nitrogen-fixing and metal tolerance phenotypes.\n"
+ },
+ "functional_role": [
+ "PRIMARY_DEGRADER",
+ "CROSS_FEEDER",
+ "NITROGEN_FIXING_SYMBIONT"
+ ],
+ "abundance_level": "COMMON",
+ "abundance_value": "Three isolates from P. pinnata nodules",
+ "evidence": [
+ {
+ "reference": "doi:10.3389/fmicb.2023.1078333",
+ "supports": "SUPPORT",
+ "evidence_source": "IN_VIVO",
+ "snippet": "Based on the phylogenetic analysis of 16S rRNA and four house-keeping genes (atpD, recA, rpoB, glnII), twelve isolates were identified as Bradyrhizobium pachyrhizi, four as Ochrobactrum anthropic, three as Rhizobium selenitireducens and one as Rhizobium pisi",
+ "explanation": "Documents R. selenitireducens presence in tailings rhizobia"
+ },
+ {
+ "reference": "doi:10.3389/fmicb.2023.1078333",
+ "supports": "SUPPORT",
+ "evidence_source": "IN_VIVO",
+ "snippet": "effective rhizobia strains for bioremediation of VTM tailings or other contaminated soils",
+ "explanation": "Establishes metal tolerance and bioremediation potential"
+ }
+ ]
+ },
+ "message": "Taxon 'Rhizobium selenitireducens' has no interactions",
+ "severity": "warning"
+ },
{
"record": "Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom",
"type": "UNKNOWN_TARGET",
diff --git a/reports/causal_graph_review/validation-20261007-batch82.json b/reports/causal_graph_review/validation-20261007-batch82.json
new file mode 100644
index 000000000..5de697b26
--- /dev/null
+++ b/reports/causal_graph_review/validation-20261007-batch82.json
@@ -0,0 +1,1810 @@
+{
+ "base_commit": "c2f23b2053bde3329f2619bc45accadcec415d19",
+ "scope": [
+ "kb/communities/Panzhihua_Vanadium_Titanium_Tailings.yaml",
+ "kb/communities/Parachlorella_Saccharomyces_Mutualistic_Coculture.yaml",
+ "kb/communities/Parmigiano_NWS_Set2_LAB_Triculture.yaml",
+ "kb/communities/Peanut_Seed_Bacterial_CS_SynCom.yaml"
+ ],
+ "reference_validator_version": "0.1.7",
+ "results": [
+ {
+ "check": "Parmigiano_NWS_Set2_LAB_Triculture-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Parmigiano_NWS_Set2_LAB_Triculture.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch82/Parmigiano_NWS_Set2_LAB_Triculture-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Parmigiano_NWS_Set2_LAB_Triculture-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch82/Parmigiano_NWS_Set2_LAB_Triculture-strict.tsv",
+ "kb/communities/Parmigiano_NWS_Set2_LAB_Triculture.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch82/Parmigiano_NWS_Set2_LAB_Triculture-strict.log",
+ "log_sha256": "54336b2cab32be4050221616be938dd272665931d66660d9bf91038cf490d124",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch82/src/communitymech/schema/communitymech.yaml\n\n=== validate-strict summary ===\n files scanned: 1\n files with ERROR: 0\n total ERROR rows: 0\n TSV: /private/tmp/communitymech-batch82/Parmigiano_NWS_Set2_LAB_Triculture-strict.tsv\n"
+ },
+ {
+ "check": "Parmigiano_NWS_Set2_LAB_Triculture-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Parmigiano_NWS_Set2_LAB_Triculture.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch82/Parmigiano_NWS_Set2_LAB_Triculture-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Parmigiano_NWS_Set2_LAB_Triculture-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Parmigiano_NWS_Set2_LAB_Triculture.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch82/Parmigiano_NWS_Set2_LAB_Triculture-references.log",
+ "log_sha256": "fe44cafb66ec8e3c1dbe94b7416b9219ec627b7292ffaf8075f3f584210e16d6",
+ "output_tail": "Validating kb/communities/Parmigiano_NWS_Set2_LAB_Triculture.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n",
+ "explained_output_tail": "Validating kb/communities/Parmigiano_NWS_Set2_LAB_Triculture.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n"
+ },
+ {
+ "check": "Parmigiano_NWS_Set2_LAB_Triculture-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Parmigiano_NWS_Set2_LAB_Triculture.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
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+ "expected_exit_codes": [
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+ ],
+ "log": "/private/tmp/communitymech-batch82/Parmigiano_NWS_Set2_LAB_Triculture-snippets.log",
+ "log_sha256": "32d5c17677a000100a0b22db07734e7af95b7e2b40f82a74ed21b581b1a6d4f5",
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+ },
+ {
+ "check": "Parmigiano_NWS_Set2_LAB_Triculture-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Parmigiano_NWS_Set2_LAB_Triculture.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch82/Parmigiano_NWS_Set2_LAB_Triculture-rank.log",
+ "log_sha256": "54da650ebda0543bb006588c73586444e9b560c79838c18542c254365653fe03",
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+ {
+ "check": "Parmigiano_NWS_Set2_LAB_Triculture-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Parmigiano_NWS_Set2_LAB_Triculture/2026-10-07T064410Z-codex-83f8ae.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch82/Parmigiano_NWS_Set2_LAB_Triculture-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Panzhihua_Vanadium_Titanium_Tailings-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
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+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch82/Panzhihua_Vanadium_Titanium_Tailings-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Panzhihua_Vanadium_Titanium_Tailings-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch82/Panzhihua_Vanadium_Titanium_Tailings-strict.tsv",
+ "kb/communities/Panzhihua_Vanadium_Titanium_Tailings.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch82/Panzhihua_Vanadium_Titanium_Tailings-strict.log",
+ "log_sha256": "03f9cd2decfb00a336ac2d01b12e683cfc2f4a40fee5393ed97127a59656baf7",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch82/src/communitymech/schema/communitymech.yaml\n\n=== validate-strict summary ===\n files scanned: 1\n files with ERROR: 0\n total ERROR rows: 0\n TSV: /private/tmp/communitymech-batch82/Panzhihua_Vanadium_Titanium_Tailings-strict.tsv\n"
+ },
+ {
+ "check": "Panzhihua_Vanadium_Titanium_Tailings-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Panzhihua_Vanadium_Titanium_Tailings.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch82/Panzhihua_Vanadium_Titanium_Tailings-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Panzhihua_Vanadium_Titanium_Tailings-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Panzhihua_Vanadium_Titanium_Tailings.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch82/Panzhihua_Vanadium_Titanium_Tailings-references.log",
+ "log_sha256": "3f64ba449b8387132fae50f534230df4316ad26b52101be583e5235733defe42",
+ "output_tail": "Validating kb/communities/Panzhihua_Vanadium_Titanium_Tailings.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n",
+ "explained_output_tail": "Validating kb/communities/Panzhihua_Vanadium_Titanium_Tailings.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n"
+ },
+ {
+ "check": "Panzhihua_Vanadium_Titanium_Tailings-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Panzhihua_Vanadium_Titanium_Tailings.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch82/Panzhihua_Vanadium_Titanium_Tailings-snippets.log",
+ "log_sha256": "c6a2cbc65462837d05b8f423e5c9f2afd274b753c96bc99871f5d542998b97e6",
+ "output_tail": "# 41 evidence snippets scanned across 1 files\n MATCH 40\n RENDERING 1\n ASSEMBLED 0\n WEAK 0\n MISMATCH 0\n NOCONTENT 0\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n\n# MISMATCH/WEAK detail\n\n# Files by RENDERING (faithful quote; differs from cache only by\n# punctuation/whitespace/Greek \u2014 this is what validate-references flags)\n 1 kb/communities/Panzhihua_Vanadium_Titanium_Tailings.yaml\n\n# Top files by NOCONTENT (unverifiable; cache stub/missing)\n\n# ASSEMBLED (every part is in the source; the join is not \u2014\n# a table flattened into prose, or a quote welded from two places)\n"
+ },
+ {
+ "check": "Panzhihua_Vanadium_Titanium_Tailings-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Panzhihua_Vanadium_Titanium_Tailings.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch82/Panzhihua_Vanadium_Titanium_Tailings-rank.log",
+ "log_sha256": "0fff273d158acbbf7b1fae08c067bbe3fd9bfa6fb8f7c2223c3c28ca16a08e17",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000051\",\n \"name\": \"Panzhihua Vanadium Titanium Tailings Community\",\n \"score\": 57.5,\n \"taxonomy\": 6,\n \"connected_taxa\": 3,\n \"disconnected_taxa\": 3,\n \"ecological_interactions\": 3,\n \"downstream_edges\": 0,\n \"interaction_evidence\": 8,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"downstream\",\n \"metabolites_or_biological_processes\",\n \"interaction_type\",\n \"disconnected_taxa\"\n ],\n \"path\": \"kb/communities/Panzhihua_Vanadium_Titanium_Tailings.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Panzhihua_Vanadium_Titanium_Tailings-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Panzhihua_Vanadium_Titanium_Tailings/2026-10-07T064410Z-codex-cbadb7.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch82/Panzhihua_Vanadium_Titanium_Tailings-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Parachlorella_Saccharomyces_Mutualistic_Coculture-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Parachlorella_Saccharomyces_Mutualistic_Coculture.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch82/Parachlorella_Saccharomyces_Mutualistic_Coculture-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Parachlorella_Saccharomyces_Mutualistic_Coculture-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch82/Parachlorella_Saccharomyces_Mutualistic_Coculture-strict.tsv",
+ "kb/communities/Parachlorella_Saccharomyces_Mutualistic_Coculture.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch82/Parachlorella_Saccharomyces_Mutualistic_Coculture-strict.log",
+ "log_sha256": "de5fb648f5a61d8d2c7e3c0147dcaabbd06dd732376d09071bdf0c6d7e116598",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch82/src/communitymech/schema/communitymech.yaml\n\n=== validate-strict summary ===\n files scanned: 1\n files with ERROR: 0\n total ERROR rows: 0\n TSV: /private/tmp/communitymech-batch82/Parachlorella_Saccharomyces_Mutualistic_Coculture-strict.tsv\n"
+ },
+ {
+ "check": "Parachlorella_Saccharomyces_Mutualistic_Coculture-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Parachlorella_Saccharomyces_Mutualistic_Coculture.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch82/Parachlorella_Saccharomyces_Mutualistic_Coculture-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Parachlorella_Saccharomyces_Mutualistic_Coculture-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Parachlorella_Saccharomyces_Mutualistic_Coculture.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch82/Parachlorella_Saccharomyces_Mutualistic_Coculture-references.log",
+ "log_sha256": "40a95601fdbdd613f1b71acc5b28890e9c22fe0091c2cfe03e04fb05fa7632c1",
+ "output_tail": "Validating kb/communities/Parachlorella_Saccharomyces_Mutualistic_Coculture.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n",
+ "explained_output_tail": "Validating kb/communities/Parachlorella_Saccharomyces_Mutualistic_Coculture.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n"
+ },
+ {
+ "check": "Parachlorella_Saccharomyces_Mutualistic_Coculture-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Parachlorella_Saccharomyces_Mutualistic_Coculture.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch82/Parachlorella_Saccharomyces_Mutualistic_Coculture-snippets.log",
+ "log_sha256": "1835af07ebf0373785ca2d25de18c6984a3cbcfdec0d2610f1d8437504408710",
+ "output_tail": "# 10 evidence snippets scanned across 1 files\n MATCH 10\n RENDERING 0\n ASSEMBLED 0\n WEAK 0\n MISMATCH 0\n NOCONTENT 0\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n\n# MISMATCH/WEAK detail\n\n# Files by RENDERING (faithful quote; differs from cache only by\n# punctuation/whitespace/Greek \u2014 this is what validate-references flags)\n\n# Top files by NOCONTENT (unverifiable; cache stub/missing)\n\n# ASSEMBLED (every part is in the source; the join is not \u2014\n# a table flattened into prose, or a quote welded from two places)\n"
+ },
+ {
+ "check": "Parachlorella_Saccharomyces_Mutualistic_Coculture-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Parachlorella_Saccharomyces_Mutualistic_Coculture.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch82/Parachlorella_Saccharomyces_Mutualistic_Coculture-rank.log",
+ "log_sha256": "e9bac370ad2bfe7af9f6b575a0570e16cff68b3efaf0427108783c11b56fa14e",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000295\",\n \"name\": \"Parachlorella kessleri + Saccharomyces cerevisiae Mutualistic Co-culture\",\n \"score\": 90.0,\n \"taxonomy\": 2,\n \"connected_taxa\": 2,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 4,\n \"downstream_edges\": 2,\n \"interaction_evidence\": 4,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Parachlorella_Saccharomyces_Mutualistic_Coculture.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Parachlorella_Saccharomyces_Mutualistic_Coculture-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Parachlorella_Saccharomyces_Mutualistic_Coculture/2026-10-07T064410Z-codex-f546b7.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch82/Parachlorella_Saccharomyces_Mutualistic_Coculture-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Peanut_Seed_Bacterial_CS_SynCom-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Peanut_Seed_Bacterial_CS_SynCom.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch82/Peanut_Seed_Bacterial_CS_SynCom-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Peanut_Seed_Bacterial_CS_SynCom-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch82/Peanut_Seed_Bacterial_CS_SynCom-strict.tsv",
+ "kb/communities/Peanut_Seed_Bacterial_CS_SynCom.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch82/Peanut_Seed_Bacterial_CS_SynCom-strict.log",
+ "log_sha256": "ab3f60036b4bfdce3e678ae1cabd41e5cb25ad37cf2eef1f315dcc482009797d",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch82/src/communitymech/schema/communitymech.yaml\n\n=== validate-strict summary ===\n files scanned: 1\n files with ERROR: 0\n total ERROR rows: 0\n TSV: /private/tmp/communitymech-batch82/Peanut_Seed_Bacterial_CS_SynCom-strict.tsv\n"
+ },
+ {
+ "check": "Peanut_Seed_Bacterial_CS_SynCom-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Peanut_Seed_Bacterial_CS_SynCom.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch82/Peanut_Seed_Bacterial_CS_SynCom-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Peanut_Seed_Bacterial_CS_SynCom-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Peanut_Seed_Bacterial_CS_SynCom.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch82/Peanut_Seed_Bacterial_CS_SynCom-references.log",
+ "log_sha256": "daf681cc2b2be74ede5f55cee39bd6564756930eeb6796441d7ff47a5b5b0924",
+ "output_tail": "Validating kb/communities/Peanut_Seed_Bacterial_CS_SynCom.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n",
+ "explained_output_tail": "Validating kb/communities/Peanut_Seed_Bacterial_CS_SynCom.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n"
+ },
+ {
+ "check": "Peanut_Seed_Bacterial_CS_SynCom-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Peanut_Seed_Bacterial_CS_SynCom.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch82/Peanut_Seed_Bacterial_CS_SynCom-snippets.log",
+ "log_sha256": "aec1f2712a64b5cd549f668dd69d5e1ab54d6d5693d8f53bbce26317b755b383",
+ "output_tail": "# 11 evidence snippets scanned across 1 files\n MATCH 11\n RENDERING 0\n ASSEMBLED 0\n WEAK 0\n MISMATCH 0\n NOCONTENT 0\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n\n# MISMATCH/WEAK detail\n\n# Files by RENDERING (faithful quote; differs from cache only by\n# punctuation/whitespace/Greek \u2014 this is what validate-references flags)\n\n# Top files by NOCONTENT (unverifiable; cache stub/missing)\n\n# ASSEMBLED (every part is in the source; the join is not \u2014\n# a table flattened into prose, or a quote welded from two places)\n"
+ },
+ {
+ "check": "Peanut_Seed_Bacterial_CS_SynCom-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Peanut_Seed_Bacterial_CS_SynCom.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch82/Peanut_Seed_Bacterial_CS_SynCom-rank.log",
+ "log_sha256": "2f5e8d5cad6af64e885b42c22df0af806ff22b003755ea2870afbd9ad1f68e2d",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000102\",\n \"name\": \"Peanut Seed Bacterial CS SynCom\",\n \"score\": 90.0,\n \"taxonomy\": 1,\n \"connected_taxa\": 1,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 4,\n \"downstream_edges\": 1,\n \"interaction_evidence\": 5,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"additional_downstream\"\n ],\n \"path\": \"kb/communities/Peanut_Seed_Bacterial_CS_SynCom.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Peanut_Seed_Bacterial_CS_SynCom-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Peanut_Seed_Bacterial_CS_SynCom/2026-10-07T064410Z-codex-0a3882.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch82/Peanut_Seed_Bacterial_CS_SynCom-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "inventory",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "reports/causal_graph_review/build_inventory.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch82/inventory.log",
+ "log_sha256": "958411d1fafdae087f258654ffd58045e7a8cc6a128d9add53f36748cd6dae48",
+ "output_tail": "{\n \"scope\": \"Every YAML under kb/communities and data/isolates; filesystem discovery includes hidden/ignored files.\",\n \"semantic_review_rule\": \"Structural checks and readiness scores do not establish causal support. Completed reviews must match the current record SHA-256, cover every node once with a rationale, and reproduce the current edge list.\",\n \"records\": 460,\n \"nodes\": 1439,\n \"edges\": 601,\n \"records_without_nodes\": 8,\n \"records_without_edges\": 170,\n \"review_status_counts\": {\n \"needs_research\": 39,\n \"pending\": 164,\n \"reviewed\": 257\n },\n \"structural_defects\": []\n}\n"
+ },
+ {
+ "check": "network",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "communitymech.cli",
+ "audit-network",
+ "--json"
+ ],
+ "exit_code": 1,
+ "expected_exit_codes": [
+ 1
+ ],
+ "log": "/private/tmp/communitymech-batch82/network.log",
+ "log_sha256": "c4ff432a38a90ba8d231a4f632b4fefacb5bd830c2612cdd13de01b353c37f9f",
+ "output_tail": " \"evidence\": [\n {\n \"reference\": \"doi:10.3389/fmicb.2023.1078333\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VIVO\",\n \"snippet\": \"Based on the phylogenetic analysis of 16S rRNA and four house-keeping genes (atpD, recA, rpoB, glnII), twelve isolates were identified as Bradyrhizobium pachyrhizi, four as Ochrobactrum anthropic, three as Rhizobium selenitireducens and one as Rhizobium pisi\",\n \"explanation\": \"Documents R. selenitireducens presence in tailings rhizobia\"\n },\n {\n \"reference\": \"doi:10.3389/fmicb.2023.1078333\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VIVO\",\n \"snippet\": \"effective rhizobia strains for bioremediation of VTM tailings or other contaminated soils\",\n \"explanation\": \"Establishes metal tolerance and bioremediation potential\"\n }\n ]\n },\n \"message\": \"Taxon 'Rhizobium selenitireducens' has no interactions\"\n }\n ],\n \"Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom\": [\n {\n \"type\": \"UNKNOWN_TARGET\",\n \"interaction\": \"Twelve-Strain SynCom Suppression of Sclerotinia Sclerotia\",\n \"interaction_index\": 0,\n \"taxon\": \"Sclerotinia sclerotiorum\",\n \"severity\": \"warning\",\n \"message\": \"Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)\"\n },\n {\n \"type\": \"UNKNOWN_TARGET\",\n \"interaction\": \"Trinickia MC Key Contribution to Sclerotia Mortality\",\n \"interaction_index\": 1,\n \"taxon\": \"Sclerotinia sclerotiorum\",\n \"severity\": \"warning\",\n \"message\": \"Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)\"\n }\n ],\n \"Space_Habitat_SevenMember_Stress_Tolerance_SynCom\": [\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Acinetobacter radioresistens 50V1\",\n \"taxon_id\": \"NCBITaxon:40216\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Acinetobacter radioresistens 50V1\",\n \"term\": {\n \"id\": \"NCBITaxon:40216\",\n \"label\": \"Acinetobacter radioresistens\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The isolate came from the preflight Mars Odyssey Orbiter; ontology grounding is at species level.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"50V1\",\n \"genome_accession\": \"GCA_002834555.1\"\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Acinetobacter radioresistens | 50V1 | Preflight Mars Odyssey Orbiter | \\u2013 | Mccoy et al., 2012 | GCA_002834555.1 | TSYB/TSYA | 37 \\u00b0C | 16\\u201318 h\",\n \"explanation\": \"Identifies A. radioresistens 50V1 as a consortium member and gives its spacecraft-associated source, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Acinetobacter radioresistens 50V1' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Micrococcus luteus W4-Al-K1\",\n \"taxon_id\": \"NCBITaxon:1270\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Micrococcus luteus W4-Al-K1\",\n \"term\": {\n \"id\": \"NCBITaxon:1270\",\n \"label\": \"Micrococcus luteus\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The isolate was recovered from an ISS aluminum-case touch array; ontology grounding is at species level.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"W4-Al-K1\",\n \"genome_accession\": \"GCA_057816565.1\"\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Micrococcus luteus | W4-Al-K1 | ISS, Touch Array Aluminum Case | - | Kr\\u00e4mer et al., 2025 | GCA_057816565.1 | NB, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies M. luteus W4-Al-K1 as a consortium member and gives its ISS source, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Micrococcus luteus W4-Al-K1' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Propionibacterium cyclohexanicum TA-12T\",\n \"taxon_id\": \"NCBITaxon:64702\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Propionibacterium cyclohexanicum TA-12T\",\n \"term\": {\n \"id\": \"NCBITaxon:64702\",\n \"label\": \"Propionibacterium cyclohexanicum\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the P. cyclohexanicum type strain as a biosafety-level-1 representative.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"TA-12T\",\n \"genome_accession\": \"GCA_900111365\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"16859\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Propionibacterium cyclohexanicum | TA-12 T | Spoilt Orange Juice | DSM 16859 T | Kusano et al., 1997 | GCA_900111365 | BHI, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies P. cyclohexanicum TA-12T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Propionibacterium cyclohexanicum TA-12T' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Pseudomonas antarctica CMS 35T\",\n \"taxon_id\": \"NCBITaxon:219572\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Pseudomonas antarctica CMS 35T\",\n \"term\": {\n \"id\": \"NCBITaxon:219572\",\n \"label\": \"Pseudomonas antarctica\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the P. antarctica type strain as a biosafety-level-1 Pseudomonas surrogate.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"CMS 35T\",\n \"genome_accession\": \"GCA_010634845\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"15318\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Pseudomonas antarctica | CMS 35 T | Antarctica | DSM 15318 T | Reddy et al., 2004 | GCA_010634845 | TSYB/TSYA | Ambient | 12\\u201316 h\",\n \"explanation\": \"Identifies P. antarctica CMS 35T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Pseudomonas antarctica CMS 35T' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Staphylococcus capitis K1-2-2-23\",\n \"taxon_id\": \"NCBITaxon:29388\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Staphylococcus capitis K1-2-2-23\",\n \"term\": {\n \"id\": \"NCBITaxon:29388\",\n \"label\": \"Staphylococcus capitis\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The isolate was recovered from ISS V2A steel; ontology grounding is at species level.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"K1-2-2-23\",\n \"genome_accession\": \"GCA_025272695\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"111179\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Staphylococcus capitis | K1-2-2-23 | ISS, V2A Steel | DSM 111179 | Sobisch et al., 2019 | GCA_025272695 | TSYB/TSYA | 37 \\u00b0C | 16\\u201324 h\",\n \"explanation\": \"Identifies S. capitis K1-2-2-23 as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Staphylococcus capitis K1-2-2-23' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Streptococcus halotolerans HTS9T\",\n \"taxon_id\": \"NCBITaxon:1814128\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Streptococcus halotolerans HTS9T\",\n \"term\": {\n \"id\": \"NCBITaxon:1814128\",\n \"label\": \"Streptococcus halotolerans\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the S. halotolerans type strain as a biosafety-level-1 representative.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"HTS9T\",\n \"genome_accession\": \"GCA_001598035\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"101996\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Streptococcus halotolerans | HTS9 T | Respiratory Tract of Marmota himalayana | DSM 101996 T | Niu et al., 2016 | GCA_001598035 | 2xLB, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies S. halotolerans HTS9T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Streptococcus halotolerans HTS9T' has no interactions\"\n }\n ]\n}\n"
+ },
+ {
+ "check": "rank-all",
+ "command": [
+ "just",
+ "rank-causal-graphs"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
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+ ],
+ "log": "/private/tmp/communitymech-batch82/rank-all.log",
+ "log_sha256": "7a025a86407b974399d9d33d9ef37aac5375177c69294aa1c4756d3bbb36e46f",
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Consortium\t4\t4\t0\t4\t2\t5\t\t0\t0\n406\t100.0\tkb/communities/Subsurface_Carboxydocella_CO_Aquifer_Community.yaml\tCommunityMech:000251\tSubsurface Carboxydocella CO-Oxidation Aquifer Community\t1\t1\t0\t5\t2\t5\t\t0\t0\n407\t100.0\tkb/communities/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom.yaml\tCommunityMech:000312\tSuillus clintonianus-Bacillus altitudinis Thiamine Cross-Feeding SynCom\t3\t3\t0\t4\t3\t4\t\t0\t0\n408\t100.0\tkb/communities/Sulfide_Spring_Autotrophic_CPR_Biofilm.yaml\tCommunityMech:000222\tSulfide Spring Autotrophic CPR-Hosting Biofilm\t3\t3\t0\t3\t2\t4\t\t0\t0\n409\t100.0\tkb/communities/SynComBac10_Chicken_Intestinal_SynCom.yaml\tCommunityMech:000127\tSynComBac10 Chicken Intestinal SynCom\t3\t3\t0\t3\t2\t3\t\t0\t0\n410\t100.0\tkb/communities/SynCom_ARC_Peanut_Aflatoxin_Nodulation.yaml\tCommunityMech:000314\tSynCom ARC Peanut Aflatoxin-Control and Nodulation-Coupling Community\t5\t5\t0\t3\t2\t3\t\t0\t0\n411\t100.0\tkb/communities/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation.yaml\tCommunityMech:000278\tSynCom BsBv Cigar Tobacco Leaf Fermentation\t2\t2\t0\t3\t2\t3\t\t0\t0\n412\t100.0\tkb/communities/SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System.yaml\tCommunityMech:000285\tSynCom + Chlorella sorokiniana Biogas-slurry Coupling System\t2\t2\t0\t5\t3\t5\t\t0\t0\n413\t100.0\tkb/communities/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience.yaml\tCommunityMech:000302\tSynCom MetG2 Rhizobacteria Sugarcane Stress Resilience\t2\t2\t0\t3\t2\t4\t\t0\t0\n414\t100.0\tkb/communities/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus.yaml\tCommunityMech:000283\tSesame-flavor Baijiu Fuqu SynCom (13-genus)\t13\t13\t0\t3\t2\t3\t\t0\t0\n415\t100.0\tkb/communities/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture.yaml\tCommunityMech:000272\tSynCom Y Agrobacterium-Bacillus Biofilm Biocontrol 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SynCom\t4\t4\t0\t3\t2\t4\t\t0\t0\n456\t100.0\tkb/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml\tCommunityMech:000354\tYarrowia lipolytica Division-of-Labor Lipid Consortium\t2\t2\t0\t3\t2\t3\t\t0\t0\n457\t100.0\tkb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml\tCommunityMech:000164\tYogurt Two-Species Starter Culture\t2\t2\t0\t4\t2\t9\t\t0\t0\n458\t100.0\tkb/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml\tCommunityMech:000210\tZymomonas-E. coli Exometabolomics-Designed Obligate Mutualism\t2\t2\t0\t3\t2\t6\t\t0\t0\n459\t100.0\tkb/communities/hCom2_Complex_Gut_Microbiome.yaml\tCommunityMech:000123\thCom2 Complex Gut Microbiome\t1\t1\t0\t3\t2\t3\t\t0\t0\n460\t100.0\tkb/communities/mCAFEs_Brachypodium_RCC.yaml\tCommunityMech:000078\tm-CAFEs Brachypodium Reduced Complexity Consortia\t10\t10\t0\t6\t2\t11\t\t0\t0\nPYTHONPATH=src uv run python scripts/rank_causal_graph_readiness.py \n"
+ },
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+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
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+ ],
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+ "expected_exit_codes": [
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+ "log": "/private/tmp/communitymech-batch82/render.log",
+ "log_sha256": "8d8364aefe8fc80f3bab81d6a141b0b3feac2a8c24f7b40d96d7508833de5276",
+ "output_tail": "sm.html\n \u2713 Synechococcus_Bacillus_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch82/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch82/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch82/docs/index.html\n"
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+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
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+ "communitymech.render"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch82/render-repeat.log",
+ "log_sha256": "8d8364aefe8fc80f3bab81d6a141b0b3feac2a8c24f7b40d96d7508833de5276",
+ "output_tail": "sm.html\n \u2713 Synechococcus_Bacillus_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch82/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch82/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch82/docs/index.html\n"
+ },
+ {
+ "check": "connectivity-survey",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-c",
+ "import json,pathlib,runpy\nfn=runpy.run_path('tests/test_community_level_connectivity_credit.py')['_survey']\nresult={}\nfor name,root in [('baseline',pathlib.Path('/private/tmp/communitymech-causal-batch81')),('current',pathlib.Path.cwd())]:\n paths=sorted(p for r in ['kb/communities','data/isolates'] for p in (root/r).rglob('*.yaml'))\n assert len(paths)==460\n fn.__globals__['record_files']=lambda:paths\n result[name]=fn()\nprint(json.dumps(result))\n"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch82/connectivity-survey.log",
+ "log_sha256": "52c3470443d3c017a6c5f5ffed2fbb43348feee7fe8afbea853d97b3c39e9ed4",
+ "output_tail": "{\"baseline\": {\"records\": 460, \"with_community_level\": 393, \"mixed\": 125, \"community_level_only\": 268, \"taxa\": 1511, \"credited_solely_by_the_rule\": 1240}, \"current\": {\"records\": 460, \"with_community_level\": 393, \"mixed\": 125, \"community_level_only\": 268, \"taxa\": 1511, \"credited_solely_by_the_rule\": 1240}}\n"
+ },
+ {
+ "check": "regressions",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "pytest",
+ "-q",
+ "tests/test_causal_review_batch10.py",
+ "tests/test_causal_review_batch11.py",
+ "tests/test_causal_review_batch12.py",
+ "tests/test_causal_review_batch13.py",
+ "tests/test_causal_review_batch14.py",
+ "tests/test_causal_review_batch15.py",
+ "tests/test_causal_review_batch16.py",
+ "tests/test_causal_review_batch17.py",
+ "tests/test_causal_review_batch18.py",
+ "tests/test_causal_review_batch19.py",
+ "tests/test_causal_review_batch20.py",
+ "tests/test_causal_review_batch21.py",
+ "tests/test_causal_review_batch22.py",
+ "tests/test_causal_review_batch23.py",
+ "tests/test_causal_review_batch24.py",
+ "tests/test_causal_review_batch25.py",
+ "tests/test_causal_review_batch27.py",
+ "tests/test_causal_review_batch28.py",
+ "tests/test_causal_review_batch29.py",
+ "tests/test_causal_review_batch30.py",
+ "tests/test_causal_review_batch31.py",
+ "tests/test_causal_review_batch32.py",
+ "tests/test_causal_review_batch33.py",
+ "tests/test_causal_review_batch34.py",
+ "tests/test_causal_review_batch35.py",
+ "tests/test_causal_review_batch36.py",
+ "tests/test_causal_review_batch37.py",
+ "tests/test_causal_review_batch38.py",
+ "tests/test_causal_review_batch39.py",
+ "tests/test_causal_review_batch40.py",
+ "tests/test_causal_review_batch41.py",
+ "tests/test_causal_review_batch42.py",
+ "tests/test_causal_review_batch43.py",
+ "tests/test_causal_review_batch44.py",
+ "tests/test_causal_review_batch45.py",
+ "tests/test_causal_review_batch46.py",
+ "tests/test_causal_review_batch47.py",
+ "tests/test_causal_review_batch48.py",
+ "tests/test_causal_review_batch49.py",
+ "tests/test_causal_review_batch5.py",
+ "tests/test_causal_review_batch50.py",
+ "tests/test_causal_review_batch51.py",
+ "tests/test_causal_review_batch52.py",
+ "tests/test_causal_review_batch53.py",
+ "tests/test_causal_review_batch54.py",
+ "tests/test_causal_review_batch55.py",
+ "tests/test_causal_review_batch56.py",
+ "tests/test_causal_review_batch57.py",
+ "tests/test_causal_review_batch58.py",
+ "tests/test_causal_review_batch59.py",
+ "tests/test_causal_review_batch6.py",
+ "tests/test_causal_review_batch60.py",
+ "tests/test_causal_review_batch61.py",
+ "tests/test_causal_review_batch62.py",
+ "tests/test_causal_review_batch63.py",
+ "tests/test_causal_review_batch64.py",
+ "tests/test_causal_review_batch65.py",
+ "tests/test_causal_review_batch66.py",
+ "tests/test_causal_review_batch67.py",
+ "tests/test_causal_review_batch68.py",
+ "tests/test_causal_review_batch69.py",
+ "tests/test_causal_review_batch7.py",
+ "tests/test_causal_review_batch70.py",
+ "tests/test_causal_review_batch71.py",
+ "tests/test_causal_review_batch72.py",
+ "tests/test_causal_review_batch73.py",
+ "tests/test_causal_review_batch74.py",
+ "tests/test_causal_review_batch75.py",
+ "tests/test_causal_review_batch76.py",
+ "tests/test_causal_review_batch77.py",
+ "tests/test_causal_review_batch78.py",
+ "tests/test_causal_review_batch79.py",
+ "tests/test_causal_review_batch8.py",
+ "tests/test_causal_review_batch80.py",
+ "tests/test_causal_review_batch81.py",
+ "tests/test_causal_review_batch82.py",
+ "tests/test_causal_review_batch9.py",
+ "tests/test_site_audit_fixes.py",
+ "tests/test_causal_review_inventory.py",
+ "tests/test_rank_causal_graph_readiness.py",
+ "tests/test_network_auditor.py",
+ "tests/test_participating_taxa.py",
+ "tests/test_causal_descriptions_are_published.py",
+ "tests/test_published_pages_name_real_records.py",
+ "tests/test_reference_validator_actually_validates.py",
+ "tests/test_snippet_audit_artefact_classes.py",
+ "tests/test_reference_error_annotation.py",
+ "tests/test_community_level_connectivity_credit.py",
+ "tests/test_no_paywalled_text_in_repo.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch82/regressions.log",
+ "log_sha256": "71fa2b17dcc6d9605ad8e66c4dbdd5ea2b66f10cce890993b073ee87b48c4e21",
+ "output_tail": "........................................................................ [ 9%]\n........................................................................ [ 19%]\n........................................................................ [ 29%]\n........................................................................ [ 39%]\n........................................................................ [ 48%]\n........................................................................ [ 58%]\n........................................................................ [ 68%]\n........................................................................ [ 78%]\n........................................................................ [ 88%]\n........................................................................ [ 97%]\n................ [100%]\n736 passed in 494.44s (0:08:14)\n"
+ },
+ {
+ "check": "black",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/3Q_kifQtLB624D5bBWGIf/bin/black",
+ "--check",
+ "tests/test_causal_review_batch82.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch82/black.log",
+ "log_sha256": "1a56c7cd8457fd05d978cfbd139d7bfd86e86acaa9b57668e718ef8bccc0cf48",
+ "output_tail": "All done! \u2728 \ud83c\udf70 \u2728\n1 file would be left unchanged.\n"
+ },
+ {
+ "check": "ruff",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/wCcxEYRM4HeHgwYPZemHX/bin/ruff",
+ "check",
+ "tests/test_causal_review_batch82.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch82/ruff.log",
+ "log_sha256": "82b3e6a6c090a57601d22943bd23fca9218d1031dbe5a7b754092f9a156b4f18",
+ "output_tail": "All checks passed!\n"
+ },
+ {
+ "check": "diff-check",
+ "command": [
+ "git",
+ "diff",
+ "--check"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch82/diff-check.log",
+ "log_sha256": "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855",
+ "output_tail": ""
+ },
+ {
+ "check": "primary-graph-proof",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-c",
+ "import hashlib,json,pathlib,subprocess,yaml\nP=pathlib.Path\nledger=yaml.safe_load(P('reports/causal_graph_review/decisions/20261007-four-records-batch82.yaml').read_text())\nfor p,h in ledger['primary_artifacts'].items(): assert hashlib.sha256(P(p).read_bytes()).hexdigest()==h\nfor c in ledger['snippet_checks']:\n doc=yaml.safe_load(P('kb/communities/'+c['record']+'.yaml').read_text())\n node=next(n for n in doc['ecological_interactions'] if n['name']==c['node'])\n source=''.join(P(c['matched_artifact']).read_text().split())\n assert all(''.join(e['snippet'].split()) in source for e in node['evidence'] if e['reference']==c['reference'])\nassert len(ledger['snippet_checks'])==25\nassert all(c['independent_primary_match'] and c['cache_matched'] for c in ledger['snippet_checks'])\nassert sum(len(r['node_decisions']) for r in ledger['records'])==15\nassert sum(len(r['removed_node_decisions']) for r in ledger['records'])==5\nassert sum(len(r['edges_before']) for r in ledger['records'])==11\nassert sum(len(r['edges_after']) for r in ledger['records'])==3\nassert sum(len(r['removed_edge_decisions']) for r in ledger['records'])==8\nassert [r['status'] for r in ledger['records']]==['needs_research','needs_research','reviewed','needs_research']\nmanifest=json.loads(P('/private/tmp/communitymech-batch82/primary-manifest.json').read_text())\nsources={v['reference']:''.join(P(v['extracted_body']).read_text().split()) for v in manifest.values()}\ndiscussions=0\nfor r in ledger['records']:\n old=yaml.safe_load(subprocess.check_output(['git','show',ledger['base_commit']+':'+r['path']],text=True))\n old_ids={d['discussion_id'] for d in old.get('discussions',[])}\n doc=yaml.safe_load(P(r['path']).read_text())\n for d in doc['discussions']:\n if d['discussion_id'] in old_ids: continue\n for e in d.get('evidence',[]):\n assert ''.join(e['snippet'].split()) in sources[e['reference']],(r['path'],d['discussion_id'],e['snippet'])\n discussions+=1\nprint(json.dumps(dict(fresh_primary_matched=25,cache_matched=25,new_discussion_quotations_fresh_primary_matched=discussions,new_nodes_or_arrows=0,retained_nodes=15,removed_nodes=5,retained_arrows=3,removed_arrows=8,complete_fresh_main_texts_read=4,additional_abstracts_read=7,review_abstract_context_only=1,original_figure_pixels_supplements_raw_data_audited=False)))\n"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch82/primary-graph-proof.log",
+ "log_sha256": "12c806b30ecd316c72ee1f8cd94c8726f9adc0d4ab34fba970c5688e132d5ceb",
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+ {
+ "check": "focused-final",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "pytest",
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+ "log_sha256": "836f3dc4d24eeea7e57031f6f7fe974237b23528bd3a267bc61082fefabfcdbe",
+ "output_tail": ".......... [100%]\n10 passed in 12.69s\n"
+ }
+ ],
+ "limitations": [
+ "Fresh pre-paper baseline:460records/920caches across both roots. Four whole records,20existing nodes and11arrows reviewed.15nodes/3arrows retained;5nodes/8arrows removed with explicit dispositions. No new topology.",
+ "Four complete fresh primary main texts/captions read:2023rhizobia,2014bulk-soil bacteria,2018S.saheli and2026milk. Seven further abstracts checked; one is a2023vanadium review, context only. Original figure pixels, separate supplements and raw data not audited. Exact matching does not establish entailment.",
+ "Normal publisher access for algae returned403 and peanut DOI delivery was unavailable. No bypass attempted, and no inference that unseen full-text assays do not exist. Primary evidence copies remain outside the repository; unchanged caches are not globally recertified.",
+ "Tailings is a composite record with unresolved canonical identities, source/site mismatches and internally inconsistent2023species/metal labels. Positive nodulation/N enrichment, Bacillus metal tolerance and Ochrobactrum production survive. The carbon-remediation result remains evidence-backed in discussion, not assigned to an unsupported pair or every canonical member. Removed Polaromonas and redundancy claims expose genuine disconnected taxa; no auditor or taxonomy changes.",
+ "Algal fourfold culture output, yeast-associated algal support, viability and biophysical observations survive. Gas exchange is contextual/proposed and EPS transfer is explicitly possible. Full text and future biophysical topology remain1681. No algal-only biomass assignment or mutualistic benefit inferred from bulk output.",
+ "Milk retains four positive/negative assay phenotypes, exact set2rate exception and mixed D-lactate pool. Two arrows were subset comparison and measurement-to-inference, not causal mediation. Prior1077-1079fixes and molecular gap preserved; no broad downgrade of the controlled fermentation comparisons.",
+ "Peanut retains four biological outcomes and the author-reported SA-to-resistance direction as partial. Two methods nodes/four workflow arrows removed. Toxin reduction is not automatically chemical degradation; abstract growth conclusion is not CS-specific. Raw engineering/taxonomy/environment YAML anchors preserved.",
+ "954all-state issue titles/bodies searched; all5matched bodies1077-1079,497,258read, plus prior milk review and Polaromonas author-request lead.64local matching files from ignored/hidden-inclusive search excluding.git/docs/site/references_cache. No exhaustive historical PR/comment audit. Some combined/cache outputs truncated; relevant fresh main texts read in bounded chunks, and absence claims do not depend on truncated output.",
+ "One9111character one-community algae Edison causal dry run; zero provider submissions/credits. Scoped paid question unanswered. Earlier paid denials and pending scopes unchanged. Repair1676-1679remainOPENuntil protected-main merge; research1680-1682andmetadata1683remainOPENafterward.",
+ "Four append-only histories;456otherrecords920caches and all raw non-graph blocks preserved, not certified. Render/description checks are not browser screenshots. Self-adversarial review is not independent approval or completion of the corpus objective.",
+ "Final adversarial reread narrowed ambiguous Ochrobactrum IAA/siderophore overlap, removed gas-metabolite annotations from the aggregate productivity endpoint, and marked peanut toxin-mechanism evidence PARTIAL. Affected checks rerun with earlier outputs retained; four original append-only histories unchanged.",
+ "Exact HTML-description parser and repeat-render checks, not browser screenshots. Post-commit docs-current is separate."
+ ],
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+ "command": [
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+ ],
+ "log": "/private/tmp/communitymech-batch82/pre-adversarial-Peanut_Seed_Bacterial_CS_SynCom-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n",
+ "superseded_reason": "Three residual evidence/metabolite boundaries narrowed after source-based adversarial reread; all affected gates rerun."
+ },
+ {
+ "check": "Peanut_Seed_Bacterial_CS_SynCom-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Peanut_Seed_Bacterial_CS_SynCom.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch82/pre-adversarial-Peanut_Seed_Bacterial_CS_SynCom-references.log",
+ "log_sha256": "daf681cc2b2be74ede5f55cee39bd6564756930eeb6796441d7ff47a5b5b0924",
+ "output_tail": "Validating kb/communities/Peanut_Seed_Bacterial_CS_SynCom.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n",
+ "explained_output_tail": "Validating kb/communities/Peanut_Seed_Bacterial_CS_SynCom.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n",
+ "superseded_reason": "Three residual evidence/metabolite boundaries narrowed after source-based adversarial reread; all affected gates rerun."
+ },
+ {
+ "check": "Peanut_Seed_Bacterial_CS_SynCom-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Peanut_Seed_Bacterial_CS_SynCom.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch82/pre-adversarial-Peanut_Seed_Bacterial_CS_SynCom-snippets.log",
+ "log_sha256": "aec1f2712a64b5cd549f668dd69d5e1ab54d6d5693d8f53bbce26317b755b383",
+ "output_tail": "# 11 evidence snippets scanned across 1 files\n MATCH 11\n RENDERING 0\n ASSEMBLED 0\n WEAK 0\n MISMATCH 0\n NOCONTENT 0\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n\n# MISMATCH/WEAK detail\n\n# Files by RENDERING (faithful quote; differs from cache only by\n# punctuation/whitespace/Greek \u2014 this is what validate-references flags)\n\n# Top files by NOCONTENT (unverifiable; cache stub/missing)\n\n# ASSEMBLED (every part is in the source; the join is not \u2014\n# a table flattened into prose, or a quote welded from two places)\n",
+ "superseded_reason": "Three residual evidence/metabolite boundaries narrowed after source-based adversarial reread; all affected gates rerun."
+ },
+ {
+ "check": "Peanut_Seed_Bacterial_CS_SynCom-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Peanut_Seed_Bacterial_CS_SynCom.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch82/pre-adversarial-Peanut_Seed_Bacterial_CS_SynCom-rank.log",
+ "log_sha256": "2f5e8d5cad6af64e885b42c22df0af806ff22b003755ea2870afbd9ad1f68e2d",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000102\",\n \"name\": \"Peanut Seed Bacterial CS SynCom\",\n \"score\": 90.0,\n \"taxonomy\": 1,\n \"connected_taxa\": 1,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 4,\n \"downstream_edges\": 1,\n \"interaction_evidence\": 5,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"additional_downstream\"\n ],\n \"path\": \"kb/communities/Peanut_Seed_Bacterial_CS_SynCom.yaml\"\n }\n]\n",
+ "superseded_reason": "Three residual evidence/metabolite boundaries narrowed after source-based adversarial reread; all affected gates rerun."
+ },
+ {
+ "check": "Peanut_Seed_Bacterial_CS_SynCom-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Peanut_Seed_Bacterial_CS_SynCom/2026-10-07T064410Z-codex-0a3882.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch82/pre-adversarial-Peanut_Seed_Bacterial_CS_SynCom-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n",
+ "superseded_reason": "Three residual evidence/metabolite boundaries narrowed after source-based adversarial reread; all affected gates rerun."
+ },
+ {
+ "check": "inventory",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "reports/causal_graph_review/build_inventory.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch82/pre-adversarial-inventory.log",
+ "log_sha256": "958411d1fafdae087f258654ffd58045e7a8cc6a128d9add53f36748cd6dae48",
+ "output_tail": "{\n \"scope\": \"Every YAML under kb/communities and data/isolates; filesystem discovery includes hidden/ignored files.\",\n \"semantic_review_rule\": \"Structural checks and readiness scores do not establish causal support. Completed reviews must match the current record SHA-256, cover every node once with a rationale, and reproduce the current edge list.\",\n \"records\": 460,\n \"nodes\": 1439,\n \"edges\": 601,\n \"records_without_nodes\": 8,\n \"records_without_edges\": 170,\n \"review_status_counts\": {\n \"needs_research\": 39,\n \"pending\": 164,\n \"reviewed\": 257\n },\n \"structural_defects\": []\n}\n",
+ "superseded_reason": "Three residual evidence/metabolite boundaries narrowed after source-based adversarial reread; all affected gates rerun."
+ },
+ {
+ "check": "network",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "communitymech.cli",
+ "audit-network",
+ "--json"
+ ],
+ "exit_code": 1,
+ "expected_exit_codes": [
+ 1
+ ],
+ "log": "/private/tmp/communitymech-batch82/pre-adversarial-network.log",
+ "log_sha256": "c4ff432a38a90ba8d231a4f632b4fefacb5bd830c2612cdd13de01b353c37f9f",
+ "output_tail": " \"evidence\": [\n {\n \"reference\": \"doi:10.3389/fmicb.2023.1078333\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VIVO\",\n \"snippet\": \"Based on the phylogenetic analysis of 16S rRNA and four house-keeping genes (atpD, recA, rpoB, glnII), twelve isolates were identified as Bradyrhizobium pachyrhizi, four as Ochrobactrum anthropic, three as Rhizobium selenitireducens and one as Rhizobium pisi\",\n \"explanation\": \"Documents R. selenitireducens presence in tailings rhizobia\"\n },\n {\n \"reference\": \"doi:10.3389/fmicb.2023.1078333\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VIVO\",\n \"snippet\": \"effective rhizobia strains for bioremediation of VTM tailings or other contaminated soils\",\n \"explanation\": \"Establishes metal tolerance and bioremediation potential\"\n }\n ]\n },\n \"message\": \"Taxon 'Rhizobium selenitireducens' has no interactions\"\n }\n ],\n \"Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom\": [\n {\n \"type\": \"UNKNOWN_TARGET\",\n \"interaction\": \"Twelve-Strain SynCom Suppression of Sclerotinia Sclerotia\",\n \"interaction_index\": 0,\n \"taxon\": \"Sclerotinia sclerotiorum\",\n \"severity\": \"warning\",\n \"message\": \"Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)\"\n },\n {\n \"type\": \"UNKNOWN_TARGET\",\n \"interaction\": \"Trinickia MC Key Contribution to Sclerotia Mortality\",\n \"interaction_index\": 1,\n \"taxon\": \"Sclerotinia sclerotiorum\",\n \"severity\": \"warning\",\n \"message\": \"Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)\"\n }\n ],\n \"Space_Habitat_SevenMember_Stress_Tolerance_SynCom\": [\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Acinetobacter radioresistens 50V1\",\n \"taxon_id\": \"NCBITaxon:40216\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Acinetobacter radioresistens 50V1\",\n \"term\": {\n \"id\": \"NCBITaxon:40216\",\n \"label\": \"Acinetobacter radioresistens\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The isolate came from the preflight Mars Odyssey Orbiter; ontology grounding is at species level.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"50V1\",\n \"genome_accession\": \"GCA_002834555.1\"\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Acinetobacter radioresistens | 50V1 | Preflight Mars Odyssey Orbiter | \\u2013 | Mccoy et al., 2012 | GCA_002834555.1 | TSYB/TSYA | 37 \\u00b0C | 16\\u201318 h\",\n \"explanation\": \"Identifies A. radioresistens 50V1 as a consortium member and gives its spacecraft-associated source, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Acinetobacter radioresistens 50V1' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Micrococcus luteus W4-Al-K1\",\n \"taxon_id\": \"NCBITaxon:1270\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Micrococcus luteus W4-Al-K1\",\n \"term\": {\n \"id\": \"NCBITaxon:1270\",\n \"label\": \"Micrococcus luteus\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The isolate was recovered from an ISS aluminum-case touch array; ontology grounding is at species level.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"W4-Al-K1\",\n \"genome_accession\": \"GCA_057816565.1\"\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Micrococcus luteus | W4-Al-K1 | ISS, Touch Array Aluminum Case | - | Kr\\u00e4mer et al., 2025 | GCA_057816565.1 | NB, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies M. luteus W4-Al-K1 as a consortium member and gives its ISS source, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Micrococcus luteus W4-Al-K1' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Propionibacterium cyclohexanicum TA-12T\",\n \"taxon_id\": \"NCBITaxon:64702\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Propionibacterium cyclohexanicum TA-12T\",\n \"term\": {\n \"id\": \"NCBITaxon:64702\",\n \"label\": \"Propionibacterium cyclohexanicum\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the P. cyclohexanicum type strain as a biosafety-level-1 representative.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"TA-12T\",\n \"genome_accession\": \"GCA_900111365\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"16859\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Propionibacterium cyclohexanicum | TA-12 T | Spoilt Orange Juice | DSM 16859 T | Kusano et al., 1997 | GCA_900111365 | BHI, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies P. cyclohexanicum TA-12T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Propionibacterium cyclohexanicum TA-12T' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Pseudomonas antarctica CMS 35T\",\n \"taxon_id\": \"NCBITaxon:219572\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Pseudomonas antarctica CMS 35T\",\n \"term\": {\n \"id\": \"NCBITaxon:219572\",\n \"label\": \"Pseudomonas antarctica\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the P. antarctica type strain as a biosafety-level-1 Pseudomonas surrogate.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"CMS 35T\",\n \"genome_accession\": \"GCA_010634845\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"15318\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Pseudomonas antarctica | CMS 35 T | Antarctica | DSM 15318 T | Reddy et al., 2004 | GCA_010634845 | TSYB/TSYA | Ambient | 12\\u201316 h\",\n \"explanation\": \"Identifies P. antarctica CMS 35T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Pseudomonas antarctica CMS 35T' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Staphylococcus capitis K1-2-2-23\",\n \"taxon_id\": \"NCBITaxon:29388\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Staphylococcus capitis K1-2-2-23\",\n \"term\": {\n \"id\": \"NCBITaxon:29388\",\n \"label\": \"Staphylococcus capitis\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The isolate was recovered from ISS V2A steel; ontology grounding is at species level.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"K1-2-2-23\",\n \"genome_accession\": \"GCA_025272695\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"111179\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Staphylococcus capitis | K1-2-2-23 | ISS, V2A Steel | DSM 111179 | Sobisch et al., 2019 | GCA_025272695 | TSYB/TSYA | 37 \\u00b0C | 16\\u201324 h\",\n \"explanation\": \"Identifies S. capitis K1-2-2-23 as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Staphylococcus capitis K1-2-2-23' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Streptococcus halotolerans HTS9T\",\n \"taxon_id\": \"NCBITaxon:1814128\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Streptococcus halotolerans HTS9T\",\n \"term\": {\n \"id\": \"NCBITaxon:1814128\",\n \"label\": \"Streptococcus halotolerans\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the S. halotolerans type strain as a biosafety-level-1 representative.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"HTS9T\",\n \"genome_accession\": \"GCA_001598035\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"101996\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Streptococcus halotolerans | HTS9 T | Respiratory Tract of Marmota himalayana | DSM 101996 T | Niu et al., 2016 | GCA_001598035 | 2xLB, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies S. halotolerans HTS9T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Streptococcus halotolerans HTS9T' has no interactions\"\n }\n ]\n}\n",
+ "superseded_reason": "Three residual evidence/metabolite boundaries narrowed after source-based adversarial reread; all affected gates rerun."
+ },
+ {
+ "check": "rank-all",
+ "command": [
+ "just",
+ "rank-causal-graphs"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch82/pre-adversarial-rank-all.log",
+ "log_sha256": "7a025a86407b974399d9d33d9ef37aac5375177c69294aa1c4756d3bbb36e46f",
+ "output_tail": "ities/Soybean_N_Fixation_sfSynCom.yaml\tCommunityMech:000064\tSoybean N-Fixation Simplified SynCom\t4\t4\t0\t3\t2\t3\t\t0\t0\n402\t100.0\tkb/communities/Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture.yaml\tCommunityMech:000267\tSphingobium-Rhodococcus Lignin-Dimer Valorization Coculture\t2\t2\t0\t3\t2\t7\t\t0\t0\n403\t100.0\tkb/communities/Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture.yaml\tCommunityMech:000326\tStaphylococcus-Candida Context-Dependent Biofilm Coculture\t2\t2\t0\t6\t2\t13\t\t0\t0\n404\t100.0\tkb/communities/Stordalen_Mire_Methylotrophic_Methanogenesis_Community.yaml\tCommunityMech:000254\tStordalen Mire Methylotrophic Methanogenesis Community\t3\t3\t0\t4\t4\t9\t\t0\t0\n405\t100.0\tkb/communities/Streptomyces_A2_A5_A11_M7_Pesticide_Consortium.yaml\tCommunityMech:000335\tStreptomyces A2-A5-A11-M7 Pesticide-Bioremediation Consortium\t4\t4\t0\t4\t2\t5\t\t0\t0\n406\t100.0\tkb/communities/Subsurface_Carboxydocella_CO_Aquifer_Community.yaml\tCommunityMech:000251\tSubsurface Carboxydocella CO-Oxidation Aquifer Community\t1\t1\t0\t5\t2\t5\t\t0\t0\n407\t100.0\tkb/communities/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom.yaml\tCommunityMech:000312\tSuillus clintonianus-Bacillus altitudinis Thiamine Cross-Feeding SynCom\t3\t3\t0\t4\t3\t4\t\t0\t0\n408\t100.0\tkb/communities/Sulfide_Spring_Autotrophic_CPR_Biofilm.yaml\tCommunityMech:000222\tSulfide Spring Autotrophic CPR-Hosting Biofilm\t3\t3\t0\t3\t2\t4\t\t0\t0\n409\t100.0\tkb/communities/SynComBac10_Chicken_Intestinal_SynCom.yaml\tCommunityMech:000127\tSynComBac10 Chicken Intestinal SynCom\t3\t3\t0\t3\t2\t3\t\t0\t0\n410\t100.0\tkb/communities/SynCom_ARC_Peanut_Aflatoxin_Nodulation.yaml\tCommunityMech:000314\tSynCom ARC Peanut Aflatoxin-Control and Nodulation-Coupling Community\t5\t5\t0\t3\t2\t3\t\t0\t0\n411\t100.0\tkb/communities/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation.yaml\tCommunityMech:000278\tSynCom BsBv Cigar Tobacco Leaf Fermentation\t2\t2\t0\t3\t2\t3\t\t0\t0\n412\t100.0\tkb/communities/SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System.yaml\tCommunityMech:000285\tSynCom + Chlorella sorokiniana Biogas-slurry Coupling System\t2\t2\t0\t5\t3\t5\t\t0\t0\n413\t100.0\tkb/communities/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience.yaml\tCommunityMech:000302\tSynCom MetG2 Rhizobacteria Sugarcane Stress Resilience\t2\t2\t0\t3\t2\t4\t\t0\t0\n414\t100.0\tkb/communities/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus.yaml\tCommunityMech:000283\tSesame-flavor Baijiu Fuqu SynCom (13-genus)\t13\t13\t0\t3\t2\t3\t\t0\t0\n415\t100.0\tkb/communities/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture.yaml\tCommunityMech:000272\tSynCom Y Agrobacterium-Bacillus Biofilm Biocontrol Co-culture\t2\t2\t0\t4\t2\t6\t\t0\t0\n416\t100.0\tkb/communities/Synechococcus_Azotobacter_Photoproduction_Mutualism.yaml\tCommunityMech:000207\tSynechococcus-Azotobacter Photoproduction Mutualism\t2\t2\t0\t3\t2\t6\t\t0\t0\n417\t100.0\tkb/communities/Synechococcus_Bacillus_SPC.yaml\tCommunityMech:000065\tSynechococcus-Bacillus Synthetic Photosynthetic Consortium\t2\t2\t0\t3\t2\t4\t\t0\t0\n418\t100.0\tkb/communities/Synechococcus_Ecoli_SPC.yaml\tCommunityMech:000066\tSynechococcus-E.coli Synthetic Photosynthetic Consortium\t2\t2\t0\t3\t2\t4\t\t0\t0\n419\t100.0\tkb/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml\tCommunityMech:000198\tSynechococcus-Halomonas Light-Driven PHB Coculture\t2\t2\t0\t3\t2\t6\t\t0\t0\n420\t100.0\tkb/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml\tCommunityMech:000167\tSynechococcus-Pseudomonas Phototrophic PHA and DNT Coculture\t2\t2\t0\t4\t2\t8\t\t0\t0\n421\t100.0\tkb/communities/Synechococcus_Saccharomyces_SPC.yaml\tCommunityMech:000067\tSynechococcus-Saccharomyces Synthetic Photosynthetic Consortium\t2\t2\t0\t3\t2\t4\t\t0\t0\n422\t100.0\tkb/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml\tCommunityMech:000211\tSynechococcus-Shewanella D-Lactate Biophotovoltaic Consortium\t2\t2\t0\t3\t2\t6\t\t0\t0\n423\t100.0\tkb/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml\tCommunityMech:000149\tSynthetic Lichen Synechococcus-Rhodotorula Coculture\t2\t2\t0\t3\t2\t4\t\t0\t0\n424\t100.0\tkb/communities/Syntrophobacter_Methanobacterium_Syntrophy.yaml\tCommunityMech:000068\tSyntrophobacter-Methanobacterium Syntrophic Consortium\t2\t2\t0\t3\t3\t8\t\t0\t0\n425\t100.0\tkb/communities/Syntrophobacter_Methanospirillum_Syntrophy.yaml\tCommunityMech:000069\tSyntrophobacter-Methanospirillum Syntrophic 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Community\t6\t6\t0\t5\t3\t6\t\t0\t0\n441\t100.0\tkb/communities/Tobacco_Chemotactic_Biocontrol_SynCom.yaml\tCommunityMech:000106\tTobacco Chemotactic Biocontrol SynCom\t2\t2\t0\t3\t2\t4\t\t0\t0\n442\t100.0\tkb/communities/Tomato_Oxylipin_SynCom3.yaml\tCommunityMech:000107\tTomato Oxylipin-Protective SynCom3\t3\t3\t0\t3\t2\t4\t\t0\t0\n443\t100.0\tkb/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml\tCommunityMech:000112\tTribromophenol Anaerobic Bioremediation SynCom\t3\t3\t0\t4\t3\t5\t\t0\t0\n444\t100.0\tkb/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml\tCommunityMech:000188\tTrichococcus-Syntrophomonas-Methanospirillum Butyrate Coculture\t3\t3\t0\t3\t2\t6\t\t0\t0\n445\t100.0\tkb/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml\tCommunityMech:000205\tTrichoderma-E. coli Cellulosic Isobutanol 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Community\t5\t5\t0\t3\t2\t5\t\t0\t0\n451\t100.0\tkb/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml\tCommunityMech:000213\tVariovorax-Cryptococcus Vitamin Cross-Feeding Microcosm\t2\t2\t0\t3\t2\t4\t\t0\t0\n452\t100.0\tkb/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml\tCommunityMech:000328\tWaste-Sludge Electro-Fermentation Biofilm-Suspension Community\t5\t5\t0\t4\t2\t6\t\t0\t0\n453\t100.0\tkb/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.yaml\tCommunityMech:000098\tWatermelon Rhizosphere Fusarium-Protective SynCom8\t2\t2\t0\t3\t2\t7\t\t0\t0\n454\t100.0\tkb/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml\tCommunityMech:000255\tWetland Oxygen-Sulfate Greenhouse Gas Microcosm Community\t3\t3\t0\t3\t2\t6\t\t0\t0\n455\t100.0\tkb/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.yaml\tCommunityMech:000118\tWheat Straw Biogas Pretreatment SynCom\t4\t4\t0\t3\t2\t4\t\t0\t0\n456\t100.0\tkb/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml\tCommunityMech:000354\tYarrowia lipolytica Division-of-Labor Lipid Consortium\t2\t2\t0\t3\t2\t3\t\t0\t0\n457\t100.0\tkb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml\tCommunityMech:000164\tYogurt Two-Species Starter Culture\t2\t2\t0\t4\t2\t9\t\t0\t0\n458\t100.0\tkb/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml\tCommunityMech:000210\tZymomonas-E. coli Exometabolomics-Designed Obligate Mutualism\t2\t2\t0\t3\t2\t6\t\t0\t0\n459\t100.0\tkb/communities/hCom2_Complex_Gut_Microbiome.yaml\tCommunityMech:000123\thCom2 Complex Gut Microbiome\t1\t1\t0\t3\t2\t3\t\t0\t0\n460\t100.0\tkb/communities/mCAFEs_Brachypodium_RCC.yaml\tCommunityMech:000078\tm-CAFEs Brachypodium Reduced Complexity Consortia\t10\t10\t0\t6\t2\t11\t\t0\t0\nPYTHONPATH=src uv run python scripts/rank_causal_graph_readiness.py \n",
+ "superseded_reason": "Three residual evidence/metabolite boundaries narrowed after source-based adversarial reread; all affected gates rerun."
+ },
+ {
+ "check": "render",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "communitymech.render"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch82/pre-adversarial-render.log",
+ "log_sha256": "8d8364aefe8fc80f3bab81d6a141b0b3feac2a8c24f7b40d96d7508833de5276",
+ "output_tail": "sm.html\n \u2713 Synechococcus_Bacillus_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch82/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch82/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch82/docs/index.html\n",
+ "superseded_reason": "Three residual evidence/metabolite boundaries narrowed after source-based adversarial reread; all affected gates rerun."
+ },
+ {
+ "check": "render-repeat",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "communitymech.render"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch82/pre-adversarial-render-repeat.log",
+ "log_sha256": "8d8364aefe8fc80f3bab81d6a141b0b3feac2a8c24f7b40d96d7508833de5276",
+ "output_tail": "sm.html\n \u2713 Synechococcus_Bacillus_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch82/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch82/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch82/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch82/docs/index.html\n",
+ "superseded_reason": "Three residual evidence/metabolite boundaries narrowed after source-based adversarial reread; all affected gates rerun."
+ },
+ {
+ "check": "connectivity-survey",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-c",
+ "import json,pathlib,runpy\nfn=runpy.run_path('tests/test_community_level_connectivity_credit.py')['_survey']\nresult={}\nfor name,root in [('baseline',pathlib.Path('/private/tmp/communitymech-causal-batch81')),('current',pathlib.Path.cwd())]:\n paths=sorted(p for r in ['kb/communities','data/isolates'] for p in (root/r).rglob('*.yaml'))\n assert len(paths)==460\n fn.__globals__['record_files']=lambda:paths\n result[name]=fn()\nprint(json.dumps(result))\n"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch82/pre-adversarial-connectivity-survey.log",
+ "log_sha256": "52c3470443d3c017a6c5f5ffed2fbb43348feee7fe8afbea853d97b3c39e9ed4",
+ "output_tail": "{\"baseline\": {\"records\": 460, \"with_community_level\": 393, \"mixed\": 125, \"community_level_only\": 268, \"taxa\": 1511, \"credited_solely_by_the_rule\": 1240}, \"current\": {\"records\": 460, \"with_community_level\": 393, \"mixed\": 125, \"community_level_only\": 268, \"taxa\": 1511, \"credited_solely_by_the_rule\": 1240}}\n",
+ "superseded_reason": "Three residual evidence/metabolite boundaries narrowed after source-based adversarial reread; all affected gates rerun."
+ },
+ {
+ "check": "regressions",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "pytest",
+ "-q",
+ "tests/test_causal_review_batch10.py",
+ "tests/test_causal_review_batch11.py",
+ "tests/test_causal_review_batch12.py",
+ "tests/test_causal_review_batch13.py",
+ "tests/test_causal_review_batch14.py",
+ "tests/test_causal_review_batch15.py",
+ "tests/test_causal_review_batch16.py",
+ "tests/test_causal_review_batch17.py",
+ "tests/test_causal_review_batch18.py",
+ "tests/test_causal_review_batch19.py",
+ "tests/test_causal_review_batch20.py",
+ "tests/test_causal_review_batch21.py",
+ "tests/test_causal_review_batch22.py",
+ "tests/test_causal_review_batch23.py",
+ "tests/test_causal_review_batch24.py",
+ "tests/test_causal_review_batch25.py",
+ "tests/test_causal_review_batch27.py",
+ "tests/test_causal_review_batch28.py",
+ "tests/test_causal_review_batch29.py",
+ "tests/test_causal_review_batch30.py",
+ "tests/test_causal_review_batch31.py",
+ "tests/test_causal_review_batch32.py",
+ "tests/test_causal_review_batch33.py",
+ "tests/test_causal_review_batch34.py",
+ "tests/test_causal_review_batch35.py",
+ "tests/test_causal_review_batch36.py",
+ "tests/test_causal_review_batch37.py",
+ "tests/test_causal_review_batch38.py",
+ "tests/test_causal_review_batch39.py",
+ "tests/test_causal_review_batch40.py",
+ "tests/test_causal_review_batch41.py",
+ "tests/test_causal_review_batch42.py",
+ "tests/test_causal_review_batch43.py",
+ "tests/test_causal_review_batch44.py",
+ "tests/test_causal_review_batch45.py",
+ "tests/test_causal_review_batch46.py",
+ "tests/test_causal_review_batch47.py",
+ "tests/test_causal_review_batch48.py",
+ "tests/test_causal_review_batch49.py",
+ "tests/test_causal_review_batch5.py",
+ "tests/test_causal_review_batch50.py",
+ "tests/test_causal_review_batch51.py",
+ "tests/test_causal_review_batch52.py",
+ "tests/test_causal_review_batch53.py",
+ "tests/test_causal_review_batch54.py",
+ "tests/test_causal_review_batch55.py",
+ "tests/test_causal_review_batch56.py",
+ "tests/test_causal_review_batch57.py",
+ "tests/test_causal_review_batch58.py",
+ "tests/test_causal_review_batch59.py",
+ "tests/test_causal_review_batch6.py",
+ "tests/test_causal_review_batch60.py",
+ "tests/test_causal_review_batch61.py",
+ "tests/test_causal_review_batch62.py",
+ "tests/test_causal_review_batch63.py",
+ "tests/test_causal_review_batch64.py",
+ "tests/test_causal_review_batch65.py",
+ "tests/test_causal_review_batch66.py",
+ "tests/test_causal_review_batch67.py",
+ "tests/test_causal_review_batch68.py",
+ "tests/test_causal_review_batch69.py",
+ "tests/test_causal_review_batch7.py",
+ "tests/test_causal_review_batch70.py",
+ "tests/test_causal_review_batch71.py",
+ "tests/test_causal_review_batch72.py",
+ "tests/test_causal_review_batch73.py",
+ "tests/test_causal_review_batch74.py",
+ "tests/test_causal_review_batch75.py",
+ "tests/test_causal_review_batch76.py",
+ "tests/test_causal_review_batch77.py",
+ "tests/test_causal_review_batch78.py",
+ "tests/test_causal_review_batch79.py",
+ "tests/test_causal_review_batch8.py",
+ "tests/test_causal_review_batch80.py",
+ "tests/test_causal_review_batch81.py",
+ "tests/test_causal_review_batch82.py",
+ "tests/test_causal_review_batch9.py",
+ "tests/test_site_audit_fixes.py",
+ "tests/test_causal_review_inventory.py",
+ "tests/test_rank_causal_graph_readiness.py",
+ "tests/test_network_auditor.py",
+ "tests/test_participating_taxa.py",
+ "tests/test_causal_descriptions_are_published.py",
+ "tests/test_published_pages_name_real_records.py",
+ "tests/test_reference_validator_actually_validates.py",
+ "tests/test_snippet_audit_artefact_classes.py",
+ "tests/test_reference_error_annotation.py",
+ "tests/test_community_level_connectivity_credit.py",
+ "tests/test_no_paywalled_text_in_repo.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch82/pre-adversarial-regressions.log",
+ "log_sha256": "42dbef829076b5967e1836e093f0b7b48e1d9a284691df6a7ab1006d7ed8f794",
+ "output_tail": "........................................................................ [ 9%]\n........................................................................ [ 19%]\n........................................................................ [ 29%]\n........................................................................ [ 39%]\n........................................................................ [ 48%]\n........................................................................ [ 58%]\n........................................................................ [ 68%]\n........................................................................ [ 78%]\n........................................................................ [ 88%]\n........................................................................ [ 97%]\n................ [100%]\n736 passed in 208.53s (0:03:28)\n",
+ "superseded_reason": "Three residual evidence/metabolite boundaries narrowed after source-based adversarial reread; all affected gates rerun."
+ },
+ {
+ "check": "black",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/3Q_kifQtLB624D5bBWGIf/bin/black",
+ "--check",
+ "tests/test_causal_review_batch82.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch82/pre-adversarial-black.log",
+ "log_sha256": "1a56c7cd8457fd05d978cfbd139d7bfd86e86acaa9b57668e718ef8bccc0cf48",
+ "output_tail": "All done! \u2728 \ud83c\udf70 \u2728\n1 file would be left unchanged.\n",
+ "superseded_reason": "Three residual evidence/metabolite boundaries narrowed after source-based adversarial reread; all affected gates rerun."
+ },
+ {
+ "check": "ruff",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/wCcxEYRM4HeHgwYPZemHX/bin/ruff",
+ "check",
+ "tests/test_causal_review_batch82.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch82/pre-adversarial-ruff.log",
+ "log_sha256": "82b3e6a6c090a57601d22943bd23fca9218d1031dbe5a7b754092f9a156b4f18",
+ "output_tail": "All checks passed!\n",
+ "superseded_reason": "Three residual evidence/metabolite boundaries narrowed after source-based adversarial reread; all affected gates rerun."
+ },
+ {
+ "check": "diff-check",
+ "command": [
+ "git",
+ "diff",
+ "--check"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch82/pre-adversarial-diff-check.log",
+ "log_sha256": "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855",
+ "output_tail": "",
+ "superseded_reason": "Three residual evidence/metabolite boundaries narrowed after source-based adversarial reread; all affected gates rerun."
+ }
+ ],
+ "snippet_counts_by_record": {
+ "kb/communities/Panzhihua_Vanadium_Titanium_Tailings.yaml": {
+ "MATCH": 40,
+ "RENDERING": 1,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Parachlorella_Saccharomyces_Mutualistic_Coculture.yaml": {
+ "MATCH": 10,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Parmigiano_NWS_Set2_LAB_Triculture.yaml": {
+ "MATCH": 20,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Peanut_Seed_Bacterial_CS_SynCom.yaml": {
+ "MATCH": 11,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ }
+ },
+ "unchanged_raw_blocks": 50,
+ "unchanged_record_files": 456,
+ "unchanged_cache_files": 920,
+ "cache_changes": [],
+ "edison": {
+ "required_for_this_repair": false,
+ "required_for_unresolved_extensions": true,
+ "provider_submissions": 0,
+ "credits_spent": 0,
+ "dry_runs": [
+ {
+ "community_id": "CommunityMech:000295",
+ "job": "LITERATURE",
+ "query_chars": 9111,
+ "query_sha256": "4515810ac69377baf2c9f943bc9854134ccf49cc1a302b3133d192fef3319ded",
+ "meta_path": "/private/tmp/communitymech-batch82/edison-algae/Parachlorella_Saccharomyces_Mutualistic_Coculture-edison-literature-causal-meta.yaml",
+ "authorization": "Scoped asynchronous question unanswered; preselection is not approval."
+ }
+ ]
+ },
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+ "/private/tmp/communitymech-batch82/vanadium-primary.txt": "7933557343c25d7e5b42283d1406d678e3b9e2b5d1fc310ecc2ecf2fb4d79fe0"
+ },
+ "network_delta": {
+ "existing_findings_preserved": 44,
+ "added_findings": {
+ "Panzhihua_Vanadium_Titanium_Tailings": [
+ {
+ "type": "DISCONNECTED",
+ "taxon": "Polaromonas species",
+ "taxon_id": "NCBITaxon:52972",
+ "taxon_data": {
+ "taxon_term": {
+ "preferred_term": "Polaromonas species",
+ "term": {
+ "id": "NCBITaxon:52972",
+ "label": "Polaromonas"
+ },
+ "gtdb_grounding_status": "GROUNDED",
+ "gtdb_classification": {
+ "gtdb_id": "GTDB:g__Polaromonas",
+ "gtdb_taxon": "Polaromonas",
+ "gtdb_lineage": "d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas",
+ "ncbi_source_id": "NCBITaxon:52972",
+ "majority_fraction": 1.0,
+ "support_genomes": 12,
+ "total_genomes": 12,
+ "is_reclassified": false,
+ "mapping_source": "kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-07-25) [grounded at g__ rank; 1 GTDB taxa under the NCBI taxon]"
+ },
+ "notes": "Betaproteobacteria capable of dissimilatory vanadium reduction in contaminated mine environments. While not specifically reported in the Panzhihua tailings studies reviewed, Polaromonas is a well-established V(V)-reducing organism in circumneutral pH vanadium mine tailings in northern China and likely present in Panzhihua tailings based on similar environmental conditions (circumneutral pH 6.5-7.5, moderate temperature, high vanadium concentrations). Polaromonas performs dissimilatory V(V) reduction to V(IV) using c-type cytochromes (cymA, omcA) and membrane-associated nitrate reductases (narG). The organism couples oxidation of organic electron donors (lactate, acetate) to V(V) reduction, decreasing vanadium solubility by 2-3 orders of magnitude through precipitation of V(IV) species. This metabolic capacity is critical for vanadium immobilization during anaerobic microsites in revegetated tailings. Polaromonas also reduces Fe(III), Mn(IV), and As(V), contributing to polymetallic redox cycling in V-Ti tailings.\n"
+ },
+ "functional_role": [
+ "PRIMARY_DEGRADER",
+ "SYNTROPHIC_PARTNER"
+ ],
+ "abundance_level": "COMMON",
+ "abundance_value": "Inferred presence based on V-reducing capacity in similar V-Ti tailings",
+ "evidence": [
+ {
+ "reference": "PMID:33125214",
+ "supports": "SUPPORT",
+ "evidence_source": "IN_VIVO",
+ "snippet": "Further, VV-reducing enrichments indicated that bacteria associated with Polaromonas, a genus belonging to the family Burkholderiaceae, were potentially responsible for VV reduction",
+ "explanation": "Establishes V(V) reduction mechanism relevant to Panzhihua conditions"
+ }
+ ]
+ },
+ "message": "Taxon 'Polaromonas species' has no interactions"
+ },
+ {
+ "type": "DISCONNECTED",
+ "taxon": "Rhizobium pisi",
+ "taxon_id": "NCBITaxon:574561",
+ "taxon_data": {
+ "taxon_term": {
+ "preferred_term": "Rhizobium pisi",
+ "term": {
+ "id": "NCBITaxon:574561",
+ "label": "Rhizobium pisi"
+ },
+ "gtdb_grounding_status": "UNRESOLVED",
+ "notes": "Fast-growing nitrogen-fixing rhizobium traditionally associated with pea (Pisum sativum) but adapted to form nodules with P. pinnata in V-Ti tailings. One isolate was identified as R. pisi, demonstrating the promiscuity of rhizobial-legume associations under metal stress conditions. R. pisi contributes to nitrogen enrichment of tailings soil through symbiotic nitrogen fixation and produces plant growth-promoting substances including IAA. The presence of R. pisi indicates that phytoremediation legumes can recruit diverse rhizobial species from indigenous tailings microbiota, not limited to traditional host-specific symbionts. This metabolic flexibility enhances the resilience and effectiveness of legume-rhizobia partnerships in contaminated environments.\n"
+ },
+ "functional_role": [
+ "PRIMARY_DEGRADER",
+ "NITROGEN_FIXING_SYMBIONT"
+ ],
+ "abundance_level": "RARE",
+ "abundance_value": "One isolate from P. pinnata nodules",
+ "evidence": [
+ {
+ "reference": "doi:10.3389/fmicb.2023.1078333",
+ "supports": "SUPPORT",
+ "evidence_source": "IN_VIVO",
+ "snippet": "Based on the phylogenetic analysis of 16S rRNA and four house-keeping genes (atpD, recA, rpoB, glnII), twelve isolates were identified as Bradyrhizobium pachyrhizi, four as Ochrobactrum anthropic, three as Rhizobium selenitireducens and one as Rhizobium pisi",
+ "explanation": "Documents R. pisi presence in V-Ti tailings rhizobia"
+ }
+ ]
+ },
+ "message": "Taxon 'Rhizobium pisi' has no interactions"
+ },
+ {
+ "type": "DISCONNECTED",
+ "taxon": "Rhizobium selenitireducens",
+ "taxon_id": "NCBITaxon:1336235",
+ "taxon_data": {
+ "taxon_term": {
+ "preferred_term": "Rhizobium selenitireducens",
+ "term": {
+ "id": "NCBITaxon:1336235",
+ "label": "Paenirhizobium selenitireducens ATCC BAA-1503"
+ },
+ "gtdb_grounding_status": "UNRESOLVED",
+ "notes": "Nitrogen-fixing alphaproteobacterium capable of selenium reduction and heavy metal tolerance, isolated from P. pinnata root nodules in V-Ti tailings. Three isolates were identified as R. selenitireducens, demonstrating nitrogen-fixing capacity and variable tolerance to Cu, Ni, Mn, and Zn. This species possesses unique metabolic capabilities including selenite reduction to elemental selenium, suggesting potential for metalloid detoxification in addition to nitrogen fixation. R. selenitireducens contributes to the functional diversity of the rhizobial community, providing complementary metal tolerance mechanisms and nitrogen enrichment. The organism forms effective symbioses with leguminous plants under metal stress conditions, promoting plant growth through nitrogen provision and IAA production. Like other tailings rhizobia, R. selenitireducens serves as a competent candidate for bioremediation of soils contaminated with multifarious metals due to its combined nitrogen-fixing and metal tolerance phenotypes.\n"
+ },
+ "functional_role": [
+ "PRIMARY_DEGRADER",
+ "CROSS_FEEDER",
+ "NITROGEN_FIXING_SYMBIONT"
+ ],
+ "abundance_level": "COMMON",
+ "abundance_value": "Three isolates from P. pinnata nodules",
+ "evidence": [
+ {
+ "reference": "doi:10.3389/fmicb.2023.1078333",
+ "supports": "SUPPORT",
+ "evidence_source": "IN_VIVO",
+ "snippet": "Based on the phylogenetic analysis of 16S rRNA and four house-keeping genes (atpD, recA, rpoB, glnII), twelve isolates were identified as Bradyrhizobium pachyrhizi, four as Ochrobactrum anthropic, three as Rhizobium selenitireducens and one as Rhizobium pisi",
+ "explanation": "Documents R. selenitireducens presence in tailings rhizobia"
+ },
+ {
+ "reference": "doi:10.3389/fmicb.2023.1078333",
+ "supports": "SUPPORT",
+ "evidence_source": "IN_VIVO",
+ "snippet": "effective rhizobia strains for bioremediation of VTM tailings or other contaminated soils",
+ "explanation": "Establishes metal tolerance and bioremediation potential"
+ }
+ ]
+ },
+ "message": "Taxon 'Rhizobium selenitireducens' has no interactions"
+ }
+ ]
+ },
+ "removed_findings": {},
+ "interpretation": "Three newly exposed Panzhihua disconnections: R.selenitireducens, R.pisi and Polaromonas. Removed unsupported redundancy/external-system claims; no invented all-member credit, taxonomy or auditor-rule change. Identity research1680/metadata1683remainOPEN."
+ },
+ "render_determinism": true,
+ "published_description_coverage": {
+ "pages": 456,
+ "nodes": 1425,
+ "arrows": 593
+ },
+ "participant_census": {
+ "measurements": {
+ "baseline": {
+ "records": 460,
+ "with_community_level": 393,
+ "mixed": 125,
+ "community_level_only": 268,
+ "taxa": 1511,
+ "credited_solely_by_the_rule": 1240
+ },
+ "current": {
+ "records": 460,
+ "with_community_level": 393,
+ "mixed": 125,
+ "community_level_only": 268,
+ "taxa": 1511,
+ "credited_solely_by_the_rule": 1240
+ }
+ },
+ "delta": {
+ "records": 0,
+ "with_community_level": 0,
+ "mixed": 0,
+ "community_level_only": 0,
+ "taxa": 0,
+ "credited_solely_by_the_rule": 0
+ },
+ "interpretation": "No scope-count change, taxonomy edit, or auditor-rule change. Aggregate outcomes do not establish member-resolved activity."
+ },
+ "network_warning_count": 47,
+ "corpus": {
+ "scope": "Every YAML under kb/communities and data/isolates; filesystem discovery includes hidden/ignored files.",
+ "records": 460,
+ "nodes": 1439,
+ "edges": 601,
+ "records_without_nodes": 8,
+ "records_without_edges": 170,
+ "review_status_counts": {
+ "needs_research": 39,
+ "pending": 164,
+ "reviewed": 257
+ },
+ "structural_defects": []
+ },
+ "tested_file_sha256": {
+ "reports/causal_graph_review/decisions/20261007-four-records-batch82.yaml": "287d391e90ad2e832c8cf57a63e6db79adfd6a73fa59a670dc6441c1466cea58",
+ "tests/test_causal_review_batch82.py": "f8a1c608f6e523301ee878e347a451309f7bb7032b631410fb4fd251bd9c481b",
+ "kb/communities/Panzhihua_Vanadium_Titanium_Tailings.yaml": "b5a4255cbaf18200e7002f843bffa20e870a5d1676d5c7cf3f4036c9ce92b0a0",
+ "kb/communities/Parachlorella_Saccharomyces_Mutualistic_Coculture.yaml": "ee3166c701c928154cb1f46337d3d43a5ee56946d75f93fcd6d4ac8ecb3f8b82",
+ "kb/communities/Parmigiano_NWS_Set2_LAB_Triculture.yaml": "1ca3e250bbd757768243c691712d2139c54a2da4e59570360417188516bb4b2c",
+ "kb/communities/Peanut_Seed_Bacterial_CS_SynCom.yaml": "faf0f4193278f1fc4c65f5666b79129629c3e1add520245a3ff941596b96513c",
+ "reports/causal_graph_review/README.md": "6a7fce42f05cab4061692231e2a17092c0554c85d1f9a520478e36cea2d69a6c"
+ },
+ "status": "verified_assay_boundary_graph_review",
+ "pre_research_baseline": {
+ "base_commit": "c2f23b2053bde3329f2619bc45accadcec415d19",
+ "base_tree": "2554aa7ffce8940a7c157483b925cd9071f5a46f",
+ "research_worktree": "/private/tmp/communitymech-causal-batch81",
+ "checks": [
+ {
+ "name": "rank",
+ "command": [
+ "just",
+ "rank-causal-graphs"
+ ],
+ "exit_code": 0,
+ "expected_exit_code": 0,
+ "log": "/private/tmp/communitymech-batch82/baseline-rank.log",
+ "sha256": "d0b983058cbe8ef90ef587d6dbf927cb92dfc7bef996d44f3fc77ce8e547960d",
+ "output_tail": "/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml\tCommunityMech:000337\tTropidoatractus magnetotacticus Magnetotactic Ciliate Tripartite Syntrophy\t3\t3\t0\t4\t2\t9\t\t0\t0\n450\t100.0\tkb/communities/Urine_Nitrification_SynCom.yaml\tCommunityMech:000117\tUrine Nitrification Synthetic Microbial Community\t5\t5\t0\t3\t2\t5\t\t0\t0\n451\t100.0\tkb/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml\tCommunityMech:000213\tVariovorax-Cryptococcus Vitamin Cross-Feeding Microcosm\t2\t2\t0\t3\t2\t4\t\t0\t0\n452\t100.0\tkb/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml\tCommunityMech:000328\tWaste-Sludge Electro-Fermentation Biofilm-Suspension Community\t5\t5\t0\t4\t2\t6\t\t0\t0\n453\t100.0\tkb/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.yaml\tCommunityMech:000098\tWatermelon Rhizosphere Fusarium-Protective SynCom8\t2\t2\t0\t3\t2\t7\t\t0\t0\n454\t100.0\tkb/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml\tCommunityMech:000255\tWetland Oxygen-Sulfate Greenhouse Gas Microcosm Community\t3\t3\t0\t3\t2\t6\t\t0\t0\n455\t100.0\tkb/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.yaml\tCommunityMech:000118\tWheat Straw Biogas Pretreatment SynCom\t4\t4\t0\t3\t2\t4\t\t0\t0\n456\t100.0\tkb/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml\tCommunityMech:000354\tYarrowia lipolytica Division-of-Labor Lipid Consortium\t2\t2\t0\t3\t2\t3\t\t0\t0\n457\t100.0\tkb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml\tCommunityMech:000164\tYogurt Two-Species Starter Culture\t2\t2\t0\t4\t2\t9\t\t0\t0\n458\t100.0\tkb/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml\tCommunityMech:000210\tZymomonas-E. coli Exometabolomics-Designed Obligate Mutualism\t2\t2\t0\t3\t2\t6\t\t0\t0\n459\t100.0\tkb/communities/hCom2_Complex_Gut_Microbiome.yaml\tCommunityMech:000123\thCom2 Complex Gut Microbiome\t1\t1\t0\t3\t2\t3\t\t0\t0\n460\t100.0\tkb/communities/mCAFEs_Brachypodium_RCC.yaml\tCommunityMech:000078\tm-CAFEs Brachypodium Reduced Complexity Consortia\t10\t10\t0\t6\t2\t11\t\t0\t0\nPYTHONPATH=src uv run python scripts/rank_causal_graph_readiness.py \n"
+ },
+ {
+ "name": "just-network",
+ "command": [
+ "just",
+ "audit-network-json"
+ ],
+ "exit_code": 2,
+ "expected_exit_code": 2,
+ "log": "/private/tmp/communitymech-batch82/baseline-just-network.log",
+ "sha256": "8595db43420d3f0a01c57acd6ad733a531a72e962486d20b4e1c2840dda55bff",
+ "output_tail": "uv run communitymech audit-network --json\nerror: Failed to spawn: `communitymech`\n Caused by: No such file or directory (os error 2)\nerror: recipe `audit-network-json` failed on line 574 with exit code 2\n"
+ },
+ {
+ "name": "network",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "communitymech.cli",
+ "audit-network",
+ "--json"
+ ],
+ "exit_code": 1,
+ "expected_exit_code": 1,
+ "log": "/private/tmp/communitymech-batch82/baseline-network.log",
+ "sha256": "dcb33d46aa53f5e1dec55b1cd6463b83d3723e2ebf8c97999c93d0a5f4a2fed1",
+ "output_tail": " \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Staphylococcus capitis | K1-2-2-23 | ISS, V2A Steel | DSM 111179 | Sobisch et al., 2019 | GCA_025272695 | TSYB/TSYA | 37 \\u00b0C | 16\\u201324 h\",\n \"explanation\": \"Identifies S. capitis K1-2-2-23 as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Staphylococcus capitis K1-2-2-23' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Streptococcus halotolerans HTS9T\",\n \"taxon_id\": \"NCBITaxon:1814128\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Streptococcus halotolerans HTS9T\",\n \"term\": {\n \"id\": \"NCBITaxon:1814128\",\n \"label\": \"Streptococcus halotolerans\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the S. halotolerans type strain as a biosafety-level-1 representative.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"HTS9T\",\n \"genome_accession\": \"GCA_001598035\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"101996\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Streptococcus halotolerans | HTS9 T | Respiratory Tract of Marmota himalayana | DSM 101996 T | Niu et al., 2016 | GCA_001598035 | 2xLB, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies S. halotolerans HTS9T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Streptococcus halotolerans HTS9T' has no interactions\"\n }\n ]\n}\n"
+ },
+ {
+ "name": "downstream",
+ "command": [
+ "rg",
+ "--no-ignore",
+ "--hidden",
+ "-n",
+ "downstream:",
+ "kb/communities",
+ "data/isolates",
+ "--glob",
+ "*.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_code": 0,
+ "log": "/private/tmp/communitymech-batch82/baseline-downstream.log",
+ "sha256": "07dd988f19b4cc1ab86e1e10bf52ac5f4fd826fadb584f0c48f5b5a6a923a41d",
+ "output_tail": "ritusphere_Niche_Succession.yaml:127: downstream:\nkb/communities/Desulfovibrio_Methanococcus_Syntrophy.yaml:138: downstream:\nkb/communities/Desulfovibrio_Methanococcus_Syntrophy.yaml:182: downstream:\nkb/communities/Desulfovibrio_Methanococcus_Syntrophy.yaml:232: downstream:\nkb/communities/Phylogenetically_Diverse_Denitrifying_SynCom.yaml:76: downstream:\nkb/communities/Phylogenetically_Diverse_Denitrifying_SynCom.yaml:95: downstream:\nkb/communities/Phylogenetically_Diverse_Denitrifying_SynCom.yaml:122: downstream:\nkb/communities/Ferroplasma_Leptospirillum_Syntrophy.yaml:125: downstream:\nkb/communities/Methylacidiphilum_Galdieria_Thermoacidophilic_Coculture.yaml:268: downstream:\nkb/communities/Methylacidiphilum_Galdieria_Thermoacidophilic_Coculture.yaml:317: downstream:\nkb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml:199: downstream:\nkb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml:267: downstream:\nkb/communities/Populus_Salt_Tolerant_SynComs.yaml:65: downstream:\nkb/communities/Populus_Salt_Tolerant_SynComs.yaml:98: downstream:\nkb/communities/Populus_Salt_Tolerant_SynComs.yaml:131: downstream:\nkb/communities/Populus_Salt_Tolerant_SynComs.yaml:155: downstream:\nkb/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml:223: downstream:\nkb/communities/Lake_Washington_Methane_Oxygen_Methylotroph_Community.yaml:342: downstream:\nkb/communities/At_RSPHERE_SynCom.yaml:207: downstream:\nkb/communities/At_RSPHERE_SynCom.yaml:249: downstream:\nkb/communities/Salar_Atacama_Lithium_Brine_Community.yaml:295: downstream:\nkb/communities/Salar_Atacama_Lithium_Brine_Community.yaml:339: downstream:\nkb/communities/Polaromonas_Vanadium_Reduction_Community.yaml:281: downstream:\nkb/communities/Polaromonas_Vanadium_Reduction_Community.yaml:401: downstream:\nkb/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml:135: downstream:\nkb/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml:177: downstream:\n"
+ }
+ ],
+ "baseline_sha256": "a88c0ecae11c7b9c0de1bd1010f2a50f81b593769a4189619bac5d50535b7c3f"
+ },
+ "reference_validator_caveat": "Four full-record reference validators exit0. CLI Total checks counts issues, not executed checks.25graph quotations independently match fresh primary content and unchanged caches. Literal matching is not entailment or whole-record provenance certification; non-graph claims/caches are preserved, not globally recertified."
+}
diff --git a/tests/test_causal_review_batch82.py b/tests/test_causal_review_batch82.py
new file mode 100644
index 000000000..e146cee81
--- /dev/null
+++ b/tests/test_causal_review_batch82.py
@@ -0,0 +1,165 @@
+"""Preserve positive phenotypes without cross-system or workflow causation."""
+
+import hashlib
+from pathlib import Path
+
+import yaml
+
+ROOT = Path(__file__).resolve().parents[1]
+LEDGER = ROOT / "reports/causal_graph_review/decisions/20261007-four-records-batch82.yaml"
+
+
+def records():
+ ledger = yaml.safe_load(LEDGER.read_text())
+ rows = ledger["records"]
+ return ledger, rows, [yaml.safe_load((ROOT / r["path"]).read_text()) for r in rows]
+
+
+def test_tailings_retains_assayed_biology_without_external_membership_credit():
+ _, rows, docs = records()
+ nitrogen, metal, ochro = docs[0]["ecological_interactions"]
+ assert all(n["scope"] == "PAIRWISE" for n in [nitrogen, metal, ochro])
+ assert all(
+ "downstream" not in n and "interaction_type" not in n for n in [nitrogen, metal, ochro]
+ )
+ assert metal["source_taxon"]["term"]["id"] == "NCBITaxon:1386"
+ assert "PP1 belongs to Rhizobium" in nitrogen["description"]
+ assert "separate nitrogen-free vermiculite" in nitrogen["description"]
+ assert "83.05" in ochro["description"]
+ assert "does not unambiguously allocate" in ochro["description"]
+ assert "Cd/Zn inconsistencies" in nitrogen["description"]
+ assert rows[0]["status"] == "needs_research" and 1680 in rows[0]["issues"]
+
+
+def test_positive_soil_carbon_is_preserved_without_a_fabricated_pair():
+ _, _, docs = records()
+ carbon = next(
+ d
+ for d in docs[0]["discussions"]
+ if d["discussion_id"] == "panzhihua-positive-soil-carbon-result"
+ )
+ assert "positive aggregate result is retained" in carbon["rationale"]
+ assert "carbon dioxide" in carbon["rationale"]
+ assert carbon["evidence"][0]["reference"] == "PMID:38744211"
+ assert len(docs[0]["taxonomy"]) == 6
+ assert all("metabolites" not in n for n in docs[0]["ecological_interactions"])
+
+
+def test_algal_positive_output_and_qualified_arrows_remain():
+ _, _, docs = records()
+ gas, growth, eps, product = docs[1]["ecological_interactions"]
+ assert product["name"] == "Fourfold Coculture Biomass and Lipid Increase"
+ assert "fourfold" in product["description"]
+ assert "metabolites" not in product
+ assert len(gas["metabolites"]) == 2
+ assert "day 6" in growth["description"]
+ assert gas["downstream"][0]["target"] == growth["downstream"][0]["target"] == product["name"]
+ assert gas["downstream"][0]["description"].startswith("HYPOTHESIZED -")
+ assert growth["downstream"][0]["description"].startswith("PARTIAL -")
+ assert all("interaction_type" not in n for n in [gas, growth, eps, product])
+
+
+def test_eps_viability_and_adhesion_do_not_become_traced_uptake():
+ _, rows, docs = records()
+ gas, _, eps, _ = docs[1]["ecological_interactions"]
+ assert all(e["supports"] == "PARTIAL" for n in [gas, eps] for e in n["evidence"])
+ assert "68%" in eps["description"] and "FluidFM" in eps["description"]
+ assert "do not by themselves demonstrate" in eps["description"]
+ assert rows[1]["status"] == "needs_research" and 1681 in rows[1]["issues"]
+
+
+def test_milk_preserves_positive_and_negative_composition_comparisons():
+ _, _, docs = records()
+ tri, pair, weaker, _ = docs[2]["ecological_interactions"]
+ assert "not uniquely superior" in tri["description"]
+ assert "higher maximum acidification rate than either" in pair["description"]
+ assert (
+ "lower maximum acidification rates than the corresponding monocultures"
+ in weaker["description"]
+ )
+ assert "75.95%" in weaker["description"]
+ assert all("downstream" not in n for n in docs[2]["ecological_interactions"])
+ assert all("interaction_type" not in n for n in docs[2]["ecological_interactions"])
+ assert all("functional_role" not in t for t in docs[2]["taxonomy"])
+
+
+def test_milk_lactate_is_a_mixed_pool_not_exclusive_c5i3_production():
+ _, _, docs = records()
+ lactate = docs[2]["ecological_interactions"][-1]
+ assert lactate["name"] == "Set 2 Triculture D-Lactate Accumulation"
+ assert "not exclusive C5I3" in lactate["description"]
+ assert "83% L-lactate" in lactate["description"]
+ assert any(
+ d["discussion_id"] == "nws_set2_molecular_cross_feeding_mechanisms"
+ for d in docs[2]["discussions"]
+ )
+
+
+def test_peanut_workflow_is_removed_but_reported_sa_direction_survives():
+ _, _, docs = records()
+ sa, rootrot, toxin, growth = docs[3]["ecological_interactions"]
+ assert sa["downstream"][0]["target"] == rootrot["name"]
+ assert sa["downstream"][0]["description"].startswith("PARTIAL -")
+ assert all("downstream" not in n for n in [rootrot, toxin, growth])
+ assert "CS showing the best effect" in rootrot["description"]
+ assert "pathway-necessity" in sa["evidence"][0]["explanation"]
+
+
+def test_peanut_toxin_and_growth_scope_remain_bounded_and_aliases_survive():
+ _, rows, docs = records()
+ _, _, toxin, growth = docs[3]["ecological_interactions"]
+ assert "chemical destruction" in toxin["description"]
+ assert toxin["evidence"][1]["supports"] == "PARTIAL"
+ assert "CS-specific growth effect size" in growth["description"]
+ raw = (ROOT / rows[3]["path"]).read_text()
+ assert "&id001" in raw and "*id001" in raw
+ assert rows[3]["status"] == "needs_research" and 1682 in rows[3]["issues"]
+
+
+def test_every_original_node_and_arrow_has_a_disposition():
+ ledger, rows, docs = records()
+ assert sum(len(r["node_decisions"]) for r in rows) == 15
+ assert sum(len(r["removed_node_decisions"]) for r in rows) == 5
+ assert sum(len(r["edges_before"]) for r in rows) == 11
+ assert sum(len(r["edges_after"]) for r in rows) == 3
+ assert sum(len(r["removed_edge_decisions"]) for r in rows) == 8
+ assert (
+ ledger["primary_graph_snippet_count"]
+ == ledger["independent_fresh_primary_graph_snippet_count"]
+ == 25
+ )
+ for row, doc in zip(rows, docs, strict=True):
+ names = {n["name"] for n in doc["ecological_interactions"]}
+ assert names == {n["node"] for n in row["node_decisions"]}
+ assert all(
+ e["target"] in names
+ for n in doc["ecological_interactions"]
+ for e in n.get("downstream", [])
+ )
+ assert all(
+ a.split("#", 1)[1] in names
+ for d in doc["discussions"]
+ for a in d["attaches_to"]
+ if a.startswith("ecological_interactions#")
+ )
+
+
+def test_history_source_and_lifecycle_boundaries_are_explicit():
+ ledger, rows, docs = records()
+ assert ledger["independent_approval"] is False
+ assert ledger["issues"] == [1676, 1677, 1678, 1679]
+ assert ledger["unresolved_research_issues"] == [1680, 1681, 1682]
+ assert ledger["unresolved_non_graph_issues"] == [1683]
+ assert ledger["cache_changes"] == []
+ assert ledger["edison"]["provider_submissions"] == ledger["edison"]["credits_spent"] == 0
+ assert ledger["edison"]["dry_runs"][0]["query_chars"] == 9111
+ for row, doc in zip(rows, docs, strict=True):
+ assert set(row["allowed_changed_fields"]) == {
+ "ecological_interactions",
+ "discussions",
+ "curation_history",
+ }
+ assert row["curation_events_added"] == len(row["history_files"]) == 1
+ assert all((ROOT / p).exists() for p in row["history_files"])
+ assert doc["curation_history"][-1]["llm_assisted"] is True
+ assert hashlib.sha256((ROOT / row["path"]).read_bytes()).hexdigest() == row["record_sha256"]