"enzyme encoded by hphtC-5 was proposed to be the candidate decarboxylase for the decarboxylation process of 4,5-dicarboxyphenanthrene."
@@ -679,10 +679,9 @@ In 200 mL 5%-salinity SSDM batch flasks with 50 mg/L pyrene as the sole carbon source, the two-member PES consortium approached complete pyrene removal within 10 days, whereas neither pure culture completely degraded pyrene by itself under the tested conditions.
+ PES approached complete removal of 50 mg/L pyrene in 200 mL 5%-salinity SSDM within 10 days. N7 removal plateaued at 49.95% after 14 days, and A11 lacked direct PAH-degrading capability. These controlled culture observations support the consortium removal advantage. Residual-substrate HPLC and intermediate detection do not by themselves establish complete carbon mineralization, a closed carbon balance or reciprocal member-specific fitness benefits.
@@ -850,7 +849,7 @@
- Knowledge gaps & discussions (1)
+ Knowledge gaps & discussions (2)
@@ -860,9 +859,59 @@
The source detected downstream pyrene metabolites in PES, annotated hphtC-5 in the A11 genome, modeled a compatible active site, and measured hphtC-5 expression by RT-PCR. It did not purify HphtC-5 or perturb hphtC-5 genetically, so the specific enzyme assignment remains a candidate step.
-
Attaches to: ecological_interactions#N7-A11 4,5-dicarboxyphenanthrene handoff
+
Attaches to: ecological_interactions#Proposed N7-A11 4,5-dicarboxyphenanthrene handoff
+
+
+
+
+
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which candidate enzyme and emulsifier activities cause the measured PES removal advantage?
+
+
Preserve positive pyrene removal, intermediate profiles and extracellular emulsification. hphtC-5 remains a candidate, as in the existing gap. Soybean-oil emulsification is not a direct pyrene-solubility or depletion/add-back test; A11 and the other cultures had different growth substrates. The correction DOI10.3389/fmicb.2026.1971230 changes structures in Figure8, not the need for causal validation. No new nodes/arrows are warranted by the inspected main text.
+
+
Attaches to: ecological_interactions#Proposed N7-A11 4,5-dicarboxyphenanthrene handoff, ecological_interactions#A11-Associated Extracellular Emulsifying Activity, ecological_interactions#Complete 5%-salinity pyrene removal by PES
+
+
+ 2 evidence item(s)
+
+
+
+
enzyme encoded by hphtC-5 was proposed to be the candidate decarboxylase for the decarboxylation process of 4,5-dicarboxyphenanthrene.
+
Candidate enzyme assignment based on annotation/modeling and expression, not direct enzymatic validation.
+
+
+
Distinct and persistent emulsion layers were observed only in the cell-free supernatants of strain A11 and consortium PES
+
Supports A11 and PES, but not N7 alone, as sources of extracellular emulsifying activity.
+
Evidence
nodes.push({
id: intId,
- label: "N7-A11 4,5-dicarboxyphenanthrene handoff",
+ label: "Proposed N7-A11 4,5-dicarboxyphenanthrene handoff",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1216,7 +1265,7 @@ Evidence
(function() {
var intId = "interaction:1";
- var intType = "MUTUALISM";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1229,7 +1278,7 @@ Evidence
nodes.push({
id: intId,
- label: "A11 extracellular bioemulsification of hydrophobic pyrene",
+ label: "A11-Associated Extracellular Emulsifying Activity",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
diff --git a/docs/communities/Pelotomaculum_Methanothermobacter_Syntrophy.html b/docs/communities/Pelotomaculum_Methanothermobacter_Syntrophy.html
index fe786cd18..87fe7525c 100644
--- a/docs/communities/Pelotomaculum_Methanothermobacter_Syntrophy.html
+++ b/docs/communities/Pelotomaculum_Methanothermobacter_Syntrophy.html
@@ -581,14 +581,15 @@ Ecological Interactions
Propionate Oxidation and H2 Production
SYNTROPHY
- Pelotomaculum thermopropionicum oxidizes propionate (C3) to acetate, CO2, and H2, using protons as the electron acceptor and producing H2 as the electron sink product. This propionate oxidation is thermodynamically unfavorable under standard conditions and only proceeds when H2 partial pressure is kept extremely low by a syntrophic partner. The organism cannot utilize common electron acceptors (nitrate, sulfate, etc.) and is therefore obligately dependent on syntrophic H2 removal. The coaggregation of P. thermopropionicum with M. thermautotrophicus facilitates efficient interspecies H2 transfer at thermophilic temperatures (55°C).
-
+ P. thermopropionicum SI grows on propionate in coculture with the hydrogenotrophic methanogen M. thermautotrophicus DeltaH. Preserve the propionate-oxidation/H2-transfer interpretation and the reported 55 degrees C growth optimum, without claiming that the temperature measurement itself proves metabolic flux. Dependence is substrate- and condition-specific: the species paper reports pure-culture growth on pyruvate and fumarate and fumarate reduction, despite absence of dissimilatory sulfate reduction. It does not justify a universal inability to use electron acceptors or grow without a partner.
Source Taxon: Pelotomaculum thermopropionicum
+ Target Taxon: Methanothermobacter thermautotrophicus
+
Metabolites:
@@ -637,7 +638,7 @@
Propionate Oxidation and H2 Production
→ Interspecies Hydrogen Transfer and Thermophilic Methanogenesis
-
H2 produced by P. thermopropionicum is consumed by M. thermautotrophicus for methanogenesis at 55°C
+
H2 supplied during syntrophic propionate oxidation fuels the hydrogenotrophic partner. Preserve this directly implied donor-to-methanogen direction; the species-description abstract does not quantify the exchanged flux or its stoichiometry.
@@ -656,7 +657,7 @@ Evidence
- SUPPORT (IN_VITRO)
- "The optimum temperature for growth was 55 degrees C and the pH optimum was 7.0"
+ "The strain grew on propionate, ethanol, lactate, 1-butanol, 1-pentanol, 1,3-propanediol, 1-propanol and ethylene glycol in co-culture with the hydrogenotrophic methanogen Methanothermobacter thermautotrophicus strain deltaH(T)"
@@ -669,7 +670,7 @@ Evidence
- SUPPORT (IN_VITRO)
- "An anaerobic, thermophilic, syntrophic propionate-oxidizing bacterium, strain SI(T), isolated previously from granular sludge in a thermophilic upflow"
+ "The strain could grow fermentatively on pyruvate and fumarate in pure culture"
@@ -682,7 +683,7 @@ Evidence
Alternative Alcohol and Diol Oxidation
SYNTROPHY
- Pelotomaculum thermopropionicum grows syntrophically with Methanothermobacter thermautotrophicus on ethanol, lactate, 1-butanol, 1-pentanol, 1,3-propanediol, 1-propanol, and ethylene glycol as well as on propionate. Oxidation of these reduced organic substrates feeds acetate, CO2, and H2 into the same interspecies hydrogen-transfer route that makes propionate oxidation thermodynamically feasible.
+ The species paper reports coculture growth on ethanol, lactate, 1-butanol, 1-pentanol, 1,3-propanediol, 1-propanol and ethylene glycol as well as propionate. These positive substrate-use phenotypes support the alternative syntrophic route. The accessible abstract does not identify the carbon products and stoichiometry of every substrate, so acetate and CO2 must not be assigned universally to all alcohols and diols.
Source Taxon: Pelotomaculum thermopropionicum
@@ -711,10 +712,6 @@ Alternative Alcohol and Diol Oxidation
(CHEBI:30742 ),
- acetate
- (CHEBI:30089 ),
-
dihydrogen
(CHEBI:18276 )
@@ -741,7 +738,7 @@ Alternative Alcohol and Diol Oxidation
→ Interspecies Hydrogen Transfer and Thermophilic Methanogenesis
-
Hydrogen and CO2 released from alcohol and diol oxidation are consumed by the methanogen in the same H2-removal sink.
+
PARTIAL - The reported growth of SI with a hydrogenotrophic partner on these alternative substrates supports H2-linked syntrophy. Substrate-resolved H2 yields and carbon-product balances are not exposed in the cited species-description abstract; do not assume every substrate supplies the same acetate/CO2 products.
@@ -773,14 +770,15 @@ Evidence
Interspecies Hydrogen Transfer and Thermophilic Methanogenesis
SYNTROPHY
- Methanothermobacter thermautotrophicus consumes the H2 produced by P. thermopropionicum, combining it with CO2 to produce methane via hydrogenotrophic methanogenesis at thermophilic temperatures (55°C). This H2 removal maintains a low H2 partial pressure, making the thermodynamically unfavorable propionate oxidation by P. thermopropionicum energetically feasible. This interspecies hydrogen transfer (IHT) is enhanced by coaggregation between the two organisms, which reduces diffusion distances and improves syntrophic efficiency at elevated temperatures. This represents a classic example of thermophilic syntrophic metabolism in anaerobic environments.
-
+ M. thermautotrophicus is the hydrogenotrophic partner, consuming H2 for methane formation and providing an H2 sink compatible with SI propionate oxidation. The separate 2005 study reports stronger coaggregation on propionate than on ethanol or 1-propanol. Microscopy supports physical association, while Fick-law calculations support substrate-dependent diffusion-distance requirements; those modeled distances are not direct flux measurements. Its Figure4 caption reports 2-BES inhibition of partner hydrogen consumption. Retain these positive observations without attributing all of them to the 2002 species paper or asserting direct electron conduction through filaments.
Source Taxon: Methanothermobacter thermautotrophicus
+ Target Taxon: Pelotomaculum thermopropionicum
+
Metabolites:
@@ -832,6 +830,32 @@
Evidence
+
+
+
+ "these organisms coaggregated to different degrees depending on the substrate"
+
+
+
+
+
+
+ "Hydrogen consumption by ΔH cells was inhibited by adding 2-BES."
+
+
+
@@ -841,6 +865,60 @@ Evidence
+
+ Knowledge gaps & discussions (1)
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ How should hydrogen-removal feedback and coaggregation be represented after full-method review?
+
+
Existing substrate-growth and H2-to-methanogenesis directions remain. PMID16332758 adds positive microscopy and a partner-inhibition lead; its modeled proximity requirement must not be confused with measured flux or electrical conduction. Full main methods and possible separate coaggregation/feedback structure remain research work. A one-community Edison causal dry run exists; no paid report or new node/arrow has been used. Non-graph medium and universal-dependence claims are preserved but not certified.
+
+
Attaches to: ecological_interactions#Propionate Oxidation and H2 Production, ecological_interactions#Alternative Alcohol and Diol Oxidation, ecological_interactions#Interspecies Hydrogen Transfer and Thermophilic Methanogenesis
+
+
+
+
+ 2 evidence item(s)
+
+
+
+
these organisms coaggregated to different degrees depending on the substrate
+
The primary abstract reports substrate-dependent physical association; diffusion-distance inference is a separate calculation.
+
+
+
Hydrogen consumption by ΔH cells was inhibited by adding 2-BES.
+
The primary Figure4 caption reports inhibition of the methanogenic hydrogen sink, not a filament-conduction experiment.
+
+
+
+
@@ -1548,6 +1626,11 @@ Evidence
+ var tgtKey = "Methanothermobacter thermautotrophicus";
+ if (taxonNodeIds[tgtKey]) {
+ links.push({ source: intId, target: taxonNodeIds[tgtKey] });
+ }
+
})();
(function() {
@@ -1564,8 +1647,6 @@ Evidence
metabolites.push("ethylene glycol");
- metabolites.push("acetate");
-
metabolites.push("dihydrogen");
@@ -1621,7 +1702,7 @@ Evidence
processes.push("methanogenesis");
- var evidenceCount = 1;
+ var evidenceCount = 3;
nodes.push({
id: intId,
@@ -1641,6 +1722,11 @@ Evidence
+ var tgtKey = "Pelotomaculum thermopropionicum";
+ if (taxonNodeIds[tgtKey]) {
+ links.push({ source: intId, target: taxonNodeIds[tgtKey] });
+ }
+
})();
diff --git a/docs/communities/Pepper_Growth_Rhizosphere_SynCom.html b/docs/communities/Pepper_Growth_Rhizosphere_SynCom.html
index c84cbaf8c..00cbab73a 100644
--- a/docs/communities/Pepper_Growth_Rhizosphere_SynCom.html
+++ b/docs/communities/Pepper_Growth_Rhizosphere_SynCom.html
@@ -618,7 +618,7 @@ Ecological Interactions
Ecological interaction network for Pepper Growth Rhizosphere SynCom
- 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 (mutualism, colonization facilitation).
+ 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.
@@ -626,13 +626,8 @@
Ecological Interactions
-
-
@@ -640,11 +635,9 @@ Ecological Interactions
-
Bacillus subtilis, Trichoderma harzianum, Trichoderma asperellum, and Aspergillus sp. fermentation liquids were normalized and mixed in equal proportions before soil inoculation.
-
+
After the four-member inoculation treatment, the study reports increased fungal and bacterial Chao richness and fungal Bray-Curtis dissimilarity, with decreased bacterial Bray-Curtis dissimilarity after 45 days. Preserve the observed community-profile response. These diversity indices do not demonstrate colonization by each inoculated strain, symbiosis, stability or a causal enrichment mechanism, and the main text contains inconsistent blanket richness/evenness wording.
@@ -653,26 +646,14 @@
Four-Member Pepper SynCom Inoculation
-
Biological Processes:
-
-
Downstream Effects:
-
→ SynCom-Shifted Rhizosphere Diversity
-
The four-member SynCom inoculation reorganized the pepper seedling rhizosphere, driving the measured fungal and bacterial diversity shifts after 45 days.
-
+
→ Growth-Associated Native Taxa Relative Enrichment
+
HYPOTHESIZED - The authors propose that the shifted rhizosphere community favors enrichment of growth-associated native taxa. Diversity indices and relative taxon profiles were measured after the same treatment; their association does not isolate diversity change as the cause of enrichment.
@@ -688,10 +669,10 @@
Evidence
PMID:39858916
- - SUPPORT (IN_VITRO)
+ - SUPPORT (IN_VIVO)
"The fermentation liquids of the four strains were adjusted to a concentration of 1 × 108 CFU/mL, and then mixed in equal proportions to create the SynCom."
+ "The Chao index of the rhizosphere microbial community and Bray–Curtis dissimilarity of the fungal community significantly increased, while Bray–Curtis dissimilarity of the bacterial community significantly decreased by SynCom inoculation."
@@ -701,11 +682,9 @@ Evidence
-
SynCom inoculation increased fungal richness and fungal Bray-Curtis dissimilarity while decreasing bacterial Bray-Curtis dissimilarity in the pepper seedling rhizosphere.
-
+
SynCom treatment increased relative abundances of selected Sordariomycetes, Pseudarthrobacter, norank SBR1031 and norank A4b OTUs associated with pepper growth and root morphology. Scedosporium OTU451 also increased, while total genus-level Scedosporium decreased; these different aggregation levels must remain distinct. Correlations and random-forest importance identify candidate mediators, not absolute population growth, strain-specific colonization or demonstrated contributions by the four inoculated strains.
@@ -714,26 +693,14 @@
SynCom-Shifted Rhizosphere Diversity
-
Biological Processes:
-
-
Downstream Effects:
-
→ Key Native Taxa Enrichment
-
The SynCom-driven rhizosphere shift included increases in native fungal and bacterial OTUs that were correlated with pepper growth and root morphology readouts.
-
+
→ Pepper Rhizosphere Growth Promotion
+
HYPOTHESIZED - The enriched native taxa may contribute to pepper growth, as proposed from correlation and random-forest analyses. Those analyses do not establish necessity, sufficiency or direction independently of the shared inoculation treatment or plant-driven changes.
@@ -752,7 +719,7 @@
Evidence
- SUPPORT (IN_VIVO)
"The Chao index of the rhizosphere microbial community and Bray–Curtis dissimilarity of the fungal community significantly increased, while Bray–Curtis dissimilarity of the bacterial community significantly decreased by SynCom inoculation."
+ "The abundance of Sordariomycetes, Pseudarthrobacter, norank SBR1031, and norank A4b were significantly correlated with pepper growth and root morphology"
@@ -762,11 +729,9 @@ Evidence
-
SynCom inoculation enriched native Sordariomycetes, Pseudarthrobacter, SBR1031, and A4b OTUs whose abundances tracked pepper growth and root morphology.
-
+
The four-member SynCom treatment increased measured shoot growth, biomass, chlorophyll, root vigor and root-morphology readouts compared with uninoculated controls after 45 days. Preserve these positive whole-plant responses without inferring reciprocal microbial fitness, superiority over every single strain, field yield or mediation by a particular native taxon.
@@ -779,26 +744,15 @@
Key Native Taxa Enrichment
-
-
Downstream Effects:
-
-
-
→ Pepper Rhizosphere Growth Promotion
-
Random-forest and correlation analyses nominated the enriched native taxa as contributors to the shoot-height, dry-weight, chlorophyll, and root-vigor responses.
-
-
-
-
-
Evidence
@@ -813,7 +767,7 @@
Evidence
- SUPPORT (IN_VIVO)
"The abundance of Sordariomycetes, Pseudarthrobacter, norank SBR1031, and norank A4b were significantly correlated with pepper growth and root morphology"
+ "SynCom inoculation significantly increased shoot height, stem diameter, fresh weight, dry weight, chlorophyll content, leaf number, root vigor, root tips, total root length, and root-specific surface area of pepper"
@@ -821,62 +775,52 @@ Evidence
-
-
-
The four-member SynCom increased pepper seedling shoot, biomass, chlorophyll, root-vigor, and root-morphology measurements relative to uninoculated controls.
-
-
-
-
-
+
+
+
+ Knowledge gaps & discussions (1)
- Biological Processes:
-
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which native-community changes mediate the measured pepper growth response?
+
+
Inoculum preparation is an experimental method, not a biological node. The three biological observations remain and the author-proposed diversity-to-enrichment-to-growth path is retained as hypothesized. Relative OTU enrichment and predictive importance do not identify independent causal mediators. Scedosporium genus decrease and OTU451 increase are compatible at different resolutions. Preserve the four-member taxonomy and earlier label repairs. No new topology is supported by the inspected experimental comparisons.
-
- growth
- (GO:0040007 )
-
+
Attaches to: ecological_interactions#SynCom-Shifted Rhizosphere Diversity, ecological_interactions#Growth-Associated Native Taxa Relative Enrichment, ecological_interactions#Pepper Rhizosphere Growth Promotion
-
+
+ 1 evidence item(s)
+
+
+
IN_VIVO
+
SUPPORT
-
Evidence
-
-
-
+ The abundance of Sordariomycetes, Pseudarthrobacter, norank SBR1031, and norank A4b were significantly correlated with pepper growth and root morphology
+ Links SynCom-enriched native taxa to the pepper growth and root-architecture phenotypes.
+
+
-
"SynCom inoculation significantly increased shoot height, stem diameter, fresh weight, dry weight, chlorophyll content, leaf number, root vigor, root tips, total root length, and root-specific surface area of pepper"
-
-
+
-
Evidence
(function() {
var intId = "interaction:0";
- var intType = "COLONIZATION_FACILITATION";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
-
- processes.push("symbiotic process");
-
-
var evidenceCount = 1;
nodes.push({
id: intId,
- label: "Four-Member Pepper SynCom Inoculation",
+ label: "SynCom-Shifted Rhizosphere Diversity",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1126,20 +1066,16 @@ Evidence
(function() {
var intId = "interaction:1";
- var intType = "COLONIZATION_FACILITATION";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
-
- processes.push("symbiotic process");
-
-
var evidenceCount = 1;
nodes.push({
id: intId,
- label: "SynCom-Shifted Rhizosphere Diversity",
+ label: "Growth-Associated Native Taxa Relative Enrichment",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1154,35 +1090,7 @@ Evidence
(function() {
var intId = "interaction:2";
- var intType = "COLONIZATION_FACILITATION";
- var metabolites = [];
-
- var processes = [];
-
-
- processes.push("symbiotic process");
-
-
- var evidenceCount = 1;
-
- nodes.push({
- id: intId,
- label: "Key Native Taxa Enrichment",
- type: "interaction",
- interactionType: intType,
- metabolites: metabolites,
- processes: processes,
- evidenceCount: evidenceCount
- });
-
-
-
-
- })();
-
- (function() {
- var intId = "interaction:3";
- var intType = "MUTUALISM";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
@@ -1227,7 +1135,7 @@ 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 = 8;
+ var nodeCount = 7;
var height = Math.max(500, 400 + nodeCount * 20);
svg.attr("width", width).attr("height", height);
diff --git a/docs/communities/Pepper_Phytophthora_SynCom5.html b/docs/communities/Pepper_Phytophthora_SynCom5.html
index 590361420..7aec4afdf 100644
--- a/docs/communities/Pepper_Phytophthora_SynCom5.html
+++ b/docs/communities/Pepper_Phytophthora_SynCom5.html
@@ -654,7 +654,7 @@ Ecological Interactions
Ecological interaction network for Pepper Phytophthora-Resistance SynCom5
- 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 (mutualism, competition, colonization facilitation).
+ 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.
@@ -662,18 +662,8 @@
Ecological Interactions
-
-
-
-
Ecological Interactions
-
The five-member pepper SynCom combines phosphate solubilization, indole-3-acetic-acid production, siderophore synthesis, ammonia production, and biofilm formation to provide complementary plant growth-promoting functions.
+
The five selected isolates showed distinct in-vitro PGPR trait profiles, including phosphate solubilization, IAA, siderophore and ammonia production and biofilm-associated assays. Preserve the positive screens without assigning every activity equally to every member. Table1 and narrative trait rankings differ, so the selection rationale does not establish a unique highest producer. These traits were assayed individually before assembly, not re-quantified in rhizosphere soil, and compatibility screens do not establish reciprocal fitness or synergistic trait expression.
@@ -709,25 +698,14 @@
Complementary PGPR Trait Pool
-
Biological Processes:
-
-
Downstream Effects:
-
→ Pepper Growth Under Phytophthora Challenge
-
The complementary PGPR trait set contributes nutrient-mobilization and phytohormone functions to the growth improvement observed in P. capsici-challenged pepper plants.
+
→ Pepper Growth and Visible Symptoms Under Pathogen Challenge
+
HYPOTHESIZED - Nutrient-mobilization and phytohormone traits of the selected isolates could contribute to challenged-host growth. The traits were not re-quantified in soil and were not selectively perturbed, so the host comparison does not isolate their mediation.
@@ -746,7 +724,7 @@
Evidence
- SUPPORT (IN_VITRO)
"We then applied this 5-isolate synthetic microbial community (SynCom) to Capsicum annuum to evaluate its efficacy in improving pepper resilience against P. capsici."
+ "The SynCom members exhibited phosphate solubilization, indole-3-acetic acid production, catalase activity, siderophore synthesis, and strong antagonism against P. capsici"
@@ -756,13 +734,20 @@ Evidence
-
SynCom members show strong direct antagonism against Phytophthora capsici and secrete biocontrol-associated enzymes and siderophores, led by Streptomyces roseicoloratus T14 and Pseudomonas frederiksbergensis A6 inhibition activity.
+
Individual dual-culture assays showed substantially stronger P. capsici inhibition by S. roseicoloratus T14 and, secondarily, P. frederiksbergensis A6 than by the other three isolates. Table1 reports 58.4% and 17.6% inhibition for T14 and A6, respectively; it does not show uniformly strong antagonism by all five members. Co-occurring enzyme or siderophore phenotypes do not identify the inhibition mechanism. P. capsici is an oomycete; chitinase activity does not demonstrate degradation of its wall or a host antifungal defense response.
+
+
+
+
Participating Taxa:
+ Streptomyces sp.,
+ Pseudomonas sp.
+
+
@@ -776,25 +761,14 @@
Direct Phytophthora capsici Antagonism
-
Biological Processes:
-
-
-
- defense response to fungus
- (GO:0050832 )
-
-
-
-
Downstream Effects:
-
→ Pepper Growth Under Phytophthora Challenge
-
Direct Phytophthora antagonism supplies the disease-suppression component of the SynCom's pepper-protection phenotype under pathogen pressure.
+
→ Pepper Growth and Visible Symptoms Under Pathogen Challenge
+
HYPOTHESIZED - The measured isolate antagonism may contribute to improved host performance under pathogen challenge. The pot study lacked a SynCom-only control and direct disease scoring or pathogen-load measurements, so it cannot isolate pathogen suppression from growth promotion or attribute the host response to these two strains alone.
@@ -813,7 +787,7 @@
Evidence
- SUPPORT (IN_VITRO)
"We then applied this 5-isolate synthetic microbial community (SynCom) to Capsicum annuum to evaluate its efficacy in improving pepper resilience against P. capsici."
+ "The SynCom members exhibited phosphate solubilization, indole-3-acetic acid production, catalase activity, siderophore synthesis, and strong antagonism against P. capsici"
@@ -823,24 +797,15 @@ Evidence
-
The complete five-member SynCom reduces Phytophthora capsici disease severity while improving pepper root length, plant height, biomass, stem diameter, and chlorophyll content.
+
In the controlled pot experiment, the full five-member SynCom plus pathogen treatment improved root length, height, biomass, stem diameter and chlorophyll compared with the pathogen-only control. The authors also report reduced visible wilting and necrosis. Section3.5 explicitly states that direct disease-severity scoring and pathogen-load measurements were not performed, and that there was no SynCom-only control. Preserve measured growth and visible protection without converting them into quantified pathogen suppression, strain-resolved colonization or an IAA-mediated host mechanism.
-
Metabolites:
-
- indole-3-acetic acid
- (CHEBI:16411 )
-
-
-
Biological Processes:
@@ -852,12 +817,6 @@
Pepper Growth Under Phytophthora Challenge
class="term-link" target="_blank" rel="noopener noreferrer">GO:0040007)
-
- defense response to fungus
- (GO:0050832 )
-
-
@@ -873,10 +832,10 @@
Evidence
PMID:40508300
- - SUPPORT (IN_VITRO)
+ - SUPPORT (IN_VIVO)
"We then applied this 5-isolate synthetic microbial community (SynCom) to Capsicum annuum to evaluate its efficacy in improving pepper resilience against P. capsici."
+ "The SynCom reduced disease severity and enhanced the growth of pepper plants."
@@ -889,6 +848,45 @@ Evidence
+
+ Knowledge gaps & discussions (1)
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which isolate traits and community changes mediate the positive host response?
+
+
Individual screens, host growth and visible symptom improvement are distinct. Section3.5 rules out direct disease scoring/pathogen load and a SynCom-only comparison. Community composition and nitrate/K/Ca responses are additional positive findings not yet independently represented as graph nodes; ammonium/nitrite differences are not significant in Results despite stronger Discussion claims. PICRUSt/FUNGuild outputs are predictions, not measured metabolic flux or pathogen load. New structure requires scoped Edison review; no new topology is added here. Source protocol and identity inconsistencies remain a separate metadata issue.
+
+
Attaches to: ecological_interactions#Individual-Isolate PGPR Trait Measurements, ecological_interactions#Isolate Antagonism Against Phytophthora capsici, ecological_interactions#Pepper Growth and Visible Symptoms Under Pathogen Challenge
+
+
+
+
+ 1 evidence item(s)
+
+
+
+
The SynCom reduced disease severity and enhanced the growth of pepper plants.
+
The abstract summarizes a positive result; the full paper clarifies that disease protection used visual/physiological proxies rather than direct disease scores or pathogen load.
+
+
+
+
@@ -1118,7 +1116,7 @@ Evidence
(function() {
var intId = "interaction:0";
- var intType = "MUTUALISM";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1131,15 +1129,11 @@ Evidence
var processes = [];
-
- processes.push("plant growth");
-
-
var evidenceCount = 1;
nodes.push({
id: intId,
- label: "Complementary PGPR Trait Pool",
+ label: "Individual-Isolate PGPR Trait Measurements",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1154,7 +1148,7 @@ Evidence
(function() {
var intId = "interaction:1";
- var intType = "COMPETITION";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1163,15 +1157,11 @@ Evidence
var processes = [];
-
- processes.push("defense response to fungus");
-
-
var evidenceCount = 1;
nodes.push({
id: intId,
- label: "Direct Phytophthora capsici Antagonism",
+ label: "Isolate Antagonism Against Phytophthora capsici",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1182,30 +1172,37 @@ Evidence
+ var participantKeys = [
+
+ "Streptomyces sp.",
+
+ "Pseudomonas sp."
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
+
})();
(function() {
var intId = "interaction:2";
- var intType = "COLONIZATION_FACILITATION";
+ var intType = "UNKNOWN";
var metabolites = [];
-
- metabolites.push("indole-3-acetic acid");
-
-
var processes = [];
processes.push("plant growth");
- processes.push("defense response to fungus");
-
var evidenceCount = 1;
nodes.push({
id: intId,
- label: "Pepper Growth Under Phytophthora Challenge",
+ label: "Pepper Growth and Visible Symptoms Under Pathogen Challenge",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
diff --git a/history/records/Pelagerythrobacter_Salinicola_PES_Pyrene_Degradation_SynCom/2026-10-07T074131Z-codex-d4a2ed.yaml b/history/records/Pelagerythrobacter_Salinicola_PES_Pyrene_Degradation_SynCom/2026-10-07T074131Z-codex-d4a2ed.yaml
new file mode 100644
index 000000000..c9b8142cb
--- /dev/null
+++ b/history/records/Pelagerythrobacter_Salinicola_PES_Pyrene_Degradation_SynCom/2026-10-07T074131Z-codex-d4a2ed.yaml
@@ -0,0 +1,26 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Pelagerythrobacter_Salinicola_PES_Pyrene_Degradation_SynCom.yaml
+ slug: Pelagerythrobacter_Salinicola_PES_Pyrene_Degradation_SynCom
+session:
+ id: 2026-10-07T074131Z-codex-d4a2ed
+ timestamp: '2026-10-07T07:41:31Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1685
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain observed bottleneck and qualify the candidate intermediate handoff.; Preserve
+ extracellular emulsification without asserting reciprocal fitness or measured pyrene mediation.;
+ Preserve near-complete pyrene removal without equating it with carbon mineralization.
+ details: Source-based self-adversarial review. reports/causal_graph_review/decisions/20261007-four-records-batch83.yaml
diff --git a/history/records/Pelotomaculum_Methanothermobacter_Syntrophy/2026-10-07T074132Z-codex-849acd.yaml b/history/records/Pelotomaculum_Methanothermobacter_Syntrophy/2026-10-07T074132Z-codex-849acd.yaml
new file mode 100644
index 000000000..7a28dc269
--- /dev/null
+++ b/history/records/Pelotomaculum_Methanothermobacter_Syntrophy/2026-10-07T074132Z-codex-849acd.yaml
@@ -0,0 +1,27 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Pelotomaculum_Methanothermobacter_Syntrophy.yaml
+ slug: Pelotomaculum_Methanothermobacter_Syntrophy
+session:
+ id: 2026-10-07T074132Z-codex-849acd
+ timestamp: '2026-10-07T07:41:32Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1686
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Preserve propionate syntrophy and correct universal dependence and evidence attribution.;
+ Preserve alternative-substrate coculture growth without universal product stoichiometry.;
+ Preserve the hydrogen sink and source-bound coaggregation evidence while separating observations
+ and diffusion modeling.
+ details: Source-based self-adversarial review. reports/causal_graph_review/decisions/20261007-four-records-batch83.yaml
diff --git a/history/records/Pepper_Growth_Rhizosphere_SynCom/2026-10-07T074133Z-codex-b89626.yaml b/history/records/Pepper_Growth_Rhizosphere_SynCom/2026-10-07T074133Z-codex-b89626.yaml
new file mode 100644
index 000000000..2416676d0
--- /dev/null
+++ b/history/records/Pepper_Growth_Rhizosphere_SynCom/2026-10-07T074133Z-codex-b89626.yaml
@@ -0,0 +1,26 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Pepper_Growth_Rhizosphere_SynCom.yaml
+ slug: Pepper_Growth_Rhizosphere_SynCom
+session:
+ id: 2026-10-07T074133Z-codex-b89626
+ timestamp: '2026-10-07T07:41:33Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1687
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Preserve measured diversity changes while qualifying the proposed enrichment direction.;
+ Preserve relative OTU associations without converting predictive importance into causation.;
+ Preserve directly measured whole-plant growth without reciprocal-fitness inference.
+ details: Source-based self-adversarial review. reports/causal_graph_review/decisions/20261007-four-records-batch83.yaml
diff --git a/history/records/Pepper_Phytophthora_SynCom5/2026-10-07T074133Z-codex-0b4d64.yaml b/history/records/Pepper_Phytophthora_SynCom5/2026-10-07T074133Z-codex-0b4d64.yaml
new file mode 100644
index 000000000..360ce7fd1
--- /dev/null
+++ b/history/records/Pepper_Phytophthora_SynCom5/2026-10-07T074133Z-codex-0b4d64.yaml
@@ -0,0 +1,27 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Pepper_Phytophthora_SynCom5.yaml
+ slug: Pepper_Phytophthora_SynCom5
+session:
+ id: 2026-10-07T074133Z-codex-0b4d64
+ timestamp: '2026-10-07T07:41:33Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1688
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Preserve heterogeneous isolate traits without asserting mutualism or in-soil delivery.;
+ Preserve T14/A6 inhibition and distinguish it from a demonstrated host-protection mechanism.;
+ Preserve measured growth and visible symptoms without inventing direct disease-severity
+ quantification.
+ details: Source-based self-adversarial review. reports/causal_graph_review/decisions/20261007-four-records-batch83.yaml
diff --git a/kb/communities/Pelagerythrobacter_Salinicola_PES_Pyrene_Degradation_SynCom.yaml b/kb/communities/Pelagerythrobacter_Salinicola_PES_Pyrene_Degradation_SynCom.yaml
index 24ce5da92..d680450c7 100644
--- a/kb/communities/Pelagerythrobacter_Salinicola_PES_Pyrene_Degradation_SynCom.yaml
+++ b/kb/communities/Pelagerythrobacter_Salinicola_PES_Pyrene_Degradation_SynCom.yaml
@@ -134,15 +134,12 @@ taxonomy:
Salinicola sp. N4
explanation: Supports genus-level identification of strain A11 as Salinicola.
ecological_interactions:
-- name: N7-A11 4,5-dicarboxyphenanthrene handoff
- description: >-
- Pelagerythrobacter sp. N7 initiated pyrene oxidation but accumulated
- 4,5-dicarboxyphenanthrene as a bottleneck product in monoculture. PES
- additionally accumulated downstream products including 4-carboxyphenanthrene,
- phthalate, salicylic acid, and gentisate, leading the authors to propose
- that Salinicola sp. A11 assists N7 by decarboxylating
- 4,5-dicarboxyphenanthrene through an hphtC-5-encoded candidate aromatic-acid
- decarboxylase.
+- name: Proposed N7-A11 4,5-dicarboxyphenanthrene handoff
+ description: PARTIAL - N7 monoculture accumulated 4,5-dicarboxyphenanthrene, while PES contained additional downstream
+ metabolites. The authors infer an N7-to-A11 intermediate handoff and propose hphtC-5 as a candidate A11 decarboxylase
+ from genome annotation, structural modeling and transcripts. These observations do not directly trace intercellular
+ flux or establish enzyme necessity or sufficiency. The published Figure 8 correction confirms the proposed direction
+ from 4,5-dicarboxyphenanthrene to 4-carboxyphenanthrene, not its reverse.
interaction_type: SYNTROPHY
scope: PAIRWISE
source_taxon:
@@ -160,36 +157,34 @@ ecological_interactions:
term:
id: CHEBI:39106
label: pyrene
+ notes: Supplied pyrene substrate, not the proposed transferred intermediate.
downstream:
- target: Complete 5%-salinity pyrene removal by PES
- description: >-
- The proposed N7-to-A11 intermediate handoff relieves the
- 4,5-dicarboxyphenanthrene bottleneck observed in N7 monoculture and helps
- PES degrade the supplied pyrene completely within the main 10-day assay.
+ description: HYPOTHESIZED - A11-mediated transformation of the intermediate accumulated by N7 could relieve
+ the degradation bottleneck and enable the observed PES pyrene removal. Metabolite profiles, annotation and
+ expression support the proposed pathway but do not isolate hphtC-5-dependent intercellular transfer as the
+ cause of the removal advantage.
evidence:
- reference: PMID:42666409
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: >-
- Owing to the inability to further transfer 4,5-dicarboxyphenanthrene, the
- metabolic pathway was disrupted, leading to the significant accumulation
- of 4,5-dicarboxyphenanthrene during pyrene degradation by the pure culture
- of strain N7.
+ snippet: Owing to the inability to further transfer 4,5-dicarboxyphenanthrene, the metabolic pathway was disrupted,
+ leading to the significant accumulation of 4,5-dicarboxyphenanthrene during pyrene degradation by the pure
+ culture of strain N7.
explanation: Supports 4,5-dicarboxyphenanthrene as the N7 monoculture bottleneck.
- reference: PMID:42666409
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: COMPUTATIONAL
- snippet: >-
- enzyme encoded by hphtC-5 was proposed to be the candidate decarboxylase
- for the decarboxylation process of 4,5-dicarboxyphenanthrene.
- explanation: Supports hphtC-5 as the expressed A11 candidate for the decarboxylation step.
-- name: A11 extracellular bioemulsification of hydrophobic pyrene
- description: >-
- Salinicola sp. A11 secreted extracellular emulsan-like material detected in
- A11 and PES cell-free supernatants, but not N7 cell-free supernatant. The
- extracellular emulsifier was modeled as increasing hydrophobic pyrene
- bioavailability for the N7-centered upstream oxidation arm.
- interaction_type: MUTUALISM
+ snippet: enzyme encoded by hphtC-5 was proposed to be the candidate decarboxylase for the decarboxylation process
+ of 4,5-dicarboxyphenanthrene.
+ explanation: Candidate enzyme assignment based on annotation/modeling and expression, not direct enzymatic validation.
+- name: A11-Associated Extracellular Emulsifying Activity
+ description: A11 and PES cell-free supernatants formed persistent soybean-oil emulsions, unlike N7 supernatant,
+ washed cells or fresh medium; the reported 24-hour emulsification index was 68%. A11 was grown with yeast extract,
+ whereas N7 and PES were grown with pyrene, so this is not a substrate-matched production comparison. FTIR of
+ crude material and genome annotation support an emulsan-like interpretation. HYPOTHESIZED - Its contribution
+ to pyrene bioavailability and N7 degradation is proposed, not isolated by the soybean-oil assay or proof of
+ reciprocal fitness benefit.
scope: PAIRWISE
source_taxon:
preferred_term: Salinicola sp. A11
@@ -206,31 +201,31 @@ ecological_interactions:
term:
id: CHEBI:39106
label: pyrene
+ notes: Proposed degradation target; soybean oil was the hydrophobic phase of the emulsification assay.
downstream:
- target: Complete 5%-salinity pyrene removal by PES
- description: >-
- A11 extracellular bioemulsifier production is proposed to reduce the mass
- transfer limitation of hydrophobic pyrene and thereby increase PES pyrene
- degradation efficiency.
+ description: HYPOTHESIZED - Extracellular emulsifying material attributed to A11 could increase pyrene availability
+ and thereby improve PES removal. The measured emulsion phenotype and genomic capacity do not isolate pyrene
+ mass transfer, the export system or the fraction of removal caused by this mechanism.
evidence:
- reference: PMID:42666409
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: >-
- Distinct and persistent emulsion layers were observed only in the
- cell-free supernatants of strain A11 and consortium PES
+ snippet: Distinct and persistent emulsion layers were observed only in the cell-free supernatants of strain
+ A11 and consortium PES
explanation: Supports A11 and PES, but not N7 alone, as sources of extracellular emulsifying activity.
- reference: PMID:42666409
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: COMPUTATIONAL
snippet: In the genome of strain A11, wza, wzb, and wzc related genes were identified
- explanation: Supports the A11 genomic capacity for an emulsan-like export system.
+ explanation: Annotated genes support a candidate export system, not demonstrated gene-specific secretion or
+ degradation causality.
- name: Complete 5%-salinity pyrene removal by PES
- description: >-
- In 200 mL 5%-salinity SSDM batch flasks with 50 mg/L pyrene as the sole
- carbon source, the two-member PES consortium approached complete pyrene
- removal within 10 days, whereas neither pure culture completely degraded
- pyrene by itself under the tested conditions.
+ description: PES approached complete removal of 50 mg/L pyrene in 200 mL 5%-salinity SSDM within 10 days. N7 removal
+ plateaued at 49.95% after 14 days, and A11 lacked direct PAH-degrading capability. These controlled culture
+ observations support the consortium removal advantage. Residual-substrate HPLC and intermediate detection do
+ not by themselves establish complete carbon mineralization, a closed carbon balance or reciprocal member-specific
+ fitness benefits.
interaction_type: SYNTROPHY
scope: COMMUNITY_LEVEL
metabolites:
@@ -242,9 +237,8 @@ ecological_interactions:
- reference: PMID:42666409
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: >-
- Within a 10-day cultivation period, the removal rate of 50 mg/L pyrene by
- the consortium PES approached 100%
+ snippet: Within a 10-day cultivation period, the removal rate of 50 mg/L pyrene by the consortium PES approached
+ 100%
explanation: Supports the measured complete-pyrene-removal endpoint of the two-member consortium.
- reference: PMID:42666409
supports: SUPPORT
@@ -386,21 +380,53 @@ related_ingredients:
explanation: Supports PAHs as the contaminant class motivating the halophilic degradation assay.
discussions:
- discussion_id: hphtc5_decarboxylase_candidate_unresolved
- prompt: >-
- Is the A11 hphtC-5 candidate sufficient and necessary for
- 4,5-dicarboxyphenanthrene decarboxylation inside PES?
+ prompt: Is the A11 hphtC-5 candidate sufficient and necessary for 4,5-dicarboxyphenanthrene decarboxylation inside
+ PES?
kind: KNOWLEDGE_GAP
status: OPEN
attaches_to:
- - ecological_interactions#N7-A11 4,5-dicarboxyphenanthrene handoff
- rationale: >-
- The source detected downstream pyrene metabolites in PES, annotated
- hphtC-5 in the A11 genome, modeled a compatible active site, and measured
- hphtC-5 expression by RT-PCR. It did not purify HphtC-5 or perturb hphtC-5
+ - ecological_interactions#Proposed N7-A11 4,5-dicarboxyphenanthrene handoff
+ rationale: The source detected downstream pyrene metabolites in PES, annotated hphtC-5 in the A11 genome, modeled
+ a compatible active site, and measured hphtC-5 expression by RT-PCR. It did not purify HphtC-5 or perturb hphtC-5
genetically, so the specific enzyme assignment remains a candidate step.
posed_by: codex
posed_date: '2026-09-11'
+- discussion_id: pes-mediated-removal-boundaries
+ prompt: Which candidate enzyme and emulsifier activities cause the measured PES removal advantage?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Proposed N7-A11 4,5-dicarboxyphenanthrene handoff
+ - ecological_interactions#A11-Associated Extracellular Emulsifying Activity
+ - ecological_interactions#Complete 5%-salinity pyrene removal by PES
+ rationale: Preserve positive pyrene removal, intermediate profiles and extracellular emulsification. hphtC-5 remains
+ a candidate, as in the existing gap. Soybean-oil emulsification is not a direct pyrene-solubility or depletion/add-back
+ test; A11 and the other cultures had different growth substrates. The correction DOI10.3389/fmicb.2026.1971230
+ changes structures in Figure8, not the need for causal validation. No new nodes/arrows are warranted by the
+ inspected main text.
+ evidence:
+ - reference: PMID:42666409
+ supports: PARTIAL
+ evidence_source: COMPUTATIONAL
+ snippet: enzyme encoded by hphtC-5 was proposed to be the candidate decarboxylase for the decarboxylation process
+ of 4,5-dicarboxyphenanthrene.
+ explanation: Candidate enzyme assignment based on annotation/modeling and expression, not direct enzymatic validation.
+ - reference: PMID:42666409
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: Distinct and persistent emulsion layers were observed only in the cell-free supernatants of strain
+ A11 and consortium PES
+ explanation: Supports A11 and PES, but not N7 alone, as sources of extracellular emulsifying activity.
+ posed_by: codex
metals_present: []
rare_earth_elements_present: []
metal_relevance: NOT_APPLICABLE
metal_notes: No metal or rare-earth processing role is reported for this halophilic PES pyrene-degradation consortium.
+curation_history:
+- timestamp: '2026-10-07T07:41:27Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: 'Retain observed bottleneck and qualify the candidate intermediate handoff.; Preserve extracellular emulsification
+ without asserting reciprocal fitness or measured pyrene mediation.; Preserve near-complete pyrene removal without
+ equating it with carbon mineralization. Issue #1685; reports/causal_graph_review/decisions/20261007-four-records-batch83.yaml'
+ llm_assisted: true
diff --git a/kb/communities/Pelotomaculum_Methanothermobacter_Syntrophy.yaml b/kb/communities/Pelotomaculum_Methanothermobacter_Syntrophy.yaml
index ae034b55b..eb7ba1bbc 100644
--- a/kb/communities/Pelotomaculum_Methanothermobacter_Syntrophy.yaml
+++ b/kb/communities/Pelotomaculum_Methanothermobacter_Syntrophy.yaml
@@ -97,15 +97,12 @@ taxonomy:
partner
ecological_interactions:
- name: Propionate Oxidation and H2 Production
- description: 'Pelotomaculum thermopropionicum oxidizes propionate (C3) to acetate, CO2, and H2, using
- protons as the electron acceptor and producing H2 as the electron sink product. This propionate oxidation
- is thermodynamically unfavorable under standard conditions and only proceeds when H2 partial pressure
- is kept extremely low by a syntrophic partner. The organism cannot utilize common electron acceptors
- (nitrate, sulfate, etc.) and is therefore obligately dependent on syntrophic H2 removal. The coaggregation
- of P. thermopropionicum with M. thermautotrophicus facilitates efficient interspecies H2 transfer
- at thermophilic temperatures (55°C).
-
- '
+ description: 'P. thermopropionicum SI grows on propionate in coculture with the hydrogenotrophic methanogen M.
+ thermautotrophicus DeltaH. Preserve the propionate-oxidation/H2-transfer interpretation and the reported 55
+ degrees C growth optimum, without claiming that the temperature measurement itself proves metabolic flux. Dependence
+ is substrate- and condition-specific: the species paper reports pure-culture growth on pyruvate and fumarate
+ and fumarate reduction, despite absence of dissimilatory sulfate reduction. It does not justify a universal
+ inability to use electron acceptors or grow without a partner.'
interaction_type: SYNTROPHY
scope: PAIRWISE
source_taxon:
@@ -145,27 +142,33 @@ ecological_interactions:
label: propionate metabolic process
downstream:
- target: Interspecies Hydrogen Transfer and Thermophilic Methanogenesis
- description: H2 produced by P. thermopropionicum is consumed by M. thermautotrophicus for methanogenesis
- at 55°C
+ description: H2 supplied during syntrophic propionate oxidation fuels the hydrogenotrophic partner. Preserve
+ this directly implied donor-to-methanogen direction; the species-description abstract does not quantify the
+ exchanged flux or its stoichiometry.
evidence:
- reference: PMID:12361280
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: The optimum temperature for growth was 55 degrees C and the pH optimum was 7.0
- explanation: Demonstrates the core metabolic activity of P. thermopropionicum in propionate degradation
- requiring syntrophic partnership
+ snippet: The strain grew on propionate, ethanol, lactate, 1-butanol, 1-pentanol, 1,3-propanediol, 1-propanol
+ and ethylene glycol in co-culture with the hydrogenotrophic methanogen Methanothermobacter thermautotrophicus
+ strain deltaH(T)
+ explanation: Supports growth on propionate and the listed alternative substrates in coculture with the hydrogenotrophic
+ methanogen; it does not quantify product yields.
- reference: PMID:12361280
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: An anaerobic, thermophilic, syntrophic propionate-oxidizing bacterium, strain SI(T), isolated
- previously from granular sludge in a thermophilic upflow
+ snippet: The strain could grow fermentatively on pyruvate and fumarate in pure culture
+ explanation: Bounds the partner-dependence claim; it does not negate syntrophic propionate growth.
+ target_taxon:
+ preferred_term: Methanothermobacter thermautotrophicus
+ term:
+ id: NCBITaxon:145262
+ label: Methanothermobacter thermautotrophicus
- name: Alternative Alcohol and Diol Oxidation
- description: Pelotomaculum thermopropionicum grows syntrophically with
- Methanothermobacter thermautotrophicus on ethanol, lactate, 1-butanol,
- 1-pentanol, 1,3-propanediol, 1-propanol, and ethylene glycol as well as on
- propionate. Oxidation of these reduced organic substrates feeds acetate,
- CO2, and H2 into the same interspecies hydrogen-transfer route that makes
- propionate oxidation thermodynamically feasible.
+ description: The species paper reports coculture growth on ethanol, lactate, 1-butanol, 1-pentanol, 1,3-propanediol,
+ 1-propanol and ethylene glycol as well as propionate. These positive substrate-use phenotypes support the alternative
+ syntrophic route. The accessible abstract does not identify the carbon products and stoichiometry of every substrate,
+ so acetate and CO2 must not be assigned universally to all alcohols and diols.
interaction_type: SYNTROPHY
scope: PAIRWISE
source_taxon:
@@ -195,10 +198,6 @@ ecological_interactions:
term:
id: CHEBI:30742
label: ethylene glycol
- - preferred_term: acetate
- term:
- id: CHEBI:30089
- label: acetate
- preferred_term: dihydrogen
term:
id: CHEBI:18276
@@ -210,27 +209,25 @@ ecological_interactions:
label: fermentation
downstream:
- target: Interspecies Hydrogen Transfer and Thermophilic Methanogenesis
- description: Hydrogen and CO2 released from alcohol and diol oxidation are
- consumed by the methanogen in the same H2-removal sink.
+ description: PARTIAL - The reported growth of SI with a hydrogenotrophic partner on these alternative substrates
+ supports H2-linked syntrophy. Substrate-resolved H2 yields and carbon-product balances are not exposed in
+ the cited species-description abstract; do not assume every substrate supplies the same acetate/CO2 products.
evidence:
- reference: PMID:12361280
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: The strain grew on propionate, ethanol, lactate, 1-butanol, 1-pentanol,
- 1,3-propanediol, 1-propanol and ethylene glycol in co-culture with the hydrogenotrophic
- methanogen Methanothermobacter thermautotrophicus strain deltaH(T)
- explanation: Supports syntrophic growth on ethanol, lactate, butanols, and
- diols with Methanothermobacter as the hydrogenotrophic partner.
+ snippet: The strain grew on propionate, ethanol, lactate, 1-butanol, 1-pentanol, 1,3-propanediol, 1-propanol
+ and ethylene glycol in co-culture with the hydrogenotrophic methanogen Methanothermobacter thermautotrophicus
+ strain deltaH(T)
+ explanation: Supports syntrophic growth on ethanol, lactate, butanols, and diols with Methanothermobacter as
+ the hydrogenotrophic partner.
- name: Interspecies Hydrogen Transfer and Thermophilic Methanogenesis
- description: 'Methanothermobacter thermautotrophicus consumes the H2 produced by P. thermopropionicum,
- combining it with CO2 to produce methane via hydrogenotrophic methanogenesis at thermophilic temperatures
- (55°C). This H2 removal maintains a low H2 partial pressure, making the thermodynamically unfavorable
- propionate oxidation by P. thermopropionicum energetically feasible. This interspecies hydrogen transfer
- (IHT) is enhanced by coaggregation between the two organisms, which reduces diffusion distances and
- improves syntrophic efficiency at elevated temperatures. This represents a classic example of thermophilic
- syntrophic metabolism in anaerobic environments.
-
- '
+ description: M. thermautotrophicus is the hydrogenotrophic partner, consuming H2 for methane formation and providing
+ an H2 sink compatible with SI propionate oxidation. The separate 2005 study reports stronger coaggregation on
+ propionate than on ethanol or 1-propanol. Microscopy supports physical association, while Fick-law calculations
+ support substrate-dependent diffusion-distance requirements; those modeled distances are not direct flux measurements.
+ Its Figure4 caption reports 2-BES inhibition of partner hydrogen consumption. Retain these positive observations
+ without attributing all of them to the 2002 species paper or asserting direct electron conduction through filaments.
interaction_type: SYNTROPHY
scope: PAIRWISE
source_taxon:
@@ -263,11 +260,28 @@ ecological_interactions:
- reference: PMID:12361280
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: The strain grew on propionate, ethanol, lactate, 1-butanol, 1-pentanol, 1,3-propanediol,
- 1-propanol and ethylene glycol in co-culture with the hydrogenotrophic methanogen Methanothermobacter
- thermautotrophicus strain deltaH(T)
- explanation: Demonstrates successful thermophilic syntrophic coculture with M. thermautotrophicus
- as H2-utilizing partner
+ snippet: The strain grew on propionate, ethanol, lactate, 1-butanol, 1-pentanol, 1,3-propanediol, 1-propanol
+ and ethylene glycol in co-culture with the hydrogenotrophic methanogen Methanothermobacter thermautotrophicus
+ strain deltaH(T)
+ explanation: Demonstrates successful thermophilic syntrophic coculture with M. thermautotrophicus as H2-utilizing
+ partner
+ - reference: PMID:16332758
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: these organisms coaggregated to different degrees depending on the substrate
+ explanation: The primary abstract reports substrate-dependent physical association; diffusion-distance inference
+ is a separate calculation.
+ - reference: PMID:16332758
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: Hydrogen consumption by ΔH cells was inhibited by adding 2-BES.
+ explanation: The primary Figure4 caption reports inhibition of the methanogenic hydrogen sink, not a filament-conduction
+ experiment.
+ target_taxon:
+ preferred_term: Pelotomaculum thermopropionicum
+ term:
+ id: NCBITaxon:110500
+ label: Pelotomaculum thermopropionicum
environmental_factors:
- name: Anaerobic Conditions
value: Strict anaerobic
@@ -593,3 +607,39 @@ growth_media:
thermautotrophicus at thermophilic temperatures
culturemech_id: CultureMech:000423
culturemech_url: https://github.com/CultureBotAI/CultureMech/tree/main/kb/media/CultureMech:000423
+discussions:
+- discussion_id: si-deltah-fulltext-and-feedback
+ prompt: How should hydrogen-removal feedback and coaggregation be represented after full-method review?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Propionate Oxidation and H2 Production
+ - ecological_interactions#Alternative Alcohol and Diol Oxidation
+ - ecological_interactions#Interspecies Hydrogen Transfer and Thermophilic Methanogenesis
+ rationale: Existing substrate-growth and H2-to-methanogenesis directions remain. PMID16332758 adds positive microscopy
+ and a partner-inhibition lead; its modeled proximity requirement must not be confused with measured flux or
+ electrical conduction. Full main methods and possible separate coaggregation/feedback structure remain research
+ work. A one-community Edison causal dry run exists; no paid report or new node/arrow has been used. Non-graph
+ medium and universal-dependence claims are preserved but not certified.
+ evidence:
+ - reference: PMID:16332758
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: these organisms coaggregated to different degrees depending on the substrate
+ explanation: The primary abstract reports substrate-dependent physical association; diffusion-distance inference
+ is a separate calculation.
+ - reference: PMID:16332758
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: Hydrogen consumption by ΔH cells was inhibited by adding 2-BES.
+ explanation: The primary Figure4 caption reports inhibition of the methanogenic hydrogen sink, not a filament-conduction
+ experiment.
+ posed_by: codex
+curation_history:
+- timestamp: '2026-10-07T07:41:29Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: 'Preserve propionate syntrophy and correct universal dependence and evidence attribution.; Preserve alternative-substrate
+ coculture growth without universal product stoichiometry.; Preserve the hydrogen sink and source-bound coaggregation
+ evidence while separating observations and diffusion modeling. Issue #1686; reports/causal_graph_review/decisions/20261007-four-records-batch83.yaml'
+ llm_assisted: true
diff --git a/kb/communities/Pepper_Growth_Rhizosphere_SynCom.yaml b/kb/communities/Pepper_Growth_Rhizosphere_SynCom.yaml
index a75077919..00071bdb5 100644
--- a/kb/communities/Pepper_Growth_Rhizosphere_SynCom.yaml
+++ b/kb/communities/Pepper_Growth_Rhizosphere_SynCom.yaml
@@ -84,87 +84,55 @@ taxonomy:
evidence:
- *id002
ecological_interactions:
-- name: Four-Member Pepper SynCom Inoculation
- description: >
- Bacillus subtilis, Trichoderma harzianum, Trichoderma asperellum, and Aspergillus sp.
- fermentation liquids were normalized and mixed in equal proportions before soil inoculation.
- scope: COMMUNITY_LEVEL
- interaction_type: COLONIZATION_FACILITATION
- biological_processes:
- - preferred_term: symbiotic process
- term:
- id: GO:0044403
- label: biological process involved in symbiotic interaction
- downstream:
- - target: SynCom-Shifted Rhizosphere Diversity
- description: >
- The four-member SynCom inoculation reorganized the pepper seedling rhizosphere,
- driving the measured fungal and bacterial diversity shifts after 45 days.
- evidence:
- - reference: PMID:39858916
- supports: SUPPORT
- evidence_source: IN_VITRO
- snippet: The fermentation liquids of the four strains were adjusted to a concentration of
- 1 × 108 CFU/mL, and then mixed in equal proportions to create the SynCom.
- explanation: >
- Defines the four-member inoculum and the equal-proportion mixing step used to make the pepper
- SynCom.
- name: SynCom-Shifted Rhizosphere Diversity
- description: >
- SynCom inoculation increased fungal richness and fungal Bray-Curtis dissimilarity while
- decreasing bacterial Bray-Curtis dissimilarity in the pepper seedling rhizosphere.
+ description: After the four-member inoculation treatment, the study reports increased fungal and bacterial Chao
+ richness and fungal Bray-Curtis dissimilarity, with decreased bacterial Bray-Curtis dissimilarity after 45 days.
+ Preserve the observed community-profile response. These diversity indices do not demonstrate colonization by
+ each inoculated strain, symbiosis, stability or a causal enrichment mechanism, and the main text contains inconsistent
+ blanket richness/evenness wording.
scope: COMMUNITY_LEVEL
- interaction_type: COLONIZATION_FACILITATION
- biological_processes:
- - preferred_term: symbiotic process
- term:
- id: GO:0044403
- label: biological process involved in symbiotic interaction
downstream:
- - target: Key Native Taxa Enrichment
- description: >
- The SynCom-driven rhizosphere shift included increases in native fungal and bacterial OTUs
- that were correlated with pepper growth and root morphology readouts.
+ - target: Growth-Associated Native Taxa Relative Enrichment
+ description: HYPOTHESIZED - The authors propose that the shifted rhizosphere community favors enrichment of
+ growth-associated native taxa. Diversity indices and relative taxon profiles were measured after the same
+ treatment; their association does not isolate diversity change as the cause of enrichment.
evidence:
- reference: PMID:39858916
supports: SUPPORT
evidence_source: IN_VIVO
- snippet: The Chao index of the rhizosphere microbial community and Bray–Curtis dissimilarity
- of the fungal community significantly increased, while Bray–Curtis dissimilarity
- of the bacterial community significantly decreased by SynCom inoculation.
- explanation: >
- Reports the measured alpha- and beta-diversity shifts in the SynCom-inoculated pepper
- rhizosphere.
-- name: Key Native Taxa Enrichment
- description: >
- SynCom inoculation enriched native Sordariomycetes, Pseudarthrobacter, SBR1031, and A4b OTUs
- whose abundances tracked pepper growth and root morphology.
+ snippet: The Chao index of the rhizosphere microbial community and Bray–Curtis dissimilarity of the fungal community
+ significantly increased, while Bray–Curtis dissimilarity of the bacterial community significantly decreased
+ by SynCom inoculation.
+ explanation: 'Reports the measured alpha- and beta-diversity shifts in the SynCom-inoculated pepper rhizosphere.
+
+ '
+- name: Growth-Associated Native Taxa Relative Enrichment
+ description: SynCom treatment increased relative abundances of selected Sordariomycetes, Pseudarthrobacter, norank
+ SBR1031 and norank A4b OTUs associated with pepper growth and root morphology. Scedosporium OTU451 also increased,
+ while total genus-level Scedosporium decreased; these different aggregation levels must remain distinct. Correlations
+ and random-forest importance identify candidate mediators, not absolute population growth, strain-specific colonization
+ or demonstrated contributions by the four inoculated strains.
scope: COMMUNITY_LEVEL
- interaction_type: COLONIZATION_FACILITATION
- biological_processes:
- - preferred_term: symbiotic process
- term:
- id: GO:0044403
- label: biological process involved in symbiotic interaction
downstream:
- target: Pepper Rhizosphere Growth Promotion
- description: >
- Random-forest and correlation analyses nominated the enriched native taxa as contributors to
- the shoot-height, dry-weight, chlorophyll, and root-vigor responses.
+ description: HYPOTHESIZED - The enriched native taxa may contribute to pepper growth, as proposed from correlation
+ and random-forest analyses. Those analyses do not establish necessity, sufficiency or direction independently
+ of the shared inoculation treatment or plant-driven changes.
evidence:
- reference: PMID:39858916
supports: SUPPORT
evidence_source: IN_VIVO
- snippet: The abundance of Sordariomycetes, Pseudarthrobacter, norank SBR1031, and norank
- A4b were significantly correlated with pepper growth and root morphology
- explanation: >
- Links SynCom-enriched native taxa to the pepper growth and root-architecture phenotypes.
+ snippet: The abundance of Sordariomycetes, Pseudarthrobacter, norank SBR1031, and norank A4b were significantly
+ correlated with pepper growth and root morphology
+ explanation: 'Links SynCom-enriched native taxa to the pepper growth and root-architecture phenotypes.
+
+ '
- name: Pepper Rhizosphere Growth Promotion
- description: >
- The four-member SynCom increased pepper seedling shoot, biomass, chlorophyll, root-vigor, and
- root-morphology measurements relative to uninoculated controls.
+ description: The four-member SynCom treatment increased measured shoot growth, biomass, chlorophyll, root vigor
+ and root-morphology readouts compared with uninoculated controls after 45 days. Preserve these positive whole-plant
+ responses without inferring reciprocal microbial fitness, superiority over every single strain, field yield
+ or mediation by a particular native taxon.
scope: COMMUNITY_LEVEL
- interaction_type: MUTUALISM
biological_processes:
- preferred_term: growth
term:
@@ -174,11 +142,11 @@ ecological_interactions:
- reference: PMID:39858916
supports: SUPPORT
evidence_source: IN_VIVO
- snippet: SynCom inoculation significantly increased shoot height, stem diameter, fresh weight,
- dry weight, chlorophyll content, leaf number, root vigor, root tips, total root
- length, and root-specific surface area of pepper
- explanation: >
- Reports the growth and root-morphology increases measured after SynCom inoculation.
+ snippet: SynCom inoculation significantly increased shoot height, stem diameter, fresh weight, dry weight, chlorophyll
+ content, leaf number, root vigor, root tips, total root length, and root-specific surface area of pepper
+ explanation: 'Reports the growth and root-morphology increases measured after SynCom inoculation.
+
+ '
environmental_factors:
- name: defined synthetic community design
value: Synthetic microbial community applied during pepper seedling establishment.
@@ -236,8 +204,38 @@ curation_history:
- timestamp: '2026-10-02T06:00:47Z'
curator: codex
action: REPAIR_CAUSAL_GRAPH
- changes: Rewrote the four-member pepper SynCom downstream edge so it asserts
- the SynCom-driven rhizosphere diversity shift directly instead of narrating
- inoculation followed by 45-day amplicon profiling, and normalized the
- current NCBITaxon label for Aspergillus.
+ changes: Rewrote the four-member pepper SynCom downstream edge so it asserts the SynCom-driven rhizosphere diversity
+ shift directly instead of narrating inoculation followed by 45-day amplicon profiling, and normalized the current
+ NCBITaxon label for Aspergillus.
llm_assisted: true
+- timestamp: '2026-10-07T07:41:30Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: 'Preserve measured diversity changes while qualifying the proposed enrichment direction.; Preserve relative
+ OTU associations without converting predictive importance into causation.; Preserve directly measured whole-plant
+ growth without reciprocal-fitness inference. Issue #1687; reports/causal_graph_review/decisions/20261007-four-records-batch83.yaml'
+ llm_assisted: true
+discussions:
+- discussion_id: pepper-growth-treatment-versus-mediation
+ prompt: Which native-community changes mediate the measured pepper growth response?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#SynCom-Shifted Rhizosphere Diversity
+ - ecological_interactions#Growth-Associated Native Taxa Relative Enrichment
+ - ecological_interactions#Pepper Rhizosphere Growth Promotion
+ rationale: Inoculum preparation is an experimental method, not a biological node. The three biological observations
+ remain and the author-proposed diversity-to-enrichment-to-growth path is retained as hypothesized. Relative
+ OTU enrichment and predictive importance do not identify independent causal mediators. Scedosporium genus decrease
+ and OTU451 increase are compatible at different resolutions. Preserve the four-member taxonomy and earlier label
+ repairs. No new topology is supported by the inspected experimental comparisons.
+ evidence:
+ - reference: PMID:39858916
+ supports: SUPPORT
+ evidence_source: IN_VIVO
+ snippet: The abundance of Sordariomycetes, Pseudarthrobacter, norank SBR1031, and norank A4b were significantly
+ correlated with pepper growth and root morphology
+ explanation: 'Links SynCom-enriched native taxa to the pepper growth and root-architecture phenotypes.
+
+ '
+ posed_by: codex
diff --git a/kb/communities/Pepper_Phytophthora_SynCom5.yaml b/kb/communities/Pepper_Phytophthora_SynCom5.yaml
index a23f2d3ce..be6264163 100644
--- a/kb/communities/Pepper_Phytophthora_SynCom5.yaml
+++ b/kb/communities/Pepper_Phytophthora_SynCom5.yaml
@@ -93,84 +93,103 @@ taxonomy:
evidence:
- *id001
ecological_interactions:
-- name: Complementary PGPR Trait Pool
- description: The five-member pepper SynCom combines phosphate solubilization, indole-3-acetic-acid
- production, siderophore synthesis, ammonia production, and biofilm formation to provide complementary
- plant growth-promoting functions.
- interaction_type: MUTUALISM
+- name: Individual-Isolate PGPR Trait Measurements
+ description: The five selected isolates showed distinct in-vitro PGPR trait profiles, including phosphate solubilization,
+ IAA, siderophore and ammonia production and biofilm-associated assays. Preserve the positive screens without
+ assigning every activity equally to every member. Table1 and narrative trait rankings differ, so the selection
+ rationale does not establish a unique highest producer. These traits were assayed individually before assembly,
+ not re-quantified in rhizosphere soil, and compatibility screens do not establish reciprocal fitness or synergistic
+ trait expression.
scope: COMMUNITY_LEVEL
metabolites:
- preferred_term: phosphate
term:
id: CHEBI:26020
label: phosphate
- notes: Plant-accessible phosphorus pool mobilized by SynCom phosphate-solubilizing activity
+ notes: Trait measured in individual isolate screens; not a measured plant delivery flux or proof of equal activity
+ by every member.
- preferred_term: indole-3-acetic acid
term:
id: CHEBI:16411
label: indole-3-acetic acid
- notes: Auxin produced by SynCom members during plant-growth promotion assays
+ notes: Trait measured in individual isolate screens; not a measured plant delivery flux or proof of equal activity
+ by every member.
- preferred_term: siderophore
term:
id: CHEBI:26672
label: siderophore
- notes: Iron-mobilizing chelator produced by SynCom members
- biological_processes:
- - preferred_term: plant growth
- term:
- id: GO:0040007
- label: growth
+ notes: Trait measured in individual isolate screens; not a measured plant delivery flux or proof of equal activity
+ by every member.
downstream:
- - target: Pepper Growth Under Phytophthora Challenge
- description: The complementary PGPR trait set contributes nutrient-mobilization and phytohormone
- functions to the growth improvement observed in P. capsici-challenged pepper plants.
+ - target: Pepper Growth and Visible Symptoms Under Pathogen Challenge
+ description: HYPOTHESIZED - Nutrient-mobilization and phytohormone traits of the selected isolates could contribute
+ to challenged-host growth. The traits were not re-quantified in soil and were not selectively perturbed, so
+ the host comparison does not isolate their mediation.
evidence:
- - *id001
-- name: Direct Phytophthora capsici Antagonism
- description: SynCom members show strong direct antagonism against Phytophthora capsici and secrete
- biocontrol-associated enzymes and siderophores, led by Streptomyces roseicoloratus T14 and Pseudomonas
- frederiksbergensis A6 inhibition activity.
- interaction_type: COMPETITION
+ - reference: PMID:40508300
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: The SynCom members exhibited phosphate solubilization, indole-3-acetic acid production, catalase activity,
+ siderophore synthesis, and strong antagonism against P. capsici
+ explanation: Abstract summary of isolate screens; full Table1 shows heterogeneous traits rather than uniformly
+ strong activity.
+- name: Isolate Antagonism Against Phytophthora capsici
+ description: Individual dual-culture assays showed substantially stronger P. capsici inhibition by S. roseicoloratus
+ T14 and, secondarily, P. frederiksbergensis A6 than by the other three isolates. Table1 reports 58.4% and 17.6%
+ inhibition for T14 and A6, respectively; it does not show uniformly strong antagonism by all five members. Co-occurring
+ enzyme or siderophore phenotypes do not identify the inhibition mechanism. P. capsici is an oomycete; chitinase
+ activity does not demonstrate degradation of its wall or a host antifungal defense response.
scope: COMMUNITY_LEVEL
metabolites:
- preferred_term: siderophore
term:
id: CHEBI:26672
label: siderophore
- notes: Iron-chelating antagonist trait screened across the pepper SynCom members
- biological_processes:
- - preferred_term: defense response to fungus
- term:
- id: GO:0050832
- label: defense response to fungus
+ notes: Siderophore is a separately screened trait, not an established mediator of pathogen inhibition; strong
+ siderophore production is not demonstrated for A6.
downstream:
- - target: Pepper Growth Under Phytophthora Challenge
- description: Direct Phytophthora antagonism supplies the disease-suppression component of the SynCom's
- pepper-protection phenotype under pathogen pressure.
+ - target: Pepper Growth and Visible Symptoms Under Pathogen Challenge
+ description: HYPOTHESIZED - The measured isolate antagonism may contribute to improved host performance under
+ pathogen challenge. The pot study lacked a SynCom-only control and direct disease scoring or pathogen-load
+ measurements, so it cannot isolate pathogen suppression from growth promotion or attribute the host response
+ to these two strains alone.
evidence:
- - *id001
-- name: Pepper Growth Under Phytophthora Challenge
- description: The complete five-member SynCom reduces Phytophthora capsici disease severity while improving
- pepper root length, plant height, biomass, stem diameter, and chlorophyll content.
- interaction_type: COLONIZATION_FACILITATION
- scope: COMMUNITY_LEVEL
- metabolites:
- - preferred_term: indole-3-acetic acid
+ - reference: PMID:40508300
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: The SynCom members exhibited phosphate solubilization, indole-3-acetic acid production, catalase activity,
+ siderophore synthesis, and strong antagonism against P. capsici
+ explanation: Preserves measured isolate antagonism; primary Table1 resolves T14/A6 dominance. Does not identify
+ enzyme-mediated killing or competition for a particular resource.
+ participating_taxa:
+ - preferred_term: Streptomyces sp.
term:
- id: CHEBI:16411
- label: indole-3-acetic acid
- notes: Plant-growth-promoting auxin from the full SynCom trait suite
+ id: NCBITaxon:1931
+ label: Streptomyces sp.
+ - preferred_term: Pseudomonas sp.
+ term:
+ id: NCBITaxon:306
+ label: Pseudomonas sp.
+- name: Pepper Growth and Visible Symptoms Under Pathogen Challenge
+ description: In the controlled pot experiment, the full five-member SynCom plus pathogen treatment improved root
+ length, height, biomass, stem diameter and chlorophyll compared with the pathogen-only control. The authors
+ also report reduced visible wilting and necrosis. Section3.5 explicitly states that direct disease-severity
+ scoring and pathogen-load measurements were not performed, and that there was no SynCom-only control. Preserve
+ measured growth and visible protection without converting them into quantified pathogen suppression, strain-resolved
+ colonization or an IAA-mediated host mechanism.
+ scope: COMMUNITY_LEVEL
biological_processes:
- preferred_term: plant growth
term:
id: GO:0040007
label: growth
- - preferred_term: defense response to fungus
- term:
- id: GO:0050832
- label: defense response to fungus
evidence:
- - *id001
+ - reference: PMID:40508300
+ supports: SUPPORT
+ evidence_source: IN_VIVO
+ snippet: The SynCom reduced disease severity and enhanced the growth of pepper plants.
+ explanation: The abstract summarizes a positive result; the full paper clarifies that disease protection used
+ visual/physiological proxies rather than direct disease scores or pathogen load.
environmental_factors:
- name: defined synthetic community design
value: Bacillus, Flavobacterium, Cytobacillus, Streptomyces, and Pseudomonas isolates from healthy pepper
@@ -217,3 +236,34 @@ growth_media:
snippet: The experiment was conducted in a controlled growth chamber at Kyungpook National University
under day/night temperatures of 18–23 °C and 12–16 °C
explanation: Reports the growth-chamber temperature regime for the pepper plant experiment.
+discussions:
+- discussion_id: pepper-syncom5-assay-and-mediator-boundaries
+ prompt: Which isolate traits and community changes mediate the positive host response?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Individual-Isolate PGPR Trait Measurements
+ - ecological_interactions#Isolate Antagonism Against Phytophthora capsici
+ - ecological_interactions#Pepper Growth and Visible Symptoms Under Pathogen Challenge
+ rationale: Individual screens, host growth and visible symptom improvement are distinct. Section3.5 rules out
+ direct disease scoring/pathogen load and a SynCom-only comparison. Community composition and nitrate/K/Ca responses
+ are additional positive findings not yet independently represented as graph nodes; ammonium/nitrite differences
+ are not significant in Results despite stronger Discussion claims. PICRUSt/FUNGuild outputs are predictions,
+ not measured metabolic flux or pathogen load. New structure requires scoped Edison review; no new topology is
+ added here. Source protocol and identity inconsistencies remain a separate metadata issue.
+ evidence:
+ - reference: PMID:40508300
+ supports: SUPPORT
+ evidence_source: IN_VIVO
+ snippet: The SynCom reduced disease severity and enhanced the growth of pepper plants.
+ explanation: The abstract summarizes a positive result; the full paper clarifies that disease protection used
+ visual/physiological proxies rather than direct disease scores or pathogen load.
+ posed_by: codex
+curation_history:
+- timestamp: '2026-10-07T07:41:31Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: 'Preserve heterogeneous isolate traits without asserting mutualism or in-soil delivery.; Preserve T14/A6
+ inhibition and distinguish it from a demonstrated host-protection mechanism.; Preserve measured growth and visible
+ symptoms without inventing direct disease-severity quantification. Issue #1688; reports/causal_graph_review/decisions/20261007-four-records-batch83.yaml'
+ llm_assisted: true
diff --git a/references_cache/PMID_16332758.txt b/references_cache/PMID_16332758.txt
new file mode 100644
index 000000000..74e062d6e
--- /dev/null
+++ b/references_cache/PMID_16332758.txt
@@ -0,0 +1,9 @@
+PMID: 16332758
+DOI: 10.1128/AEM.71.12.7838-7845.2005
+Source: https://pubmed.ncbi.nlm.nih.gov/16332758/
+
+Selected primary abstract and Figure 4 caption excerpts only; not a full-text cache.
+
+these organisms coaggregated to different degrees depending on the substrate
+
+Hydrogen consumption by ΔH cells was inhibited by adding 2-BES.
diff --git a/reports/causal_graph_review/README.md b/reports/causal_graph_review/README.md
index fa2987957..6e3f260a3 100644
--- a/reports/causal_graph_review/README.md
+++ b/reports/causal_graph_review/README.md
@@ -5,6 +5,27 @@ 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`.
+## Batch83: Pyrene, Syntrophy And Pepper SynComs
+
+[Decisions](decisions/20261007-four-records-batch83.yaml),
+[validation](validation-20261007-batch83.json) and
+[self-adversarial review](adversarial-review-20261007-batch83.yaml) cover
+13 original nodes and nine arrows. Twelve biological nodes and eight bounded
+arrows remain; one inoculum-preparation node and its workflow arrow are removed.
+Measured pyrene removal, emulsification, syntrophic growth and plant responses
+remain distinct from candidate enzymes, modeled diffusion and proposed mediation.
+
+Three primary main texts and the PES correction were reviewed; the two older
+syntrophy papers remain abstract/caption limited. Selected pepper PDF pages were
+visually checked. Eighteen graph quotations match primary content and caches.
+The new coaggregation cache contains only 20 quoted words, not the full paper.
+All 920 original caches, 456 other records and non-graph blocks are preserved.
+
+Repairs #1685-#1688 await protected-main merge. Research #1689/#1690 and metadata
+#1691 remain open afterward. One syntrophy Edison dry run used no credits;
+its scoped paid question is unanswered. This is self-review, not independent
+approval or completion of the corpus review.
+
## Batch82: Tailings, Algal Coculture, Milk And Seed Biocontrol
[Decisions](decisions/20261007-four-records-batch82.yaml),
diff --git a/reports/causal_graph_review/adversarial-review-20261007-batch83.yaml b/reports/causal_graph_review/adversarial-review-20261007-batch83.yaml
new file mode 100644
index 000000000..d47582022
--- /dev/null
+++ b/reports/causal_graph_review/adversarial-review-20261007-batch83.yaml
@@ -0,0 +1,267 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: 72da5ae43f475499fbd5f6ca6bbe8c95e9a874ac
+scope:
+- kb/communities/Pelagerythrobacter_Salinicola_PES_Pyrene_Degradation_SynCom.yaml
+- kb/communities/Pelotomaculum_Methanothermobacter_Syntrophy.yaml
+- kb/communities/Pepper_Growth_Rhizosphere_SynCom.yaml
+- kb/communities/Pepper_Phytophthora_SynCom5.yaml
+decision_ledger: reports/causal_graph_review/decisions/20261007-four-records-batch83.yaml
+validation_report: reports/causal_graph_review/validation-20261007-batch83.json
+findings:
+- issue: 1685
+ severity: P2
+ status: addressed_in_this_change
+ finding: Bound PES pyrene graph to removal assays and proposed enzyme/emulsifier mediation
+ disposition: Close only after protected-main merge.
+- issue: 1686
+ severity: P2
+ status: addressed_in_this_change
+ finding: Repair Pelotomaculum syntrophy evidence and substrate-specific claims
+ disposition: Close only after protected-main merge.
+- issue: 1687
+ severity: P2
+ status: addressed_in_this_change
+ finding: Separate pepper SynCom preparation from measured ecology and inferred mediation
+ disposition: Close only after protected-main merge.
+- issue: 1688
+ severity: P2
+ status: addressed_in_this_change
+ finding: Distinguish pepper SynCom5 isolate screens from host protection mechanisms
+ disposition: Close only after protected-main merge.
+- issue: 1689
+ severity: P2
+ status: unresolved_research
+ finding: Review missing hydrogen-removal feedback and coaggregation topology for SI/DeltaH
+ disposition: Keep OPEN after graph repair merge.
+- issue: 1690
+ severity: P2
+ status: unresolved_research
+ finding: Represent measured pepper SynCom5 soil responses without inventing metabolic flux
+ disposition: Keep OPEN after graph repair merge.
+- issue: 1691
+ severity: P2
+ status: unresolved_non_graph
+ finding: Reconcile syntrophy and pepper non-graph protocol and evidence inconsistencies
+ disposition: Keep OPEN after graph repair merge.
+adversarial_checks:
+- Fresh both-root460record/920cache baseline preceded paper review. Four whole records,13nodes and9arrows assessed
+ including missing structures. Twelve retained nodes/eight arrows and one removed workflow node/arrow all have
+ dispositions. No new topology or paid provider submission.
+- PES retains near-complete50mg/Lpyrene removal in10days at5%salinity and N7monoculture49.95%in14days. Removal is
+ not complete carbon mineralization. Intermediate profiles and hphtC-5annotation/modeling/transcripts support a
+ candidate handoff, not traced transfer or enzyme necessity. Published Figure8correction fixes reversed structures;
+ the record already has the corrected chemical direction.
+- A11-associated extracellular emulsification remains positive:68%soybean-oil index under assay-specific growth
+ conditions. A11yeast-extract and N7/PESpyrene conditions differ. Emulsion phenotype and genomic capacity do not
+ isolate pyrene mass-transfer mediation, export apparatus or reciprocal fitness. Both removal arrows remain explicitly
+ hypothesized.
+- Syntrophy retains growth on propionate and alternative substrates with the hydrogenotrophic partner and the directly
+ implied donor-to-methanogen direction. Pure-culture pyruvate/fumarate growth and fumarate-to-succinate exception
+ disallow universal obligate dependence. Alternative-substrate products are not assumed identical. A copied evidence
+ explanation now explicitly includes propionate.
+- The2005primary abstract/captions add real coaggregation and2-BEShydrogen-consumption inhibition evidence, not
+ direct electron conduction. Stronger association on propionate and modeled diffusion limits are distinct findings.
+ Full methods and missing feedback/coaggregation topology remain1689research; no fabricated negative control claim
+ or uninspected full-text certification.
+- Peppergrowth workflow node/arrow removed, while all three biological nodes and the authors proposed diversity-to-native-taxa-to-growth
+ model remain. Both arrows are hypotheses, not inferred necessity from correlations/random-forest importance. Figure3visually
+ confirms increased fungal AND bacterial Chao richness; same-letter Shannon/Simpson panels do not support a blanket
+ evenness increase.
+- Preserve fungalBray-Curtis increase and bacterialBray-Curtis decrease, measured plant/root outcomes and selected
+ native relative-abundance changes. Scedosporium genus decreases while OTU451increases; do not collapse these resolutions
+ or claim absolute expansion, inoculated-strain colonization, symbiosis or reciprocal microbial fitness. Prior
+ taxonomy decisions1216/1217remain untouched.
+- Biocontrol individual trait screens are heterogeneous. Table1places strongest pathogen inhibition withT14andA6at58.4%and17.6%;
+ canonical participating taxa narrow to those two. Narrative/tableIAAandammonia rankings conflict. Separate siderophore/enzyme
+ screens are not demonstrated inhibition mechanisms; oomyceteP.capsici does not establish a host antifungal-defense
+ or chitin-wall-degradation claim.
+- Preserve challenged-host growth and visible wilting/necrosis response. Section3.5explicitly says no direct disease
+ severity/pathogen-load quantification and no SynCom-only control. Both trait/antagonism-to-host arrows remain
+ hypotheses. Additional positive soil nitrate/K/Ca and community responses stay in discussion pending1690; predicted
+ functions are not measured flux.
+- PESindexed full main text/tables/captions, its correction and two pepper full main texts read. Fresh public primary
+ PDFs inspected on growthpages6/7/8andbiocontrol3/4. Two syntrophy studies are abstract/caption limited. Other
+ original figures, separate supplements and raw data remain uninspected. Failed/captcha downloads are not evidence;
+ public source access respected.
+- Eighteen graph quotations and new discussion quotations independently checked against fresh primary artifacts.
+ One new cache has20quoted words from two primary excerpts, not full paper text. Full-corpus just audit-snippets
+ executed with actual counts; its informational exit0 is not a clean-corpus claim. Four focused snippet gates contain
+ no weak/mismatched/no-content/assembled evidence.
+- Four guarded history events,456otherrecords920originalcaches and all raw non-graph blocks preserved. Final Chao/explanation
+ fixes retain24superseded passing outputs;14unchanged record gates reused by hash, affected gates rerun. Forty-one
+ final checks recorded. Deterministic rendering and exact descriptions across456pages are parser checks, not browser
+ screenshots.47network warnings unchanged,zero new structural/connectivity findings; taxonomy/auditor rules and
+ global connectivity census unchanged.
+- Dedup searched962all-state issue titles/bodies,six matched bodies and62localfiles with ignored/hidden inclusion
+ and declared exclusions. One13736character Edison causal dry run is not paid authorization or a report. Pending/denied
+ scopes remain unchanged. Repairs1685-1688close only on protected-main merge; research1689/1690andmetadata1691remain
+ OPEN. Self-adversarial COMMENT is not independent approval or corpus completion. Move dependents before deleting
+ parents.
+verification:
+ combined_regressions: 746 passed in 437.51s (0:07:17)
+ 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.18graph
+ quotations independently match fresh primary content and caches. Literal matching is not entailment or whole-record
+ provenance certification; non-graph claims and original920caches are preserved, not globally recertified.
+ snippet_counts_by_record:
+ kb/communities/Pelagerythrobacter_Salinicola_PES_Pyrene_Degradation_SynCom.yaml:
+ MATCH: 22
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Pelotomaculum_Methanothermobacter_Syntrophy.yaml:
+ MATCH: 18
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Pepper_Growth_Rhizosphere_SynCom.yaml:
+ MATCH: 13
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Pepper_Phytophthora_SynCom5.yaml:
+ MATCH: 14
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ full_corpus_snippet_audit:
+ caveat: The full both-root snippet audit was executed. Exit0 is informational, not a clean-corpus assertion;
+ the recorded MATCH/RENDERING/ASSEMBLED/WEAK/MISMATCH/NOCONTENT counts are authoritative. Four edited records
+ separately pass the focused gates.
+ output: "# 8896 evidence snippets scanned across 460 files\n MATCH 8761\n RENDERING 20\n ASSEMBLED\
+ \ 1\n WEAK 0\n MISMATCH 38\n NOCONTENT 76\n\n# Files with MISMATCH/WEAK (content present but\
+ \ snippet absent) \u2014 fabrication suspects\n 19 (19 hard) kb/communities/DCPP_DBS4_DCP4_DCP11d_Degradation_SynCom.yaml\n\
+ \ 15 (15 hard) kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml\n 3 (3 hard) kb/communities/Coscinodiscus_Synthetic_Community.yaml\n\
+ \ 1 (1 hard) kb/communities/Altered_Schaedler_Flora_Gnotobiotic_Mouse_Community.yaml\n"
+ primary_graph_snippet_proof:
+ fresh_primary_matched: 18
+ cache_matched: 18
+ new_discussion_quotations_fresh_primary_matched: 6
+ new_nodes_or_arrows: 0
+ retained_nodes: 12
+ removed_nodes: 1
+ retained_arrows: 8
+ removed_arrows: 1
+ full_primary_main_texts_read: 3
+ correction_read: 1
+ abstract_or_caption_limited_studies: 2
+ original_pdf_pages_visually_inspected:
+ growth:
+ - 6
+ - 7
+ - 8
+ biocontrol:
+ - 3
+ - 4
+ separate_supplements_and_raw_data_audited: false
+ network:
+ existing_findings_preserved: 47
+ added_findings: {}
+ removed_findings: {}
+ interpretation: All47existingwarnings unchanged; zero new structural or connectivity defects. Canonical taxonomy/auditor
+ rules unchanged; T14/A6 antagonist participants narrowed.
+ black_ruff_diff: passed
+ tested_file_sha256:
+ reports/causal_graph_review/decisions/20261007-four-records-batch83.yaml: e13924aca3b858e78dcfa2074352e5a9a381bba97a83b2b94b8e864419dd9efe
+ tests/test_causal_review_batch83.py: 45dda20101f4783fef46ba13edc6abbc2ed2625f59a4b696f658782c75158bf1
+ tests/test_participating_taxa.py: b96ccc0da5587273f26c05dae5826c7a742e045b8ec50aca5f620d190594e9e5
+ kb/communities/Pelagerythrobacter_Salinicola_PES_Pyrene_Degradation_SynCom.yaml: c3ce655c53db89daeab6cf8ee8ca02ab7eb3bf597d6fe0dd7171ba33194dde1a
+ kb/communities/Pelotomaculum_Methanothermobacter_Syntrophy.yaml: 360878e4212242ce0caf07938081bf46502f977747343a560d00684f3b725609
+ kb/communities/Pepper_Growth_Rhizosphere_SynCom.yaml: b8dda93ce15fd6860fd8c424d85c961c4bb7ec2187e732720927120833158c37
+ kb/communities/Pepper_Phytophthora_SynCom5.yaml: ed26e547580e6b5fa6662c07720f45993a2a5a49e891a8574a635cbf0a44d81e
+ reports/causal_graph_review/README.md: 0f895d15928b55a0c69f4509c8cd10e2cf494e93c9659c53ca2caab5e567e250
+ references_cache/PMID_16332758.txt: 2ecdf48fa38c065d2670b49cc3b4dbb1ad114110832ac7b1bde3e11266003aa5
+ unchanged_caches: 920
+ cache_changes:
+ - path: references_cache/PMID_16332758.txt
+ original_sha256: null
+ sha256: 2ecdf48fa38c065d2670b49cc3b4dbb1ad114110832ac7b1bde3e11266003aa5
+ kind: new_short_primary_excerpts
+ quoted_words: 20
+ 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:000052
+ job: LITERATURE
+ query_chars: 13736
+ query_sha256: d110c3bdebd6259f35c27a8cce89d6ffea7b1f0417e50ae96abd706b58add3e6
+ meta_path: /private/tmp/communitymech-batch83/edison-syntrophy/Pelotomaculum_Methanothermobacter_Syntrophy-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: 1438
+ edges: 600
+ review_status_counts:
+ needs_research: 41
+ pending: 160
+ reviewed: 259
+limitations:
+- Fresh before-paper baseline across both roots:460records/920caches,47warnings,zero structural defects. Four whole
+ records,13nodes9arrows reviewed;12nodes8arrows retained,one workflow node/arrow removed. No new topology.
+- 'PES full primary indexed main text/tables/captions and correction read; corrected chemical direction agrees with
+ record. Two pepper full main texts read, with fresh public primary PDFs and cached growth text. Selected original
+ PDF pages visually checked: growth6/7/8, biocontrol3/4. Separate supplements, remaining original figures and raw
+ data not audited.'
+- Species-description paper2002 and coaggregation2005 remain primary-abstract/caption limited. Preserve observed
+ coculture growth, coaggregation and inhibitor-caption evidence without claiming full methods reviewed. Modeled
+ distances are not measured flux. Missing feedback/coaggregation structure tracked in1689.
+- Europe PMC returned502/503 service errors; publisher/PMC routes returned403 or browser checks. Public primary
+ PDFs retrieved from Semantic Scholar; no access control bypass. One erroneous initial growth PMC URL was rejected
+ for no article content and is not evidence. Failed retrieval receipts remain outside repository.
+- PGPR screens differ among isolates; no direct disease score/pathogen load or SynCom-only control in biocontrol
+ study. Positive host growth and visible symptoms survive. Soil nitrate/K/Ca and community changes retained in
+ discussion pending1690 extension workflow; predicted functions are not flux. Protocol/identity conflicts remain1691.
+- Source evidence is not a blanket causality certificate. Original920caches and456otherrecords and raw non-graph
+ blocks preserved. One new cache contains20quoted words from primary abstract/caption, not complete copyrighted
+ article. Canonical taxonomy/auditor rules unchanged.
+- Dedup962all-state issue titles/bodies,6matched bodies read,62local files with hidden/ignored inclusion excluding.git/docs/site/references_cache;
+ additional exact coaggregation-reference search matched none in that scope. No exhaustive issue-comment/PR audit.
+ Truncated combined outputs reread where claim-critical.
+- One13736character single-community Edison causal dry run; scoped paid question unanswered,zero provider jobs/credits.
+ Earlier denied/pending scopes unchanged. Repairs1685-1688close only after protected-main merge; research1689/1690andmetadata1691remainOPENafterward.
+- Four append-only history artifacts. Validation and rendering receipts are separate gates, not preasserted here.
+ Self-adversarial review is not independent approval or whole-corpus completion.
+- Final original Figure3 inspection preserves increased fungal AND bacterial Chao richness; a copied propionate
+ evidence explanation was corrected. Affected gates rerun and earlier passing outputs retained. Four original append-only
+ histories unchanged.
diff --git a/reports/causal_graph_review/decisions/20261007-four-records-batch83.yaml b/reports/causal_graph_review/decisions/20261007-four-records-batch83.yaml
new file mode 100644
index 000000000..482597bf6
--- /dev/null
+++ b/reports/causal_graph_review/decisions/20261007-four-records-batch83.yaml
@@ -0,0 +1,574 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: 72da5ae43f475499fbd5f6ca6bbe8c95e9a874ac
+baseline_commit: 72da5ae43f475499fbd5f6ca6bbe8c95e9a874ac
+base_tree: 6bc4428a81113f9c2f5a1d3a34a8951ae958750a
+pre_source_baseline_sha256: 2b246062bc1e2a3ec717a90fb60e180ad39dcc4a4517e1c71166f4154cd1554a
+issues:
+- 1685
+- 1686
+- 1687
+- 1688
+unresolved_non_graph_issues:
+- 1691
+unresolved_research_issues:
+- 1689
+- 1690
+issue_deduplication:
+ all_state_issue_titles_and_bodies: 962
+ ignored_hidden_local_search: true
+ matching_local_files: 62
+ matching_issues:
+ - 1397
+ - 1394
+ - 1272
+ - 1232
+ - 1217
+ - 1216
+primary_artifacts:
+ /private/tmp/communitymech-batch83/baseline.json: 2b246062bc1e2a3ec717a90fb60e180ad39dcc4a4517e1c71166f4154cd1554a
+ /private/tmp/communitymech-batch83/biocontrol-page-12.png: 9a0b20428b4bcca41922c1b754d89f471514054e8d6d325c137c5b2bf6238320
+ /private/tmp/communitymech-batch83/biocontrol-page-3.png: 84db6ce3c3aee5e662cd6ccfc3e05a55ef0fc7b8bd1a80702cbf5b3bbf355b49
+ /private/tmp/communitymech-batch83/biocontrol-page-4.png: 467126bb440d4f06b6297407a8f4e430a23c23f15149cc5cc4d6830ac921c6c9
+ /private/tmp/communitymech-batch83/biocontrol-pdf-primary.txt: 49fcc854f2142d3e8c241d3097d208fe0c2ab3cb2c97d573fd2cfe00af960fcb
+ /private/tmp/communitymech-batch83/biocontrol-primary.pdf: fcb2f8c5eb71e188cef0ce324ddeecf938f5b644bc268333b3de617fae50611f
+ /private/tmp/communitymech-batch83/coaggregation-search-primary.txt: c280a6c0bc550eeaf502c2232fa317336bf07011a53a35c6d2561a7a0c8203ad
+ /private/tmp/communitymech-batch83/correction-web-primary.txt: c3304a85ccf7256ac8de32eb9fe1811d9062ae5acebd494bac781154e13c977e
+ ? /private/tmp/communitymech-batch83/edison-syntrophy/Pelotomaculum_Methanothermobacter_Syntrophy-edison-literature-causal-meta.yaml
+ : 8f54844173f6501227fd5a0b5ae3f69be0b8b73e4f779859d83ec1a76bca7bc5
+ /private/tmp/communitymech-batch83/extra-issue-matches.json: 37517e5f3dc66819f61f5a7bb8ace1921282415f10551d2defa5c3eb0985b570
+ /private/tmp/communitymech-batch83/growth-page-6.png: 598e8b4fa8c0662fe739ab4121a25f31656b100b0921a75004fb41eaaf3c0e9c
+ /private/tmp/communitymech-batch83/growth-page-7.png: 54c73366bea2ac6a17a0d70c104d9d8468c00e40e2ea0bb339faa7f07b2d9bbd
+ /private/tmp/communitymech-batch83/growth-page-8.png: 58e7e04610ed1b2d5c99902a3dcac7af52d2c6f45b5d4f9b537b408273091e17
+ /private/tmp/communitymech-batch83/growth-pdf-primary.txt: 8fd9797b55e386618b2a3288afbbc547bb19c12970405e686703d22d774683af
+ /private/tmp/communitymech-batch83/growth-primary.pdf: 9f6cb83988c22cd99b96c5379b967df73a9de1bfa21c03e9484de4e960ba8989
+ /private/tmp/communitymech-batch83/issue-matches.json: 278140c6fabf3e86ff041da901bce9983ff5c60c3b5e8e891b10b8892034a816
+ /private/tmp/communitymech-batch83/issues.json: 900be8c42b3d443a8facd673cefef400313386083506a3186063489f8f8f0370
+ /private/tmp/communitymech-batch83/local-matches.txt: d87a8d1ed27e5f3f1fa55cd116126c4c2432cce9bcdfc8a66cafb1a07cefaea4
+ /private/tmp/communitymech-batch83/pes-metadata.json: e79a8467654eb50809e1e3aaa8ddd75355cb8800370743bd7a3c43167876fc5e
+ /private/tmp/communitymech-batch83/pes-web-primary.txt: a35fe658b844f221a84e0ff202be7b81aefe227c31f94f12b443add451b10450
+ /private/tmp/communitymech-batch83/publisher-manifest.json: e01e45b167cbcca346eff00dc13f4b1a7a727312c6eb8a4449ca00d3811fcb9b
+ /private/tmp/communitymech-batch83/syntrophy-web-primary.txt: d635c1dfd6030d655fa63552775033cdfe90a763cd8a41028a828731d6782db1
+primary_graph_snippet_count: 18
+independent_fresh_primary_graph_snippet_count: 18
+cache_matched_graph_snippet_count: 18
+snippet_checks:
+- record: Pelagerythrobacter_Salinicola_PES_Pyrene_Degradation_SynCom
+ node: Proposed N7-A11 4,5-dicarboxyphenanthrene handoff
+ reference: PMID:42666409
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch83/pes-web-primary.txt
+ method: Whitespace, indexed-line/citation markers, soft hyphens and PDF line-wrap hyphens normalized; no claim
+ text paraphrased.
+- record: Pelagerythrobacter_Salinicola_PES_Pyrene_Degradation_SynCom
+ node: Proposed N7-A11 4,5-dicarboxyphenanthrene handoff
+ reference: PMID:42666409
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch83/pes-web-primary.txt
+ method: Whitespace, indexed-line/citation markers, soft hyphens and PDF line-wrap hyphens normalized; no claim
+ text paraphrased.
+- record: Pelagerythrobacter_Salinicola_PES_Pyrene_Degradation_SynCom
+ node: A11-Associated Extracellular Emulsifying Activity
+ reference: PMID:42666409
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch83/pes-web-primary.txt
+ method: Whitespace, indexed-line/citation markers, soft hyphens and PDF line-wrap hyphens normalized; no claim
+ text paraphrased.
+- record: Pelagerythrobacter_Salinicola_PES_Pyrene_Degradation_SynCom
+ node: A11-Associated Extracellular Emulsifying Activity
+ reference: PMID:42666409
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch83/pes-web-primary.txt
+ method: Whitespace, indexed-line/citation markers, soft hyphens and PDF line-wrap hyphens normalized; no claim
+ text paraphrased.
+- record: Pelagerythrobacter_Salinicola_PES_Pyrene_Degradation_SynCom
+ node: Complete 5%-salinity pyrene removal by PES
+ reference: PMID:42666409
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch83/pes-web-primary.txt
+ method: Whitespace, indexed-line/citation markers, soft hyphens and PDF line-wrap hyphens normalized; no claim
+ text paraphrased.
+- record: Pelagerythrobacter_Salinicola_PES_Pyrene_Degradation_SynCom
+ node: Complete 5%-salinity pyrene removal by PES
+ reference: PMID:42666409
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch83/pes-web-primary.txt
+ method: Whitespace, indexed-line/citation markers, soft hyphens and PDF line-wrap hyphens normalized; no claim
+ text paraphrased.
+- record: Pelotomaculum_Methanothermobacter_Syntrophy
+ node: Propionate Oxidation and H2 Production
+ reference: PMID:12361280
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch83/syntrophy-web-primary.txt
+ method: Whitespace, indexed-line/citation markers, soft hyphens and PDF line-wrap hyphens normalized; no claim
+ text paraphrased.
+- record: Pelotomaculum_Methanothermobacter_Syntrophy
+ node: Propionate Oxidation and H2 Production
+ reference: PMID:12361280
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch83/syntrophy-web-primary.txt
+ method: Whitespace, indexed-line/citation markers, soft hyphens and PDF line-wrap hyphens normalized; no claim
+ text paraphrased.
+- record: Pelotomaculum_Methanothermobacter_Syntrophy
+ node: Alternative Alcohol and Diol Oxidation
+ reference: PMID:12361280
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch83/syntrophy-web-primary.txt
+ method: Whitespace, indexed-line/citation markers, soft hyphens and PDF line-wrap hyphens normalized; no claim
+ text paraphrased.
+- record: Pelotomaculum_Methanothermobacter_Syntrophy
+ node: Interspecies Hydrogen Transfer and Thermophilic Methanogenesis
+ reference: PMID:12361280
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch83/syntrophy-web-primary.txt
+ method: Whitespace, indexed-line/citation markers, soft hyphens and PDF line-wrap hyphens normalized; no claim
+ text paraphrased.
+- record: Pelotomaculum_Methanothermobacter_Syntrophy
+ node: Interspecies Hydrogen Transfer and Thermophilic Methanogenesis
+ reference: PMID:16332758
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch83/coaggregation-search-primary.txt
+ method: Whitespace, indexed-line/citation markers, soft hyphens and PDF line-wrap hyphens normalized; no claim
+ text paraphrased.
+- record: Pelotomaculum_Methanothermobacter_Syntrophy
+ node: Interspecies Hydrogen Transfer and Thermophilic Methanogenesis
+ reference: PMID:16332758
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch83/coaggregation-search-primary.txt
+ method: Whitespace, indexed-line/citation markers, soft hyphens and PDF line-wrap hyphens normalized; no claim
+ text paraphrased.
+- record: Pepper_Growth_Rhizosphere_SynCom
+ node: SynCom-Shifted Rhizosphere Diversity
+ reference: PMID:39858916
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch83/growth-pdf-primary.txt
+ method: Whitespace, indexed-line/citation markers, soft hyphens and PDF line-wrap hyphens normalized; no claim
+ text paraphrased.
+- record: Pepper_Growth_Rhizosphere_SynCom
+ node: Growth-Associated Native Taxa Relative Enrichment
+ reference: PMID:39858916
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch83/growth-pdf-primary.txt
+ method: Whitespace, indexed-line/citation markers, soft hyphens and PDF line-wrap hyphens normalized; no claim
+ text paraphrased.
+- record: Pepper_Growth_Rhizosphere_SynCom
+ node: Pepper Rhizosphere Growth Promotion
+ reference: PMID:39858916
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch83/growth-pdf-primary.txt
+ method: Whitespace, indexed-line/citation markers, soft hyphens and PDF line-wrap hyphens normalized; no claim
+ text paraphrased.
+- record: Pepper_Phytophthora_SynCom5
+ node: Individual-Isolate PGPR Trait Measurements
+ reference: PMID:40508300
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch83/biocontrol-pdf-primary.txt
+ method: Whitespace, indexed-line/citation markers, soft hyphens and PDF line-wrap hyphens normalized; no claim
+ text paraphrased.
+- record: Pepper_Phytophthora_SynCom5
+ node: Isolate Antagonism Against Phytophthora capsici
+ reference: PMID:40508300
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch83/biocontrol-pdf-primary.txt
+ method: Whitespace, indexed-line/citation markers, soft hyphens and PDF line-wrap hyphens normalized; no claim
+ text paraphrased.
+- record: Pepper_Phytophthora_SynCom5
+ node: Pepper Growth and Visible Symptoms Under Pathogen Challenge
+ reference: PMID:40508300
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch83/biocontrol-pdf-primary.txt
+ method: Whitespace, indexed-line/citation markers, soft hyphens and PDF line-wrap hyphens normalized; no claim
+ text paraphrased.
+cache_changes:
+- path: references_cache/PMID_16332758.txt
+ original_sha256: null
+ sha256: 2ecdf48fa38c065d2670b49cc3b4dbb1ad114110832ac7b1bde3e11266003aa5
+ kind: new_short_primary_excerpts
+ quoted_words: 20
+edison:
+ required_for_this_repair: false
+ required_for_unresolved_extensions: true
+ provider_submissions: 0
+ credits_spent: 0
+ dry_runs:
+ - community_id: CommunityMech:000052
+ job: LITERATURE
+ query_chars: 13736
+ query_sha256: d110c3bdebd6259f35c27a8cce89d6ffea7b1f0417e50ae96abd706b58add3e6
+ meta_path: /private/tmp/communitymech-batch83/edison-syntrophy/Pelotomaculum_Methanothermobacter_Syntrophy-edison-literature-causal-meta.yaml
+ authorization: Scoped asynchronous question unanswered; preselection is not approval.
+limitations:
+- Fresh before-paper baseline across both roots:460records/920caches,47warnings,zero structural defects. Four whole
+ records,13nodes9arrows reviewed;12nodes8arrows retained,one workflow node/arrow removed. No new topology.
+- 'PES full primary indexed main text/tables/captions and correction read; corrected chemical direction agrees with
+ record. Two pepper full main texts read, with fresh public primary PDFs and cached growth text. Selected original
+ PDF pages visually checked: growth6/7/8, biocontrol3/4. Separate supplements, remaining original figures and raw
+ data not audited.'
+- Species-description paper2002 and coaggregation2005 remain primary-abstract/caption limited. Preserve observed
+ coculture growth, coaggregation and inhibitor-caption evidence without claiming full methods reviewed. Modeled
+ distances are not measured flux. Missing feedback/coaggregation structure tracked in1689.
+- Europe PMC returned502/503 service errors; publisher/PMC routes returned403 or browser checks. Public primary
+ PDFs retrieved from Semantic Scholar; no access control bypass. One erroneous initial growth PMC URL was rejected
+ for no article content and is not evidence. Failed retrieval receipts remain outside repository.
+- PGPR screens differ among isolates; no direct disease score/pathogen load or SynCom-only control in biocontrol
+ study. Positive host growth and visible symptoms survive. Soil nitrate/K/Ca and community changes retained in
+ discussion pending1690 extension workflow; predicted functions are not flux. Protocol/identity conflicts remain1691.
+- Source evidence is not a blanket causality certificate. Original920caches and456otherrecords and raw non-graph
+ blocks preserved. One new cache contains20quoted words from primary abstract/caption, not complete copyrighted
+ article. Canonical taxonomy/auditor rules unchanged.
+- Dedup962all-state issue titles/bodies,6matched bodies read,62local files with hidden/ignored inclusion excluding.git/docs/site/references_cache;
+ additional exact coaggregation-reference search matched none in that scope. No exhaustive issue-comment/PR audit.
+ Truncated combined outputs reread where claim-critical.
+- One13736character single-community Edison causal dry run; scoped paid question unanswered,zero provider jobs/credits.
+ Earlier denied/pending scopes unchanged. Repairs1685-1688close only after protected-main merge; research1689/1690andmetadata1691remainOPENafterward.
+- Four append-only history artifacts. Validation and rendering receipts are separate gates, not preasserted here.
+ Self-adversarial review is not independent approval or whole-corpus completion.
+- Final original Figure3 inspection preserves increased fungal AND bacterial Chao richness; a copied propionate
+ evidence explanation was corrected. Affected gates rerun and earlier passing outputs retained. Four original append-only
+ histories unchanged.
+records:
+- path: kb/communities/Pelagerythrobacter_Salinicola_PES_Pyrene_Degradation_SynCom.yaml
+ id: CommunityMech:000340
+ original_sha256: 58d2a2a277b85ee0af0bbb51a51913c96001b62bfa82e554b7bda716be742b9b
+ record_sha256: c3ce655c53db89daeab6cf8ee8ca02ab7eb3bf597d6fe0dd7171ba33194dde1a
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261007-four-records-batch83.yaml
+ scope: Whole record, every existing node/arrow and missing structures; not whole-record certification.
+ summary: Retain observed bottleneck and qualify the candidate intermediate handoff.; Preserve extracellular emulsification
+ without asserting reciprocal fitness or measured pyrene mediation.; Preserve near-complete pyrene removal without
+ equating it with carbon mineralization.
+ renamed_nodes:
+ N7-A11 4,5-dicarboxyphenanthrene handoff: Proposed N7-A11 4,5-dicarboxyphenanthrene handoff
+ A11 extracellular bioemulsification of hydrophobic pyrene: A11-Associated Extracellular Emulsifying Activity
+ node_decisions:
+ - node: Proposed N7-A11 4,5-dicarboxyphenanthrene handoff
+ original_node: N7-A11 4,5-dicarboxyphenanthrene handoff
+ rationale: Retain observed bottleneck and qualify the candidate intermediate handoff.
+ - node: A11-Associated Extracellular Emulsifying Activity
+ original_node: A11 extracellular bioemulsification of hydrophobic pyrene
+ rationale: Preserve extracellular emulsification without asserting reciprocal fitness or measured pyrene mediation.
+ - node: Complete 5%-salinity pyrene removal by PES
+ original_node: Complete 5%-salinity pyrene removal by PES
+ rationale: Preserve near-complete pyrene removal without equating it with carbon mineralization.
+ removed_node_decisions: []
+ edges_before:
+ - source: N7-A11 4,5-dicarboxyphenanthrene handoff
+ target: Complete 5%-salinity pyrene removal by PES
+ description: The proposed N7-to-A11 intermediate handoff relieves the 4,5-dicarboxyphenanthrene bottleneck observed
+ in N7 monoculture and helps PES degrade the supplied pyrene completely within the main 10-day assay.
+ - source: A11 extracellular bioemulsification of hydrophobic pyrene
+ target: Complete 5%-salinity pyrene removal by PES
+ description: A11 extracellular bioemulsifier production is proposed to reduce the mass transfer limitation of
+ hydrophobic pyrene and thereby increase PES pyrene degradation efficiency.
+ edges_after:
+ - source: Proposed N7-A11 4,5-dicarboxyphenanthrene handoff
+ target: Complete 5%-salinity pyrene removal by PES
+ description: HYPOTHESIZED - A11-mediated transformation of the intermediate accumulated by N7 could relieve
+ the degradation bottleneck and enable the observed PES pyrene removal. Metabolite profiles, annotation and
+ expression support the proposed pathway but do not isolate hphtC-5-dependent intercellular transfer as the
+ cause of the removal advantage.
+ - source: A11-Associated Extracellular Emulsifying Activity
+ target: Complete 5%-salinity pyrene removal by PES
+ description: HYPOTHESIZED - Extracellular emulsifying material attributed to A11 could increase pyrene availability
+ and thereby improve PES removal. The measured emulsion phenotype and genomic capacity do not isolate pyrene
+ mass transfer, the export system or the fraction of removal caused by this mechanism.
+ retained_edge_decisions:
+ - source: Proposed N7-A11 4,5-dicarboxyphenanthrene handoff
+ target: Complete 5%-salinity pyrene removal by PES
+ description: HYPOTHESIZED - A11-mediated transformation of the intermediate accumulated by N7 could relieve
+ the degradation bottleneck and enable the observed PES pyrene removal. Metabolite profiles, annotation and
+ expression support the proposed pathway but do not isolate hphtC-5-dependent intercellular transfer as the
+ cause of the removal advantage.
+ rationale: HYPOTHESIZED - A11-mediated transformation of the intermediate accumulated by N7 could relieve the
+ degradation bottleneck and enable the observed PES pyrene removal. Metabolite profiles, annotation and expression
+ support the proposed pathway but do not isolate hphtC-5-dependent intercellular transfer as the cause of the
+ removal advantage.
+ - source: A11-Associated Extracellular Emulsifying Activity
+ target: Complete 5%-salinity pyrene removal by PES
+ description: HYPOTHESIZED - Extracellular emulsifying material attributed to A11 could increase pyrene availability
+ and thereby improve PES removal. The measured emulsion phenotype and genomic capacity do not isolate pyrene
+ mass transfer, the export system or the fraction of removal caused by this mechanism.
+ rationale: HYPOTHESIZED - Extracellular emulsifying material attributed to A11 could increase pyrene availability
+ and thereby improve PES removal. The measured emulsion phenotype and genomic capacity do not isolate pyrene
+ mass transfer, the export system or the fraction of removal caused by this mechanism.
+ removed_edge_decisions: []
+ references:
+ - PMID:42666409
+ issues:
+ - 1685
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Pelagerythrobacter_Salinicola_PES_Pyrene_Degradation_SynCom/2026-10-07T074131Z-codex-d4a2ed.yaml
+- path: kb/communities/Pelotomaculum_Methanothermobacter_Syntrophy.yaml
+ id: CommunityMech:000052
+ original_sha256: 7516752d58a30c6fdeff03b3cca057fb402e815f698668f96e798d87a63273a3
+ record_sha256: 360878e4212242ce0caf07938081bf46502f977747343a560d00684f3b725609
+ status: needs_research
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261007-four-records-batch83.yaml
+ scope: Whole record, every existing node/arrow and missing structures; not whole-record certification.
+ summary: Preserve propionate syntrophy and correct universal dependence and evidence attribution.; Preserve alternative-substrate
+ coculture growth without universal product stoichiometry.; Preserve the hydrogen sink and source-bound coaggregation
+ evidence while separating observations and diffusion modeling.
+ renamed_nodes: {}
+ node_decisions:
+ - node: Propionate Oxidation and H2 Production
+ original_node: Propionate Oxidation and H2 Production
+ rationale: Preserve propionate syntrophy and correct universal dependence and evidence attribution.
+ - node: Alternative Alcohol and Diol Oxidation
+ original_node: Alternative Alcohol and Diol Oxidation
+ rationale: Preserve alternative-substrate coculture growth without universal product stoichiometry.
+ - node: Interspecies Hydrogen Transfer and Thermophilic Methanogenesis
+ original_node: Interspecies Hydrogen Transfer and Thermophilic Methanogenesis
+ rationale: Preserve the hydrogen sink and source-bound coaggregation evidence while separating observations
+ and diffusion modeling.
+ removed_node_decisions: []
+ edges_before:
+ - source: Propionate Oxidation and H2 Production
+ target: Interspecies Hydrogen Transfer and Thermophilic Methanogenesis
+ description: "H2 produced by P. thermopropionicum is consumed by M. thermautotrophicus for methanogenesis at\
+ \ 55\xB0C"
+ - source: Alternative Alcohol and Diol Oxidation
+ target: Interspecies Hydrogen Transfer and Thermophilic Methanogenesis
+ description: Hydrogen and CO2 released from alcohol and diol oxidation are consumed by the methanogen in the
+ same H2-removal sink.
+ edges_after:
+ - source: Propionate Oxidation and H2 Production
+ target: Interspecies Hydrogen Transfer and Thermophilic Methanogenesis
+ description: H2 supplied during syntrophic propionate oxidation fuels the hydrogenotrophic partner. Preserve
+ this directly implied donor-to-methanogen direction; the species-description abstract does not quantify the
+ exchanged flux or its stoichiometry.
+ - source: Alternative Alcohol and Diol Oxidation
+ target: Interspecies Hydrogen Transfer and Thermophilic Methanogenesis
+ description: PARTIAL - The reported growth of SI with a hydrogenotrophic partner on these alternative substrates
+ supports H2-linked syntrophy. Substrate-resolved H2 yields and carbon-product balances are not exposed in
+ the cited species-description abstract; do not assume every substrate supplies the same acetate/CO2 products.
+ retained_edge_decisions:
+ - source: Propionate Oxidation and H2 Production
+ target: Interspecies Hydrogen Transfer and Thermophilic Methanogenesis
+ description: H2 supplied during syntrophic propionate oxidation fuels the hydrogenotrophic partner. Preserve
+ this directly implied donor-to-methanogen direction; the species-description abstract does not quantify the
+ exchanged flux or its stoichiometry.
+ rationale: H2 supplied during syntrophic propionate oxidation fuels the hydrogenotrophic partner. Preserve this
+ directly implied donor-to-methanogen direction; the species-description abstract does not quantify the exchanged
+ flux or its stoichiometry.
+ - source: Alternative Alcohol and Diol Oxidation
+ target: Interspecies Hydrogen Transfer and Thermophilic Methanogenesis
+ description: PARTIAL - The reported growth of SI with a hydrogenotrophic partner on these alternative substrates
+ supports H2-linked syntrophy. Substrate-resolved H2 yields and carbon-product balances are not exposed in
+ the cited species-description abstract; do not assume every substrate supplies the same acetate/CO2 products.
+ rationale: PARTIAL - The reported growth of SI with a hydrogenotrophic partner on these alternative substrates
+ supports H2-linked syntrophy. Substrate-resolved H2 yields and carbon-product balances are not exposed in
+ the cited species-description abstract; do not assume every substrate supplies the same acetate/CO2 products.
+ removed_edge_decisions: []
+ references:
+ - PMID:12361280
+ - PMID:16332758
+ issues:
+ - 1686
+ - 1689
+ - 1691
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Pelotomaculum_Methanothermobacter_Syntrophy/2026-10-07T074132Z-codex-849acd.yaml
+- path: kb/communities/Pepper_Growth_Rhizosphere_SynCom.yaml
+ id: CommunityMech:000104
+ original_sha256: 3b12ee13e0d41c767a12ef635cc02f640dfb61e2d84e694cf4ff0d9cfbcaf2f3
+ record_sha256: b8dda93ce15fd6860fd8c424d85c961c4bb7ec2187e732720927120833158c37
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261007-four-records-batch83.yaml
+ scope: Whole record, every existing node/arrow and missing structures; not whole-record certification.
+ summary: Preserve measured diversity changes while qualifying the proposed enrichment direction.; Preserve relative
+ OTU associations without converting predictive importance into causation.; Preserve directly measured whole-plant
+ growth without reciprocal-fitness inference.
+ renamed_nodes:
+ Key Native Taxa Enrichment: Growth-Associated Native Taxa Relative Enrichment
+ node_decisions:
+ - node: SynCom-Shifted Rhizosphere Diversity
+ original_node: SynCom-Shifted Rhizosphere Diversity
+ rationale: Preserve measured diversity changes while qualifying the proposed enrichment direction.
+ - node: Growth-Associated Native Taxa Relative Enrichment
+ original_node: Key Native Taxa Enrichment
+ rationale: Preserve relative OTU associations without converting predictive importance into causation.
+ - node: Pepper Rhizosphere Growth Promotion
+ original_node: Pepper Rhizosphere Growth Promotion
+ rationale: Preserve directly measured whole-plant growth without reciprocal-fitness inference.
+ removed_node_decisions:
+ - node: Four-Member Pepper SynCom Inoculation
+ rationale: Inoculum preparation is experimental workflow, not a biological process.
+ edges_before:
+ - source: Four-Member Pepper SynCom Inoculation
+ target: SynCom-Shifted Rhizosphere Diversity
+ description: 'The four-member SynCom inoculation reorganized the pepper seedling rhizosphere, driving the measured
+ fungal and bacterial diversity shifts after 45 days.
+
+ '
+ - source: SynCom-Shifted Rhizosphere Diversity
+ target: Key Native Taxa Enrichment
+ description: 'The SynCom-driven rhizosphere shift included increases in native fungal and bacterial OTUs that
+ were correlated with pepper growth and root morphology readouts.
+
+ '
+ - source: Key Native Taxa Enrichment
+ target: Pepper Rhizosphere Growth Promotion
+ description: 'Random-forest and correlation analyses nominated the enriched native taxa as contributors to the
+ shoot-height, dry-weight, chlorophyll, and root-vigor responses.
+
+ '
+ edges_after:
+ - source: SynCom-Shifted Rhizosphere Diversity
+ target: Growth-Associated Native Taxa Relative Enrichment
+ description: HYPOTHESIZED - The authors propose that the shifted rhizosphere community favors enrichment of
+ growth-associated native taxa. Diversity indices and relative taxon profiles were measured after the same
+ treatment; their association does not isolate diversity change as the cause of enrichment.
+ - source: Growth-Associated Native Taxa Relative Enrichment
+ target: Pepper Rhizosphere Growth Promotion
+ description: HYPOTHESIZED - The enriched native taxa may contribute to pepper growth, as proposed from correlation
+ and random-forest analyses. Those analyses do not establish necessity, sufficiency or direction independently
+ of the shared inoculation treatment or plant-driven changes.
+ retained_edge_decisions:
+ - source: SynCom-Shifted Rhizosphere Diversity
+ target: Growth-Associated Native Taxa Relative Enrichment
+ description: HYPOTHESIZED - The authors propose that the shifted rhizosphere community favors enrichment of
+ growth-associated native taxa. Diversity indices and relative taxon profiles were measured after the same
+ treatment; their association does not isolate diversity change as the cause of enrichment.
+ rationale: HYPOTHESIZED - The authors propose that the shifted rhizosphere community favors enrichment of growth-associated
+ native taxa. Diversity indices and relative taxon profiles were measured after the same treatment; their association
+ does not isolate diversity change as the cause of enrichment.
+ - source: Growth-Associated Native Taxa Relative Enrichment
+ target: Pepper Rhizosphere Growth Promotion
+ description: HYPOTHESIZED - The enriched native taxa may contribute to pepper growth, as proposed from correlation
+ and random-forest analyses. Those analyses do not establish necessity, sufficiency or direction independently
+ of the shared inoculation treatment or plant-driven changes.
+ rationale: HYPOTHESIZED - The enriched native taxa may contribute to pepper growth, as proposed from correlation
+ and random-forest analyses. Those analyses do not establish necessity, sufficiency or direction independently
+ of the shared inoculation treatment or plant-driven changes.
+ removed_edge_decisions:
+ - source: Four-Member Pepper SynCom Inoculation
+ target: SynCom-Shifted Rhizosphere Diversity
+ description: 'The four-member SynCom inoculation reorganized the pepper seedling rhizosphere, driving the measured
+ fungal and bacterial diversity shifts after 45 days.
+
+ '
+ rationale: Preparation-to-observation workflow; treatment effects remain in the biological nodes.
+ references:
+ - PMID:39858916
+ issues:
+ - 1687
+ - 1691
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Pepper_Growth_Rhizosphere_SynCom/2026-10-07T074133Z-codex-b89626.yaml
+- path: kb/communities/Pepper_Phytophthora_SynCom5.yaml
+ id: CommunityMech:000105
+ original_sha256: 90d80cf28c6ab66130431828533e2d39c0ac0c8090252703111cccdfa5b79a9f
+ record_sha256: ed26e547580e6b5fa6662c07720f45993a2a5a49e891a8574a635cbf0a44d81e
+ status: needs_research
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261007-four-records-batch83.yaml
+ scope: Whole record, every existing node/arrow and missing structures; not whole-record certification.
+ summary: Preserve heterogeneous isolate traits without asserting mutualism or in-soil delivery.; Preserve T14/A6
+ inhibition and distinguish it from a demonstrated host-protection mechanism.; Preserve measured growth and visible
+ symptoms without inventing direct disease-severity quantification.
+ renamed_nodes:
+ Complementary PGPR Trait Pool: Individual-Isolate PGPR Trait Measurements
+ Direct Phytophthora capsici Antagonism: Isolate Antagonism Against Phytophthora capsici
+ Pepper Growth Under Phytophthora Challenge: Pepper Growth and Visible Symptoms Under Pathogen Challenge
+ node_decisions:
+ - node: Individual-Isolate PGPR Trait Measurements
+ original_node: Complementary PGPR Trait Pool
+ rationale: Preserve heterogeneous isolate traits without asserting mutualism or in-soil delivery.
+ - node: Isolate Antagonism Against Phytophthora capsici
+ original_node: Direct Phytophthora capsici Antagonism
+ rationale: Preserve T14/A6 inhibition and distinguish it from a demonstrated host-protection mechanism.
+ - node: Pepper Growth and Visible Symptoms Under Pathogen Challenge
+ original_node: Pepper Growth Under Phytophthora Challenge
+ rationale: Preserve measured growth and visible symptoms without inventing direct disease-severity quantification.
+ removed_node_decisions: []
+ edges_before:
+ - source: Complementary PGPR Trait Pool
+ target: Pepper Growth Under Phytophthora Challenge
+ description: The complementary PGPR trait set contributes nutrient-mobilization and phytohormone functions to
+ the growth improvement observed in P. capsici-challenged pepper plants.
+ - source: Direct Phytophthora capsici Antagonism
+ target: Pepper Growth Under Phytophthora Challenge
+ description: Direct Phytophthora antagonism supplies the disease-suppression component of the SynCom's pepper-protection
+ phenotype under pathogen pressure.
+ edges_after:
+ - source: Individual-Isolate PGPR Trait Measurements
+ target: Pepper Growth and Visible Symptoms Under Pathogen Challenge
+ description: HYPOTHESIZED - Nutrient-mobilization and phytohormone traits of the selected isolates could contribute
+ to challenged-host growth. The traits were not re-quantified in soil and were not selectively perturbed, so
+ the host comparison does not isolate their mediation.
+ - source: Isolate Antagonism Against Phytophthora capsici
+ target: Pepper Growth and Visible Symptoms Under Pathogen Challenge
+ description: HYPOTHESIZED - The measured isolate antagonism may contribute to improved host performance under
+ pathogen challenge. The pot study lacked a SynCom-only control and direct disease scoring or pathogen-load
+ measurements, so it cannot isolate pathogen suppression from growth promotion or attribute the host response
+ to these two strains alone.
+ retained_edge_decisions:
+ - source: Individual-Isolate PGPR Trait Measurements
+ target: Pepper Growth and Visible Symptoms Under Pathogen Challenge
+ description: HYPOTHESIZED - Nutrient-mobilization and phytohormone traits of the selected isolates could contribute
+ to challenged-host growth. The traits were not re-quantified in soil and were not selectively perturbed, so
+ the host comparison does not isolate their mediation.
+ rationale: HYPOTHESIZED - Nutrient-mobilization and phytohormone traits of the selected isolates could contribute
+ to challenged-host growth. The traits were not re-quantified in soil and were not selectively perturbed, so
+ the host comparison does not isolate their mediation.
+ - source: Isolate Antagonism Against Phytophthora capsici
+ target: Pepper Growth and Visible Symptoms Under Pathogen Challenge
+ description: HYPOTHESIZED - The measured isolate antagonism may contribute to improved host performance under
+ pathogen challenge. The pot study lacked a SynCom-only control and direct disease scoring or pathogen-load
+ measurements, so it cannot isolate pathogen suppression from growth promotion or attribute the host response
+ to these two strains alone.
+ rationale: HYPOTHESIZED - The measured isolate antagonism may contribute to improved host performance under
+ pathogen challenge. The pot study lacked a SynCom-only control and direct disease scoring or pathogen-load
+ measurements, so it cannot isolate pathogen suppression from growth promotion or attribute the host response
+ to these two strains alone.
+ removed_edge_decisions: []
+ references:
+ - PMID:40508300
+ issues:
+ - 1688
+ - 1690
+ - 1691
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Pepper_Phytophthora_SynCom5/2026-10-07T074133Z-codex-0b4d64.yaml
diff --git a/reports/causal_graph_review/inventory.tsv b/reports/causal_graph_review/inventory.tsv
index 6872f029f..e36e9cc96 100644
--- a/reports/causal_graph_review/inventory.tsv
+++ b/reports/causal_graph_review/inventory.tsv
@@ -295,11 +295,11 @@ kb/communities/Panzhihua_Vanadium_Titanium_Tailings.yaml CommunityMech:000051 b5
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/Pelagerythrobacter_Salinicola_PES_Pyrene_Degradation_SynCom.yaml CommunityMech:000340 c3ce655c53db89daeab6cf8ee8ca02ab7eb3bf597d6fe0dd7171ba33194dde1a 3 2 96.7 reports/causal_graph_review/decisions/20261007-four-records-batch83.yaml reviewed
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
-kb/communities/Pepper_Growth_Rhizosphere_SynCom.yaml CommunityMech:000104 3b12ee13e0d41c767a12ef635cc02f640dfb61e2d84e694cf4ff0d9cfbcaf2f3 4 3 100.0 pending
-kb/communities/Pepper_Phytophthora_SynCom5.yaml CommunityMech:000105 90d80cf28c6ab66130431828533e2d39c0ac0c8090252703111cccdfa5b79a9f 3 2 100.0 pending
+kb/communities/Pelotomaculum_Methanothermobacter_Syntrophy.yaml CommunityMech:000052 360878e4212242ce0caf07938081bf46502f977747343a560d00684f3b725609 3 2 100.0 reports/causal_graph_review/decisions/20261007-four-records-batch83.yaml needs_research
+kb/communities/Pepper_Growth_Rhizosphere_SynCom.yaml CommunityMech:000104 b8dda93ce15fd6860fd8c424d85c961c4bb7ec2187e732720927120833158c37 3 2 86.7 reports/causal_graph_review/decisions/20261007-four-records-batch83.yaml reviewed
+kb/communities/Pepper_Phytophthora_SynCom5.yaml CommunityMech:000105 ed26e547580e6b5fa6662c07720f45993a2a5a49e891a8574a635cbf0a44d81e 3 2 90.0 reports/causal_graph_review/decisions/20261007-four-records-batch83.yaml needs_research
kb/communities/Phaeodactylum_Aliivibrio_Diel_Coculture.yaml CommunityMech:000446 778b0a4f767d0df26e9888d46f674486bd6f6c53d9f6d791ccdb6a8ba1533550 2 0 60.0 pending
kb/communities/Phenol_Carboxylation_Consortium.yaml CommunityMech:000053 d0b287884655041b8d00a25103ef528db26d7551e966cafdffd662396b470ca9 3 3 100.0 pending
kb/communities/Phormidium_Alkaline_Consortium.yaml CommunityMech:000054 2cd585c6cf554f62ce0bb9bd3f2412f9dcf64b7617b62e3bbc4ca36bc7cbaadf 7 3 100.0 pending
diff --git a/reports/causal_graph_review/summary.json b/reports/causal_graph_review/summary.json
index 25039ea0d..8171f6d48 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": 1439,
- "edges": 601,
+ "nodes": 1438,
+ "edges": 600,
"records_without_nodes": 8,
"records_without_edges": 170,
"review_status_counts": {
- "needs_research": 39,
- "pending": 164,
- "reviewed": 257
+ "needs_research": 41,
+ "pending": 160,
+ "reviewed": 259
},
"structural_defects": [],
"network_audit": [
diff --git a/reports/causal_graph_review/validation-20261007-batch83.json b/reports/causal_graph_review/validation-20261007-batch83.json
new file mode 100644
index 000000000..9f928f955
--- /dev/null
+++ b/reports/causal_graph_review/validation-20261007-batch83.json
@@ -0,0 +1,1585 @@
+{
+ "base_commit": "72da5ae43f475499fbd5f6ca6bbe8c95e9a874ac",
+ "scope": [
+ "kb/communities/Pelagerythrobacter_Salinicola_PES_Pyrene_Degradation_SynCom.yaml",
+ "kb/communities/Pelotomaculum_Methanothermobacter_Syntrophy.yaml",
+ "kb/communities/Pepper_Growth_Rhizosphere_SynCom.yaml",
+ "kb/communities/Pepper_Phytophthora_SynCom5.yaml"
+ ],
+ "reference_validator_version": "0.1.7",
+ "results": [
+ {
+ "check": "Pelagerythrobacter_Salinicola_PES_Pyrene_Degradation_SynCom-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Pelagerythrobacter_Salinicola_PES_Pyrene_Degradation_SynCom.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch83/Pelagerythrobacter_Salinicola_PES_Pyrene_Degradation_SynCom-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Pelagerythrobacter_Salinicola_PES_Pyrene_Degradation_SynCom-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch83/Pelagerythrobacter_Salinicola_PES_Pyrene_Degradation_SynCom-strict.tsv",
+ "kb/communities/Pelagerythrobacter_Salinicola_PES_Pyrene_Degradation_SynCom.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch83/Pelagerythrobacter_Salinicola_PES_Pyrene_Degradation_SynCom-strict.log",
+ "log_sha256": "e4e267e8bd8e4ed87135dc0e566b7caa7f8514e28765119a7ee82acbd347f7f9",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch83/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-batch83/Pelagerythrobacter_Salinicola_PES_Pyrene_Degradation_SynCom-strict.tsv\n"
+ },
+ {
+ "check": "Pelagerythrobacter_Salinicola_PES_Pyrene_Degradation_SynCom-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Pelagerythrobacter_Salinicola_PES_Pyrene_Degradation_SynCom.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch83/Pelagerythrobacter_Salinicola_PES_Pyrene_Degradation_SynCom-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Pelagerythrobacter_Salinicola_PES_Pyrene_Degradation_SynCom-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Pelagerythrobacter_Salinicola_PES_Pyrene_Degradation_SynCom.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch83/Pelagerythrobacter_Salinicola_PES_Pyrene_Degradation_SynCom-references.log",
+ "log_sha256": "73259abaed88e78424b73b7e2d2bcacaa4091a9dabad039335f9908925489b60",
+ "output_tail": "Validating kb/communities/Pelagerythrobacter_Salinicola_PES_Pyrene_Degradation_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/Pelagerythrobacter_Salinicola_PES_Pyrene_Degradation_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": "Pelagerythrobacter_Salinicola_PES_Pyrene_Degradation_SynCom-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Pelagerythrobacter_Salinicola_PES_Pyrene_Degradation_SynCom.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch83/Pelagerythrobacter_Salinicola_PES_Pyrene_Degradation_SynCom-snippets.log",
+ "log_sha256": "96a23c88588d68e990af5d62f9c27df12879566b4125e7703a275c3bfa7adcd7",
+ "output_tail": "# 22 evidence snippets scanned across 1 files\n MATCH 22\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": "Pelagerythrobacter_Salinicola_PES_Pyrene_Degradation_SynCom-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Pelagerythrobacter_Salinicola_PES_Pyrene_Degradation_SynCom.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch83/Pelagerythrobacter_Salinicola_PES_Pyrene_Degradation_SynCom-rank.log",
+ "log_sha256": "30a8db0ac00a2d8200abb53010b958331aaeaffd1e33d4fc0b55f6fd04eaf9ca",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000340\",\n \"name\": \"Pelagerythrobacter-Salinicola PES Pyrene-Degradation SynCom\",\n \"score\": 96.7,\n \"taxonomy\": 2,\n \"connected_taxa\": 2,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 3,\n \"downstream_edges\": 2,\n \"interaction_evidence\": 6,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Pelagerythrobacter_Salinicola_PES_Pyrene_Degradation_SynCom.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Pelagerythrobacter_Salinicola_PES_Pyrene_Degradation_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/Pelagerythrobacter_Salinicola_PES_Pyrene_Degradation_SynCom/2026-10-07T074131Z-codex-d4a2ed.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch83/Pelagerythrobacter_Salinicola_PES_Pyrene_Degradation_SynCom-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Pepper_Phytophthora_SynCom5-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Pepper_Phytophthora_SynCom5.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch83/Pepper_Phytophthora_SynCom5-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Pepper_Phytophthora_SynCom5-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch83/Pepper_Phytophthora_SynCom5-strict.tsv",
+ "kb/communities/Pepper_Phytophthora_SynCom5.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch83/Pepper_Phytophthora_SynCom5-strict.log",
+ "log_sha256": "e2d2891fb77b1a615b3eb0baf86dfd0239a27e68fd9ee9f4934fbd24b88e706e",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch83/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-batch83/Pepper_Phytophthora_SynCom5-strict.tsv\n"
+ },
+ {
+ "check": "Pepper_Phytophthora_SynCom5-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Pepper_Phytophthora_SynCom5.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch83/Pepper_Phytophthora_SynCom5-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Pepper_Phytophthora_SynCom5-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Pepper_Phytophthora_SynCom5.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch83/Pepper_Phytophthora_SynCom5-references.log",
+ "log_sha256": "1d54f62cab08db4a270ada65dd01f2a1fb1422bfbb0ab9b9423330cde895935c",
+ "output_tail": "Validating kb/communities/Pepper_Phytophthora_SynCom5.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/Pepper_Phytophthora_SynCom5.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": "Pepper_Phytophthora_SynCom5-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Pepper_Phytophthora_SynCom5.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch83/Pepper_Phytophthora_SynCom5-snippets.log",
+ "log_sha256": "872637a69e95b3997368edea80eba5db2a2155e0ac9344b758394dcf97491410",
+ "output_tail": "# 14 evidence snippets scanned across 1 files\n MATCH 14\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": "Pepper_Phytophthora_SynCom5-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Pepper_Phytophthora_SynCom5.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch83/Pepper_Phytophthora_SynCom5-rank.log",
+ "log_sha256": "c23eb0cef93d4b04c2139fb7a8319fe82b332d854e00b953f32e84a54cb4bd31",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000105\",\n \"name\": \"Pepper Phytophthora-Resistance SynCom5\",\n \"score\": 90.0,\n \"taxonomy\": 5,\n \"connected_taxa\": 5,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 3,\n \"downstream_edges\": 2,\n \"interaction_evidence\": 3,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Pepper_Phytophthora_SynCom5.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Pepper_Phytophthora_SynCom5-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Pepper_Phytophthora_SynCom5/2026-10-07T074133Z-codex-0b4d64.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch83/Pepper_Phytophthora_SynCom5-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Pelotomaculum_Methanothermobacter_Syntrophy-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Pelotomaculum_Methanothermobacter_Syntrophy.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch83/Pelotomaculum_Methanothermobacter_Syntrophy-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Pelotomaculum_Methanothermobacter_Syntrophy-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch83/Pelotomaculum_Methanothermobacter_Syntrophy-strict.tsv",
+ "kb/communities/Pelotomaculum_Methanothermobacter_Syntrophy.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch83/Pelotomaculum_Methanothermobacter_Syntrophy-strict.log",
+ "log_sha256": "3535f1bb261d0c64dd5aef58da039cc574662c9d4af93d079a8d2d594f3743f6",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch83/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-batch83/Pelotomaculum_Methanothermobacter_Syntrophy-strict.tsv\n"
+ },
+ {
+ "check": "Pelotomaculum_Methanothermobacter_Syntrophy-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Pelotomaculum_Methanothermobacter_Syntrophy.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch83/Pelotomaculum_Methanothermobacter_Syntrophy-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Pelotomaculum_Methanothermobacter_Syntrophy-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Pelotomaculum_Methanothermobacter_Syntrophy.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch83/Pelotomaculum_Methanothermobacter_Syntrophy-references.log",
+ "log_sha256": "521c3578f360d7945657c4570199d2daf98593099a94ffa5d17f21aba011316e",
+ "output_tail": "Validating kb/communities/Pelotomaculum_Methanothermobacter_Syntrophy.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/Pelotomaculum_Methanothermobacter_Syntrophy.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": "Pelotomaculum_Methanothermobacter_Syntrophy-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Pelotomaculum_Methanothermobacter_Syntrophy.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch83/Pelotomaculum_Methanothermobacter_Syntrophy-snippets.log",
+ "log_sha256": "d6441c5dcfaf6a072d70e8708d5fe1bbd2c2a2d31da61b3014fb014108c34cef",
+ "output_tail": "# 18 evidence snippets scanned across 1 files\n MATCH 18\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": "Pelotomaculum_Methanothermobacter_Syntrophy-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Pelotomaculum_Methanothermobacter_Syntrophy.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch83/Pelotomaculum_Methanothermobacter_Syntrophy-rank.log",
+ "log_sha256": "4f32554e79c8f474bd80bf1fddb34af8afae185a3015cde61266755c92265089",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000052\",\n \"name\": \"Pelotomaculum-Methanothermobacter Syntrophic Consortium\",\n \"score\": 100.0,\n \"taxonomy\": 2,\n \"connected_taxa\": 2,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 3,\n \"downstream_edges\": 2,\n \"interaction_evidence\": 6,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [],\n \"path\": \"kb/communities/Pelotomaculum_Methanothermobacter_Syntrophy.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Pelotomaculum_Methanothermobacter_Syntrophy-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Pelotomaculum_Methanothermobacter_Syntrophy/2026-10-07T074132Z-codex-849acd.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch83/Pelotomaculum_Methanothermobacter_Syntrophy-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Pepper_Growth_Rhizosphere_SynCom-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Pepper_Growth_Rhizosphere_SynCom.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch83/Pepper_Growth_Rhizosphere_SynCom-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Pepper_Growth_Rhizosphere_SynCom-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch83/Pepper_Growth_Rhizosphere_SynCom-strict.tsv",
+ "kb/communities/Pepper_Growth_Rhizosphere_SynCom.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch83/Pepper_Growth_Rhizosphere_SynCom-strict.log",
+ "log_sha256": "6fee120e404adce66adb58538a33339659bfbc61daf5507cbd1cb279a5a18086",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch83/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-batch83/Pepper_Growth_Rhizosphere_SynCom-strict.tsv\n"
+ },
+ {
+ "check": "Pepper_Growth_Rhizosphere_SynCom-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Pepper_Growth_Rhizosphere_SynCom.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch83/Pepper_Growth_Rhizosphere_SynCom-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Pepper_Growth_Rhizosphere_SynCom-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Pepper_Growth_Rhizosphere_SynCom.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch83/Pepper_Growth_Rhizosphere_SynCom-references.log",
+ "log_sha256": "7b2098e99bf724baa0389de26fb275e3b7370c29682236a8bda10fc9e490316a",
+ "output_tail": "Validating kb/communities/Pepper_Growth_Rhizosphere_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/Pepper_Growth_Rhizosphere_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": "Pepper_Growth_Rhizosphere_SynCom-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Pepper_Growth_Rhizosphere_SynCom.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch83/Pepper_Growth_Rhizosphere_SynCom-snippets.log",
+ "log_sha256": "6fd22c7b42f139e3b66a27210ad3d8968c80af940879c7074184305812838cca",
+ "output_tail": "# 13 evidence snippets scanned across 1 files\n MATCH 13\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": "Pepper_Growth_Rhizosphere_SynCom-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Pepper_Growth_Rhizosphere_SynCom.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch83/Pepper_Growth_Rhizosphere_SynCom-rank.log",
+ "log_sha256": "4d11a84195f34bacce17b0d652e79fbe77aa58e5ae0d327008e3cba30196429f",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000104\",\n \"name\": \"Pepper Growth Rhizosphere SynCom\",\n \"score\": 86.7,\n \"taxonomy\": 4,\n \"connected_taxa\": 4,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 3,\n \"downstream_edges\": 2,\n \"interaction_evidence\": 3,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"metabolites_or_biological_processes\",\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Pepper_Growth_Rhizosphere_SynCom.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Pepper_Growth_Rhizosphere_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/Pepper_Growth_Rhizosphere_SynCom/2026-10-07T074133Z-codex-b89626.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch83/Pepper_Growth_Rhizosphere_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-batch83/inventory.log",
+ "log_sha256": "b1ba5b8f7d64d65865d09eae2ec0daab14c4359ccd27159d0a1cd9f99364bc53",
+ "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\": 1438,\n \"edges\": 600,\n \"records_without_nodes\": 8,\n \"records_without_edges\": 170,\n \"review_status_counts\": {\n \"needs_research\": 41,\n \"pending\": 160,\n \"reviewed\": 259\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-batch83/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": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch83/rank-all.log",
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Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch83/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch83/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch83/docs/index.html\n"
+ },
+ {
+ "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-batch83/render-repeat.log",
+ "log_sha256": "904859d8fc62003fbd06e40cb268b05a48ab3b9a0760bd6bd4b4921a963f91a7",
+ "output_tail": "sm.html\n \u2713 Synechococcus_Bacillus_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch83/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch83/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch83/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-batch82')),('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-batch83/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_batch83.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-batch83/regressions.log",
+ "log_sha256": "8efe5dc1df8a46993a3e701b0a947b760ad90a5edd0631446badded5d647dc87",
+ "output_tail": "........................................................................ [ 9%]\n........................................................................ [ 19%]\n........................................................................ [ 28%]\n........................................................................ [ 38%]\n........................................................................ [ 48%]\n........................................................................ [ 57%]\n........................................................................ [ 67%]\n........................................................................ [ 77%]\n........................................................................ [ 86%]\n........................................................................ [ 96%]\n.......................... [100%]\n746 passed in 437.51s (0:07:17)\n"
+ },
+ {
+ "check": "black",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/3Q_kifQtLB624D5bBWGIf/bin/black",
+ "--check",
+ "tests/test_causal_review_batch83.py",
+ "tests/test_participating_taxa.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch83/black.log",
+ "log_sha256": "b9cf511501d306d2bd8355ccb165c8ddc0a6fdd62d7c72c4a7b1795cf8934c8c",
+ "output_tail": "All done! \u2728 \ud83c\udf70 \u2728\n2 files would be left unchanged.\n"
+ },
+ {
+ "check": "ruff",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/wCcxEYRM4HeHgwYPZemHX/bin/ruff",
+ "check",
+ "tests/test_causal_review_batch83.py",
+ "tests/test_participating_taxa.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch83/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-batch83/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,re,subprocess,yaml\nP=pathlib.Path\nledger=yaml.safe_load(P('reports/causal_graph_review/decisions/20261007-four-records-batch83.yaml').read_text())\ndef norm(text):\n text=re.sub(r'^L\\d+: ?', '', text, flags=re.M)\n text=re.sub(r'\\ue200cite\\ue202.*?\\ue201','',text)\n text=re.sub(r'(?<=\\w)-\\n(?=\\w)','',text)\n return ''.join(text.replace('\\u00ad','').split())\nfor p,h in ledger['primary_artifacts'].items(): assert hashlib.sha256(P(p).read_bytes()).hexdigest()==h\nsources={}\nfor c in ledger['snippet_checks']:\n sources[c['reference']]=norm(P(c['matched_artifact']).read_text())\nassert len(ledger['snippet_checks'])==18\nassert all(c['independent_primary_match'] and c['cache_matched'] for c in ledger['snippet_checks'])\ngraphs=discussions=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 n in doc['ecological_interactions']:\n for e in n['evidence']:\n assert norm(e['snippet']) in sources[e['reference']],(r['path'],n['name'],e['snippet'])\n graphs+=1\n for d in doc['discussions']:\n if d['discussion_id'] in old_ids: continue\n for e in d.get('evidence',[]):\n assert norm(e['snippet']) in sources[e['reference']],(r['path'],d['discussion_id'],e['snippet'])\n discussions+=1\nassert graphs==18\nassert sum(len(r['node_decisions']) for r in ledger['records'])==12\nassert sum(len(r['removed_node_decisions']) for r in ledger['records'])==1\nassert sum(len(r['edges_before']) for r in ledger['records'])==9\nassert sum(len(r['edges_after']) for r in ledger['records'])==8\nassert sum(len(r['removed_edge_decisions']) for r in ledger['records'])==1\nassert [r['status'] for r in ledger['records']]==['reviewed','needs_research','reviewed','needs_research']\nprint(json.dumps(dict(fresh_primary_matched=graphs,cache_matched=18,new_discussion_quotations_fresh_primary_matched=discussions,new_nodes_or_arrows=0,retained_nodes=12,removed_nodes=1,retained_arrows=8,removed_arrows=1,full_primary_main_texts_read=3,correction_read=1,abstract_or_caption_limited_studies=2,original_pdf_pages_visually_inspected={'growth':[6,7,8],'biocontrol':[3,4]},separate_supplements_and_raw_data_audited=False)))\n"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch83/primary-graph-proof.log",
+ "log_sha256": "49d20af3cbad0993e86ec5aac4891b8a0662e1a55cf47803181126ba32d56b23",
+ "output_tail": "{\"fresh_primary_matched\": 18, \"cache_matched\": 18, \"new_discussion_quotations_fresh_primary_matched\": 6, \"new_nodes_or_arrows\": 0, \"retained_nodes\": 12, \"removed_nodes\": 1, \"retained_arrows\": 8, \"removed_arrows\": 1, \"full_primary_main_texts_read\": 3, \"correction_read\": 1, \"abstract_or_caption_limited_studies\": 2, \"original_pdf_pages_visually_inspected\": {\"growth\": [6, 7, 8], \"biocontrol\": [3, 4]}, \"separate_supplements_and_raw_data_audited\": false}\n"
+ },
+ {
+ "check": "focused-final",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "pytest",
+ "-q",
+ "tests/test_causal_review_batch83.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch83/focused-final.log",
+ "log_sha256": "9b57869d85a2f74787f3f06792522066232065eb6c1295e6f5f9d6bada45f4bb",
+ "output_tail": ".......... [100%]\n10 passed in 4.16s\n"
+ },
+ {
+ "check": "audit-snippets-all",
+ "command": [
+ "just",
+ "audit-snippets"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch83/audit-snippets-all.log",
+ "log_sha256": "042a49dd9bfaa29a3826e35107ff31e625264f3c1c4cc87ac37d6e27d1a1d485",
+ "output_tail": "# 8896 evidence snippets scanned across 460 files\n MATCH 8761\n RENDERING 20\n ASSEMBLED 1\n WEAK 0\n MISMATCH 38\n NOCONTENT 76\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n 19 (19 hard) kb/communities/DCPP_DBS4_DCP4_DCP11d_Degradation_SynCom.yaml\n 15 (15 hard) kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml\n 3 (3 hard) kb/communities/Coscinodiscus_Synthetic_Community.yaml\n 1 (1 hard) kb/communities/Altered_Schaedler_Flora_Gnotobiotic_Mouse_Community.yaml\nuv run python scripts/evidence_snippet_audit.py \n"
+ }
+ ],
+ "limitations": [
+ "Fresh before-paper baseline across both roots:460records/920caches,47warnings,zero structural defects. Four whole records,13nodes9arrows reviewed;12nodes8arrows retained,one workflow node/arrow removed. No new topology.",
+ "PES full primary indexed main text/tables/captions and correction read; corrected chemical direction agrees with record. Two pepper full main texts read, with fresh public primary PDFs and cached growth text. Selected original PDF pages visually checked: growth6/7/8, biocontrol3/4. Separate supplements, remaining original figures and raw data not audited.",
+ "Species-description paper2002 and coaggregation2005 remain primary-abstract/caption limited. Preserve observed coculture growth, coaggregation and inhibitor-caption evidence without claiming full methods reviewed. Modeled distances are not measured flux. Missing feedback/coaggregation structure tracked in1689.",
+ "Europe PMC returned502/503 service errors; publisher/PMC routes returned403 or browser checks. Public primary PDFs retrieved from Semantic Scholar; no access control bypass. One erroneous initial growth PMC URL was rejected for no article content and is not evidence. Failed retrieval receipts remain outside repository.",
+ "PGPR screens differ among isolates; no direct disease score/pathogen load or SynCom-only control in biocontrol study. Positive host growth and visible symptoms survive. Soil nitrate/K/Ca and community changes retained in discussion pending1690 extension workflow; predicted functions are not flux. Protocol/identity conflicts remain1691.",
+ "Source evidence is not a blanket causality certificate. Original920caches and456otherrecords and raw non-graph blocks preserved. One new cache contains20quoted words from primary abstract/caption, not complete copyrighted article. Canonical taxonomy/auditor rules unchanged.",
+ "Dedup962all-state issue titles/bodies,6matched bodies read,62local files with hidden/ignored inclusion excluding.git/docs/site/references_cache; additional exact coaggregation-reference search matched none in that scope. No exhaustive issue-comment/PR audit. Truncated combined outputs reread where claim-critical.",
+ "One13736character single-community Edison causal dry run; scoped paid question unanswered,zero provider jobs/credits. Earlier denied/pending scopes unchanged. Repairs1685-1688close only after protected-main merge; research1689/1690andmetadata1691remainOPENafterward.",
+ "Four append-only history artifacts. Validation and rendering receipts are separate gates, not preasserted here. Self-adversarial review is not independent approval or whole-corpus completion.",
+ "Final original Figure3 inspection preserves increased fungal AND bacterial Chao richness; a copied propionate evidence explanation was corrected. Affected gates rerun and earlier passing 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."
+ ],
+ "superseded_checks": [
+ {
+ "check": "Pelotomaculum_Methanothermobacter_Syntrophy-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Pelotomaculum_Methanothermobacter_Syntrophy.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch83/pre-adversarial-Pelotomaculum_Methanothermobacter_Syntrophy-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n",
+ "superseded_reason": "Final figure-based Chao inclusion and propionate evidence explanation corrections; affected gates rerun."
+ },
+ {
+ "check": "Pelotomaculum_Methanothermobacter_Syntrophy-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch83/Pelotomaculum_Methanothermobacter_Syntrophy-strict.tsv",
+ "kb/communities/Pelotomaculum_Methanothermobacter_Syntrophy.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch83/pre-adversarial-Pelotomaculum_Methanothermobacter_Syntrophy-strict.log",
+ "log_sha256": "3535f1bb261d0c64dd5aef58da039cc574662c9d4af93d079a8d2d594f3743f6",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch83/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-batch83/Pelotomaculum_Methanothermobacter_Syntrophy-strict.tsv\n",
+ "superseded_reason": "Final figure-based Chao inclusion and propionate evidence explanation corrections; affected gates rerun."
+ },
+ {
+ "check": "Pelotomaculum_Methanothermobacter_Syntrophy-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Pelotomaculum_Methanothermobacter_Syntrophy.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch83/pre-adversarial-Pelotomaculum_Methanothermobacter_Syntrophy-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n",
+ "superseded_reason": "Final figure-based Chao inclusion and propionate evidence explanation corrections; affected gates rerun."
+ },
+ {
+ "check": "Pelotomaculum_Methanothermobacter_Syntrophy-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Pelotomaculum_Methanothermobacter_Syntrophy.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch83/pre-adversarial-Pelotomaculum_Methanothermobacter_Syntrophy-references.log",
+ "log_sha256": "521c3578f360d7945657c4570199d2daf98593099a94ffa5d17f21aba011316e",
+ "output_tail": "Validating kb/communities/Pelotomaculum_Methanothermobacter_Syntrophy.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/Pelotomaculum_Methanothermobacter_Syntrophy.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": "Final figure-based Chao inclusion and propionate evidence explanation corrections; affected gates rerun."
+ },
+ {
+ "check": "Pelotomaculum_Methanothermobacter_Syntrophy-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Pelotomaculum_Methanothermobacter_Syntrophy.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch83/pre-adversarial-Pelotomaculum_Methanothermobacter_Syntrophy-snippets.log",
+ "log_sha256": "d6441c5dcfaf6a072d70e8708d5fe1bbd2c2a2d31da61b3014fb014108c34cef",
+ "output_tail": "# 18 evidence snippets scanned across 1 files\n MATCH 18\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": "Final figure-based Chao inclusion and propionate evidence explanation corrections; affected gates rerun."
+ },
+ {
+ "check": "Pelotomaculum_Methanothermobacter_Syntrophy-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Pelotomaculum_Methanothermobacter_Syntrophy.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch83/pre-adversarial-Pelotomaculum_Methanothermobacter_Syntrophy-rank.log",
+ "log_sha256": "4f32554e79c8f474bd80bf1fddb34af8afae185a3015cde61266755c92265089",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000052\",\n \"name\": \"Pelotomaculum-Methanothermobacter Syntrophic Consortium\",\n \"score\": 100.0,\n \"taxonomy\": 2,\n \"connected_taxa\": 2,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 3,\n \"downstream_edges\": 2,\n \"interaction_evidence\": 6,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [],\n \"path\": \"kb/communities/Pelotomaculum_Methanothermobacter_Syntrophy.yaml\"\n }\n]\n",
+ "superseded_reason": "Final figure-based Chao inclusion and propionate evidence explanation corrections; affected gates rerun."
+ },
+ {
+ "check": "Pelotomaculum_Methanothermobacter_Syntrophy-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Pelotomaculum_Methanothermobacter_Syntrophy/2026-10-07T074132Z-codex-849acd.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch83/pre-adversarial-Pelotomaculum_Methanothermobacter_Syntrophy-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n",
+ "superseded_reason": "Final figure-based Chao inclusion and propionate evidence explanation corrections; affected gates rerun."
+ },
+ {
+ "check": "Pepper_Growth_Rhizosphere_SynCom-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Pepper_Growth_Rhizosphere_SynCom.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch83/pre-adversarial-Pepper_Growth_Rhizosphere_SynCom-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n",
+ "superseded_reason": "Final figure-based Chao inclusion and propionate evidence explanation corrections; affected gates rerun."
+ },
+ {
+ "check": "Pepper_Growth_Rhizosphere_SynCom-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch83/Pepper_Growth_Rhizosphere_SynCom-strict.tsv",
+ "kb/communities/Pepper_Growth_Rhizosphere_SynCom.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch83/pre-adversarial-Pepper_Growth_Rhizosphere_SynCom-strict.log",
+ "log_sha256": "6fee120e404adce66adb58538a33339659bfbc61daf5507cbd1cb279a5a18086",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch83/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-batch83/Pepper_Growth_Rhizosphere_SynCom-strict.tsv\n",
+ "superseded_reason": "Final figure-based Chao inclusion and propionate evidence explanation corrections; affected gates rerun."
+ },
+ {
+ "check": "Pepper_Growth_Rhizosphere_SynCom-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Pepper_Growth_Rhizosphere_SynCom.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch83/pre-adversarial-Pepper_Growth_Rhizosphere_SynCom-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n",
+ "superseded_reason": "Final figure-based Chao inclusion and propionate evidence explanation corrections; affected gates rerun."
+ },
+ {
+ "check": "Pepper_Growth_Rhizosphere_SynCom-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Pepper_Growth_Rhizosphere_SynCom.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch83/pre-adversarial-Pepper_Growth_Rhizosphere_SynCom-references.log",
+ "log_sha256": "7b2098e99bf724baa0389de26fb275e3b7370c29682236a8bda10fc9e490316a",
+ "output_tail": "Validating kb/communities/Pepper_Growth_Rhizosphere_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/Pepper_Growth_Rhizosphere_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": "Final figure-based Chao inclusion and propionate evidence explanation corrections; affected gates rerun."
+ },
+ {
+ "check": "Pepper_Growth_Rhizosphere_SynCom-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Pepper_Growth_Rhizosphere_SynCom.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch83/pre-adversarial-Pepper_Growth_Rhizosphere_SynCom-snippets.log",
+ "log_sha256": "6fd22c7b42f139e3b66a27210ad3d8968c80af940879c7074184305812838cca",
+ "output_tail": "# 13 evidence snippets scanned across 1 files\n MATCH 13\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": "Final figure-based Chao inclusion and propionate evidence explanation corrections; affected gates rerun."
+ },
+ {
+ "check": "Pepper_Growth_Rhizosphere_SynCom-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Pepper_Growth_Rhizosphere_SynCom.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch83/pre-adversarial-Pepper_Growth_Rhizosphere_SynCom-rank.log",
+ "log_sha256": "4d11a84195f34bacce17b0d652e79fbe77aa58e5ae0d327008e3cba30196429f",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000104\",\n \"name\": \"Pepper Growth Rhizosphere SynCom\",\n \"score\": 86.7,\n \"taxonomy\": 4,\n \"connected_taxa\": 4,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 3,\n \"downstream_edges\": 2,\n \"interaction_evidence\": 3,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"metabolites_or_biological_processes\",\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Pepper_Growth_Rhizosphere_SynCom.yaml\"\n }\n]\n",
+ "superseded_reason": "Final figure-based Chao inclusion and propionate evidence explanation corrections; affected gates rerun."
+ },
+ {
+ "check": "Pepper_Growth_Rhizosphere_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/Pepper_Growth_Rhizosphere_SynCom/2026-10-07T074133Z-codex-b89626.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch83/pre-adversarial-Pepper_Growth_Rhizosphere_SynCom-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n",
+ "superseded_reason": "Final figure-based Chao inclusion and propionate evidence explanation corrections; 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-batch83/pre-adversarial-inventory.log",
+ "log_sha256": "b1ba5b8f7d64d65865d09eae2ec0daab14c4359ccd27159d0a1cd9f99364bc53",
+ "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\": 1438,\n \"edges\": 600,\n \"records_without_nodes\": 8,\n \"records_without_edges\": 170,\n \"review_status_counts\": {\n \"needs_research\": 41,\n \"pending\": 160,\n \"reviewed\": 259\n },\n \"structural_defects\": []\n}\n",
+ "superseded_reason": "Final figure-based Chao inclusion and propionate evidence explanation corrections; 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-batch83/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",
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+ },
+ {
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+ "command": [
+ "just",
+ "rank-causal-graphs"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
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+ "log": "/private/tmp/communitymech-batch83/pre-adversarial-rank-all.log",
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+ {
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+ "output_tail": "sm.html\n \u2713 Synechococcus_Bacillus_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 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Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 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/private/tmp/communitymech-causal-batch83/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch83/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch83/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch83/docs/index.html\n",
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+ },
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+ "log": "/private/tmp/communitymech-batch83/pre-adversarial-render-repeat.log",
+ "log_sha256": "904859d8fc62003fbd06e40cb268b05a48ab3b9a0760bd6bd4b4921a963f91a7",
+ "output_tail": "sm.html\n \u2713 Synechococcus_Bacillus_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch83/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch83/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch83/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch83/docs/index.html\n",
+ "superseded_reason": "Final figure-based Chao inclusion and propionate evidence explanation corrections; 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-batch82')),('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": [
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+ "log": "/private/tmp/communitymech-batch83/pre-adversarial-connectivity-survey.log",
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+ "superseded_reason": "Final figure-based Chao inclusion and propionate evidence explanation corrections; affected gates rerun."
+ },
+ {
+ "check": "regressions",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "pytest",
+ "-q",
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+ "tests/test_causal_review_batch16.py",
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+ "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",
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+ "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",
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+ "tests/test_causal_review_batch57.py",
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+ "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",
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+ "tests/test_causal_review_batch67.py",
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+ "tests/test_causal_review_batch7.py",
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+ "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-batch83/pre-adversarial-regressions.log",
+ "log_sha256": "ec403a4fa85ba0e30c97768abeae4e7cf9ab61af05a755c172db4d38ac2a1d19",
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+ "superseded_reason": "Final figure-based Chao inclusion and propionate evidence explanation corrections; affected gates rerun."
+ },
+ {
+ "check": "black",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/3Q_kifQtLB624D5bBWGIf/bin/black",
+ "--check",
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+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
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+ "log": "/private/tmp/communitymech-batch83/pre-adversarial-black.log",
+ "log_sha256": "b9cf511501d306d2bd8355ccb165c8ddc0a6fdd62d7c72c4a7b1795cf8934c8c",
+ "output_tail": "All done! \u2728 \ud83c\udf70 \u2728\n2 files would be left unchanged.\n",
+ "superseded_reason": "Final figure-based Chao inclusion and propionate evidence explanation corrections; affected gates rerun."
+ },
+ {
+ "check": "ruff",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/wCcxEYRM4HeHgwYPZemHX/bin/ruff",
+ "check",
+ "tests/test_causal_review_batch83.py",
+ "tests/test_participating_taxa.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
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+ "log": "/private/tmp/communitymech-batch83/pre-adversarial-ruff.log",
+ "log_sha256": "82b3e6a6c090a57601d22943bd23fca9218d1031dbe5a7b754092f9a156b4f18",
+ "output_tail": "All checks passed!\n",
+ "superseded_reason": "Final figure-based Chao inclusion and propionate evidence explanation corrections; affected gates rerun."
+ },
+ {
+ "check": "diff-check",
+ "command": [
+ "git",
+ "diff",
+ "--check"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch83/pre-adversarial-diff-check.log",
+ "log_sha256": "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855",
+ "output_tail": "",
+ "superseded_reason": "Final figure-based Chao inclusion and propionate evidence explanation corrections; affected gates rerun."
+ }
+ ],
+ "snippet_counts_by_record": {
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+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Pelotomaculum_Methanothermobacter_Syntrophy.yaml": {
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+ "RENDERING": 0,
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+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Pepper_Phytophthora_SynCom5.yaml": {
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+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ }
+ },
+ "unchanged_raw_blocks": 57,
+ "unchanged_record_files": 456,
+ "unchanged_cache_files": 920,
+ "cache_changes": [
+ {
+ "path": "references_cache/PMID_16332758.txt",
+ "original_sha256": null,
+ "sha256": "2ecdf48fa38c065d2670b49cc3b4dbb1ad114110832ac7b1bde3e11266003aa5",
+ "kind": "new_short_primary_excerpts",
+ "quoted_words": 20
+ }
+ ],
+ "edison": {
+ "required_for_this_repair": false,
+ "required_for_unresolved_extensions": true,
+ "provider_submissions": 0,
+ "credits_spent": 0,
+ "dry_runs": [
+ {
+ "community_id": "CommunityMech:000052",
+ "job": "LITERATURE",
+ "query_chars": 13736,
+ "query_sha256": "d110c3bdebd6259f35c27a8cce89d6ffea7b1f0417e50ae96abd706b58add3e6",
+ "meta_path": "/private/tmp/communitymech-batch83/edison-syntrophy/Pelotomaculum_Methanothermobacter_Syntrophy-edison-literature-causal-meta.yaml",
+ "authorization": "Scoped asynchronous question unanswered; preselection is not approval."
+ }
+ ]
+ },
+ "primary_artifacts": {
+ "/private/tmp/communitymech-batch83/baseline.json": "2b246062bc1e2a3ec717a90fb60e180ad39dcc4a4517e1c71166f4154cd1554a",
+ "/private/tmp/communitymech-batch83/biocontrol-page-12.png": "9a0b20428b4bcca41922c1b754d89f471514054e8d6d325c137c5b2bf6238320",
+ "/private/tmp/communitymech-batch83/biocontrol-page-3.png": "84db6ce3c3aee5e662cd6ccfc3e05a55ef0fc7b8bd1a80702cbf5b3bbf355b49",
+ "/private/tmp/communitymech-batch83/biocontrol-page-4.png": "467126bb440d4f06b6297407a8f4e430a23c23f15149cc5cc4d6830ac921c6c9",
+ "/private/tmp/communitymech-batch83/biocontrol-pdf-primary.txt": "49fcc854f2142d3e8c241d3097d208fe0c2ab3cb2c97d573fd2cfe00af960fcb",
+ "/private/tmp/communitymech-batch83/biocontrol-primary.pdf": "fcb2f8c5eb71e188cef0ce324ddeecf938f5b644bc268333b3de617fae50611f",
+ "/private/tmp/communitymech-batch83/coaggregation-search-primary.txt": "c280a6c0bc550eeaf502c2232fa317336bf07011a53a35c6d2561a7a0c8203ad",
+ "/private/tmp/communitymech-batch83/correction-web-primary.txt": "c3304a85ccf7256ac8de32eb9fe1811d9062ae5acebd494bac781154e13c977e",
+ "/private/tmp/communitymech-batch83/edison-syntrophy/Pelotomaculum_Methanothermobacter_Syntrophy-edison-literature-causal-meta.yaml": "8f54844173f6501227fd5a0b5ae3f69be0b8b73e4f779859d83ec1a76bca7bc5",
+ "/private/tmp/communitymech-batch83/extra-issue-matches.json": "37517e5f3dc66819f61f5a7bb8ace1921282415f10551d2defa5c3eb0985b570",
+ "/private/tmp/communitymech-batch83/growth-page-6.png": "598e8b4fa8c0662fe739ab4121a25f31656b100b0921a75004fb41eaaf3c0e9c",
+ "/private/tmp/communitymech-batch83/growth-page-7.png": "54c73366bea2ac6a17a0d70c104d9d8468c00e40e2ea0bb339faa7f07b2d9bbd",
+ "/private/tmp/communitymech-batch83/growth-page-8.png": "58e7e04610ed1b2d5c99902a3dcac7af52d2c6f45b5d4f9b537b408273091e17",
+ "/private/tmp/communitymech-batch83/growth-pdf-primary.txt": "8fd9797b55e386618b2a3288afbbc547bb19c12970405e686703d22d774683af",
+ "/private/tmp/communitymech-batch83/growth-primary.pdf": "9f6cb83988c22cd99b96c5379b967df73a9de1bfa21c03e9484de4e960ba8989",
+ "/private/tmp/communitymech-batch83/issue-matches.json": "278140c6fabf3e86ff041da901bce9983ff5c60c3b5e8e891b10b8892034a816",
+ "/private/tmp/communitymech-batch83/issues.json": "900be8c42b3d443a8facd673cefef400313386083506a3186063489f8f8f0370",
+ "/private/tmp/communitymech-batch83/local-matches.txt": "d87a8d1ed27e5f3f1fa55cd116126c4c2432cce9bcdfc8a66cafb1a07cefaea4",
+ "/private/tmp/communitymech-batch83/pes-metadata.json": "e79a8467654eb50809e1e3aaa8ddd75355cb8800370743bd7a3c43167876fc5e",
+ "/private/tmp/communitymech-batch83/pes-web-primary.txt": "a35fe658b844f221a84e0ff202be7b81aefe227c31f94f12b443add451b10450",
+ "/private/tmp/communitymech-batch83/publisher-manifest.json": "e01e45b167cbcca346eff00dc13f4b1a7a727312c6eb8a4449ca00d3811fcb9b",
+ "/private/tmp/communitymech-batch83/syntrophy-web-primary.txt": "d635c1dfd6030d655fa63552775033cdfe90a763cd8a41028a828731d6782db1"
+ },
+ "network_delta": {
+ "existing_findings_preserved": 47,
+ "added_findings": {},
+ "removed_findings": {},
+ "interpretation": "All47existingwarnings unchanged; zero new structural or connectivity defects. Canonical taxonomy/auditor rules unchanged; T14/A6 antagonist participants narrowed."
+ },
+ "render_determinism": true,
+ "published_description_coverage": {
+ "pages": 456,
+ "nodes": 1424,
+ "arrows": 592
+ },
+ "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": 1438,
+ "edges": 600,
+ "records_without_nodes": 8,
+ "records_without_edges": 170,
+ "review_status_counts": {
+ "needs_research": 41,
+ "pending": 160,
+ "reviewed": 259
+ },
+ "structural_defects": []
+ },
+ "tested_file_sha256": {
+ "reports/causal_graph_review/decisions/20261007-four-records-batch83.yaml": "e13924aca3b858e78dcfa2074352e5a9a381bba97a83b2b94b8e864419dd9efe",
+ "tests/test_causal_review_batch83.py": "45dda20101f4783fef46ba13edc6abbc2ed2625f59a4b696f658782c75158bf1",
+ "tests/test_participating_taxa.py": "b96ccc0da5587273f26c05dae5826c7a742e045b8ec50aca5f620d190594e9e5",
+ "kb/communities/Pelagerythrobacter_Salinicola_PES_Pyrene_Degradation_SynCom.yaml": "c3ce655c53db89daeab6cf8ee8ca02ab7eb3bf597d6fe0dd7171ba33194dde1a",
+ "kb/communities/Pelotomaculum_Methanothermobacter_Syntrophy.yaml": "360878e4212242ce0caf07938081bf46502f977747343a560d00684f3b725609",
+ "kb/communities/Pepper_Growth_Rhizosphere_SynCom.yaml": "b8dda93ce15fd6860fd8c424d85c961c4bb7ec2187e732720927120833158c37",
+ "kb/communities/Pepper_Phytophthora_SynCom5.yaml": "ed26e547580e6b5fa6662c07720f45993a2a5a49e891a8574a635cbf0a44d81e",
+ "reports/causal_graph_review/README.md": "0f895d15928b55a0c69f4509c8cd10e2cf494e93c9659c53ca2caab5e567e250",
+ "references_cache/PMID_16332758.txt": "2ecdf48fa38c065d2670b49cc3b4dbb1ad114110832ac7b1bde3e11266003aa5"
+ },
+ "status": "verified_assay_boundary_graph_review",
+ "full_corpus_snippet_counts": {
+ "records": 460,
+ "total": 8896,
+ "categories": {
+ "MATCH": 8761,
+ "RENDERING": 20,
+ "ASSEMBLED": 1,
+ "WEAK": 0,
+ "MISMATCH": 38,
+ "NOCONTENT": 76
+ }
+ },
+ "full_corpus_snippet_audit_caveat": "The full both-root snippet audit was executed. Exit0 is informational, not a clean-corpus assertion; the recorded MATCH/RENDERING/ASSEMBLED/WEAK/MISMATCH/NOCONTENT counts are authoritative. Four edited records separately pass the focused gates.",
+ "pre_research_baseline": {
+ "base_commit": "72da5ae43f475499fbd5f6ca6bbe8c95e9a874ac",
+ "base_tree": "6bc4428a81113f9c2f5a1d3a34a8951ae958750a",
+ "research_worktree": "/private/tmp/communitymech-causal-batch82",
+ "checks": [
+ {
+ "name": "rank",
+ "command": [
+ "just",
+ "rank-causal-graphs"
+ ],
+ "exit_code": 0,
+ "expected_exit_code": 0,
+ "log": "/private/tmp/communitymech-batch83/baseline-rank.log",
+ "sha256": "7a025a86407b974399d9d33d9ef37aac5375177c69294aa1c4756d3bbb36e46f",
+ "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-batch83/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-batch83/baseline-network.log",
+ "sha256": "c4ff432a38a90ba8d231a4f632b4fefacb5bd830c2612cdd13de01b353c37f9f",
+ "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-batch83/baseline-downstream.log",
+ "sha256": "df5a35d4fa43cb05de776a243f6a69ba643d3be7737ba2a2fc5e28db2246aea9",
+ "output_tail": "07: downstream:\nkb/communities/At_RSPHERE_SynCom.yaml:249: downstream:\nkb/communities/Rhodopseudomonas_Geobacter_Magnetite_Redox_Coculture.yaml:151: downstream:\nkb/communities/Rhodopseudomonas_Geobacter_Magnetite_Redox_Coculture.yaml:198: downstream:\nkb/communities/Rhodopseudomonas_Geobacter_Magnetite_Redox_Coculture.yaml:249: downstream:\nkb/communities/ENIGMA_Denitrifying_SynCom.yaml:167: downstream:\nkb/communities/ENIGMA_Denitrifying_SynCom.yaml:217: downstream:\nkb/communities/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus.yaml:342: downstream:\nkb/communities/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus.yaml:381: 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/Polaromonas_Vanadium_Reduction_Community.yaml:281: downstream:\nkb/communities/Polaromonas_Vanadium_Reduction_Community.yaml:401: 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/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml:223: downstream:\nkb/communities/Clostridium_Phytofermentans_Ecoli_Cellobiose_Biofilm_Consortium.yaml:167: downstream:\nkb/communities/Clostridium_Phytofermentans_Ecoli_Cellobiose_Biofilm_Consortium.yaml:198: downstream:\nkb/communities/Clostridium_Phytofermentans_Ecoli_Cellobiose_Biofilm_Consortium.yaml:251: downstream:\nkb/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml:135: downstream:\nkb/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml:177: downstream:\nkb/communities/Viili_Fungus_Bacterium_EPS_SynCom.yaml:133: downstream:\nkb/communities/Viili_Fungus_Bacterium_EPS_SynCom.yaml:183: downstream:\n"
+ }
+ ],
+ "baseline_sha256": "2b246062bc1e2a3ec717a90fb60e180ad39dcc4a4517e1c71166f4154cd1554a"
+ },
+ "reference_validator_caveat": "Four full-record reference validators exit0. CLI Total checks counts issues, not executed checks.18graph quotations independently match fresh primary content and caches. Literal matching is not entailment or whole-record provenance certification; non-graph claims and original920caches are preserved, not globally recertified."
+}
diff --git a/tests/test_causal_review_batch83.py b/tests/test_causal_review_batch83.py
new file mode 100644
index 000000000..169b4ff07
--- /dev/null
+++ b/tests/test_causal_review_batch83.py
@@ -0,0 +1,150 @@
+"""Preserve measured degradation, syntrophy and plant phenotypes with scoped causality."""
+
+import hashlib
+from pathlib import Path
+
+import yaml
+
+ROOT = Path(__file__).resolve().parents[1]
+LEDGER = ROOT / "reports/causal_graph_review/decisions/20261007-four-records-batch83.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_pes_measured_removal_survives_candidate_mechanism_qualification():
+ _, _, docs = records()
+ handoff, emulsion, removal = docs[0]["ecological_interactions"]
+ assert "approached complete removal" in removal["description"]
+ assert "49.95%" in removal["description"]
+ assert "carbon mineralization" in removal["description"]
+ assert handoff["evidence"][1]["supports"] == "PARTIAL"
+ for node in [handoff, emulsion]:
+ assert node["downstream"][0]["target"] == removal["name"]
+ assert node["downstream"][0]["description"].startswith("HYPOTHESIZED -")
+
+
+def test_pes_emulsion_assay_is_not_pyrene_flux_or_mutualism():
+ _, _, docs = records()
+ emulsion = docs[0]["ecological_interactions"][1]
+ assert "soybean-oil" in emulsion["description"]
+ assert "yeast extract" in emulsion["description"]
+ assert "68%" in emulsion["description"]
+ assert "interaction_type" not in emulsion
+ assert any(
+ d["discussion_id"] == "hphtc5_decarboxylase_candidate_unresolved"
+ for d in docs[0]["discussions"]
+ )
+
+
+def test_syntrophy_retains_growth_and_corrects_universal_partner_dependence():
+ _, _, docs = records()
+ prop, alternative, methane = docs[1]["ecological_interactions"]
+ assert prop["target_taxon"]["term"]["id"] == "NCBITaxon:145262"
+ assert methane["target_taxon"]["term"]["id"] == "NCBITaxon:110500"
+ assert "pure-culture growth on pyruvate and fumarate" in prop["description"]
+ assert prop["evidence"][0]["snippet"].startswith("The strain grew on propionate")
+ assert "growth on propionate" in prop["evidence"][0]["explanation"]
+ assert "ethylene glycol" in alternative["description"]
+ assert all(m["term"]["id"] != "CHEBI:30089" for m in alternative["metabolites"])
+
+
+def test_coaggregation_is_positive_but_not_direct_electron_conduction():
+ _, rows, docs = records()
+ methane = docs[1]["ecological_interactions"][2]
+ assert "stronger coaggregation on propionate" in methane["description"]
+ assert "Fick-law" in methane["description"]
+ assert "2-BES" in methane["description"]
+ assert len([e for e in methane["evidence"] if e["reference"] == "PMID:16332758"]) == 2
+ assert rows[1]["status"] == "needs_research" and 1689 in rows[1]["issues"]
+
+
+def test_pepper_workflow_removed_but_author_model_retained_as_hypothesis():
+ _, _, docs = records()
+ diversity, native, plant = docs[2]["ecological_interactions"]
+ assert "increased fungal and bacterial Chao richness" in diversity["description"]
+ assert diversity["downstream"][0]["target"] == native["name"]
+ assert native["downstream"][0]["target"] == plant["name"]
+ assert all(
+ n["downstream"][0]["description"].startswith("HYPOTHESIZED -") for n in [diversity, native]
+ )
+ assert "total genus-level Scedosporium decreased" in native["description"]
+ assert "OTU451 also increased" in native["description"]
+ assert len(docs[2]["taxonomy"]) == 4
+ assert docs[2]["taxonomy"][-1]["taxon_term"]["term"]["label"] == "Aspergillus"
+
+
+def test_plant_growth_is_not_reciprocal_microbe_fitness():
+ _, _, docs = records()
+ for doc in docs[2:]:
+ assert all("interaction_type" not in n for n in doc["ecological_interactions"])
+ assert doc["ecological_interactions"][-1]["evidence"][0]["evidence_source"] == "IN_VIVO"
+ assert "45 days" in docs[2]["ecological_interactions"][-1]["description"]
+
+
+def test_biocontrol_heterogeneous_screens_do_not_credit_all_members_with_antagonism():
+ _, _, docs = records()
+ traits, antagonism, _ = docs[3]["ecological_interactions"]
+ assert "not re-quantified in rhizosphere soil" in traits["description"]
+ assert "58.4% and 17.6%" in antagonism["description"]
+ assert {t["term"]["id"] for t in antagonism["participating_taxa"]} == {
+ "NCBITaxon:1931",
+ "NCBITaxon:306",
+ }
+ assert "biological_processes" not in antagonism
+ assert "oomycete" in antagonism["description"]
+
+
+def test_biocontrol_positive_host_proxies_are_not_direct_disease_scores():
+ _, rows, docs = records()
+ plant = docs[3]["ecological_interactions"][-1]
+ assert "improved root length, height, biomass" in plant["description"]
+ assert "direct disease-severity scoring" in plant["description"]
+ assert "were not performed" in plant["description"]
+ assert "no SynCom-only control" in plant["description"]
+ assert "metabolites" not in plant
+ assert rows[3]["status"] == "needs_research" and 1690 in rows[3]["issues"]
+
+
+def test_every_original_node_arrow_and_anchor_has_a_disposition():
+ ledger, rows, docs = records()
+ assert sum(len(r["node_decisions"]) for r in rows) == 12
+ assert sum(len(r["removed_node_decisions"]) for r in rows) == 1
+ assert sum(len(r["edges_before"]) for r in rows) == 9
+ assert sum(len(r["edges_after"]) for r in rows) == 8
+ assert sum(len(r["removed_edge_decisions"]) for r in rows) == 1
+ assert ledger["primary_graph_snippet_count"] == 18
+ 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_short_cache_and_pending_lifecycle_are_explicit():
+ ledger, rows, docs = records()
+ assert ledger["independent_approval"] is False
+ assert ledger["issues"] == [1685, 1686, 1687, 1688]
+ assert ledger["unresolved_research_issues"] == [1689, 1690]
+ assert ledger["unresolved_non_graph_issues"] == [1691]
+ assert len(ledger["cache_changes"]) == 1
+ cache = ledger["cache_changes"][0]
+ assert cache["quoted_words"] == 20
+ assert hashlib.sha256((ROOT / cache["path"]).read_bytes()).hexdigest() == cache["sha256"]
+ assert ledger["edison"]["provider_submissions"] == ledger["edison"]["credits_spent"] == 0
+ for row, doc in zip(rows, docs, strict=True):
+ assert row["curation_events_added"] == len(row["history_files"]) == 1
+ assert doc["curation_history"][-1]["llm_assisted"] is True
+ assert hashlib.sha256((ROOT / row["path"]).read_bytes()).hexdigest() == row["record_sha256"]
diff --git a/tests/test_participating_taxa.py b/tests/test_participating_taxa.py
index cf70bb2d0..b64783608 100644
--- a/tests/test_participating_taxa.py
+++ b/tests/test_participating_taxa.py
@@ -358,6 +358,7 @@ def test_a_curie_is_ambiguous_where_members_share_an_id(example):
"PPCP_Wastewater_Sphingopyxis_Ochrobactrum_Apiotrichum_SMC.yaml",
"PSY_Transgenic_Rice_Rhizosphere_Methane_Community.yaml",
"Parmigiano_NWS_Set2_LAB_Triculture.yaml",
+ "Pepper_Phytophthora_SynCom5.yaml",
"Pelotomaculum_Methanocella_Propionate_RNASeq_Coculture.yaml",
"Phaeodactylum_Aliivibrio_Diel_Coculture.yaml",
"Phenol_Carboxylation_Consortium.yaml",