diff --git a/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html b/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html
index b78192085..34b348024 100644
--- a/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html
+++ b/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html
@@ -598,7 +598,7 @@ Ecological Interactions
Cyanobacterial Organic-Carbon Provisioning
CROSS_FEEDING
- Under illuminated coculture conditions, XZ-Cy5 secreted organic carbon that supported Chelatococcus sp. XZ-Ab1 heterotrophic growth; 13CO2 NanoSIMS tracing directly detected transfer of cyanobacterium-derived carbon to the heterotroph.
+ Illuminated XZ-Cy5/XZ-Ab1 coculture supports organic-carbon provision from the cyanobacterium to the heterotroph. The abstract reports heterotrophic growth benefit and direct NanoSIMS detection of photoautotroph-derived carbon after 13CO2 labeling. Retain this experimentally supported cross-feeding without assigning an identified secreted molecule or extending the carbon tracer result to nitrogen or oxygen transfer.
Source Taxon: Thermoleptolyngbya sichuanensis XZ-Cy5
@@ -664,7 +664,7 @@ Evidence
Chelatococcus Arsenite Detoxification
MUTUALISM
- Chelatococcus sp. XZ-Ab1 used cyanobacterium-derived carbon and oxygen to oxidize toxic arsenite to less-toxic arsenate, relieving arsenite stress that otherwise damaged XZ-Cy5 chlorophyll content and photosynthetic activity.
+ Chelatococcus sp. XZ-Ab1 oxidizes arsenite to less-toxic arsenate and promotes XZ-Cy5 growth in coculture. Together with the reciprocal heterotrophic benefit from photosynthetic carbon, this supports mutualism under the tested arsenic-stress conditions. The cyanobacterial monoculture did not oxidize arsenite, whereas the heterotroph did so when supplied organic carbon and oxygen. PARTIAL for the exact oxygen-supply route in coculture: genomic interpretation and a supplemented pure-culture comparison are not direct tracing of cyanobacterial oxygen into arsenite oxidation. No nitrogen transfer or thermodynamic product-removal dependence is asserted.
Source Taxon: Chelatococcus sp. XZ-Ab1
@@ -695,6 +695,19 @@ Chelatococcus Arsenite Detoxification
Evidence
+
+
+
+ "Chelatococcus sp. XZ-Ab1 promoted growth of "T. sichuanensis" XZ-Cy5"
+
+
+
@@ -721,6 +734,19 @@
Evidence
+
+
+
+ "a pure culture of the mat-derived heterotroph Chelatococcus sp. XZ-Ab1 could oxidize As(Ⅲ) quickly with the addition of organic carbon and oxygen"
+
+
+
Evidence
- Knowledge gaps & discussions (1)
+ Knowledge gaps & discussions (2)
@@ -746,6 +772,41 @@
+
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which chemical and oxygen-supply routes account for the measured XZ-Cy5/XZ-Ab1 mutualism?
+
+
The primary abstract directly supports carbon transfer and reciprocal growth. It separately interprets metabolic complementarity from genomes, including nitrogen provision and oxygen production. These are not equivalent to isotope-resolved oxygen or nitrogen transfer. Full primary methods and route-specific evidence would resolve these details; missing detail does not negate the positive carbon and growth results. The earlier culture-conditions discussion remains open. No new node or arrow is introduced.
+
+
Attaches to: ecological_interactions#Cyanobacterial Organic-Carbon Provisioning, ecological_interactions#Chelatococcus Arsenite Detoxification
+
+
+
+
+ 1 evidence item(s)
+
+
+
+
Metagenomic and genomic analyses indicated several mechanisms for metabolic complementarity between the two strains
+
+
+
+
@@ -987,7 +1048,7 @@ Environmental Factors
processes.push("response to toxic substance");
- var evidenceCount = 2;
+ var evidenceCount = 4;
nodes.push({
id: intId,
diff --git a/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html b/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html
index 25a88fdd7..bfa5ebff6 100644
--- a/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html
+++ b/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html
@@ -852,7 +852,7 @@ Ecological Interactions
Ecological interaction network for Thermophilic Ex-Situ Biomethanation Mixed Culture
- Bipartite graph where circles represent taxa and non-circular symbols represent interactions, with distinct shapes and colours for cross-feeding, syntrophy.
+ Bipartite graph where circles represent taxa and non-circular symbols represent interactions. Rare or untyped interactions share the Other symbol; exact curated types remain in the interaction details.
@@ -860,13 +860,8 @@
Ecological Interactions
-
-
@@ -875,9 +870,8 @@ Ecological Interactions
-
The conditioned archaeal fraction used H2 and CO2 to produce CH4 under a 4:1 H2:CO2 gas feed at 50 C; the final phase favoured hydrogenotrophic Methanobacteria, with Methanosarcina contributing at lower abundance through hydrogenotrophic and acetoclastic metabolism.
+
A conditioned mixed culture converted externally supplied H2/CO2 to methane in a single proof-of-concept CSTR. Output methane content reached 86% by day 69 in the final thermophilic phase; exceeding 90% was proposed, not observed. Cylinder-fed gas conversion is not itself interspecies cross-feeding. Methanobacteria enrichment and contributions by Methanosarcina are source interpretations informed by group-specific qPCR and community profiles, not taxon-resolved flux measurements. The listed phylum, class and genus are overlapping taxonomic summaries rather than independent strain members. Sequential conditioning and washout changes do not independently isolate temperature as the cause of every performance difference.
@@ -939,7 +933,7 @@
Evidence
- SUPPORT (IN_VITRO)
"The high H₂: CO₂ throughput at 50"
+ "H₂ and CO₂ gases were supplied from pressurised gas cylinders"
@@ -952,7 +946,7 @@ Evidence
- SUPPORT (IN_VITRO)
- "favoured hydrogenotrophic Methanobacteria"
+ "CH₄ levels in the output gas steadily increased with each washout, reaching 86% by day 69"
@@ -962,10 +956,10 @@ Evidence
PMID:42293522
- - SUPPORT (IN_VITRO)
+ - PARTIAL (OTHER)
- "levels in the output gas steadily increased with each washout, reaching 86% by day 69"
+ "favoured hydrogenotrophic Methanobacteria"
@@ -975,10 +969,9 @@ Evidence
-
Thermophilic bacterial partners produced and transformed volatile fatty acids while archaeal acetoclastic methanogens consumed acetate for methane production; by day 69, VFA concentrations fell to approximately 3.5 g/L and were dominated by acetate.
+
The measured VFA pool fell from approximately 5 to 3.5 g/L during the final phase and ended with 73% acetate, 16% propionic acid and 10% n-butyric acid. These are pool measurements during washout-managed operation, not direct rates of metabolite exchange. PARTIAL: the authors interpret Firmicutes as VFA producers, Coprothermobacterota as acetate oxidizers and Methanosaeta/Methanothrix as acetoclastic methanogens, with Methanosarcina potentially using both substrates. Group abundance and gene copies do not demonstrate those exact taxa executing each route, metabolic activity per cell, or product-removal-dependent thermodynamic cooperation. Washout and substrate-pool changes remain alternatives to attributing every VFA decrease to consumption.
@@ -1064,7 +1057,7 @@
Evidence
PMID:42293522
- - SUPPORT (IN_VITRO)
+ - PARTIAL (OTHER)
"Overall, in the final phase, the system exhibited a balanced microbial community"
@@ -1077,7 +1070,7 @@ Evidence
PMID:42293522
- - SUPPORT (IN_VITRO)
+ - PARTIAL (OTHER)
"Coprothermobacterota converting acetate"
@@ -1090,13 +1083,26 @@ Evidence
PMID:42293522
- - SUPPORT (IN_VITRO)
+ - PARTIAL (OTHER)
"Methanosaeta converting acetate"
+
+
+
+ "VFA concentrations were measured immediately before washout, capturing peak accumulation prior to dilution or biomass replacement"
+
+
+
@@ -1107,7 +1113,7 @@ Evidence
- Knowledge gaps & discussions (2)
+ Knowledge gaps & discussions (3)
@@ -1179,6 +1185,41 @@
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which taxon-specific VFA and methane routes were active beyond the bulk chemistry and DNA profiles?
+
+
The study follows one reactor through sequential temperature, gas and washout changes. Methane production is measured, but its organism-specific allocation and interspecies fluxes are inferred. Direct sludge qPCR/16S can include DNA from killed or inactive cells; bacterial plate recovery is a separate culturable fraction. The original taxonomy-resolution and industrial-stability discussions remain open. No new causal link between the two process nodes is introduced.
+
+
Attaches to: ecological_interactions#Thermophilic H2/CO2 Biomethanation, ecological_interactions#VFA dynamics and inferred interspecies turnover
+
+
+
+
+ 1 evidence item(s)
+
+
+
+
These approaches reflect the total microbial DNA pool
+
+
+
+
+
@@ -1632,7 +1673,7 @@ Evidence
(function() {
var intId = "interaction:0";
- var intType = "CROSS_FEEDING";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1683,7 +1724,7 @@ Evidence
(function() {
var intId = "interaction:1";
- var intType = "SYNTROPHY";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1706,11 +1747,11 @@ Evidence
processes.push("methanogenesis");
- var evidenceCount = 4;
+ var evidenceCount = 5;
nodes.push({
id: intId,
- label: "VFA Syntrophic Turnover",
+ label: "VFA dynamics and inferred interspecies turnover",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
diff --git a/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html b/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html
index b852718ba..572e59292 100644
--- a/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html
+++ b/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html
@@ -684,7 +684,7 @@ Ecological Interactions
Ecological interaction network for Thermophilic Lignocellulose-degrading Composting SynCom
- Bipartite graph where circles represent taxa and non-circular symbols represent interactions, with distinct shapes and colours for mutualism, competition.
+ Bipartite graph where circles represent taxa and non-circular symbols represent interactions. Rare or untyped interactions share the Other symbol; exact curated types remain in the interaction details.
@@ -692,13 +692,8 @@
Ecological Interactions
-
-
@@ -706,10 +701,9 @@ Ecological Interactions
-
The five-member SynCom intensifies thermophilic fermentation, rapidly lowers the carbon/nitrogen ratio, and enhances humification in the manure-composting matrix.
+
The five-member inoculum is reported to intensify thermophilic fermentation, lower the compost carbon/nitrogen ratio and increase humification. These are community-treatment and substrate outcomes, not evidence that all five inoculated members obtain reciprocal fitness benefits. The accessible abstract relates maturation to resistance-gene attenuation using Mantel correlation; it does not resolve individual-strain contributions or a uniquely demonstrated causal mediator.
@@ -735,13 +729,8 @@
SynCom-driven lignocellulose decomposition and humification
Downstream Effects:
-
→ Community-level bio-sanitization of high-risk pathogens
-
Intensified thermophilic fermentation and faster organic-matter turnover create the SynCom-driven composting trajectory linked to deep bio-sanitization and high-risk pathogen elimination.
-
-
-
-
→ SynCom-driven suppression of horizontal gene transfer
-
The SynCom-driven composting trajectory is tied to metabolic reprogramming away from a biofilm-dependent defense-survival mode, restricting horizontal gene transfer opportunities in the compost.
+
→ Reported compost resistome and pathogen attenuation
+
PARTIAL: intensified fermentation and the correlated C/N decrease and humification are proposed environmental contributors to later ARG and pathogen attenuation. Mantel association and the common inoculation treatment support this interpretation, not selective demonstration that maturation alone mediates elimination or prevents every gene-transfer event.
Evidence
PMID:41839407
- - SUPPORT (IN_VIVO)
+ - SUPPORT (OTHER)
"SynCom-driven rapid decrease in carbon/nitrogen ratio and enhanced humification"
+
+
+
+ "Mantel correlation analysis revealed"
+
+
+
-
By intensifying thermophilic fermentation and driving down the carbon/nitrogen ratio, the SynCom collapses high-risk ARG-mobilome interactomes and eliminates high-risk pathogens including Pseudomonas aeruginosa, an emergent community-level function rather than a single pairwise edge.
+
The abstract reports a transient ARG rebound after SynCom inoculation followed by attenuation, reduced multidrug-resistance genes and virulence factors, and elimination of source-identified high-risk pathogens. Preserve this reported bio-sanitization result without equating metagenomic or network signals with demonstrated loss of every viable pathogen, universal fertilizer biosafety, or bilateral negative fitness effects. The accessible abstract does not resolve the viability-detection limits or provide a direct causal competition assay.
@@ -782,17 +783,6 @@
Community-level bio-sanitization of high-risk pathogens
-
Biological Processes:
-
-
-
- biological process involved in interspecies interaction between organisms
- (GO:0044419 )
-
-
-
-
@@ -806,23 +796,35 @@
Evidence
PMID:41839407
- - SUPPORT (IN_VIVO)
+ - SUPPORT (OTHER)
"deep bio-sanitization was achieved by synchronously eliminating high-risk pathogens (e.g., Pseudomonas aeruginosa), phytopathogens, and specific virulence factors"
+
+
+
+ "Metagenomic analysis showed SynCom inoculation caused a transient ARG rebound followed by profound attenuation"
+
+
+
-
SynCom inoculation reprograms community metabolism from a biofilm-dependent defense-survival model to an active motility-metabolism mode (depleted lipopolysaccharide biosynthesis, enriched flagellar assembly), a fitness-cost trade-off that physically restricts horizontal gene transfer and suppresses key recombinases (XerD, IntI1).
+
KEGG and metagenomic analyses suggest a shift in functional potential from biofilm-associated defense toward motility/metabolism, with lower lipopolysaccharide biosynthesis and higher flagellar-assembly representation. The reported network change includes 26.6% fewer potential host-gene associations. PARTIAL: reduced HGT opportunity, recombinase suppression and physical restriction of transfer are source interpretations, not measurements of conjugation frequency, gene expression, actual cell motility or proven necessity of a particular route. Potential host-gene associations are not a count of observed horizontal-transfer events.
@@ -855,13 +857,39 @@
Evidence
PMID:41839407
- - SUPPORT (IN_VIVO)
+ - SUPPORT (COMPUTATIONAL)
"a pivotal metabolic reprogramming from a biofilm-dependent defense-survival model to an active motility-metabolism mode, characterized by depleted lipopolysaccharide biosynthesis and enriched flagellar assembly"
+
+
+
+ "reducing potential host-gene associations by 26.6%"
+
+
+
+
+
+
+ "This metabolic shift implies a fitness cost trade-off that physically restricts horizontal gene transfer (HGT) opportunities"
+
+
+
@@ -871,6 +899,45 @@ Evidence
+
+ Knowledge gaps & discussions (1)
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which inferred compost mechanisms explain attenuation beyond metagenomic and correlation-based evidence?
+
+
The abstract describes treatment-associated chemistry, a transient ARG rebound, later attenuation, KEGG interpretation and potential host-gene networks. It does not resolve causal necessity or viable-pathogen detection limits. Full methods and direct functional evidence are needed to distinguish the proposed HGT restriction and environmental mediation from parallel responses to inoculation. This uncertainty does not erase the reported positive bio-sanitization outcome.
+
+
Attaches to: ecological_interactions#SynCom-associated compost maturation, ecological_interactions#Reported compost resistome and pathogen attenuation, ecological_interactions#Metagenomic signatures of reduced HGT potential
+
+
+
+
+ 1 evidence item(s)
+
+
+
+
This metabolic shift implies a fitness cost trade-off that physically restricts horizontal gene transfer (HGT) opportunities
+
+
+
+
+
@@ -1067,7 +1134,7 @@ Evidence
(function() {
var intId = "interaction:0";
- var intType = "MUTUALISM";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
@@ -1076,11 +1143,11 @@ Evidence
processes.push("cellulose catabolic process");
- var evidenceCount = 1;
+ var evidenceCount = 2;
nodes.push({
id: intId,
- label: "SynCom-driven lignocellulose decomposition and humification",
+ label: "SynCom-associated compost maturation",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1095,20 +1162,16 @@ Evidence
(function() {
var intId = "interaction:1";
- var intType = "COMPETITION";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
-
- processes.push("biological process involved in interspecies interaction between organisms");
-
-
- var evidenceCount = 1;
+ var evidenceCount = 2;
nodes.push({
id: intId,
- label: "Community-level bio-sanitization of high-risk pathogens",
+ label: "Reported compost resistome and pathogen attenuation",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1123,7 +1186,7 @@ Evidence
(function() {
var intId = "interaction:2";
- var intType = "COMPETITION";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
@@ -1132,11 +1195,11 @@ Evidence
processes.push("horizontal gene transfer");
- var evidenceCount = 1;
+ var evidenceCount = 3;
nodes.push({
id: intId,
- label: "SynCom-driven suppression of horizontal gene transfer",
+ label: "Metagenomic signatures of reduced HGT potential",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
diff --git a/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html b/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html
index 229e55aba..b67945135 100644
--- a/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html
+++ b/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html
@@ -558,7 +558,7 @@ Ecological Interactions
Ecological interaction network for Tobacco Chemotactic Biocontrol SynCom
- Bipartite graph where circles represent taxa and non-circular symbols represent interactions, with distinct shapes and colours for colonization facilitation.
+ Bipartite graph where circles represent taxa and non-circular symbols represent interactions. Rare or untyped interactions share the Other symbol; exact curated types remain in the interaction details.
@@ -566,8 +566,8 @@
Ecological Interactions
@@ -575,10 +575,9 @@ Ecological Interactions
-
Root-exudate-derived vitamin C, propionic acid, and esculetin stimulate growth of the chemotactic SynCom strains and increase the antagonistic activity of their fermentation broth against Ralstonia solanacearum.
+
Added resource compounds produced strain-specific growth and cell-free broth responses. Vitamin C increased Y364 broth antagonism; selected compounds including propionic acid and esculetin increased Y832 broth antagonism. No tested compound significantly enhanced Y878 broth inhibition relative to its mock treatment. Growth screening and broth inhibition are distinct assays, and the selected compounds did not show uniform benefit across every isolate. The resource library drew on compounds commonly found in tomato root exudates; these assays do not demonstrate that all were secreted by tobacco roots in the field.
@@ -609,8 +608,8 @@
Root-Exudate Prebiotic Enhancement
Downstream Effects:
-
→ Chemotactic Bacterial Wilt Suppression
-
Prebiotic-stimulated SynCom growth and antagonistic bioactivity strengthen the chemotactic consortium's suppression of Ralstonia.
+
→ Antagonism by cheA-positive SynCom isolates
+
Selected compound additions enhanced broth antagonism in particular isolate assays. PARTIAL for growth as the mediator: growth, broth chemistry and residual additives were not selectively separated. The Y878 null enhancement result prevents generalizing this effect to all three members, and the comparison does not establish enhanced chemotaxis or root colonization.
Evidence
-
-
-
-
-
-
-
Chemotactic SynCom members colonize the rhizosphere and suppress Ralstonia invasion.
-
+
+
+ "for Y878, none of the tested compounds showed a significant difference compared with the mock treatment"
+
-
Metabolites:
+
- L-ascorbic acid
- (CHEBI:29073 ),
+
CHEBI:30768 ),
+
+
+
The selected Y364, Y832 and Y878 isolates showed antagonism against Ralstonia solanacearum, mutual compatibility and PCR detection of cheA. The source identifies two Pseudomonas strains and one Bacillus strain; the canonical two-row taxonomy remains a broad, incomplete representation. cheA detection supports chemotaxis potential, not directly measured root migration or colonization. Strong antagonism was also observed among cheA-negative screened isolates. Compatibility and pathogen inhibition do not establish within-SynCom cross-feeding or facilitation of another member's establishment.
- esculetin
- (
CHEBI:490095 )
-
-
Biological Processes:
-
@@ -685,7 +669,7 @@
Chemotactic Bacterial Wilt Suppression
→ Tobacco Field Protection and Yield Enhancement
-
Rhizosphere colonization and antagonism by the chemotactic SynCom carry through the bioorganic fertilizer into lower field Ralstonia invasion and higher tobacco yield.
+
PARTIAL: laboratory antagonism is a candidate contribution to the field benefit of the formulated SynCom fertilizer. The field contrast combined strains, prebiotics and an organic matrix against conventional cow-manure fertilization; it did not isolate chemotaxis, colonization or broth antagonism as the mediator. The authors explicitly identify non-chemotactic SynCom controls as future work.
Evidence
- SUPPORT (IN_VITRO)
- "we constructed a chemotactic SynCom comprising two Pseudomonas strains and one Bacillus strain."
+ "exhibited strong antagonism against R. solanacearum, harbored the chemotaxis gene cheA, and showed mutual compatibility"
@@ -717,7 +701,7 @@ Evidence
- SUPPORT (IN_VITRO)
- "vitamin C, propionic acid, and esculetin significantly promoted the growth and antagonistic ability of chemotactic SynCom strains"
+ "another half of isolated strains, which lacked cheA gene, still displayed strong antagonistic activity"
@@ -728,9 +712,8 @@ Evidence
-
Bioorganic fertilizer carrying the chemotactic SynCom protects diseased tobacco fields from Ralstonia solanacearum invasion and increases crop yield under field conditions.
+
In the reported tobacco field trial, the SynCom-containing bioorganic fertilizer plus prebiotics was associated with a lower disease index, lower Ralstonia qPCR abundance and nearly doubled crop yield relative to conventional fertilization. This is a positive combined-treatment result, not an independently isolated effect of chemotaxis or microbial colonization facilitation. qPCR abundance is not a direct viable-cell count, and Tax4Fun predictions of indigenous-community functions do not establish active pathways or strain-resolved establishment of the inoculum.
@@ -739,17 +722,6 @@
Tobacco Field Protection and Yield Enhancement
-
Biological Processes:
-
-
@@ -770,6 +742,19 @@
Evidence
+
+
+
+ "the chemotactic SynCom fertilizer nearly doubled crop yield"
+
+
+
Evidence
+
+ Knowledge gaps & discussions (1)
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ How much of the tobacco field benefit specifically depends on chemotaxis or the tested broth effects?
+
+
The field comparison combines the inoculum, prebiotics and fertilizer matrix. It does not isolate chemotaxis, and the authors explicitly identify non-chemotactic controls as future work. cheA PCR and Tax4Fun inference should not stand in for measured root migration, strain persistence or active metabolic pathways. The paper also differs between Results and Discussion on resource counts and has tomato wording in some captions despite a tobacco trial; those details are not silently reconciled or used to erase the positive field outcome.
+
+
Attaches to: ecological_interactions#Strain-specific prebiotic enhancement, ecological_interactions#Antagonism by cheA-positive SynCom isolates, ecological_interactions#Tobacco Field Protection and Yield Enhancement
+
+
+
+
+ 1 evidence item(s)
+
+
+
+
future studies should include non-chemotactic SynCom as experimental controls
+
+
+
+
+
@@ -972,7 +996,7 @@ Evidence
(function() {
var intId = "interaction:0";
- var intType = "COLONIZATION_FACILITATION";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -985,11 +1009,11 @@ Evidence
var processes = [];
- var evidenceCount = 1;
+ var evidenceCount = 2;
nodes.push({
id: intId,
- label: "Root-Exudate Prebiotic Enhancement",
+ label: "Strain-specific prebiotic enhancement",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1004,28 +1028,16 @@ Evidence
(function() {
var intId = "interaction:1";
- var intType = "COLONIZATION_FACILITATION";
+ var intType = "UNKNOWN";
var metabolites = [];
-
- metabolites.push("L-ascorbic acid");
-
- metabolites.push("propionic acid");
-
- metabolites.push("esculetin");
-
-
var processes = [];
-
- processes.push("chemotaxis");
-
-
var evidenceCount = 2;
nodes.push({
id: intId,
- label: "Chemotactic Bacterial Wilt Suppression",
+ label: "Antagonism by cheA-positive SynCom isolates",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1040,16 +1052,12 @@ Evidence
(function() {
var intId = "interaction:2";
- var intType = "COLONIZATION_FACILITATION";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
-
- processes.push("chemotaxis");
-
-
- var evidenceCount = 1;
+ var evidenceCount = 2;
nodes.push({
id: intId,
diff --git a/history/records/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture/2026-10-08T141541Z-codex-62412f.yaml b/history/records/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture/2026-10-08T141541Z-codex-62412f.yaml
new file mode 100644
index 000000000..39e596669
--- /dev/null
+++ b/history/records/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture/2026-10-08T141541Z-codex-62412f.yaml
@@ -0,0 +1,26 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml
+ slug: Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture
+session:
+ id: 2026-10-08T141541Z-codex-62412f
+ timestamp: '2026-10-08T14:15:41Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1931
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain experimentally supported carbon cross-feeding and tracer direction without
+ inventing a compound or nitrogen flux.; Retain reciprocal-growth mutualism with direct
+ growth evidence, bounding supplemented-culture comparisons and genomic route inference.
+ details: Source-based self-adversarial graph review; reports/causal_graph_review/decisions/20261008-four-records-batch120.yaml
diff --git a/history/records/Thermophilic_ExSitu_Biomethanation_Mixed_Culture/2026-10-08T141542Z-codex-8205c5.yaml b/history/records/Thermophilic_ExSitu_Biomethanation_Mixed_Culture/2026-10-08T141542Z-codex-8205c5.yaml
new file mode 100644
index 000000000..8892d8f44
--- /dev/null
+++ b/history/records/Thermophilic_ExSitu_Biomethanation_Mixed_Culture/2026-10-08T141542Z-codex-8205c5.yaml
@@ -0,0 +1,26 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml
+ slug: Thermophilic_ExSitu_Biomethanation_Mixed_Culture
+session:
+ id: 2026-10-08T141542Z-codex-8205c5
+ timestamp: '2026-10-08T14:15:42Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1932
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain measured external-gas methane production without coding abiotic supply as
+ microbial cross-feeding or qPCR as activity.; Retain VFA measurements and source interpretations
+ while removing an unsupported demonstrated-syntrophy type.
+ details: Source-based self-adversarial graph review; reports/causal_graph_review/decisions/20261008-four-records-batch120.yaml
diff --git a/history/records/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization/2026-10-08T141542Z-codex-0c3005.yaml b/history/records/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization/2026-10-08T141542Z-codex-0c3005.yaml
new file mode 100644
index 000000000..643fc2416
--- /dev/null
+++ b/history/records/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization/2026-10-08T141542Z-codex-0c3005.yaml
@@ -0,0 +1,28 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml
+ slug: Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization
+session:
+ id: 2026-10-08T141542Z-codex-0c3005
+ timestamp: '2026-10-08T14:15:42Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1933
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain reported maturation without coding aggregate improvement as mutualism; bound
+ the remaining environmental-mediation arrow.; Retain positive later attenuation and the
+ early rebound without claiming universal viable-pathogen elimination or bilateral competition.;
+ Represent KEGG and network findings as HGT potential, not measured transfer, expression
+ or motility.
+ details: Source-based self-adversarial graph review; reports/causal_graph_review/decisions/20261008-four-records-batch120.yaml
diff --git a/history/records/Tobacco_Chemotactic_Biocontrol_SynCom/2026-10-08T141542Z-codex-fb2ec0.yaml b/history/records/Tobacco_Chemotactic_Biocontrol_SynCom/2026-10-08T141542Z-codex-fb2ec0.yaml
new file mode 100644
index 000000000..50a7fc881
--- /dev/null
+++ b/history/records/Tobacco_Chemotactic_Biocontrol_SynCom/2026-10-08T141542Z-codex-fb2ec0.yaml
@@ -0,0 +1,27 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Tobacco_Chemotactic_Biocontrol_SynCom.yaml
+ slug: Tobacco_Chemotactic_Biocontrol_SynCom
+session:
+ id: 2026-10-08T141542Z-codex-fb2ec0
+ timestamp: '2026-10-08T14:15:42Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1934
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain positive compound responses with isolate-specific limits and the Y878 null
+ result.; Keep antagonism and compatibility distinct from cheA-based potential and unmeasured
+ colonization.; Preserve the positive field co-treatment outcome while bounding qPCR, Tax4Fun
+ and mechanistic attribution.
+ details: Source-based self-adversarial graph review; reports/causal_graph_review/decisions/20261008-four-records-batch120.yaml
diff --git a/kb/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml b/kb/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml
index effa90d5a..279d9737e 100644
--- a/kb/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml
+++ b/kb/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml
@@ -86,16 +86,22 @@ taxonomy:
explanation: Identifies Chelatococcus sp. XZ-Ab1 as the heterotrophic arsenite-oxidizing partner in the coculture.
ecological_interactions:
- name: Cyanobacterial Organic-Carbon Provisioning
- description: Under illuminated coculture conditions, XZ-Cy5 secreted organic carbon that supported Chelatococcus sp. XZ-Ab1
- heterotrophic growth; 13CO2 NanoSIMS tracing directly detected transfer of cyanobacterium-derived carbon to the heterotroph.
+ description: Illuminated XZ-Cy5/XZ-Ab1 coculture supports organic-carbon provision from the cyanobacterium to
+ the heterotroph. The abstract reports heterotrophic growth benefit and direct NanoSIMS detection of photoautotroph-derived
+ carbon after 13CO2 labeling. Retain this experimentally supported cross-feeding without assigning an identified
+ secreted molecule or extending the carbon tracer result to nitrogen or oxygen transfer.
interaction_type: CROSS_FEEDING
scope: PAIRWISE
- source_taxon: &id004
+ source_taxon:
preferred_term: Thermoleptolyngbya sichuanensis XZ-Cy5
- term: *id001
- target_taxon: &id003
+ term:
+ id: NCBITaxon:3031812
+ label: Thermoleptolyngbya sichuanensis XZ-Cy5
+ target_taxon:
preferred_term: Chelatococcus sp. XZ-Ab1
- term: *id002
+ term:
+ id: NCBITaxon:3034027
+ label: Chelatococcus sp. XZ-Ab1
biological_processes:
- preferred_term: photosynthesis
term:
@@ -105,26 +111,46 @@ ecological_interactions:
- reference: PMID:42468699
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: '"T. sichuanensis" XZ-Cy5 secreted organic carbon to facilitate heterotrophic growth of Chelatococcus sp. XZ-Ab1'
+ snippet: '"T. sichuanensis" XZ-Cy5 secreted organic carbon to facilitate heterotrophic growth of Chelatococcus
+ sp. XZ-Ab1'
explanation: Supports the direction of organic-carbon cross-feeding from the cyanobacterium to Chelatococcus.
- reference: PMID:42468699
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: direct evidence of photoautotroph-derived carbon from "T. sichuanensis" XZ-Cy5 to Chelatococcus sp. XZ-Ab1
- explanation: Supports isotope-tracing evidence for cyanobacterium-derived carbon reaching the heterotrophic partner.
+ snippet: direct evidence of photoautotroph-derived carbon from "T. sichuanensis" XZ-Cy5 to Chelatococcus sp.
+ XZ-Ab1
+ explanation: Supports isotope-tracing evidence for cyanobacterium-derived carbon reaching the heterotrophic
+ partner.
- name: Chelatococcus Arsenite Detoxification
- description: Chelatococcus sp. XZ-Ab1 used cyanobacterium-derived carbon and oxygen to oxidize toxic arsenite to less-toxic
- arsenate, relieving arsenite stress that otherwise damaged XZ-Cy5 chlorophyll content and photosynthetic activity.
+ description: 'Chelatococcus sp. XZ-Ab1 oxidizes arsenite to less-toxic arsenate and promotes XZ-Cy5 growth in
+ coculture. Together with the reciprocal heterotrophic benefit from photosynthetic carbon, this supports mutualism
+ under the tested arsenic-stress conditions. The cyanobacterial monoculture did not oxidize arsenite, whereas
+ the heterotroph did so when supplied organic carbon and oxygen. PARTIAL for the exact oxygen-supply route in
+ coculture: genomic interpretation and a supplemented pure-culture comparison are not direct tracing of cyanobacterial
+ oxygen into arsenite oxidation. No nitrogen transfer or thermodynamic product-removal dependence is asserted.'
interaction_type: MUTUALISM
scope: PAIRWISE
- source_taxon: *id003
- target_taxon: *id004
+ source_taxon:
+ preferred_term: Chelatococcus sp. XZ-Ab1
+ term:
+ id: NCBITaxon:3034027
+ label: Chelatococcus sp. XZ-Ab1
+ target_taxon:
+ preferred_term: Thermoleptolyngbya sichuanensis XZ-Cy5
+ term:
+ id: NCBITaxon:3031812
+ label: Thermoleptolyngbya sichuanensis XZ-Cy5
biological_processes:
- preferred_term: response to toxic substance
term:
id: GO:0009636
label: response to toxic substance
evidence:
+ - reference: PMID:42468699
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: Chelatococcus sp. XZ-Ab1 promoted growth of "T. sichuanensis" XZ-Cy5
+ explanation: Directly cites the reported reciprocal cyanobacterial growth benefit, not only monoculture toxicity.
- reference: PMID:42468699
supports: SUPPORT
evidence_source: IN_VITRO
@@ -135,6 +161,13 @@ ecological_interactions:
evidence_source: IN_VITRO
snippet: exposure of a growing culture to 5 mM As(Ⅲ) led to rapid loss of chlorophyll and photosynthetic activity
explanation: Supports arsenite as a toxic stressor for pure XZ-Cy5 cultures.
+ - reference: PMID:42468699
+ supports: PARTIAL
+ evidence_source: IN_VITRO
+ snippet: a pure culture of the mat-derived heterotroph Chelatococcus sp. XZ-Ab1 could oxidize As(Ⅲ) quickly
+ with the addition of organic carbon and oxygen
+ explanation: Supports oxidation in supplemented heterotroph culture, not a demonstrated oxygen-source requirement
+ in coculture.
environmental_factors:
- name: High-arsenic Tibetan hot-spring mat source
value: Tibet high-As hot spring
@@ -161,19 +194,37 @@ external_resources:
explanation: Supports the DOI for the primary Thermoleptolyngbya-Chelatococcus coculture publication.
discussions:
- discussion_id: thermoleptolyngbya_chelatococcus_exact_culture_conditions
- prompt: Which medium, temperature, light regime, arsenite concentration series, inoculum densities, and time points were
- used for the XZ-Cy5/XZ-Ab1 coculture?
+ prompt: Which medium, temperature, light regime, arsenite concentration series, inoculum densities, and time points
+ were used for the XZ-Cy5/XZ-Ab1 coculture?
kind: KNOWLEDGE_GAP
status: OPEN
attaches_to:
- engineering_design
- ecological_interactions#Cyanobacterial Organic-Carbon Provisioning
- ecological_interactions#Chelatococcus Arsenite Detoxification
- rationale: The PubMed abstract names the exact strains, arsenite-detoxifying mutualism, organic-carbon transfer, oxygen
- production, NanoSIMS tracing, and pure-culture comparisons, but Europe PMC did not expose open-access full text with the
- coculture recipe or condition series.
+ rationale: The PubMed abstract names the exact strains, arsenite-detoxifying mutualism, organic-carbon transfer,
+ oxygen production, NanoSIMS tracing, and pure-culture comparisons, but Europe PMC did not expose open-access
+ full text with the coculture recipe or condition series.
posed_by: codex
posed_date: '2026-09-27'
+- discussion_id: arsenic_causal_scope_batch120
+ prompt: Which chemical and oxygen-supply routes account for the measured XZ-Cy5/XZ-Ab1 mutualism?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Cyanobacterial Organic-Carbon Provisioning
+ - ecological_interactions#Chelatococcus Arsenite Detoxification
+ rationale: The primary abstract directly supports carbon transfer and reciprocal growth. It separately interprets
+ metabolic complementarity from genomes, including nitrogen provision and oxygen production. These are not equivalent
+ to isotope-resolved oxygen or nitrogen transfer. Full primary methods and route-specific evidence would resolve
+ these details; missing detail does not negate the positive carbon and growth results. The earlier culture-conditions
+ discussion remains open. No new node or arrow is introduced.
+ evidence:
+ - reference: PMID:42468699
+ snippet: Metagenomic and genomic analyses indicated several mechanisms for metabolic complementarity between
+ the two strains
+ posed_by: codex
+ posed_date: '2026-10-08'
metals_present: []
rare_earth_elements_present: []
metal_relevance: PRIMARY
@@ -186,3 +237,10 @@ curation_history:
changes: Created CommunityMech:000454 from PMID:42468699 and DOI 10.1016/j.biortech.2026.135440 for the Thermoleptolyngbya
sichuanensis XZ-Cy5 and Chelatococcus sp. XZ-Ab1 arsenic-detoxification coculture.
llm_assisted: true
+- timestamp: '2026-10-08T14:15:39Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Retain experimentally supported carbon cross-feeding and tracer direction without inventing a compound
+ or nitrogen flux.; Retain reciprocal-growth mutualism with direct growth evidence, bounding supplemented-culture
+ comparisons and genomic route inference. Issue#1931; reports/causal_graph_review/decisions/20261008-four-records-batch120.yaml
+ llm_assisted: true
diff --git a/kb/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml b/kb/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml
index f6059419a..dd702729f 100644
--- a/kb/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml
+++ b/kb/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml
@@ -223,10 +223,13 @@ taxonomy:
explanation: Supports the acetoclastic role assigned to the Methanosaeta target.
ecological_interactions:
- name: Thermophilic H2/CO2 Biomethanation
- description: The conditioned archaeal fraction used H2 and CO2 to produce CH4 under a 4:1 H2:CO2 gas feed at 50 C; the final
- phase favoured hydrogenotrophic Methanobacteria, with Methanosarcina contributing at lower abundance through hydrogenotrophic
- and acetoclastic metabolism.
- interaction_type: CROSS_FEEDING
+ description: A conditioned mixed culture converted externally supplied H2/CO2 to methane in a single proof-of-concept
+ CSTR. Output methane content reached 86% by day 69 in the final thermophilic phase; exceeding 90% was proposed,
+ not observed. Cylinder-fed gas conversion is not itself interspecies cross-feeding. Methanobacteria enrichment
+ and contributions by Methanosarcina are source interpretations informed by group-specific qPCR and community
+ profiles, not taxon-resolved flux measurements. The listed phylum, class and genus are overlapping taxonomic
+ summaries rather than independent strain members. Sequential conditioning and washout changes do not independently
+ isolate temperature as the cause of every performance difference.
scope: COMMUNITY_LEVEL
participating_taxa:
- preferred_term: Euryarchaeota
@@ -263,23 +266,26 @@ ecological_interactions:
- reference: PMID:42293522
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: 'The high H₂: CO₂ throughput at 50'
- explanation: Supports high-throughput H2/CO2 feeding as the operational context for methanogen selection.
+ snippet: H₂ and CO₂ gases were supplied from pressurised gas cylinders
+ explanation: Identifies the external source of methanogenic substrates.
- reference: PMID:42293522
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: favoured hydrogenotrophic Methanobacteria
- explanation: Supports hydrogenotrophic methanogenesis by Methanobacteria in the final phase.
+ snippet: CH₄ levels in the output gas steadily increased with each washout, reaching 86% by day 69
+ explanation: Preserves the measured final gas-composition outcome, not a prediction above90%.
- reference: PMID:42293522
- supports: SUPPORT
- evidence_source: IN_VITRO
- snippet: levels in the output gas steadily increased with each washout, reaching 86% by day 69
- explanation: Reports the final methane-content outcome under the conditioned final-phase regime.
-- name: VFA Syntrophic Turnover
- description: Thermophilic bacterial partners produced and transformed volatile fatty acids while archaeal acetoclastic methanogens
- consumed acetate for methane production; by day 69, VFA concentrations fell to approximately 3.5 g/L and were dominated
- by acetate.
- interaction_type: SYNTROPHY
+ supports: PARTIAL
+ evidence_source: OTHER
+ snippet: favoured hydrogenotrophic Methanobacteria
+ explanation: The source interprets enrichment from group-level measurements; not organism-specific gas tracing.
+- name: VFA dynamics and inferred interspecies turnover
+ description: 'The measured VFA pool fell from approximately 5 to 3.5 g/L during the final phase and ended with
+ 73% acetate, 16% propionic acid and 10% n-butyric acid. These are pool measurements during washout-managed operation,
+ not direct rates of metabolite exchange. PARTIAL: the authors interpret Firmicutes as VFA producers, Coprothermobacterota
+ as acetate oxidizers and Methanosaeta/Methanothrix as acetoclastic methanogens, with Methanosarcina potentially
+ using both substrates. Group abundance and gene copies do not demonstrate those exact taxa executing each route,
+ metabolic activity per cell, or product-removal-dependent thermodynamic cooperation. Washout and substrate-pool
+ changes remain alternatives to attributing every VFA decrease to consumption.'
scope: COMMUNITY_LEVEL
participating_taxa:
- preferred_term: Firmicutes
@@ -333,22 +339,33 @@ ecological_interactions:
supports: SUPPORT
evidence_source: IN_VITRO
snippet: At this point, the VFAs comprised 73% acetate, 16% propionic acid, and 10% n-butyric acid
- explanation: Reports the final VFA pool available to syntrophic acetate turnover and acetoclastic methanogenesis.
+ explanation: Measured final VFA composition; it does not by itself identify producers, consumers or exchange
+ rates.
- reference: PMID:42293522
- supports: SUPPORT
- evidence_source: IN_VITRO
+ supports: PARTIAL
+ evidence_source: OTHER
snippet: Overall, in the final phase, the system exhibited a balanced microbial community
- explanation: Supports the final-phase syntrophic interpretation linking Firmicutes, Coprothermobacterota, and Methanosaeta.
+ explanation: Author interpretation integrating community profiles and bulk chemistry; not directly measured
+ taxon-specific transfer or thermodynamic dependence.
- reference: PMID:42293522
- supports: SUPPORT
- evidence_source: IN_VITRO
+ supports: PARTIAL
+ evidence_source: OTHER
snippet: Coprothermobacterota converting acetate
- explanation: Supports the acetate-oxidizing role assigned to Coprothermobacterota.
+ explanation: Author interpretation integrating community profiles and bulk chemistry; not directly measured
+ taxon-specific transfer or thermodynamic dependence.
+ - reference: PMID:42293522
+ supports: PARTIAL
+ evidence_source: OTHER
+ snippet: Methanosaeta converting acetate
+ explanation: Author interpretation integrating community profiles and bulk chemistry; not directly measured
+ taxon-specific transfer or thermodynamic dependence.
- reference: PMID:42293522
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: Methanosaeta converting acetate
- explanation: Supports acetoclastic methane production by the Methanosaeta qPCR target.
+ snippet: VFA concentrations were measured immediately before washout, capturing peak accumulation prior to dilution
+ or biomass replacement
+ explanation: The phase-1 paragraph defines this sampling context; it does not establish phase-4 sampling timing
+ or convert pool concentrations into flux.
environmental_factors:
- name: Thermophilic operating temperature
value: '50'
@@ -484,9 +501,9 @@ external_resources:
explanation: Identifies the primary publication used to curate this record.
discussions:
- discussion_id: taxonomy_resolution
- prompt: The final reactor community is resolved primarily at phylum level by 16S rRNA sequencing and by group-specific qPCR.
- Species- or MAG-level assignments for the dominant Euryarchaeota, Firmicutes, and Coprothermobacterota partners remain
- unresolved.
+ prompt: The final reactor community is resolved primarily at phylum level by 16S rRNA sequencing and by group-specific
+ qPCR. Species- or MAG-level assignments for the dominant Euryarchaeota, Firmicutes, and Coprothermobacterota
+ partners remain unresolved.
kind: KNOWLEDGE_GAP
status: OPEN
attaches_to:
@@ -509,8 +526,9 @@ discussions:
attaches_to:
- engineering_design
- cultivation_setup
- rationale: A non-sterile continuous-feeding trial would test whether the selected thermophilic consortium remains stable
- under industrially realistic operation rather than washout-managed autoclaved-sludge proof-of-concept conditions.
+ rationale: A non-sterile continuous-feeding trial would test whether the selected thermophilic consortium remains
+ stable under industrially realistic operation rather than washout-managed autoclaved-sludge proof-of-concept
+ conditions.
evidence:
- reference: PMID:42293522
supports: SUPPORT
@@ -519,10 +537,34 @@ discussions:
explanation: Names the industrial robustness gap stated by the authors.
posed_by: codex
posed_date: '2026-09-21'
+- discussion_id: biomethane_causal_scope_batch120
+ prompt: Which taxon-specific VFA and methane routes were active beyond the bulk chemistry and DNA profiles?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Thermophilic H2/CO2 Biomethanation
+ - ecological_interactions#VFA dynamics and inferred interspecies turnover
+ rationale: The study follows one reactor through sequential temperature, gas and washout changes. Methane production
+ is measured, but its organism-specific allocation and interspecies fluxes are inferred. Direct sludge qPCR/16S
+ can include DNA from killed or inactive cells; bacterial plate recovery is a separate culturable fraction. The
+ original taxonomy-resolution and industrial-stability discussions remain open. No new causal link between the
+ two process nodes is introduced.
+ evidence:
+ - reference: PMID:42293522
+ snippet: These approaches reflect the total microbial DNA pool
+ posed_by: codex
+ posed_date: '2026-10-08'
curation_history:
- timestamp: '2026-09-22T04:09:10Z'
curator: codex
action: CREATE_RECORD
- changes: Created CommunityMech:000416 for PMID:42293522, a thermophilic ex-situ biomethanation CSTR mixed culture enriched
- from autoclaved anaerobic digestate sludge.
+ changes: Created CommunityMech:000416 for PMID:42293522, a thermophilic ex-situ biomethanation CSTR mixed culture
+ enriched from autoclaved anaerobic digestate sludge.
+ llm_assisted: true
+- timestamp: '2026-10-08T14:15:40Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Retain measured external-gas methane production without coding abiotic supply as microbial cross-feeding
+ or qPCR as activity.; Retain VFA measurements and source interpretations while removing an unsupported demonstrated-syntrophy
+ type. Issue#1932; reports/causal_graph_review/decisions/20261008-four-records-batch120.yaml
llm_assisted: true
diff --git a/kb/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml b/kb/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml
index 5a58da151..0659603cb 100644
--- a/kb/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml
+++ b/kb/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml
@@ -151,11 +151,12 @@ taxonomy:
Bacillus cereus, Achromobacter sp., Pseudomonas sp., Cladosporium sp., and Trichoderma harzianum)
explanation: Names Trichoderma harzianum as a fungal member of the composting SynCom.
ecological_interactions:
-- name: SynCom-driven lignocellulose decomposition and humification
- description: The five-member SynCom intensifies thermophilic fermentation,
- rapidly lowers the carbon/nitrogen ratio, and enhances humification in the
- manure-composting matrix.
- interaction_type: MUTUALISM
+- name: SynCom-associated compost maturation
+ description: The five-member inoculum is reported to intensify thermophilic fermentation, lower the compost carbon/nitrogen
+ ratio and increase humification. These are community-treatment and substrate outcomes, not evidence that all
+ five inoculated members obtain reciprocal fitness benefits. The accessible abstract relates maturation to resistance-gene
+ attenuation using Mantel correlation; it does not resolve individual-strain contributions or a uniquely demonstrated
+ causal mediator.
scope: COMMUNITY_LEVEL
biological_processes:
- preferred_term: cellulose catabolic process
@@ -163,61 +164,77 @@ ecological_interactions:
id: GO:0030245
label: cellulose catabolic process
downstream:
- - target: Community-level bio-sanitization of high-risk pathogens
- description: Intensified thermophilic fermentation and faster organic-matter
- turnover create the SynCom-driven composting trajectory linked to deep
- bio-sanitization and high-risk pathogen elimination.
- - target: SynCom-driven suppression of horizontal gene transfer
- description: The SynCom-driven composting trajectory is tied to metabolic
- reprogramming away from a biofilm-dependent defense-survival mode,
- restricting horizontal gene transfer opportunities in the compost.
+ - target: Reported compost resistome and pathogen attenuation
+ description: 'PARTIAL: intensified fermentation and the correlated C/N decrease and humification are proposed
+ environmental contributors to later ARG and pathogen attenuation. Mantel association and the common inoculation
+ treatment support this interpretation, not selective demonstration that maturation alone mediates elimination
+ or prevents every gene-transfer event.'
evidence:
- reference: PMID:41839407
supports: SUPPORT
- evidence_source: IN_VIVO
+ evidence_source: OTHER
snippet: SynCom-driven rapid decrease in carbon/nitrogen ratio and enhanced humification
- explanation: Supports the SynCom as the driver of faster humification and
- carbon/nitrogen turnover in thermophilic compost.
-- name: Community-level bio-sanitization of high-risk pathogens
- description: By intensifying thermophilic fermentation and driving down the carbon/nitrogen ratio,
- the SynCom collapses high-risk ARG-mobilome interactomes and eliminates high-risk pathogens
- including Pseudomonas aeruginosa, an emergent community-level function rather than a single
- pairwise edge.
- interaction_type: COMPETITION
+ explanation: Abstract-reported compost maturation; the experimental venue and detailed assay design were not
+ reconstructed from full text.
+ - reference: PMID:41839407
+ supports: PARTIAL
+ evidence_source: COMPUTATIONAL
+ snippet: Mantel correlation analysis revealed
+ explanation: Identifies the association analysis underlying the environmental-driver interpretation.
+- name: Reported compost resistome and pathogen attenuation
+ description: The abstract reports a transient ARG rebound after SynCom inoculation followed by attenuation, reduced
+ multidrug-resistance genes and virulence factors, and elimination of source-identified high-risk pathogens.
+ Preserve this reported bio-sanitization result without equating metagenomic or network signals with demonstrated
+ loss of every viable pathogen, universal fertilizer biosafety, or bilateral negative fitness effects. The accessible
+ abstract does not resolve the viability-detection limits or provide a direct causal competition assay.
scope: COMMUNITY_LEVEL
- biological_processes:
- - preferred_term: biological process involved in interspecies interaction between organisms
- term:
- id: GO:0044419
- label: biological process involved in interspecies interaction between organisms
evidence:
- reference: PMID:41839407
supports: SUPPORT
- evidence_source: IN_VIVO
- snippet: deep bio-sanitization was achieved by synchronously eliminating high-risk pathogens (e.g.,
- Pseudomonas aeruginosa), phytopathogens, and specific virulence factors
- explanation: The consortium collectively suppresses and eliminates high-risk pathogens including
- P. aeruginosa.
-- name: SynCom-driven suppression of horizontal gene transfer
- description: SynCom inoculation reprograms community metabolism from a biofilm-dependent
- defense-survival model to an active motility-metabolism mode (depleted lipopolysaccharide
- biosynthesis, enriched flagellar assembly), a fitness-cost trade-off that physically restricts
- horizontal gene transfer and suppresses key recombinases (XerD, IntI1).
- interaction_type: COMPETITION
+ evidence_source: OTHER
+ snippet: deep bio-sanitization was achieved by synchronously eliminating high-risk pathogens (e.g., Pseudomonas
+ aeruginosa), phytopathogens, and specific virulence factors
+ explanation: Preserves the authors' reported bio-sanitization outcome; the abstract alone does not establish
+ viability-detection limits or universal eradication.
+ - reference: PMID:41839407
+ supports: SUPPORT
+ evidence_source: COMPUTATIONAL
+ snippet: Metagenomic analysis showed SynCom inoculation caused a transient ARG rebound followed by profound
+ attenuation
+ explanation: Retains the non-monotonic resistance-gene trajectory instead of claiming immediate uniform removal.
+- name: Metagenomic signatures of reduced HGT potential
+ description: 'KEGG and metagenomic analyses suggest a shift in functional potential from biofilm-associated defense
+ toward motility/metabolism, with lower lipopolysaccharide biosynthesis and higher flagellar-assembly representation.
+ The reported network change includes 26.6% fewer potential host-gene associations. PARTIAL: reduced HGT opportunity,
+ recombinase suppression and physical restriction of transfer are source interpretations, not measurements of
+ conjugation frequency, gene expression, actual cell motility or proven necessity of a particular route. Potential
+ host-gene associations are not a count of observed horizontal-transfer events.'
scope: COMMUNITY_LEVEL
biological_processes:
- preferred_term: horizontal gene transfer
term:
id: GO:0009292
label: horizontal gene transfer
+ notes: Inferred change in HGT potential; not a directly measured transfer rate.
evidence:
- reference: PMID:41839407
supports: SUPPORT
- evidence_source: IN_VIVO
- snippet: a pivotal metabolic reprogramming from a biofilm-dependent defense-survival model to an
- active motility-metabolism mode, characterized by depleted lipopolysaccharide biosynthesis and
- enriched flagellar assembly
- explanation: Community-level metabolic reprogramming that restricts horizontal gene transfer.
+ evidence_source: COMPUTATIONAL
+ snippet: a pivotal metabolic reprogramming from a biofilm-dependent defense-survival model to an active motility-metabolism
+ mode, characterized by depleted lipopolysaccharide biosynthesis and enriched flagellar assembly
+ explanation: KEGG-based functional interpretation; not directly measured motility, biofilm loss or transfer
+ frequency.
+ - reference: PMID:41839407
+ supports: SUPPORT
+ evidence_source: COMPUTATIONAL
+ snippet: reducing potential host-gene associations by 26.6%
+ explanation: Network statistic, not observed gene-transfer frequency.
+ - reference: PMID:41839407
+ supports: PARTIAL
+ evidence_source: COMPUTATIONAL
+ snippet: This metabolic shift implies a fitness cost trade-off that physically restricts horizontal gene transfer
+ (HGT) opportunities
+ explanation: The source labels this a mechanistic implication; it is retained as partial support only.
growth_media:
- name: Thermophilic manure-composting substrate (solid-state)
temperature: thermophilic (no numeric value reported in the abstract)
@@ -244,3 +261,32 @@ growth_media:
snippet: SynCom-driven rapid decrease in carbon/nitrogen ratio and enhanced humification
explanation: Names the C/N ratio decrease and humification that characterize the composting
substrate over time.
+discussions:
+- discussion_id: compost_causal_scope_batch120
+ prompt: Which inferred compost mechanisms explain attenuation beyond metagenomic and correlation-based evidence?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#SynCom-associated compost maturation
+ - ecological_interactions#Reported compost resistome and pathogen attenuation
+ - ecological_interactions#Metagenomic signatures of reduced HGT potential
+ rationale: The abstract describes treatment-associated chemistry, a transient ARG rebound, later attenuation,
+ KEGG interpretation and potential host-gene networks. It does not resolve causal necessity or viable-pathogen
+ detection limits. Full methods and direct functional evidence are needed to distinguish the proposed HGT restriction
+ and environmental mediation from parallel responses to inoculation. This uncertainty does not erase the reported
+ positive bio-sanitization outcome.
+ evidence:
+ - reference: PMID:41839407
+ snippet: This metabolic shift implies a fitness cost trade-off that physically restricts horizontal gene transfer
+ (HGT) opportunities
+ posed_by: codex
+ posed_date: '2026-10-08'
+curation_history:
+- timestamp: '2026-10-08T14:15:41Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Retain reported maturation without coding aggregate improvement as mutualism; bound the remaining environmental-mediation
+ arrow.; Retain positive later attenuation and the early rebound without claiming universal viable-pathogen elimination
+ or bilateral competition.; Represent KEGG and network findings as HGT potential, not measured transfer, expression
+ or motility. Issue#1933; reports/causal_graph_review/decisions/20261008-four-records-batch120.yaml
+ llm_assisted: true
diff --git a/kb/communities/Tobacco_Chemotactic_Biocontrol_SynCom.yaml b/kb/communities/Tobacco_Chemotactic_Biocontrol_SynCom.yaml
index 94dced4c7..65b8af802 100644
--- a/kb/communities/Tobacco_Chemotactic_Biocontrol_SynCom.yaml
+++ b/kb/communities/Tobacco_Chemotactic_Biocontrol_SynCom.yaml
@@ -62,12 +62,13 @@ taxonomy:
evidence:
- *id001
ecological_interactions:
-- name: Root-Exudate Prebiotic Enhancement
- description: Root-exudate-derived vitamin C, propionic acid, and esculetin
- stimulate growth of the chemotactic SynCom strains and increase the
- antagonistic activity of their fermentation broth against Ralstonia
- solanacearum.
- interaction_type: COLONIZATION_FACILITATION
+- name: Strain-specific prebiotic enhancement
+ description: Added resource compounds produced strain-specific growth and cell-free broth responses. Vitamin C
+ increased Y364 broth antagonism; selected compounds including propionic acid and esculetin increased Y832 broth
+ antagonism. No tested compound significantly enhanced Y878 broth inhibition relative to its mock treatment.
+ Growth screening and broth inhibition are distinct assays, and the selected compounds did not show uniform benefit
+ across every isolate. The resource library drew on compounds commonly found in tomato root exudates; these assays
+ do not demonstrate that all were secreted by tobacco roots in the field.
scope: COMMUNITY_LEVEL
metabolites:
- preferred_term: L-ascorbic acid
@@ -83,72 +84,70 @@ ecological_interactions:
id: CHEBI:490095
label: esculetin
downstream:
- - target: Chemotactic Bacterial Wilt Suppression
- description: Prebiotic-stimulated SynCom growth and antagonistic bioactivity
- strengthen the chemotactic consortium's suppression of Ralstonia.
+ - target: Antagonism by cheA-positive SynCom isolates
+ description: 'Selected compound additions enhanced broth antagonism in particular isolate assays. PARTIAL for
+ growth as the mediator: growth, broth chemistry and residual additives were not selectively separated. The
+ Y878 null enhancement result prevents generalizing this effect to all three members, and the comparison does
+ not establish enhanced chemotaxis or root colonization.'
evidence:
- reference: PMID:40670700
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: vitamin C, propionic acid, and esculetin significantly promoted the growth and
- antagonistic ability of chemotactic SynCom strains
- explanation: Supports the root-exudate-derived compounds as prebiotics that
- increase growth and pathogen antagonism by the chemotactic SynCom.
-- name: Chemotactic Bacterial Wilt Suppression
- description: Chemotactic SynCom members colonize the rhizosphere and suppress Ralstonia invasion.
- interaction_type: COLONIZATION_FACILITATION
+ snippet: vitamin C, propionic acid, and esculetin significantly promoted the growth and antagonistic ability
+ of chemotactic SynCom strains
+ explanation: Abstract-level summary of positive resource responses; the main Results narrow the effect to specific
+ isolate/compound combinations.
+ - reference: PMID:40670700
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: for Y878, none of the tested compounds showed a significant difference compared with the mock treatment
+ explanation: Preserves the explicit null enhancement result for the Bacillus isolate.
+- name: Antagonism by cheA-positive SynCom isolates
+ description: The selected Y364, Y832 and Y878 isolates showed antagonism against Ralstonia solanacearum, mutual
+ compatibility and PCR detection of cheA. The source identifies two Pseudomonas strains and one Bacillus strain;
+ the canonical two-row taxonomy remains a broad, incomplete representation. cheA detection supports chemotaxis
+ potential, not directly measured root migration or colonization. Strong antagonism was also observed among cheA-negative
+ screened isolates. Compatibility and pathogen inhibition do not establish within-SynCom cross-feeding or facilitation
+ of another member's establishment.
scope: COMMUNITY_LEVEL
- metabolites:
- - preferred_term: L-ascorbic acid
- term:
- id: CHEBI:29073
- label: L-ascorbic acid
- - preferred_term: propionic acid
- term:
- id: CHEBI:30768
- label: propionic acid
- - preferred_term: esculetin
- term:
- id: CHEBI:490095
- label: esculetin
- biological_processes:
- - preferred_term: chemotaxis
- term:
- id: GO:0006935
- label: chemotaxis
downstream:
- target: Tobacco Field Protection and Yield Enhancement
- description: Rhizosphere colonization and antagonism by the chemotactic
- SynCom carry through the bioorganic fertilizer into lower field
- Ralstonia invasion and higher tobacco yield.
+ description: 'PARTIAL: laboratory antagonism is a candidate contribution to the field benefit of the formulated
+ SynCom fertilizer. The field contrast combined strains, prebiotics and an organic matrix against conventional
+ cow-manure fertilization; it did not isolate chemotaxis, colonization or broth antagonism as the mediator.
+ The authors explicitly identify non-chemotactic SynCom controls as future work.'
evidence:
- - *id001
- reference: PMID:40670700
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: vitamin C, propionic acid, and esculetin significantly promoted the growth and antagonistic
- ability of chemotactic SynCom strains
- explanation: Names the three root-exudate prebiotics that promoted
- chemotactic SynCom growth and antagonism against Ralstonia solanacearum.
+ snippet: exhibited strong antagonism against R. solanacearum, harbored the chemotaxis gene cheA, and showed
+ mutual compatibility
+ explanation: Directly supports the selected isolates' screening phenotypes and marker, not measured migration.
+ - reference: PMID:40670700
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: another half of isolated strains, which lacked cheA gene, still displayed strong antagonistic activity
+ explanation: Shows that cheA positivity was not required for antagonism across the screened isolate set.
- name: Tobacco Field Protection and Yield Enhancement
- description: Bioorganic fertilizer carrying the chemotactic SynCom protects
- diseased tobacco fields from Ralstonia solanacearum invasion and increases
- crop yield under field conditions.
- interaction_type: COLONIZATION_FACILITATION
+ description: In the reported tobacco field trial, the SynCom-containing bioorganic fertilizer plus prebiotics
+ was associated with a lower disease index, lower Ralstonia qPCR abundance and nearly doubled crop yield relative
+ to conventional fertilization. This is a positive combined-treatment result, not an independently isolated effect
+ of chemotaxis or microbial colonization facilitation. qPCR abundance is not a direct viable-cell count, and
+ Tax4Fun predictions of indigenous-community functions do not establish active pathways or strain-resolved establishment
+ of the inoculum.
scope: COMMUNITY_LEVEL
- biological_processes:
- - preferred_term: chemotaxis
- term:
- id: GO:0006935
- label: chemotaxis
evidence:
- reference: PMID:40670700
supports: SUPPORT
evidence_source: IN_VIVO
- snippet: bioorganic fertilizer containing chemotactic SynCom can protect diseased tobacco
- field from R. solanacearum invasion and enhance yields
- explanation: Supports the field endpoint of the chemotactic SynCom
- bioorganic fertilizer.
+ snippet: bioorganic fertilizer containing chemotactic SynCom can protect diseased tobacco field from R. solanacearum
+ invasion and enhance yields
+ explanation: Supports the field endpoint of the chemotactic SynCom bioorganic fertilizer.
+ - reference: PMID:40670700
+ supports: SUPPORT
+ evidence_source: IN_VIVO
+ snippet: the chemotactic SynCom fertilizer nearly doubled crop yield
+ explanation: Retains the positive field result without converting it into proof of a unique mechanism.
environmental_factors:
- name: defined synthetic community design
value: Two Pseudomonas strains and one Bacillus strain selected from healthy tobacco rhizosphere isolates.
@@ -247,3 +246,30 @@ cultivation_setup:
evidence_source: IN_VITRO
snippet: During fermentation, the mixture was turned every 12 h, and a moisture
content was maintained at 40% to ensure aeration and looseness of the compost
+discussions:
+- discussion_id: tobacco_causal_scope_batch120
+ prompt: How much of the tobacco field benefit specifically depends on chemotaxis or the tested broth effects?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Strain-specific prebiotic enhancement
+ - ecological_interactions#Antagonism by cheA-positive SynCom isolates
+ - ecological_interactions#Tobacco Field Protection and Yield Enhancement
+ rationale: The field comparison combines the inoculum, prebiotics and fertilizer matrix. It does not isolate chemotaxis,
+ and the authors explicitly identify non-chemotactic controls as future work. cheA PCR and Tax4Fun inference
+ should not stand in for measured root migration, strain persistence or active metabolic pathways. The paper
+ also differs between Results and Discussion on resource counts and has tomato wording in some captions despite
+ a tobacco trial; those details are not silently reconciled or used to erase the positive field outcome.
+ evidence:
+ - reference: PMID:40670700
+ snippet: future studies should include non-chemotactic SynCom as experimental controls
+ posed_by: codex
+ posed_date: '2026-10-08'
+curation_history:
+- timestamp: '2026-10-08T14:15:41Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Retain positive compound responses with isolate-specific limits and the Y878 null result.; Keep antagonism
+ and compatibility distinct from cheA-based potential and unmeasured colonization.; Preserve the positive field
+ co-treatment outcome while bounding qPCR, Tax4Fun and mechanistic attribution. Issue#1934; reports/causal_graph_review/decisions/20261008-four-records-batch120.yaml
+ llm_assisted: true
diff --git a/reports/causal_graph_review/README.md b/reports/causal_graph_review/README.md
index 55fbde5f5..4acb4fe5b 100644
--- a/reports/causal_graph_review/README.md
+++ b/reports/causal_graph_review/README.md
@@ -5,6 +5,40 @@ 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`.
+## Batch120: Measured Outcomes And Inferred Routes
+
+[Decisions](decisions/20261008-four-records-batch120.yaml),
+[provenance](cache-provenance-20261008-batch120.json),
+[validation](validation-20261008-batch120.json), and
+[self-adversarial review](adversarial-review-20261008-batch120.yaml) cover
+the Thermoleptolyngbya-Chelatococcus arsenic pair, thermophilic ex-situ
+biomethanation, lignocellulose-composting SynCom and tobacco chemotaxis SynCom.
+All ten nodes remain, with six renames. Three existing arrows remain qualified;
+one compost arrow that confounded parallel responses to inoculation is removed.
+
+Arsenic carbon tracing and reciprocal growth remain direct positive evidence;
+genomic complementarity does not establish traced oxygen or nitrogen transfer.
+Biomethanation retains measured gas and VFA outcomes, without calling external
+gas supply cross-feeding or group-level inference demonstrated syntrophy.
+Compost retains the transient ARG rebound and later attenuation; KEGG and
+host-gene networks describe potential, not measured gene-transfer frequency.
+Tobacco retains strain-specific broth and combined field-treatment benefits,
+including the Y878 null enhancement, without equating cheA PCR with measured
+chemotaxis or isolating that mechanism from fertilizer co-treatment.
+
+Four whole records and four fresh primary abstracts were reviewed. Biomethanation
+and tobacco main-body XML, methods, results, discussion, tables and captions were
+read; original figure pixels, supplements, raw data and analysis code were not.
+Arsenic and compost repairs are abstract-bounded, not an exhaustive claim that
+full text is absent. All 33 graph/discussion quotations match primary text and
+existing caches. All 923 caches, 456 other records and unrelated raw fields are
+unchanged. Four append-only histories record the edits. No new topology,
+experimental protocol, Edison invocation or provider spend is introduced.
+
+Repairs #1931-#1934 await protected-main merge; non-graph follow-ups #1935-#1937
+remain open. Source-based self-review is not independent approval, and the
+overall review and protected merge are still incomplete.
+
## Batch119: Strain Identity And Inferred Networks
[Decisions](decisions/20261008-four-records-batch119.yaml),
diff --git a/reports/causal_graph_review/adversarial-review-20261008-batch120.yaml b/reports/causal_graph_review/adversarial-review-20261008-batch120.yaml
new file mode 100644
index 000000000..c9f016b84
--- /dev/null
+++ b/reports/causal_graph_review/adversarial-review-20261008-batch120.yaml
@@ -0,0 +1,423 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: 0c53674faea0dcf72f3fb830f46ebb656811684a
+scope:
+- kb/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml
+- kb/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml
+- kb/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml
+- kb/communities/Tobacco_Chemotactic_Biocontrol_SynCom.yaml
+decision_ledger: reports/causal_graph_review/decisions/20261008-four-records-batch120.yaml
+validation_report: reports/causal_graph_review/validation-20261008-batch120.json
+findings:
+- issue: 1931
+ severity: P2
+ finding: Separate measured carbon transfer and reciprocal benefit from predicted arsenic-coculture routes
+ status: addressed_in_this_change
+ disposition: Close only after protected-main merge.
+- issue: 1932
+ severity: P2
+ finding: Distinguish external gas conversion and inferred VFA routes in thermophilic biomethanation
+ status: addressed_in_this_change
+ disposition: Close only after protected-main merge.
+- issue: 1933
+ severity: P2
+ finding: Bound compost bio-sanitization and HGT claims to metagenomic and correlation evidence
+ status: addressed_in_this_change
+ disposition: Close only after protected-main merge.
+- issue: 1934
+ severity: P2
+ finding: Keep tobacco isolate-specific prebiotic responses separate from chemotaxis-mediated field protection
+ status: addressed_in_this_change
+ disposition: Close only after protected-main merge.
+- issue: 1935
+ severity: P2
+ finding: Audit biomethanation non-graph viability claims and group-level functional roles
+ status: open_non_graph_follow_up
+ disposition: Remain open until separately verified.
+- issue: 1936
+ severity: P2
+ finding: Qualify compost record overview and cultivation claims to the available source scope
+ status: open_non_graph_follow_up
+ disposition: Remain open until separately verified.
+- issue: 1937
+ severity: P2
+ finding: Resolve the three tobacco SynCom strains and non-graph assay boundaries
+ status: open_non_graph_follow_up
+ disposition: Remain open until separately verified.
+adversarial_checks:
+- 'All 10 original nodes and 4 arrows accounted for: 10 nodes and 3 arrows retained, one unsupported common-treatment
+ arrow removed, six renames, no new topology. Targets and discussion anchors resolve. No direction invented.'
+- Arsenic carbon transfer and reciprocal growth remain positive evidence, retaining CROSS_FEEDING and MUTUALISM.
+ Genomic complementarity is not direct nitrogen/oxygen tracing. Oxygen-supplemented pure culture is not a demonstrated
+ oxygen requirement. Exact strains and canonical identities unchanged.
+- Biomethane 86% by day 69 remains observed; above 90% remains proposed. External cylinder gas is not microbial
+ cross-feeding. qPCR/16S profiles are not viability or taxon-specific flux; positive plate recovery is separate.
+ VFA pools and inferred routes do not establish thermodynamic syntrophy. Prewashout sampling quotation explicitly
+ belongs to phase 1, not demonstrated phase 4 timing.
+- Compost retains maturation, transient ARG rebound, later attenuation and reported pathogen elimination. Aggregate
+ treatment benefit is not mutualism or bilateral competition. KEGG and potential host-gene network signals are
+ not expression, motility or actual transfer events. 26.6% refers to potential associations. One environmental-mediation
+ arrow stays PARTIAL; common-treatment maturation-to-HGT arrow removed.
+- Tobacco retains isolate-specific positive resource responses, Y878 null enhancement, compatible antagonist isolates
+ and positive combined field treatment. cheA PCR is not measured migration/colonization; cheA-negative isolates
+ also antagonize. The resource library cites tomato exudates. Missing non-chemotactic controls are explicit future
+ work. qPCR and Tax4Fun are not viability/activity. Results/Discussion counts and tomato-caption inconsistencies
+ are not silently reconciled.
+- Twenty-seven graph and six discussion quotes match fresh primary texts and all existing caches. Full main bodies,
+ methods, results, discussion, table text and captions read for biomethane and tobacco; arsenic and compost review
+ bounded to fresh primary abstracts. No original figure pixels, supplements, raw data or analysis-code audit. No
+ cache edits or full-body imports. Tobacco license is CC BY-NC-ND 4.0, not unrestricted CC BY. Matching is not
+ entailment certification.
+- 'Four guarded writes and append-only histories preserve 456 other records, all 923 caches, unrelated raw blocks
+ and previous histories/decisions. Canonical taxon identities/ranks unchanged. Metadata/composition/scope findings
+ remain separate issues #1935-#1937. Shared evidence aliases detached before edits.'
+- Fifteen focused tests and twelve control/mutation/restored-control probes pass. Mutations reject loss of positive
+ carbon/field evidence, syntrophy overclaims, oxygen inference promotion, external-gas cross-feeding, compost mutualism,
+ HGT proof promotion, loss of ARG rebound, restored common-treatment arrow, loss of Y878 null and unmeasured chemotaxis.
+ No canonical writes during probes.
+- The initial mutation harness removed a required dictionary key and stopped with KeyError before producing a report.
+ It was changed to a wrong interaction-type value so the intended scientific assertion is exercised. All 12 cases
+ then completed with restored controls; no test or canonical-record weakening.
+- 'All four records pass schema, strict, terms, full-record references, snippets, rank and history. 1131 selected
+ tests including palette pass; not full Linux CI certification. Network: 57 unchanged warnings, zero structural
+ defects. Descriptions on 456 pages, 1361 nodes and 522 arrows exactly match descriptions with deterministic rendering,
+ not screenshot QA.'
+- 'All participant lists and scopes unchanged; 299 participant-list users. Census: 414 community-level, 136 mixed,
+ 278 community-only, 1568 taxa, 1281 solely credited unchanged. Scope credit is not actual participant coverage.
+ Connectivity logic and thresholds unchanged.'
+- 'Issues #1931-#1934 addressed pending protected-main merge; #1935-#1937 remain open. No Edison extension or credits.
+ Prior Ruegeria #1883 still needs configured authentication and was not retried unchanged. Self-adversarial review
+ is not independent approval; root #1836 and actual exact-head protected checks remain required.'
+- 'Corpus: 388 reviewed, 18 pending, 54 needs_research across 460 records. Overall goal, protected merge and branch
+ deletion incomplete. Postcommit docs-current and exact-head publication are separate gates, not preasserted here.'
+adversarial_regression_proof:
+ report:
+ cases:
+ - mutation: Erase directly measured carbon cross-feeding
+ test: test_arsenic_preserves_direct_carbon_cross_feeding
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 21
+ assertion: assert node["interaction_type"] == "CROSS_FEEDING"
+ restored_control: PASS
+ changed_values:
+ - path: records/0/ecological_interactions/0/interaction_type
+ before: CROSS_FEEDING
+ after: COMPETITION
+ - mutation: Turn reciprocal benefit into thermodynamic syntrophy
+ test: test_arsenic_mutualism_keeps_actual_reciprocal_growth_evidence
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 32
+ assertion: assert node["interaction_type"] == "MUTUALISM"
+ restored_control: PASS
+ changed_values:
+ - path: records/0/ecological_interactions/1/interaction_type
+ before: MUTUALISM
+ after: SYNTROPHY
+ - mutation: Promote oxygen-supplement comparison to route proof
+ test: test_arsenic_genomic_routes_are_not_traced_oxygen_or_nitrogen
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 43
+ assertion: assert node["evidence"][-1]["supports"] == "PARTIAL"
+ restored_control: PASS
+ changed_values:
+ - path: records/0/ecological_interactions/1/evidence/3/supports
+ before: PARTIAL
+ after: SUPPORT
+ - mutation: Call external cylinder-gas supply cross-feeding
+ test: test_biomethanation_external_gas_is_not_interspecies_cross_feeding
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 54
+ assertion: assert "interaction_type" not in node
+ restored_control: PASS
+ changed_values:
+ - path: records/1/ecological_interactions/0/interaction_type
+ before: null
+ after: CROSS_FEEDING
+ - mutation: Turn VFA pool dynamics into demonstrated syntrophy
+ test: test_biomethanation_vfa_pools_do_not_prove_thermodynamic_syntrophy
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 78
+ assertion: assert "interaction_type" not in node
+ restored_control: PASS
+ changed_values:
+ - path: records/1/ecological_interactions/1/interaction_type
+ before: null
+ after: SYNTROPHY
+ - mutation: Call compost maturation microbial mutualism
+ test: test_compost_maturation_is_not_demonstrated_member_mutualism
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 91
+ assertion: assert "interaction_type" not in node
+ restored_control: PASS
+ changed_values:
+ - path: records/2/ecological_interactions/0/interaction_type
+ before: null
+ after: MUTUALISM
+ - mutation: Erase transient ARG rebound from reported trajectory
+ test: test_compost_preserves_rebound_and_later_reported_attenuation
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 103
+ assertion: '"transient ARG rebound followed by profound attenuation" in node["evidence"][1]["snippet"]'
+ restored_control: PASS
+ changed_values:
+ - path: records/2/ecological_interactions/1/evidence/1/snippet
+ before: Metagenomic analysis showed SynCom inoculation caused a transient ARG rebound followed by profound
+ attenuation
+ after: ARGs immediately declined without rebound.
+ - mutation: Promote inferred HGT restriction to demonstrated mechanism
+ test: test_compost_hgt_is_potential_not_measured_transfer_frequency
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 117
+ assertion: assert node["evidence"][2]["supports"] == "PARTIAL"
+ restored_control: PASS
+ changed_values:
+ - path: records/2/ecological_interactions/2/evidence/2/supports
+ before: PARTIAL
+ after: SUPPORT
+ - mutation: Restore common-treatment maturation-to-HGT arrow
+ test: test_compost_retains_partial_environmental_mediation_not_common_cause_arrow
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 125
+ assertion: assert len(maturation["downstream"]) == 1
+ restored_control: PASS
+ changed_values:
+ - path: records/2/ecological_interactions/0/downstream
+ before:
+ - target: Reported compost resistome and pathogen attenuation
+ description: 'PARTIAL: intensified fermentation and the correlated C/N decrease and humification are proposed
+ environmental contributors to later ARG and pathogen attenuation. Mantel association and the common
+ inoculation treatment support this interpretation, not selective demonstration that maturation alone
+ mediates elimination or prevents every gene-transfer event.'
+ after:
+ - target: Reported compost resistome and pathogen attenuation
+ description: 'PARTIAL: intensified fermentation and the correlated C/N decrease and humification are proposed
+ environmental contributors to later ARG and pathogen attenuation. Mantel association and the common
+ inoculation treatment support this interpretation, not selective demonstration that maturation alone
+ mediates elimination or prevents every gene-transfer event.'
+ - target: Metagenomic signatures of reduced HGT potential
+ description: Maturation demonstrates HGT suppression.
+ - mutation: Erase isolate-specific Y878 null enhancement
+ test: test_tobacco_prebiotic_results_are_isolate_specific_with_y878_null
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 138
+ assertion: assert "for Y878, none" in node["evidence"][1]["snippet"]
+ restored_control: PASS
+ changed_values:
+ - path: records/3/ecological_interactions/0/evidence/1/snippet
+ before: for Y878, none of the tested compounds showed a significant difference compared with the mock treatment
+ after: Every isolate showed enhanced antagonism.
+ - mutation: Treat cheA marker as measured chemotaxis
+ test: test_tobacco_chea_marker_and_compatibility_are_not_colonization_measurements
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 145
+ assertion: assert "interaction_type" not in node and "biological_processes" not in node
+ restored_control: PASS
+ changed_values:
+ - path: records/3/ecological_interactions/1/biological_processes
+ before: null
+ after:
+ - preferred_term: chemotaxis
+ term:
+ id: GO:0006935
+ label: chemotaxis
+ - mutation: Erase positive field yield result
+ test: test_tobacco_positive_field_result_is_a_combined_treatment
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 159
+ assertion: assert "nearly doubled crop yield" in node["evidence"][1]["snippet"]
+ restored_control: PASS
+ changed_values:
+ - path: records/3/ecological_interactions/2/evidence/1/snippet
+ before: the chemotactic SynCom fertilizer nearly doubled crop yield
+ after: No positive crop yield effect was observed.
+ canonical_files_unchanged: true
+ checked_file_sha256:
+ kb/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml: bc09df336e1e5a701bf24c3f47eed41c24829eb4618c8597840052a93d0f822c
+ kb/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml: 51357584e2099b2916e81f893f46fc0af8cede23e3b2616ca957adc5f7a4bf71
+ kb/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml: 9d6ab3706fb821b6231441efc4342728b21ede4ab1aad3e5962ba5dab5d79199
+ kb/communities/Tobacco_Chemotactic_Biocontrol_SynCom.yaml: 2d1851c88c385f813706b923eeb0754bf70bbac4dd94fb15369bf5e45317e371
+ tests/test_causal_review_batch120.py: 6f25ad6bbd01d3eb06b6bfd1b9f4b03372f2ccfafca2923d6f4ac9cbc7673aa4
+ probe_script_sha256: 4ee94b8660194e8e5321fd3a567be404a10fcc85fd33be08769c97b07c966bbb
+ scope: In-memory control/mutation/restored-control; no canonical writes and not additional pytest tests.
+ artifact: /private/tmp/communitymech-batch120/adversarial-regression-proof.json
+ sha256: 94b88f130c95e5183173ae781c751c0f2bd72af36b59b29056fac11b72c69cdd
+verification:
+ combined_regressions: 1131 passed in 305.98s (0:05:05)
+ new_regression_tests: 15
+ total_recorded_gate_outputs: 41
+ primary_graph_snippet_proof:
+ graph_quotations: 27
+ discussion_quotations: 6
+ fresh_primary_literal_matches: 33
+ all_cached_literal_matches: 33
+ retained_nodes: 10
+ removed_nodes: 0
+ renamed_nodes: 6
+ retained_arrows: 3
+ removed_arrows: 1
+ new_nodes_or_directions: 0
+ references: Full-record local passes are macOS, not Linux certification. Literal matching does not establish entailment.
+ Total checks in the reference CLI counts issues, not examined snippets.
+ snippet_counts_by_record:
+ kb/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml:
+ MATCH: 13
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml:
+ MATCH: 43
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml:
+ MATCH: 16
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Tobacco_Chemotactic_Biocontrol_SynCom.yaml:
+ MATCH: 17
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ full_corpus_snippet_audit:
+ counts:
+ records: 460
+ total: 9059
+ categories:
+ MATCH: 8914
+ RENDERING: 28
+ ASSEMBLED: 1
+ WEAK: 0
+ MISMATCH: 40
+ NOCONTENT: 76
+ caveat: Informational audit exit0 is not clean-corpus or entailment certification.
+ network:
+ existing_findings_preserved: 57
+ added_findings: {}
+ removed_findings: {}
+ structural_defects: 0
+ tested_file_sha256:
+ reports/causal_graph_review/decisions/20261008-four-records-batch120.yaml: 02d8e5bcf94ac4a351a5c23517211f8dfe3d3545b73c3de784f53d23ddc6105b
+ tests/test_causal_review_batch120.py: 6f25ad6bbd01d3eb06b6bfd1b9f4b03372f2ccfafca2923d6f4ac9cbc7673aa4
+ tests/test_participating_taxa.py: f438815b4a028c0f38a077df53c95f685f98b3c2b523593896a124b544269db1
+ tests/test_community_level_connectivity_credit.py: 996cc631423bfa7adc5d8e693d67d55b374a24379d119ab0fa8f1802f38f216a
+ tests/test_causal_review_batch109.py: ff8e9e26771545e1ace22b3c1d42076789c99cc4bc83e588b6a4b9ad698d3d73
+ tests/test_datamodel.py: f8d4750ad64eb4156857a86a8c6adf16dedefb09ca3c3da908f697e609a35f25
+ reports/causal_graph_review/cache-provenance-20261008-batch120.json: 151d0064a128baf905eba3e41ae9b2035d47b740eab7b134d091caf52f7a4290
+ kb/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml: bc09df336e1e5a701bf24c3f47eed41c24829eb4618c8597840052a93d0f822c
+ kb/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml: 51357584e2099b2916e81f893f46fc0af8cede23e3b2616ca957adc5f7a4bf71
+ kb/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml: 9d6ab3706fb821b6231441efc4342728b21ede4ab1aad3e5962ba5dab5d79199
+ kb/communities/Tobacco_Chemotactic_Biocontrol_SynCom.yaml: 2d1851c88c385f813706b923eeb0754bf70bbac4dd94fb15369bf5e45317e371
+ history_sha256:
+ history/records/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture/2026-10-08T141541Z-codex-62412f.yaml: 9644536c1fb24245f489189b18624c2877a158673da516875031ba5942419103
+ history/records/Thermophilic_ExSitu_Biomethanation_Mixed_Culture/2026-10-08T141542Z-codex-8205c5.yaml: 74d79e3776faa7d8a0f754652e6923b8496510ef06fc0c5a82a9638329695cee
+ history/records/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization/2026-10-08T141542Z-codex-0c3005.yaml: a1bbcfe8f0d52db5daaddd9171d68644d74c5c4f76e034ec6a00f36f1a20b294
+ history/records/Tobacco_Chemotactic_Biocontrol_SynCom/2026-10-08T141542Z-codex-fb2ec0.yaml: 4b26a768b2d5dfc11255ccf65473deb7e28591ef37d9aee8dda17f832da5f078
+ unchanged_records: 456
+ unchanged_caches: 923
+ immutable_prior_history_and_decision_files: 889
+ cache_changes: []
+ edison:
+ required_for_this_repair: false
+ provider_submissions: 0
+ credits_spent: 0
+ new_nodes_or_directions: 0
+ prior_extension_blocker: 'Ruegeria1883: configured authentication unavailable in prior approved invocation;
+ no unchanged-state retry.'
+ post_commit_docs_current: Separate publication gate,not preasserted.
+participant_census:
+ current:
+ records: 460
+ with_community_level: 414
+ mixed: 136
+ community_level_only: 278
+ taxa: 1568
+ credited_solely_by_the_rule: 1281
+ delta_from_batch119:
+ records: 0
+ with_community_level: 0
+ mixed: 0
+ community_level_only: 0
+ taxa: 0
+ credited_solely_by_the_rule: 0
+ explanation: All participant lists and scopes are unchanged;299participant-list users. Scope credit is not certification
+ of actual participant coverage. Connectivity logic and thresholds are unchanged.
+corpus:
+ records: 460
+ nodes: 1375
+ edges: 530
+ review_status_counts:
+ needs_research: 54
+ pending: 18
+ reviewed: 388
+lint_environment:
+ path: /private/tmp/communitymech-batch100/lint-env
+ scope: Temporary established Python3.13 lint environment; project dependencies unchanged.
+limitations:
+- Both-root baseline precedes primary research:460records,923caches,57existing warnings,zero structural defects.
+ All four whole records and10existing nodes/four arrows reviewed. Retain10nodes/three arrows,remove one common-cause
+ arrow,rename six nodes,no new topology.
+- All four fresh EuropePMC abstracts and Crossref identities checked. Biomethanation and tobacco complete main-body
+ XML texts read including methods,results,discussion,table text and captions. No original figure pixels,separate
+ supplementary files,raw data or analysis code audited. Figure alt text is not independent experimental evidence.
+- Arsenic and compost changes are abstract-bounded. Neither EuropePMC metadata exposed a PMC article; DOI searches
+ found publisher pages whose opens returned403. No exhaustive full-text absence claim,access bypass or author contact.
+ Existing caches retained; no article-body import. Tobacco source license is CC BY-NC-ND4.0,not unrestricted CC
+ BY.
+- Arsenic retains direct NanoSIMS carbon transfer and reciprocal-growth mutualism. Supplemented heterotroph culture
+ and genomic complementarity do not independently establish oxygen-source necessity,nitrogen transfer or the identity
+ of exchanged carbon compounds. Existing culture-conditions discussion remains open.
+- Biomethanation preserves measured methane and VFA outcomes from a single sequential CSTR. External gas supply
+ is not microbial cross-feeding. Taxon-specific routes and thermodynamic cooperation remain interpretations; qPCR
+ counts are not activity or viability. Washout affects pools,phase1sampling wording is not assigned to phase4.
+ Non-graph roles/viability claims remain1935.
+- Compost retains reported maturation,transient ARG rebound and later attenuation. KEGG and potential host-gene
+ networks are not expression,actual motility or transfer-frequency measurements. Maturation-to-attenuation remains
+ PARTIAL; no maturation-to-profile causation is inferred from shared inoculation. Non-graph overview/role/access
+ wording remains1936.
+- Tobacco keeps positive strain-specific broth and combined field-treatment results,including the Y878 null enhancement.
+ cheA positivity is potential,not measured root migration; authors call for non-chemotactic controls. Source species/strain
+ rows,resource-count discrepancies and tomato caption wording remain1937. The graph does not certify the current
+ merged two-row taxonomy.
+- Initial all-state1168issue titles/bodies searched; fresh pre-creation expanded alias/DOI search receipt records
+ exact count and local paths. Matching1160/1162 bodies read and distinct. Local searches include hidden/ignored
+ files,excluding.git,docs,site,references_cache,.env; not a historical PR-comment audit.
+- Four guarded writes preserve456otherrecords,all923caches,unrelated raw YAML blocks,all prior histories/decisions.
+ Four append-only histories and curation events. Taxon identities unchanged; evidence aliases detached. No new
+ experimental or optimization protocol.
+- 'Existing-graph repair with no new nodes/directions: no Edison run,provider submission or spend. Prior authorized
+ Ruegeria1883 authentication blocker not retried unchanged; no credential inspected. Source-based self-adversarial
+ review is not independent approval. Overall review,protected merge and branch deletion remain incomplete.'
diff --git a/reports/causal_graph_review/cache-provenance-20261008-batch120.json b/reports/causal_graph_review/cache-provenance-20261008-batch120.json
new file mode 100644
index 000000000..467800ea1
--- /dev/null
+++ b/reports/causal_graph_review/cache-provenance-20261008-batch120.json
@@ -0,0 +1,430 @@
+{
+ "changes": [],
+ "unchanged_cache_files": 923,
+ "primary_artifacts": {
+ "/private/tmp/communitymech-batch120/arsenic-abstract.txt": "a909e837092f1da517e50c42ff313c20550b11cb582d166ddf59d8586ddc2d4c",
+ "/private/tmp/communitymech-batch120/arsenic-crossref.json": "3149d8a27a6c985fa051aa8f72f0d7e9e30973772db3b6ac6f0ce9e3fa1409a9",
+ "/private/tmp/communitymech-batch120/arsenic-metadata.json": "ac574c108980520414341685d5eb2e6799b923575355b1c78c2f63c1c33c41d8",
+ "/private/tmp/communitymech-batch120/baseline.json": "d42d40339f6ba33b43924bf90686d932911392d036e74948cee75f9c42ff72f0",
+ "/private/tmp/communitymech-batch120/biomethane-abstract.txt": "ad02f9b8ff0bae6cbb65b0f27897c15e0a811df73f4ede1b030b6d3f57c691c0",
+ "/private/tmp/communitymech-batch120/biomethane-crossref.json": "a746e5cb42ee04cae8c3570416db6e71a1bd77c0ac359edf3bd3c0a31af52da2",
+ "/private/tmp/communitymech-batch120/biomethane-metadata.json": "0825df418eecc1d99e9dd929f807a1543fbc41a3770b6f2fe7f970867d751289",
+ "/private/tmp/communitymech-batch120/biomethane-primary.txt": "118147cf4280579fd51de0a87a785cfc692c3a61d3744f3654a781f199d7c982",
+ "/private/tmp/communitymech-batch120/biomethane-primary.xml": "c2fa0a603345aa191a0c2b0baf002377049dbcf1314df2a03e1547e70e9738f3",
+ "/private/tmp/communitymech-batch120/compost-abstract.txt": "292153c2db3d6d378c131f0441260289cb918332db5e54710a14d7d118a81cf1",
+ "/private/tmp/communitymech-batch120/compost-crossref.json": "ac99461fc313a7938ec8c8575672e8e953347b1585e259f725a67c8caa51ef5d",
+ "/private/tmp/communitymech-batch120/compost-metadata.json": "2a7db350a825482366f272247bed219889838e1b7c1984052d07416bb472591e",
+ "/private/tmp/communitymech-batch120/issue-dedup-current.json": "3cc0aa058fb10c87f24a23b942fce47a8522f99da4cf25f90ca959c2f7bf0696",
+ "/private/tmp/communitymech-batch120/local-matches-expanded.txt": "5463acc4575050d5644d3bcd0626f449ec01ea39f106c78e6593731682138272",
+ "/private/tmp/communitymech-batch120/local-matches.txt": "8fae12d5cc5b383bf190840897389fcb1eb473d6ac069e04336505322a475f49",
+ "/private/tmp/communitymech-batch120/primary-manifest.json": "3153d33ec4b983c9f5cd4a61126ad4b67db94f70b22494f40cc6f644276dc04f",
+ "/private/tmp/communitymech-batch120/target-baseline.json": "b3e222155b610d5d68957d5f8310c10dee71335bbc658eecbad25cd55ff3c0bf",
+ "/private/tmp/communitymech-batch120/tobacco-abstract.txt": "d43a05eae6fa9d0482997ea6ee7ab9f0ed61b69a9bd6dfe46f4bae622da2c45f",
+ "/private/tmp/communitymech-batch120/tobacco-crossref.json": "81ebdc1512fe7f4f6223878ef206fef2e00b1d89746c5fbceb62d1f2a1a6a103",
+ "/private/tmp/communitymech-batch120/tobacco-metadata.json": "0cc228df759e084065a551f5c853db1b5611d778ea598ea31bf638eb43f5747c",
+ "/private/tmp/communitymech-batch120/tobacco-primary.txt": "aab21d91bbaccd305b39a0d53a598c013717825a2d7ed294892d7b1f9329693b",
+ "/private/tmp/communitymech-batch120/tobacco-primary.xml": "a5b94ad21ff186c3bd617fa9c5a3932dc898200789bbc686a1a577cafadcd5c7",
+ "references_cache/PMID_40670700.txt": "37ffd9320d083751cc694555dd3530044fa8b1fba07d4543242aa9545028f31a",
+ "references_cache/PMID_41839407.md": "f514018cde834bbe39601275e389eaacfd7b274f4422687e713f7852f7812929",
+ "references_cache/PMID_42293522.txt": "436160c020b6dea8acef0eeba5c9ff81d7b2ba18f5ed7b400445f6fdc29541b1",
+ "references_cache/PMID_42468699.txt": "79d5c2a3114b5d25e1bc789a2288ebf584858f799b995c40adb5bf4beca4a896"
+ },
+ "source_access": {
+ "retrieval_manifest": {
+ "arsenic": {
+ "pmid": "42468699",
+ "doi": "10.1016/j.biortech.2026.135440",
+ "pmcid": null,
+ "title": "Arsenic detoxification mediated by mutualistic cross-feeding in a thermophilic microbial consortium.",
+ "metadata": "/private/tmp/communitymech-batch120/arsenic-metadata.json",
+ "metadata_sha256": "ac574c108980520414341685d5eb2e6799b923575355b1c78c2f63c1c33c41d8",
+ "retrievals": [
+ {
+ "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A42468699+AND+SRC%3AMED&format=json&resultType=core",
+ "status": "retrieved"
+ }
+ ],
+ "abstract": "/private/tmp/communitymech-batch120/arsenic-abstract.txt",
+ "abstract_sha256": "a909e837092f1da517e50c42ff313c20550b11cb582d166ddf59d8586ddc2d4c",
+ "crossref": "/private/tmp/communitymech-batch120/arsenic-crossref.json",
+ "crossref_sha256": "3149d8a27a6c985fa051aa8f72f0d7e9e30973772db3b6ac6f0ce9e3fa1409a9",
+ "crossref_license": [
+ {
+ "start": {
+ "date-parts": [
+ [
+ 2026,
+ 12,
+ 1
+ ]
+ ],
+ "date-time": "2026-12-01T00:00:00Z",
+ "timestamp": 1796083200000
+ },
+ "content-version": "tdm",
+ "delay-in-days": 0,
+ "URL": "https://www.elsevier.com/tdm/userlicense/1.0/"
+ },
+ {
+ "start": {
+ "date-parts": [
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+ ]
+ ],
+ "date-time": "2026-12-01T00:00:00Z",
+ "timestamp": 1796083200000
+ },
+ "content-version": "tdm",
+ "delay-in-days": 0,
+ "URL": "https://www.elsevier.com/legal/tdmrep-license"
+ },
+ {
+ "start": {
+ "date-parts": [
+ [
+ 2026,
+ 12,
+ 1
+ ]
+ ],
+ "date-time": "2026-12-01T00:00:00Z",
+ "timestamp": 1796083200000
+ },
+ "content-version": "stm-asf",
+ "delay-in-days": 0,
+ "URL": "https://doi.org/10.15223/policy-017"
+ },
+ {
+ "start": {
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+ ]
+ ],
+ "date-time": "2026-12-01T00:00:00Z",
+ "timestamp": 1796083200000
+ },
+ "content-version": "stm-asf",
+ "delay-in-days": 0,
+ "URL": "https://doi.org/10.15223/policy-037"
+ },
+ {
+ "start": {
+ "date-parts": [
+ [
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+ 12,
+ 1
+ ]
+ ],
+ "date-time": "2026-12-01T00:00:00Z",
+ "timestamp": 1796083200000
+ },
+ "content-version": "stm-asf",
+ "delay-in-days": 0,
+ "URL": "https://doi.org/10.15223/policy-012"
+ },
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+ },
+ "content-version": "stm-asf",
+ "delay-in-days": 0,
+ "URL": "https://doi.org/10.15223/policy-029"
+ },
+ {
+ "start": {
+ "date-parts": [
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+ ]
+ ],
+ "date-time": "2026-12-01T00:00:00Z",
+ "timestamp": 1796083200000
+ },
+ "content-version": "stm-asf",
+ "delay-in-days": 0,
+ "URL": "https://doi.org/10.15223/policy-004"
+ }
+ ]
+ },
+ "biomethane": {
+ "pmid": "42293522",
+ "doi": "10.3389/fmicb.2026.1840981",
+ "pmcid": "PMC13256089",
+ "title": "Development of a mixed microbial culture for robust high-throughput ex-situ thermophilic biomethanation.",
+ "metadata": "/private/tmp/communitymech-batch120/biomethane-metadata.json",
+ "metadata_sha256": "0825df418eecc1d99e9dd929f807a1543fbc41a3770b6f2fe7f970867d751289",
+ "retrievals": [
+ {
+ "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A42293522+AND+SRC%3AMED&format=json&resultType=core",
+ "status": "retrieved"
+ },
+ {
+ "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13256089/fullTextXML",
+ "status": "retrieved_not_yet_read"
+ }
+ ],
+ "abstract": "/private/tmp/communitymech-batch120/biomethane-abstract.txt",
+ "abstract_sha256": "ad02f9b8ff0bae6cbb65b0f27897c15e0a811df73f4ede1b030b6d3f57c691c0",
+ "xml": "/private/tmp/communitymech-batch120/biomethane-primary.xml",
+ "xml_sha256": "c2fa0a603345aa191a0c2b0baf002377049dbcf1314df2a03e1547e70e9738f3",
+ "primary_text": "/private/tmp/communitymech-batch120/biomethane-primary.txt",
+ "primary_text_sha256": "118147cf4280579fd51de0a87a785cfc692c3a61d3744f3654a781f199d7c982",
+ "license": [
+ "https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms."
+ ],
+ "crossref": "/private/tmp/communitymech-batch120/biomethane-crossref.json",
+ "crossref_sha256": "a746e5cb42ee04cae8c3570416db6e71a1bd77c0ac359edf3bd3c0a31af52da2",
+ "crossref_license": [
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+ ],
+ "date-time": "2026-05-28T00:00:00Z",
+ "timestamp": 1779926400000
+ },
+ "content-version": "vor",
+ "delay-in-days": 0,
+ "URL": "https://creativecommons.org/licenses/by/4.0/"
+ }
+ ]
+ },
+ "compost": {
+ "pmid": "41839407",
+ "doi": "10.1016/j.biortech.2026.134433",
+ "pmcid": null,
+ "title": "Metabolic reprogramming disrupts the resistome-mobilome nexus and enhances bio-sanitization in synthetic microbial community-mediated composting.",
+ "metadata": "/private/tmp/communitymech-batch120/compost-metadata.json",
+ "metadata_sha256": "2a7db350a825482366f272247bed219889838e1b7c1984052d07416bb472591e",
+ "retrievals": [
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+ "status": "retrieved"
+ }
+ ],
+ "abstract": "/private/tmp/communitymech-batch120/compost-abstract.txt",
+ "abstract_sha256": "292153c2db3d6d378c131f0441260289cb918332db5e54710a14d7d118a81cf1",
+ "crossref": "/private/tmp/communitymech-batch120/compost-crossref.json",
+ "crossref_sha256": "ac99461fc313a7938ec8c8575672e8e953347b1585e259f725a67c8caa51ef5d",
+ "crossref_license": [
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+ 1
+ ]
+ ],
+ "date-time": "2026-06-01T00:00:00Z",
+ "timestamp": 1780272000000
+ },
+ "content-version": "tdm",
+ "delay-in-days": 0,
+ "URL": "https://www.elsevier.com/tdm/userlicense/1.0/"
+ },
+ {
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+ "title": "Development of a chemotactic SynCom bioorganic fertilizer for biocontrol of bacterial wilt in tobacco fields.",
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+ "license": [
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+ "All four fresh EuropePMC abstracts and Crossref identities checked. Biomethanation and tobacco complete main-body XML texts read including methods,results,discussion,table text and captions. No original figure pixels,separate supplementary files,raw data or analysis code audited. Figure alt text is not independent experimental evidence.",
+ "Arsenic and compost changes are abstract-bounded. Neither EuropePMC metadata exposed a PMC article; DOI searches found publisher pages whose opens returned403. No exhaustive full-text absence claim,access bypass or author contact. Existing caches retained; no article-body import. Tobacco source license is CC BY-NC-ND4.0,not unrestricted CC BY.",
+ "Arsenic retains direct NanoSIMS carbon transfer and reciprocal-growth mutualism. Supplemented heterotroph culture and genomic complementarity do not independently establish oxygen-source necessity,nitrogen transfer or the identity of exchanged carbon compounds. Existing culture-conditions discussion remains open.",
+ "Biomethanation preserves measured methane and VFA outcomes from a single sequential CSTR. External gas supply is not microbial cross-feeding. Taxon-specific routes and thermodynamic cooperation remain interpretations; qPCR counts are not activity or viability. Washout affects pools,phase1sampling wording is not assigned to phase4. Non-graph roles/viability claims remain1935.",
+ "Compost retains reported maturation,transient ARG rebound and later attenuation. KEGG and potential host-gene networks are not expression,actual motility or transfer-frequency measurements. Maturation-to-attenuation remains PARTIAL; no maturation-to-profile causation is inferred from shared inoculation. Non-graph overview/role/access wording remains1936.",
+ "Tobacco keeps positive strain-specific broth and combined field-treatment results,including the Y878 null enhancement. cheA positivity is potential,not measured root migration; authors call for non-chemotactic controls. Source species/strain rows,resource-count discrepancies and tomato caption wording remain1937. The graph does not certify the current merged two-row taxonomy."
+ ]
+ },
+ "limitations": [
+ "Both-root baseline precedes primary research:460records,923caches,57existing warnings,zero structural defects. All four whole records and10existing nodes/four arrows reviewed. Retain10nodes/three arrows,remove one common-cause arrow,rename six nodes,no new topology.",
+ "All four fresh EuropePMC abstracts and Crossref identities checked. Biomethanation and tobacco complete main-body XML texts read including methods,results,discussion,table text and captions. No original figure pixels,separate supplementary files,raw data or analysis code audited. Figure alt text is not independent experimental evidence.",
+ "Arsenic and compost changes are abstract-bounded. Neither EuropePMC metadata exposed a PMC article; DOI searches found publisher pages whose opens returned403. No exhaustive full-text absence claim,access bypass or author contact. Existing caches retained; no article-body import. Tobacco source license is CC BY-NC-ND4.0,not unrestricted CC BY.",
+ "Arsenic retains direct NanoSIMS carbon transfer and reciprocal-growth mutualism. Supplemented heterotroph culture and genomic complementarity do not independently establish oxygen-source necessity,nitrogen transfer or the identity of exchanged carbon compounds. Existing culture-conditions discussion remains open.",
+ "Biomethanation preserves measured methane and VFA outcomes from a single sequential CSTR. External gas supply is not microbial cross-feeding. Taxon-specific routes and thermodynamic cooperation remain interpretations; qPCR counts are not activity or viability. Washout affects pools,phase1sampling wording is not assigned to phase4. Non-graph roles/viability claims remain1935.",
+ "Compost retains reported maturation,transient ARG rebound and later attenuation. KEGG and potential host-gene networks are not expression,actual motility or transfer-frequency measurements. Maturation-to-attenuation remains PARTIAL; no maturation-to-profile causation is inferred from shared inoculation. Non-graph overview/role/access wording remains1936.",
+ "Tobacco keeps positive strain-specific broth and combined field-treatment results,including the Y878 null enhancement. cheA positivity is potential,not measured root migration; authors call for non-chemotactic controls. Source species/strain rows,resource-count discrepancies and tomato caption wording remain1937. The graph does not certify the current merged two-row taxonomy.",
+ "Initial all-state1168issue titles/bodies searched; fresh pre-creation expanded alias/DOI search receipt records exact count and local paths. Matching1160/1162 bodies read and distinct. Local searches include hidden/ignored files,excluding.git,docs,site,references_cache,.env; not a historical PR-comment audit.",
+ "Four guarded writes preserve456otherrecords,all923caches,unrelated raw YAML blocks,all prior histories/decisions. Four append-only histories and curation events. Taxon identities unchanged; evidence aliases detached. No new experimental or optimization protocol.",
+ "Existing-graph repair with no new nodes/directions: no Edison run,provider submission or spend. Prior authorized Ruegeria1883 authentication blocker not retried unchanged; no credential inspected. Source-based self-adversarial review is not independent approval. Overall review,protected merge and branch deletion remain incomplete."
+ ]
+}
diff --git a/reports/causal_graph_review/decisions/20261008-four-records-batch120.yaml b/reports/causal_graph_review/decisions/20261008-four-records-batch120.yaml
new file mode 100644
index 000000000..05132ce9f
--- /dev/null
+++ b/reports/causal_graph_review/decisions/20261008-four-records-batch120.yaml
@@ -0,0 +1,899 @@
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+pre_source_baseline_sha256: d42d40339f6ba33b43924bf90686d932911392d036e74948cee75f9c42ff72f0
+issues:
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+- 1932
+- 1933
+- 1934
+unresolved_research_issues: []
+unresolved_non_graph_issues:
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+- 1936
+- 1937
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+ doi: 10.1016/j.biortech.2026.135440
+ pmcid: null
+ title: Arsenic detoxification mediated by mutualistic cross-feeding in a thermophilic microbial consortium.
+ metadata: /private/tmp/communitymech-batch120/arsenic-metadata.json
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+ title: Development of a mixed microbial culture for robust high-throughput ex-situ thermophilic biomethanation.
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+ is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original
+ publication in this journal is cited, in accordance with accepted academic practice. No use, distribution
+ or reproduction is permitted which does not comply with these terms.
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+ doi: 10.1016/j.biortech.2026.134433
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+ title: Metabolic reprogramming disrupts the resistome-mobilome nexus and enhances bio-sanitization in synthetic
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+ doi: 10.1007/s00253-025-13547-6
+ pmcid: PMC12267373
+ title: Development of a chemotactic SynCom bioorganic fertilizer for biocontrol of bacterial wilt in tobacco
+ fields.
+ metadata: /private/tmp/communitymech-batch120/tobacco-metadata.json
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+ status: retrieved
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+ xml: /private/tmp/communitymech-batch120/tobacco-primary.xml
+ xml_sha256: a5b94ad21ff186c3bd617fa9c5a3932dc898200789bbc686a1a577cafadcd5c7
+ primary_text: /private/tmp/communitymech-batch120/tobacco-primary.txt
+ primary_text_sha256: aab21d91bbaccd305b39a0d53a598c013717825a2d7ed294892d7b1f9329693b
+ license:
+ - "Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0\
+ \ International License, which permits any non-commercial use, sharing, distribution and reproduction in\
+ \ any medium or format, as long as you give appropriate credit to the original author(s) and the source,\
+ \ provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You\
+ \ do not have permission under this licence to share adapted material derived from this article or parts\
+ \ of it. The images or other third party material in this article are included in the article\u2019s Creative\
+ \ Commons licence, unless indicated otherwise in a credit line to the material. If material is not included\
+ \ in the article\u2019s Creative Commons licence and your intended use is not permitted by statutory regulation\
+ \ or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To\
+ \ view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/."
+ crossref: /private/tmp/communitymech-batch120/tobacco-crossref.json
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+ actual_read_scope:
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+ XML texts read including methods,results,discussion,table text and captions. No original figure pixels,separate
+ supplementary files,raw data or analysis code audited. Figure alt text is not independent experimental evidence.
+ - Arsenic and compost changes are abstract-bounded. Neither EuropePMC metadata exposed a PMC article; DOI searches
+ found publisher pages whose opens returned403. No exhaustive full-text absence claim,access bypass or author
+ contact. Existing caches retained; no article-body import. Tobacco source license is CC BY-NC-ND4.0,not unrestricted
+ CC BY.
+ - Arsenic retains direct NanoSIMS carbon transfer and reciprocal-growth mutualism. Supplemented heterotroph culture
+ and genomic complementarity do not independently establish oxygen-source necessity,nitrogen transfer or the
+ identity of exchanged carbon compounds. Existing culture-conditions discussion remains open.
+ - Biomethanation preserves measured methane and VFA outcomes from a single sequential CSTR. External gas supply
+ is not microbial cross-feeding. Taxon-specific routes and thermodynamic cooperation remain interpretations;
+ qPCR counts are not activity or viability. Washout affects pools,phase1sampling wording is not assigned to phase4.
+ Non-graph roles/viability claims remain1935.
+ - Compost retains reported maturation,transient ARG rebound and later attenuation. KEGG and potential host-gene
+ networks are not expression,actual motility or transfer-frequency measurements. Maturation-to-attenuation remains
+ PARTIAL; no maturation-to-profile causation is inferred from shared inoculation. Non-graph overview/role/access
+ wording remains1936.
+ - Tobacco keeps positive strain-specific broth and combined field-treatment results,including the Y878 null enhancement.
+ cheA positivity is potential,not measured root migration; authors call for non-chemotactic controls. Source
+ species/strain rows,resource-count discrepancies and tomato caption wording remain1937. The graph does not certify
+ the current merged two-row taxonomy.
+primary_artifacts:
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+reviewed_counts:
+ original_nodes: 10
+ retained_nodes: 10
+ removed_nodes: 0
+ original_arrows: 4
+ retained_arrows: 3
+ removed_arrows: 1
+ renamed_nodes: 6
+ graph_quotations: 27
+ discussion_quotations: 6
+ new_discussions: 4
+primary_graph_snippet_count: 27
+snippet_checks:
+- record: Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture
+ node: Cyanobacterial Organic-Carbon Provisioning
+ evidence_index: 0
+ reference: PMID:42468699
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch120/arsenic-abstract.txt
+ cache_artifact: references_cache/PMID_42468699.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture
+ node: Cyanobacterial Organic-Carbon Provisioning
+ evidence_index: 1
+ reference: PMID:42468699
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch120/arsenic-abstract.txt
+ cache_artifact: references_cache/PMID_42468699.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture
+ node: Chelatococcus Arsenite Detoxification
+ evidence_index: 0
+ reference: PMID:42468699
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch120/arsenic-abstract.txt
+ cache_artifact: references_cache/PMID_42468699.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture
+ node: Chelatococcus Arsenite Detoxification
+ evidence_index: 1
+ reference: PMID:42468699
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch120/arsenic-abstract.txt
+ cache_artifact: references_cache/PMID_42468699.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture
+ node: Chelatococcus Arsenite Detoxification
+ evidence_index: 2
+ reference: PMID:42468699
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch120/arsenic-abstract.txt
+ cache_artifact: references_cache/PMID_42468699.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture
+ node: Chelatococcus Arsenite Detoxification
+ evidence_index: 3
+ reference: PMID:42468699
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch120/arsenic-abstract.txt
+ cache_artifact: references_cache/PMID_42468699.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Thermophilic_ExSitu_Biomethanation_Mixed_Culture
+ node: Thermophilic H2/CO2 Biomethanation
+ evidence_index: 0
+ reference: PMID:42293522
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch120/biomethane-primary.txt
+ cache_artifact: references_cache/PMID_42293522.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Thermophilic_ExSitu_Biomethanation_Mixed_Culture
+ node: Thermophilic H2/CO2 Biomethanation
+ evidence_index: 1
+ reference: PMID:42293522
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch120/biomethane-primary.txt
+ cache_artifact: references_cache/PMID_42293522.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Thermophilic_ExSitu_Biomethanation_Mixed_Culture
+ node: Thermophilic H2/CO2 Biomethanation
+ evidence_index: 2
+ reference: PMID:42293522
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch120/biomethane-primary.txt
+ cache_artifact: references_cache/PMID_42293522.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Thermophilic_ExSitu_Biomethanation_Mixed_Culture
+ node: VFA dynamics and inferred interspecies turnover
+ evidence_index: 0
+ reference: PMID:42293522
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch120/biomethane-primary.txt
+ cache_artifact: references_cache/PMID_42293522.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Thermophilic_ExSitu_Biomethanation_Mixed_Culture
+ node: VFA dynamics and inferred interspecies turnover
+ evidence_index: 1
+ reference: PMID:42293522
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch120/biomethane-primary.txt
+ cache_artifact: references_cache/PMID_42293522.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Thermophilic_ExSitu_Biomethanation_Mixed_Culture
+ node: VFA dynamics and inferred interspecies turnover
+ evidence_index: 2
+ reference: PMID:42293522
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch120/biomethane-primary.txt
+ cache_artifact: references_cache/PMID_42293522.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Thermophilic_ExSitu_Biomethanation_Mixed_Culture
+ node: VFA dynamics and inferred interspecies turnover
+ evidence_index: 3
+ reference: PMID:42293522
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch120/biomethane-primary.txt
+ cache_artifact: references_cache/PMID_42293522.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Thermophilic_ExSitu_Biomethanation_Mixed_Culture
+ node: VFA dynamics and inferred interspecies turnover
+ evidence_index: 4
+ reference: PMID:42293522
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch120/biomethane-primary.txt
+ cache_artifact: references_cache/PMID_42293522.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization
+ node: SynCom-associated compost maturation
+ evidence_index: 0
+ reference: PMID:41839407
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch120/compost-abstract.txt
+ cache_artifact: references_cache/PMID_41839407.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization
+ node: SynCom-associated compost maturation
+ evidence_index: 1
+ reference: PMID:41839407
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch120/compost-abstract.txt
+ cache_artifact: references_cache/PMID_41839407.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization
+ node: Reported compost resistome and pathogen attenuation
+ evidence_index: 0
+ reference: PMID:41839407
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch120/compost-abstract.txt
+ cache_artifact: references_cache/PMID_41839407.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization
+ node: Reported compost resistome and pathogen attenuation
+ evidence_index: 1
+ reference: PMID:41839407
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch120/compost-abstract.txt
+ cache_artifact: references_cache/PMID_41839407.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization
+ node: Metagenomic signatures of reduced HGT potential
+ evidence_index: 0
+ reference: PMID:41839407
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch120/compost-abstract.txt
+ cache_artifact: references_cache/PMID_41839407.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization
+ node: Metagenomic signatures of reduced HGT potential
+ evidence_index: 1
+ reference: PMID:41839407
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch120/compost-abstract.txt
+ cache_artifact: references_cache/PMID_41839407.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization
+ node: Metagenomic signatures of reduced HGT potential
+ evidence_index: 2
+ reference: PMID:41839407
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch120/compost-abstract.txt
+ cache_artifact: references_cache/PMID_41839407.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Tobacco_Chemotactic_Biocontrol_SynCom
+ node: Strain-specific prebiotic enhancement
+ evidence_index: 0
+ reference: PMID:40670700
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch120/tobacco-primary.txt
+ cache_artifact: references_cache/PMID_40670700.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Tobacco_Chemotactic_Biocontrol_SynCom
+ node: Strain-specific prebiotic enhancement
+ evidence_index: 1
+ reference: PMID:40670700
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch120/tobacco-primary.txt
+ cache_artifact: references_cache/PMID_40670700.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Tobacco_Chemotactic_Biocontrol_SynCom
+ node: Antagonism by cheA-positive SynCom isolates
+ evidence_index: 0
+ reference: PMID:40670700
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch120/tobacco-primary.txt
+ cache_artifact: references_cache/PMID_40670700.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Tobacco_Chemotactic_Biocontrol_SynCom
+ node: Antagonism by cheA-positive SynCom isolates
+ evidence_index: 1
+ reference: PMID:40670700
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch120/tobacco-primary.txt
+ cache_artifact: references_cache/PMID_40670700.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Tobacco_Chemotactic_Biocontrol_SynCom
+ node: Tobacco Field Protection and Yield Enhancement
+ evidence_index: 0
+ reference: PMID:40670700
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch120/tobacco-primary.txt
+ cache_artifact: references_cache/PMID_40670700.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Tobacco_Chemotactic_Biocontrol_SynCom
+ node: Tobacco Field Protection and Yield Enhancement
+ evidence_index: 1
+ reference: PMID:40670700
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch120/tobacco-primary.txt
+ cache_artifact: references_cache/PMID_40670700.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+discussion_snippet_checks:
+- record: Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture
+ node: arsenic_causal_scope_batch120
+ evidence_index: 0
+ reference: PMID:42468699
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch120/arsenic-abstract.txt
+ cache_artifact: references_cache/PMID_42468699.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Thermophilic_ExSitu_Biomethanation_Mixed_Culture
+ node: taxonomy_resolution
+ evidence_index: 0
+ reference: PMID:42293522
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch120/biomethane-primary.txt
+ cache_artifact: references_cache/PMID_42293522.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Thermophilic_ExSitu_Biomethanation_Mixed_Culture
+ node: industrial_nonsterile_stability
+ evidence_index: 0
+ reference: PMID:42293522
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch120/biomethane-primary.txt
+ cache_artifact: references_cache/PMID_42293522.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Thermophilic_ExSitu_Biomethanation_Mixed_Culture
+ node: biomethane_causal_scope_batch120
+ evidence_index: 0
+ reference: PMID:42293522
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch120/biomethane-primary.txt
+ cache_artifact: references_cache/PMID_42293522.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization
+ node: compost_causal_scope_batch120
+ evidence_index: 0
+ reference: PMID:41839407
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch120/compost-abstract.txt
+ cache_artifact: references_cache/PMID_41839407.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Tobacco_Chemotactic_Biocontrol_SynCom
+ node: tobacco_causal_scope_batch120
+ evidence_index: 0
+ reference: PMID:40670700
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch120/tobacco-primary.txt
+ cache_artifact: references_cache/PMID_40670700.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+cache_changes: []
+edison:
+ required_for_this_repair: false
+ provider_submissions: 0
+ credits_spent: 0
+ new_nodes_or_directions: 0
+ prior_extension_blocker: 'Ruegeria1883: configured authentication unavailable in prior approved invocation; no
+ unchanged-state retry.'
+limitations:
+- Both-root baseline precedes primary research:460records,923caches,57existing warnings,zero structural defects.
+ All four whole records and10existing nodes/four arrows reviewed. Retain10nodes/three arrows,remove one common-cause
+ arrow,rename six nodes,no new topology.
+- All four fresh EuropePMC abstracts and Crossref identities checked. Biomethanation and tobacco complete main-body
+ XML texts read including methods,results,discussion,table text and captions. No original figure pixels,separate
+ supplementary files,raw data or analysis code audited. Figure alt text is not independent experimental evidence.
+- Arsenic and compost changes are abstract-bounded. Neither EuropePMC metadata exposed a PMC article; DOI searches
+ found publisher pages whose opens returned403. No exhaustive full-text absence claim,access bypass or author contact.
+ Existing caches retained; no article-body import. Tobacco source license is CC BY-NC-ND4.0,not unrestricted CC
+ BY.
+- Arsenic retains direct NanoSIMS carbon transfer and reciprocal-growth mutualism. Supplemented heterotroph culture
+ and genomic complementarity do not independently establish oxygen-source necessity,nitrogen transfer or the identity
+ of exchanged carbon compounds. Existing culture-conditions discussion remains open.
+- Biomethanation preserves measured methane and VFA outcomes from a single sequential CSTR. External gas supply
+ is not microbial cross-feeding. Taxon-specific routes and thermodynamic cooperation remain interpretations; qPCR
+ counts are not activity or viability. Washout affects pools,phase1sampling wording is not assigned to phase4.
+ Non-graph roles/viability claims remain1935.
+- Compost retains reported maturation,transient ARG rebound and later attenuation. KEGG and potential host-gene
+ networks are not expression,actual motility or transfer-frequency measurements. Maturation-to-attenuation remains
+ PARTIAL; no maturation-to-profile causation is inferred from shared inoculation. Non-graph overview/role/access
+ wording remains1936.
+- Tobacco keeps positive strain-specific broth and combined field-treatment results,including the Y878 null enhancement.
+ cheA positivity is potential,not measured root migration; authors call for non-chemotactic controls. Source species/strain
+ rows,resource-count discrepancies and tomato caption wording remain1937. The graph does not certify the current
+ merged two-row taxonomy.
+- Initial all-state1168issue titles/bodies searched; fresh pre-creation expanded alias/DOI search receipt records
+ exact count and local paths. Matching1160/1162 bodies read and distinct. Local searches include hidden/ignored
+ files,excluding.git,docs,site,references_cache,.env; not a historical PR-comment audit.
+- Four guarded writes preserve456otherrecords,all923caches,unrelated raw YAML blocks,all prior histories/decisions.
+ Four append-only histories and curation events. Taxon identities unchanged; evidence aliases detached. No new
+ experimental or optimization protocol.
+- 'Existing-graph repair with no new nodes/directions: no Edison run,provider submission or spend. Prior authorized
+ Ruegeria1883 authentication blocker not retried unchanged; no credential inspected. Source-based self-adversarial
+ review is not independent approval. Overall review,protected merge and branch deletion remain incomplete.'
+records:
+- path: kb/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml
+ id: CommunityMech:000454
+ original_sha256: ab97378f5f2ca6160bdceebee4eb24276dbc2ffddc1b49051355ba4609dfae35
+ record_sha256: bc09df336e1e5a701bf24c3f47eed41c24829eb4618c8597840052a93d0f822c
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261008-four-records-batch120.yaml
+ scope: Whole record and all existing nodes/arrows reviewed; existing-graph repair, not whole-record certification.
+ summary: Retain experimentally supported carbon cross-feeding and tracer direction without inventing a compound
+ or nitrogen flux.; Retain reciprocal-growth mutualism with direct growth evidence, bounding supplemented-culture
+ comparisons and genomic route inference.
+ node_decisions:
+ - node: Cyanobacterial Organic-Carbon Provisioning
+ rationale: Retain experimentally supported carbon cross-feeding and tracer direction without inventing a compound
+ or nitrogen flux.
+ - node: Chelatococcus Arsenite Detoxification
+ rationale: Retain reciprocal-growth mutualism with direct growth evidence, bounding supplemented-culture comparisons
+ and genomic route inference.
+ removed_node_decisions: []
+ renamed_nodes: {}
+ edges_before: []
+ edges_after: []
+ retained_edge_decisions: []
+ removed_edge_decisions: []
+ references:
+ - PMID:42468699
+ issues:
+ - 1931
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture/2026-10-08T141541Z-codex-62412f.yaml
+- path: kb/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml
+ id: CommunityMech:000416
+ original_sha256: 07c4856308831b4b7bdf1fc50d2442584f1a4c2e5c8431a334e81557eec66727
+ record_sha256: 51357584e2099b2916e81f893f46fc0af8cede23e3b2616ca957adc5f7a4bf71
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261008-four-records-batch120.yaml
+ scope: Whole record and all existing nodes/arrows reviewed; existing-graph repair, not whole-record certification.
+ summary: Retain measured external-gas methane production without coding abiotic supply as microbial cross-feeding
+ or qPCR as activity.; Retain VFA measurements and source interpretations while removing an unsupported demonstrated-syntrophy
+ type.
+ node_decisions:
+ - node: Thermophilic H2/CO2 Biomethanation
+ rationale: Retain measured external-gas methane production without coding abiotic supply as microbial cross-feeding
+ or qPCR as activity.
+ - node: VFA dynamics and inferred interspecies turnover
+ rationale: Retain VFA measurements and source interpretations while removing an unsupported demonstrated-syntrophy
+ type.
+ removed_node_decisions: []
+ renamed_nodes:
+ VFA Syntrophic Turnover: VFA dynamics and inferred interspecies turnover
+ edges_before: []
+ edges_after: []
+ retained_edge_decisions: []
+ removed_edge_decisions: []
+ references:
+ - PMID:42293522
+ issues:
+ - 1932
+ - 1935
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Thermophilic_ExSitu_Biomethanation_Mixed_Culture/2026-10-08T141542Z-codex-8205c5.yaml
+- path: kb/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml
+ id: CommunityMech:000282
+ original_sha256: ec822e47b495189805f5dc2fc9c555e7f987de9d9e3a4986dd7f89920b4def28
+ record_sha256: 9d6ab3706fb821b6231441efc4342728b21ede4ab1aad3e5962ba5dab5d79199
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261008-four-records-batch120.yaml
+ scope: Whole record and all existing nodes/arrows reviewed; existing-graph repair, not whole-record certification.
+ summary: Retain reported maturation without coding aggregate improvement as mutualism; bound the remaining environmental-mediation
+ arrow.; Retain positive later attenuation and the early rebound without claiming universal viable-pathogen elimination
+ or bilateral competition.; Represent KEGG and network findings as HGT potential, not measured transfer, expression
+ or motility.
+ node_decisions:
+ - node: SynCom-associated compost maturation
+ rationale: Retain reported maturation without coding aggregate improvement as mutualism; bound the remaining
+ environmental-mediation arrow.
+ - node: Reported compost resistome and pathogen attenuation
+ rationale: Retain positive later attenuation and the early rebound without claiming universal viable-pathogen
+ elimination or bilateral competition.
+ - node: Metagenomic signatures of reduced HGT potential
+ rationale: Represent KEGG and network findings as HGT potential, not measured transfer, expression or motility.
+ removed_node_decisions: []
+ renamed_nodes:
+ SynCom-driven lignocellulose decomposition and humification: SynCom-associated compost maturation
+ Community-level bio-sanitization of high-risk pathogens: Reported compost resistome and pathogen attenuation
+ SynCom-driven suppression of horizontal gene transfer: Metagenomic signatures of reduced HGT potential
+ edges_before:
+ - &id001
+ source: SynCom-driven lignocellulose decomposition and humification
+ target: Community-level bio-sanitization of high-risk pathogens
+ description: Intensified thermophilic fermentation and faster organic-matter turnover create the SynCom-driven
+ composting trajectory linked to deep bio-sanitization and high-risk pathogen elimination.
+ - &id003
+ source: SynCom-driven lignocellulose decomposition and humification
+ target: SynCom-driven suppression of horizontal gene transfer
+ description: The SynCom-driven composting trajectory is tied to metabolic reprogramming away from a biofilm-dependent
+ defense-survival mode, restricting horizontal gene transfer opportunities in the compost.
+ edges_after:
+ - &id002
+ source: SynCom-associated compost maturation
+ target: Reported compost resistome and pathogen attenuation
+ description: 'PARTIAL: intensified fermentation and the correlated C/N decrease and humification are proposed
+ environmental contributors to later ARG and pathogen attenuation. Mantel association and the common inoculation
+ treatment support this interpretation, not selective demonstration that maturation alone mediates elimination
+ or prevents every gene-transfer event.'
+ retained_edge_decisions:
+ - before: *id001
+ after: *id002
+ rationale: 'PARTIAL: intensified fermentation and the correlated C/N decrease and humification are proposed
+ environmental contributors to later ARG and pathogen attenuation. Mantel association and the common inoculation
+ treatment support this interpretation, not selective demonstration that maturation alone mediates elimination
+ or prevents every gene-transfer event.'
+ removed_edge_decisions:
+ - edge: *id003
+ rationale: Shared SynCom inoculation and parallel associations do not show that compost maturation causes the
+ separately inferred KEGG/metagenomic profile.
+ references:
+ - PMID:41839407
+ issues:
+ - 1933
+ - 1936
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization/2026-10-08T141542Z-codex-0c3005.yaml
+- path: kb/communities/Tobacco_Chemotactic_Biocontrol_SynCom.yaml
+ id: CommunityMech:000106
+ original_sha256: b4d7702d9c87b2b55cb2b3c74598aed2bfded7afd454faed5628c817b2fdfa35
+ record_sha256: 2d1851c88c385f813706b923eeb0754bf70bbac4dd94fb15369bf5e45317e371
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261008-four-records-batch120.yaml
+ scope: Whole record and all existing nodes/arrows reviewed; existing-graph repair, not whole-record certification.
+ summary: Retain positive compound responses with isolate-specific limits and the Y878 null result.; Keep antagonism
+ and compatibility distinct from cheA-based potential and unmeasured colonization.; Preserve the positive field
+ co-treatment outcome while bounding qPCR, Tax4Fun and mechanistic attribution.
+ node_decisions:
+ - node: Strain-specific prebiotic enhancement
+ rationale: Retain positive compound responses with isolate-specific limits and the Y878 null result.
+ - node: Antagonism by cheA-positive SynCom isolates
+ rationale: Keep antagonism and compatibility distinct from cheA-based potential and unmeasured colonization.
+ - node: Tobacco Field Protection and Yield Enhancement
+ rationale: Preserve the positive field co-treatment outcome while bounding qPCR, Tax4Fun and mechanistic attribution.
+ removed_node_decisions: []
+ renamed_nodes:
+ Root-Exudate Prebiotic Enhancement: Strain-specific prebiotic enhancement
+ Chemotactic Bacterial Wilt Suppression: Antagonism by cheA-positive SynCom isolates
+ edges_before:
+ - &id004
+ source: Root-Exudate Prebiotic Enhancement
+ target: Chemotactic Bacterial Wilt Suppression
+ description: Prebiotic-stimulated SynCom growth and antagonistic bioactivity strengthen the chemotactic consortium's
+ suppression of Ralstonia.
+ - &id006
+ source: Chemotactic Bacterial Wilt Suppression
+ target: Tobacco Field Protection and Yield Enhancement
+ description: Rhizosphere colonization and antagonism by the chemotactic SynCom carry through the bioorganic
+ fertilizer into lower field Ralstonia invasion and higher tobacco yield.
+ edges_after:
+ - &id005
+ source: Strain-specific prebiotic enhancement
+ target: Antagonism by cheA-positive SynCom isolates
+ description: 'Selected compound additions enhanced broth antagonism in particular isolate assays. PARTIAL for
+ growth as the mediator: growth, broth chemistry and residual additives were not selectively separated. The
+ Y878 null enhancement result prevents generalizing this effect to all three members, and the comparison does
+ not establish enhanced chemotaxis or root colonization.'
+ - &id007
+ source: Antagonism by cheA-positive SynCom isolates
+ target: Tobacco Field Protection and Yield Enhancement
+ description: 'PARTIAL: laboratory antagonism is a candidate contribution to the field benefit of the formulated
+ SynCom fertilizer. The field contrast combined strains, prebiotics and an organic matrix against conventional
+ cow-manure fertilization; it did not isolate chemotaxis, colonization or broth antagonism as the mediator.
+ The authors explicitly identify non-chemotactic SynCom controls as future work.'
+ retained_edge_decisions:
+ - before: *id004
+ after: *id005
+ rationale: 'Selected compound additions enhanced broth antagonism in particular isolate assays. PARTIAL for
+ growth as the mediator: growth, broth chemistry and residual additives were not selectively separated. The
+ Y878 null enhancement result prevents generalizing this effect to all three members, and the comparison does
+ not establish enhanced chemotaxis or root colonization.'
+ - before: *id006
+ after: *id007
+ rationale: 'PARTIAL: laboratory antagonism is a candidate contribution to the field benefit of the formulated
+ SynCom fertilizer. The field contrast combined strains, prebiotics and an organic matrix against conventional
+ cow-manure fertilization; it did not isolate chemotaxis, colonization or broth antagonism as the mediator.
+ The authors explicitly identify non-chemotactic SynCom controls as future work.'
+ removed_edge_decisions: []
+ references:
+ - PMID:40670700
+ issues:
+ - 1934
+ - 1937
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Tobacco_Chemotactic_Biocontrol_SynCom/2026-10-08T141542Z-codex-fb2ec0.yaml
diff --git a/reports/causal_graph_review/inventory.tsv b/reports/causal_graph_review/inventory.tsv
index 49409289b..de6387842 100644
--- a/reports/causal_graph_review/inventory.tsv
+++ b/reports/causal_graph_review/inventory.tsv
@@ -421,14 +421,14 @@ kb/communities/Teosinte_Maize_Biofertilizer_SynCom7.yaml CommunityMech:000100 d2
kb/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml CommunityMech:000259 8b79efb0b04a43548b3c73ac280ac987b83c4e97f2531b55da5c940f29485eae 4 2 90.0 reports/causal_graph_review/decisions/20261008-three-records-batch113.yaml reviewed
kb/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml CommunityMech:000162 f1e51614a8c4a7856a2669afe12574d1c982f12dcebf9f53f49c65d470f747d6 3 0 68.3 reports/causal_graph_review/decisions/20261008-three-records-batch113.yaml needs_research
kb/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml CommunityMech:000182 f45e52ffbf76a2c295b73efb10bf183a01ecc03056cc11f018afe3c6e3723992 3 2 100.0 reports/causal_graph_review/decisions/20261008-two-records-batch114.yaml reviewed
-kb/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml CommunityMech:000454 ab97378f5f2ca6160bdceebee4eb24276dbc2ffddc1b49051355ba4609dfae35 2 0 70.0 pending
-kb/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml CommunityMech:000416 07c4856308831b4b7bdf1fc50d2442584f1a4c2e5c8431a334e81557eec66727 2 0 70.0 pending
-kb/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml CommunityMech:000282 ec822e47b495189805f5dc2fc9c555e7f987de9d9e3a4986dd7f89920b4def28 3 2 100.0 pending
+kb/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml CommunityMech:000454 bc09df336e1e5a701bf24c3f47eed41c24829eb4618c8597840052a93d0f822c 2 0 70.0 reports/causal_graph_review/decisions/20261008-four-records-batch120.yaml reviewed
+kb/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml CommunityMech:000416 51357584e2099b2916e81f893f46fc0af8cede23e3b2616ca957adc5f7a4bf71 2 0 60.0 reports/causal_graph_review/decisions/20261008-four-records-batch120.yaml reviewed
+kb/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml CommunityMech:000282 9d6ab3706fb821b6231441efc4342728b21ede4ab1aad3e5962ba5dab5d79199 3 1 78.3 reports/causal_graph_review/decisions/20261008-four-records-batch120.yaml reviewed
kb/communities/Thermophilic_Pyrite_QS_Consortium.yaml CommunityMech:000073 05778c90ad0a5bedfde9bc406926489c4c8f70edcf59ad524f7ffb1cadf69320 6 2 89.2 reports/causal_graph_review/decisions/20261008-three-records-batch115.yaml reviewed
kb/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml CommunityMech:000186 05b09dc41d9f2e54eac83d1021d69d2ea733144e9e5386295dd99cc9cae6293c 3 2 93.3 reports/causal_graph_review/decisions/20261008-two-records-batch114.yaml reviewed
kb/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml CommunityMech:000239 0bf172f2ca5732c1c0ff0b2853f2685a65da950dface53edd4e00ba108a3c281 3 1 78.3 reports/causal_graph_review/decisions/20261008-three-records-batch115.yaml reviewed
kb/communities/Tinto_River_Iron_Cycling_Community.yaml CommunityMech:000074 0597ed078c3761a0c46d2d8590ce3c328bd9897730a232938f4f5709bba02d09 4 1 79.2 reports/causal_graph_review/decisions/20261008-three-records-batch115.yaml reviewed
-kb/communities/Tobacco_Chemotactic_Biocontrol_SynCom.yaml CommunityMech:000106 b4d7702d9c87b2b55cb2b3c74598aed2bfded7afd454faed5628c817b2fdfa35 3 2 100.0 pending
+kb/communities/Tobacco_Chemotactic_Biocontrol_SynCom.yaml CommunityMech:000106 2d1851c88c385f813706b923eeb0754bf70bbac4dd94fb15369bf5e45317e371 3 2 86.7 reports/causal_graph_review/decisions/20261008-four-records-batch120.yaml reviewed
kb/communities/Tomato_Oxylipin_SynCom3.yaml CommunityMech:000107 9c5917f46de396ed1c278b2cb65ff5d6d5a78be8aa470ce09e20a9e8550ccafe 3 2 100.0 pending
kb/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml CommunityMech:000112 1349b3976b1d7a34ce789447fa6b35e8659b80725ec6aa09694f2f8d5e1aa6a8 4 3 95.0 reports/causal_graph_review/decisions/20261008-four-records-batch117.yaml reviewed
kb/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml CommunityMech:000188 19be2baf6f39a410bce4ce119b4b192d16c49f03e57b39ba4d1a3bf59f8c1ff0 3 2 90.0 reports/causal_graph_review/decisions/20261008-seven-records-batch112.yaml reviewed
diff --git a/reports/causal_graph_review/summary.json b/reports/causal_graph_review/summary.json
index b122ffa73..649645b16 100644
--- a/reports/causal_graph_review/summary.json
+++ b/reports/causal_graph_review/summary.json
@@ -3,13 +3,13 @@
"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": 1375,
- "edges": 531,
+ "edges": 530,
"records_without_nodes": 10,
"records_without_edges": 189,
"review_status_counts": {
"needs_research": 54,
- "pending": 22,
- "reviewed": 384
+ "pending": 18,
+ "reviewed": 388
},
"structural_defects": [],
"network_audit": [
diff --git a/reports/causal_graph_review/validation-20261008-batch120.json b/reports/causal_graph_review/validation-20261008-batch120.json
new file mode 100644
index 000000000..ae6503918
--- /dev/null
+++ b/reports/causal_graph_review/validation-20261008-batch120.json
@@ -0,0 +1,1089 @@
+{
+ "base_commit": "0c53674faea0dcf72f3fb830f46ebb656811684a",
+ "scope": [
+ "kb/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml",
+ "kb/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml",
+ "kb/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml",
+ "kb/communities/Tobacco_Chemotactic_Biocontrol_SynCom.yaml"
+ ],
+ "results": [
+ {
+ "check": "focused",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "pytest",
+ "-q",
+ "tests/test_causal_review_batch120.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch120/verification/focused.log",
+ "log_sha256": "cae71f1e5ebb2a265be401160db78fa13dc64b3aa5995e706b34c667039c3a08",
+ "output_tail": "............... [100%]\n15 passed in 2.69s\n"
+ },
+ {
+ "check": "Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch120/verification/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch120/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture-strict.tsv",
+ "kb/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch120/verification/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture-strict.log",
+ "log_sha256": "1fb3449b1ea2da6815c17ec13e93ffde208f99ebbf9d555a547baf32f88c47ae",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch120/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-batch120/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture-strict.tsv\n"
+ },
+ {
+ "check": "Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch120/verification/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch120/verification/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture-references.log",
+ "log_sha256": "1cbabf0e739481b214b86cac01644bb8ad697b1cf73471157718bc8ff5777c8d",
+ "output_tail": "Validating kb/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n",
+ "explained_output_tail": "Validating kb/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n"
+ },
+ {
+ "check": "Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch120/verification/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture-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": "Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch120/verification/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture-rank.log",
+ "log_sha256": "9f9ab65f6dffc7fa86c47cf4a69cb80c6bd809db50de2fc435ca133a42c04ea0",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000454\",\n \"name\": \"Thermoleptolyngbya-Chelatococcus Arsenic Detoxification Coculture\",\n \"score\": 70.0,\n \"taxonomy\": 2,\n \"connected_taxa\": 2,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 2,\n \"downstream_edges\": 0,\n \"interaction_evidence\": 6,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"additional_interactions\",\n \"downstream\"\n ],\n \"path\": \"kb/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture/2026-10-08T141541Z-codex-62412f.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch120/verification/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Thermophilic_ExSitu_Biomethanation_Mixed_Culture-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch120/verification/Thermophilic_ExSitu_Biomethanation_Mixed_Culture-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Thermophilic_ExSitu_Biomethanation_Mixed_Culture-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch120/Thermophilic_ExSitu_Biomethanation_Mixed_Culture-strict.tsv",
+ "kb/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch120/verification/Thermophilic_ExSitu_Biomethanation_Mixed_Culture-strict.log",
+ "log_sha256": "9e1f35895497b478a0e8b3a4d378616df200cab78f12dc2f24460f4197ea5f81",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch120/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-batch120/Thermophilic_ExSitu_Biomethanation_Mixed_Culture-strict.tsv\n"
+ },
+ {
+ "check": "Thermophilic_ExSitu_Biomethanation_Mixed_Culture-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch120/verification/Thermophilic_ExSitu_Biomethanation_Mixed_Culture-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Thermophilic_ExSitu_Biomethanation_Mixed_Culture-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch120/verification/Thermophilic_ExSitu_Biomethanation_Mixed_Culture-references.log",
+ "log_sha256": "78c2caf733f45a73d80b7ea2c974e8003622237bb400ab8696c49036476c3143",
+ "output_tail": "Validating kb/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.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/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.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": "Thermophilic_ExSitu_Biomethanation_Mixed_Culture-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch120/verification/Thermophilic_ExSitu_Biomethanation_Mixed_Culture-snippets.log",
+ "log_sha256": "4aa77c860f3ea55440fba368c12e0ba54f5974232fa3488140b015299bdeedae",
+ "output_tail": "# 43 evidence snippets scanned across 1 files\n MATCH 43\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": "Thermophilic_ExSitu_Biomethanation_Mixed_Culture-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch120/verification/Thermophilic_ExSitu_Biomethanation_Mixed_Culture-rank.log",
+ "log_sha256": "8466ff2e7698b49406f8bea82422e335a6f97701bd0c1f19145e14d52eef7d7e",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000416\",\n \"name\": \"Thermophilic Ex-Situ Biomethanation Mixed Culture\",\n \"score\": 60.0,\n \"taxonomy\": 6,\n \"connected_taxa\": 6,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 2,\n \"downstream_edges\": 0,\n \"interaction_evidence\": 8,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"additional_interactions\",\n \"downstream\",\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Thermophilic_ExSitu_Biomethanation_Mixed_Culture-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Thermophilic_ExSitu_Biomethanation_Mixed_Culture/2026-10-08T141542Z-codex-8205c5.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch120/verification/Thermophilic_ExSitu_Biomethanation_Mixed_Culture-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch120/verification/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch120/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization-strict.tsv",
+ "kb/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch120/verification/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization-strict.log",
+ "log_sha256": "3307653a2ac1d7b2a0427a467ea079f93e56d22326909ce93387bc98eebce823",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch120/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-batch120/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization-strict.tsv\n"
+ },
+ {
+ "check": "Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch120/verification/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch120/verification/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization-references.log",
+ "log_sha256": "f97e27153c47c1cde55c324d70e91c5c0c563f299268676d5c310cd051907221",
+ "output_tail": "Validating kb/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.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/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.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": "Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch120/verification/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization-snippets.log",
+ "log_sha256": "f77044cea09a90a006f3fc48666f62a208521829981c6819a3a36631506c4ec1",
+ "output_tail": "# 16 evidence snippets scanned across 1 files\n MATCH 16\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": "Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch120/verification/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization-rank.log",
+ "log_sha256": "745869371755d59bba77737bf508fe47e3434df77d31c1df89e93bb293d6b857",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000282\",\n \"name\": \"Thermophilic Lignocellulose-degrading Composting SynCom\",\n \"score\": 78.3,\n \"taxonomy\": 5,\n \"connected_taxa\": 5,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 3,\n \"downstream_edges\": 1,\n \"interaction_evidence\": 7,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"additional_downstream\",\n \"metabolites_or_biological_processes\",\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization/2026-10-08T141542Z-codex-0c3005.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch120/verification/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Tobacco_Chemotactic_Biocontrol_SynCom-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Tobacco_Chemotactic_Biocontrol_SynCom.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch120/verification/Tobacco_Chemotactic_Biocontrol_SynCom-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Tobacco_Chemotactic_Biocontrol_SynCom-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch120/Tobacco_Chemotactic_Biocontrol_SynCom-strict.tsv",
+ "kb/communities/Tobacco_Chemotactic_Biocontrol_SynCom.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch120/verification/Tobacco_Chemotactic_Biocontrol_SynCom-strict.log",
+ "log_sha256": "f21ad61459e3c06aa0307a823ec09caeae29023df76f5004fca4733c58412efd",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch120/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-batch120/Tobacco_Chemotactic_Biocontrol_SynCom-strict.tsv\n"
+ },
+ {
+ "check": "Tobacco_Chemotactic_Biocontrol_SynCom-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Tobacco_Chemotactic_Biocontrol_SynCom.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch120/verification/Tobacco_Chemotactic_Biocontrol_SynCom-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Tobacco_Chemotactic_Biocontrol_SynCom-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Tobacco_Chemotactic_Biocontrol_SynCom.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch120/verification/Tobacco_Chemotactic_Biocontrol_SynCom-references.log",
+ "log_sha256": "457610b8d56e6375e40e2c8987f319fb3c9a5f2d13ccb0788a89e48ef161ecc2",
+ "output_tail": "Validating kb/communities/Tobacco_Chemotactic_Biocontrol_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/Tobacco_Chemotactic_Biocontrol_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": "Tobacco_Chemotactic_Biocontrol_SynCom-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Tobacco_Chemotactic_Biocontrol_SynCom.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch120/verification/Tobacco_Chemotactic_Biocontrol_SynCom-snippets.log",
+ "log_sha256": "5f0e8a5be45b94195ee5599498c60e06ff8db089c85d0bf23969aa37351ca96e",
+ "output_tail": "# 17 evidence snippets scanned across 1 files\n MATCH 17\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": "Tobacco_Chemotactic_Biocontrol_SynCom-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Tobacco_Chemotactic_Biocontrol_SynCom.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch120/verification/Tobacco_Chemotactic_Biocontrol_SynCom-rank.log",
+ "log_sha256": "a7026aba7f4033dba6913fd03ef4507300178072cd4d93b63cd0ae8239b2e138",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000106\",\n \"name\": \"Tobacco Chemotactic Biocontrol SynCom\",\n \"score\": 86.7,\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 \"metabolites_or_biological_processes\",\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Tobacco_Chemotactic_Biocontrol_SynCom.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Tobacco_Chemotactic_Biocontrol_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/Tobacco_Chemotactic_Biocontrol_SynCom/2026-10-08T141542Z-codex-fb2ec0.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch120/verification/Tobacco_Chemotactic_Biocontrol_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-batch120/verification/inventory.log",
+ "log_sha256": "864d691942bba499557b2f3e213fcee4ba7a124d587dce773acde424378ae5cc",
+ "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\": 1375,\n \"edges\": 530,\n \"records_without_nodes\": 10,\n \"records_without_edges\": 189,\n \"review_status_counts\": {\n \"needs_research\": 54,\n \"pending\": 18,\n \"reviewed\": 388\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-batch120/verification/network.log",
+ "log_sha256": "6a349ee70c3b3deb2e3171d0a85501f53c7faa0aca02351007a8296feed367e9",
+ "output_tail": "\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 \"Tinto_River_Iron_Cycling_Community\": [\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Basidiomycota\",\n \"taxon_id\": \"NCBITaxon:5204\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Basidiomycota\",\n \"term\": {\n \"id\": \"NCBITaxon:5204\",\n \"label\": \"Basidiomycota\"\n },\n \"gtdb_grounding_status\": \"NO_GTDB_EQUIVALENT\",\n \"notes\": \"Acidophilic fungi including Hortaea werneckii (black yeast) detected in Rio Tinto sediments and water. Fungi contribute to organic matter degradation, biofilm formation, and nutrient cycling through extracellular enzyme secretion.\\n\"\n },\n \"functional_role\": [\n \"PRIMARY_DEGRADER\"\n ],\n \"abundance_level\": \"RARE\",\n \"evidence\": [\n {\n \"reference\": \"PMID:25369810\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VIVO\",\n \"snippet\": \"Thus, interest in the biodiversity and ecology of extreme environments has grown in recent years for several reasons\",\n \"explanation\": \"Documents fungal presence\"\n }\n ]\n },\n \"message\": \"Taxon 'Basidiomycota' has no interactions\"\n }\n ]\n}\n"
+ },
+ {
+ "check": "just-network-json",
+ "command": [
+ "just",
+ "audit-network-json"
+ ],
+ "exit_code": 2,
+ "expected_exit_codes": [
+ 2
+ ],
+ "log": "/private/tmp/communitymech-batch120/verification/just-network-json.log",
+ "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"
+ },
+ {
+ "check": "rank-all",
+ "command": [
+ "just",
+ "rank-causal-graphs"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch120/verification/rank-all.log",
+ "log_sha256": "748b1981e1bf6dbe143bff0cbf11e33d13e603d03cda2292bfb398f0688f8704",
+ "output_tail": "kb/communities/Clostridium_Saccharomyces_Cellulose_Ethanol_Coculture.yaml\tCommunityMech:000206\tClostridium-Saccharomyces Cellulose Ethanol Coculture\t2\t2\t0\t3\t2\t5\tinteraction_type\t0\t0\n405\t96.7\tkb/communities/DIETsimp_Lignocellulose_to_Methane_DIET_Consortia.yaml\tCommunityMech:000297\tDIET-based Simplified Lignocellulose-to-Methane Consortia (DIETsimp)\t3\t3\t0\t3\t2\t4\tinteraction_type\t0\t0\n406\t96.7\tkb/communities/Desulfovibrio_Methanococcus_Syntrophy.yaml\tCommunityMech:000023\tDesulfovibrio-Methanococcus Syntrophic Consortium\t2\t2\t0\t3\t3\t6\tinteraction_type\t0\t0\n407\t96.7\tkb/communities/Pelagerythrobacter_Salinicola_PES_Pyrene_Degradation_SynCom.yaml\tCommunityMech:000340\tPelagerythrobacter-Salinicola PES Pyrene-Degradation SynCom\t2\t2\t0\t3\t2\t6\tinteraction_type\t0\t0\n408\t96.7\tkb/communities/Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium.yaml\tCommunityMech:000291\tPseudomonas stutzeri + Rhodococcus Naphthalene-degrading Biochar-bridged Engineered Consortium\t2\t2\t0\t3\t2\t3\tinteraction_type\t0\t0\n409\t96.7\tkb/communities/SMutans_CAlbicans_ECC_Biofilm.yaml\tCommunityMech:000083\tStreptococcus mutans - Candida albicans ECC Biofilm Model\t2\t2\t0\t3\t2\t4\tinteraction_type\t0\t0\n410\t96.7\tkb/communities/Synechococcus_Azotobacter_Photoproduction_Mutualism.yaml\tCommunityMech:000207\tSynechococcus-Azotobacter Photoproduction Mutualism\t2\t2\t0\t3\t2\t5\tinteraction_type\t0\t0\n411\t96.7\tkb/communities/Synechococcus_Ecoli_SPC.yaml\tCommunityMech:000066\tSynechococcus-E.coli Synthetic Photosynthetic Consortium\t2\t2\t0\t3\t2\t5\tinteraction_type\t0\t0\n412\t96.7\tkb/communities/Synechococcus_Saccharomyces_SPC.yaml\tCommunityMech:000067\tSynechococcus-Saccharomyces Synthetic Photosynthetic Consortium\t2\t2\t0\t3\t2\t4\tinteraction_type\t0\t0\n413\t96.7\tkb/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml\tCommunityMech:000149\tSynthetic Lichen Synechococcus-Rhodotorula Coculture\t2\t2\t0\t3\t2\t9\tinteraction_type\t0\t0\n414\t96.7\tkb/communities/Syntrophobacter_Methanobacterium_Syntrophy.yaml\tCommunityMech:000068\tSyntrophobacter-Methanobacterium Syntrophic Consortium\t2\t2\t0\t3\t3\t9\tinteraction_type\t0\t0\n415\t96.7\tkb/communities/Syntrophobacter_Methanospirillum_Syntrophy.yaml\tCommunityMech:000069\tSyntrophobacter-Methanospirillum Syntrophic Consortium\t2\t2\t0\t3\t3\t7\tinteraction_type\t0\t0\n416\t96.7\tkb/communities/Syntrophomonas_Methanospirillum_Syntrophy.yaml\tCommunityMech:000070\tSyntrophomonas-Methanospirillum Syntrophic Consortium\t2\t2\t0\t3\t3\t6\tinteraction_type\t0\t0\n417\t96.7\tkb/communities/Syntrophus_Benzoate_Degrader.yaml\tCommunityMech:000071\tSyntrophus Benzoate Degrader\t2\t2\t0\t3\t2\t6\tinteraction_type\t0\t0\n418\t96.7\tkb/communities/Trichoderma_Lactate_Platform.yaml\tCommunityMech:000075\tTrichoderma Lactate Platform for SCFA Production\t3\t3\t0\t3\t2\t4\tinteraction_type\t0\t0\n419\t97.5\tkb/communities/Anammox_Granule_Metabolic_Interaction_Community.yaml\tCommunityMech:000146\tAnammox Granule Metabolic Interaction Community\t3\t3\t0\t4\t3\t5\tinteraction_type\t0\t0\n420\t97.5\tkb/communities/ORNL_Clostridium_Desulfovibrio_Geobacter_Trophic_Model.yaml\tCommunityMech:000176\tORNL Clostridium-Desulfovibrio-Geobacter Trophic Model Community\t3\t3\t0\t4\t2\t8\tinteraction_type\t0\t0\n421\t97.5\tkb/communities/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom.yaml\tCommunityMech:000312\tSuillus clintonianus-Bacillus altitudinis Thiamine Cross-Feeding SynCom\t3\t3\t0\t4\t3\t8\tinteraction_type\t0\t0\n422\t97.5\tkb/communities/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture.yaml\tCommunityMech:000272\tSynCom Y Agrobacterium-Bacillus Biofilm Biocontrol Co-culture\t2\t2\t0\t4\t2\t8\tinteraction_type\t0\t0\n423\t97.9\tkb/communities/Maize_Drought_Response_SynCom.yaml\tCommunityMech:000103\tMaize Drought Response SynCom\t1\t1\t0\t7\t7\t8\tmetabolites_or_biological_processes\t0\t0\n424\t98.3\tkb/communities/Populus_Salt_Tolerant_SynComs.yaml\tCommunityMech:000090\tPopulus Salt-Tolerant Rhizosphere SynComs\t1\t1\t0\t3\t2\t3\tmetabolites_or_biological_processes\t0\t0\n425\t98.3\tkb/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml\tCommunityMech:000404\tWollastonite Ramichloridium-Talaromyces Fungal Consortium\t2\t2\t0\t3\t2\t5\tmetabolites_or_biological_processes\t0\t0\n426\t98.8\tdata/isolates/Chromobacterium_Gold_Biocyanidation.yaml\tCommunityMech:000273\tChromobacterium Gold Biocyanidation Platform\t1\t1\t0\t4\t2\t7\tmetabolites_or_biological_processes\t0\t0\n427\t100.0\tdata/isolates/Aspergillus_Indium_LED_Recovery.yaml\tCommunityMech:000320\tAspergillus Indium LCD Recovery Platform\t1\t1\t0\t5\t4\t6\t\t0\t0\n428\t100.0\tdata/isolates/Methylobacterium_REE_Ewaste_Platform.yaml\tCommunityMech:000322\tMethylobacterium REE E-waste Platform\t1\t1\t0\t4\t2\t6\t\t0\t0\n429\t100.0\tkb/communities/ANME_SRB_Anaerobic_Methanotrophic_Syntrophic_Consortia.yaml\tCommunityMech:000276\tANME/SRB Anaerobic Methanotrophic Syntrophic Consortia\t6\t6\t0\t3\t2\t7\t\t0\t0\n430\t100.0\tkb/communities/Anabaena_MGS1_Anaerobic_Digestion_Methanogen_Consortium.yaml\tCommunityMech:000307\tAnabaena / MGS-1 Anaerobic-Digestion Methanogen Consortium\t1\t1\t0\t5\t2\t7\t\t0\t0\n431\t100.0\tkb/communities/Avena_Rhizosphere_Detritusphere_Niche_Succession.yaml\tCommunityMech:000245\tAvena Rhizosphere and Detritusphere Niche-Differentiated Decomposer Guilds\t1\t1\t0\t5\t2\t7\t\t0\t0\n432\t100.0\tkb/communities/Bacteroides_Methanobrevibacter_Gnotobiotic_Mouse_Mutualism.yaml\tCommunityMech:000142\tBacteroides-Methanobrevibacter Gnotobiotic Mouse Mutualism\t2\t2\t0\t3\t2\t3\t\t0\t0\n433\t100.0\tkb/communities/BioModels_MODEL2405300001_Infant_Gut_HMO_SynCom.yaml\tCommunityMech:000012\tBioModels MODEL2405300001 Infant Gut HMO SynCom\t13\t13\t0\t3\t2\t6\t\t0\t0\n434\t100.0\tkb/communities/California_Grassland_Precipitation_Legacy_Soil_Community.yaml\tCommunityMech:000215\tCalifornia Grassland Precipitation Legacy Soil Community\t1\t1\t0\t3\t2\t6\t\t0\t0\n435\t100.0\tkb/communities/Cellulose_Methane_Quad_Culture_SynCom.yaml\tCommunityMech:000089\tCellulose-to-Methane Quad-Culture SynCom\t4\t4\t0\t6\t5\t9\t\t0\t0\n436\t100.0\tkb/communities/DVM_Triculture.yaml\tCommunityMech:000021\tDVM Tri-culture\t3\t3\t0\t4\t2\t7\t\t0\t0\n437\t100.0\tkb/communities/Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium.yaml\tCommunityMech:000301\tDehalococcoides mccartyi CWV2 Dechlorinating Consortium\t1\t1\t0\t5\t2\t6\t\t0\t0\n438\t100.0\tkb/communities/Ecoli_Bifidobacterium_bifidum_Infant_gut_HMO_Mutualism_Coculture.yaml\tCommunityMech:000296\tEscherichia coli + Bifidobacterium bifidum Infant-gut Mutualistic Co-culture\t2\t2\t0\t3\t2\t6\t\t0\t0\n439\t100.0\tkb/communities/High_Ammonia_Biogas_0B_Butyrate_Oxidizing_Enrichment.yaml\tCommunityMech:000350\tHigh-Ammonia Biogas 0B Butyrate-Oxidizing Enrichment\t4\t4\t0\t3\t2\t6\t\t0\t0\n440\t100.0\tkb/communities/Honeybee_Core20_Defined_Microbiota.yaml\tCommunityMech:000124\tHoneybee Core-20 Defined Microbiota\t1\t1\t0\t3\t2\t3\t\t0\t0\n441\t100.0\tkb/communities/Microbacterium_Terrabacter_Sulfadiazine_CrossFeeding_Coculture.yaml\tCommunityMech:000462\tMicrobacterium-Terrabacter Sulfadiazine Cross-Feeding Coculture\t2\t2\t0\t3\t2\t6\t\t0\t0\n442\t100.0\tkb/communities/Microcoleus_Massilia_Cyanosphere_Urea_Mutualism.yaml\tCommunityMech:000157\tMicrocoleus-Massilia Cyanosphere Urea Mutualism\t2\t2\t0\t3\t2\t5\t\t0\t0\n443\t100.0\tkb/communities/Multiomics_Corn_Straw_Degradation_SynCom.yaml\tCommunityMech:000119\tMultiomics Corn Straw Degradation SynCom\t1\t1\t0\t4\t3\t9\t\t0\t0\n444\t100.0\tkb/communities/Neocallimastix_Methanobrevibacter_Xylan_Coculture.yaml\tCommunityMech:000156\tNeocallimastix-Methanobrevibacter Xylanolytic Coculture\t2\t2\t0\t3\t2\t5\t\t0\t0\n445\t100.0\tkb/communities/Pelotomaculum_Methanocella_Propionate_RNASeq_Coculture.yaml\tCommunityMech:000190\tPelotomaculum-Methanocella Propionate RNA-Seq Coculture\t2\t2\t0\t4\t2\t9\t\t0\t0\n446\t100.0\tkb/communities/Pelotomaculum_Methanothermobacter_Syntrophy.yaml\tCommunityMech:000052\tPelotomaculum-Methanothermobacter Syntrophic Consortium\t2\t2\t0\t3\t2\t6\t\t0\t0\n447\t100.0\tkb/communities/Phenol_Carboxylation_Consortium.yaml\tCommunityMech:000053\tPhenol Carboxylation Consortium\t2\t2\t0\t3\t3\t7\t\t0\t0\n448\t100.0\tkb/communities/Phosphitivorax_Methanoculleus_Lithosyntrophy_Phosphite_Coculture.yaml\tCommunityMech:000290\tPhosphitivorax-Methanoculleus Lithosyntrophic Phosphite-Oxidizing Methanogenic Culture\t2\t2\t0\t3\t2\t4\t\t0\t0\n449\t100.0\tkb/communities/Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium.yaml\tCommunityMech:000289\tPseudomonas putida Pp-TE + Rhodococcus sp. RDK17 Terephthalic-acid Consortium\t2\t2\t0\t3\t2\t4\t\t0\t0\n450\t100.0\tkb/communities/Rhodopseudomonas_Ecoli_CrossFeeding_Coculture.yaml\tCommunityMech:000092\tRhodopseudomonas-E. coli Cross-Feeding Coculture\t2\t2\t0\t3\t2\t4\t\t0\t0\n451\t100.0\tkb/communities/Rice_Acid_Soil_Bioinoculant_SynCom.yaml\tCommunityMech:000109\tRice Acid Soil Bioinoculant SynCom\t1\t1\t0\t4\t4\t4\t\t0\t0\n452\t100.0\tkb/communities/Subsurface_Carboxydocella_CO_Aquifer_Community.yaml\tCommunityMech:000251\tSubsurface Carboxydocella CO-Oxidation Aquifer Community\t1\t1\t0\t4\t2\t4\t\t0\t0\n453\t100.0\tkb/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml\tCommunityMech:000182\tThermacetogenium-Methanothermobacter Acetate Oxidation Coculture\t2\t2\t0\t3\t2\t8\t\t0\t0\n454\t100.0\tkb/communities/Tomato_Oxylipin_SynCom3.yaml\tCommunityMech:000107\tTomato Oxylipin-Protective SynCom3\t3\t3\t0\t3\t2\t4\t\t0\t0\n455\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\n456\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\n457\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\n458\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\n459\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\n460\t100.0\tkb/communities/hCom2_Complex_Gut_Microbiome.yaml\tCommunityMech:000123\thCom2 Complex Gut Microbiome\t1\t1\t0\t3\t2\t3\t\t0\t0\nPYTHONPATH=src uv run python scripts/rank_causal_graph_readiness.py \n"
+ },
+ {
+ "check": "render",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "communitymech.render"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch120/verification/render.log",
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+ "output_tail": "unitymech-causal-batch120/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch120/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch120/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch120/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-batch120/verification/render-repeat.log",
+ "log_sha256": "490380ca7b4e748a5416fe17c85428d17c1943a997067d40fc7096cd7b82ce38",
+ "output_tail": "unitymech-causal-batch120/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch120/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch120/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch120/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch120/docs/index.html\n"
+ },
+ {
+ "check": "connectivity-survey",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-c",
+ "import json,runpy; print(json.dumps(runpy.run_path('tests/test_community_level_connectivity_credit.py')['_survey']()))"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch120/verification/connectivity-survey.log",
+ "log_sha256": "6dba3d2251cf8431c1fc7f04f3c0806d8a8c166c0901fd6be1fcbc268a1730a4",
+ "output_tail": "{\"records\": 460, \"with_community_level\": 414, \"mixed\": 136, \"community_level_only\": 278, \"taxa\": 1568, \"credited_solely_by_the_rule\": 1281}\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_batch100.py",
+ "tests/test_causal_review_batch101.py",
+ "tests/test_causal_review_batch102.py",
+ "tests/test_causal_review_batch103.py",
+ "tests/test_causal_review_batch104.py",
+ "tests/test_causal_review_batch105.py",
+ "tests/test_causal_review_batch106.py",
+ "tests/test_causal_review_batch107.py",
+ "tests/test_causal_review_batch108.py",
+ "tests/test_causal_review_batch109.py",
+ "tests/test_causal_review_batch11.py",
+ "tests/test_causal_review_batch110.py",
+ "tests/test_causal_review_batch111.py",
+ "tests/test_causal_review_batch112.py",
+ "tests/test_causal_review_batch113.py",
+ "tests/test_causal_review_batch114.py",
+ "tests/test_causal_review_batch115.py",
+ "tests/test_causal_review_batch116.py",
+ "tests/test_causal_review_batch117.py",
+ "tests/test_causal_review_batch118.py",
+ "tests/test_causal_review_batch119.py",
+ "tests/test_causal_review_batch12.py",
+ "tests/test_causal_review_batch120.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_batch84.py",
+ "tests/test_causal_review_batch85.py",
+ "tests/test_causal_review_batch86.py",
+ "tests/test_causal_review_batch87.py",
+ "tests/test_causal_review_batch88.py",
+ "tests/test_causal_review_batch89.py",
+ "tests/test_causal_review_batch9.py",
+ "tests/test_causal_review_batch90.py",
+ "tests/test_causal_review_batch91.py",
+ "tests/test_causal_review_batch92.py",
+ "tests/test_causal_review_batch93.py",
+ "tests/test_causal_review_batch94.py",
+ "tests/test_causal_review_batch95.py",
+ "tests/test_causal_review_batch96.py",
+ "tests/test_causal_review_batch97.py",
+ "tests/test_causal_review_batch98.py",
+ "tests/test_causal_review_batch99.py",
+ "tests/test_network_palette.py",
+ "tests/test_datamodel.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-batch120/verification/regressions.log",
+ "log_sha256": "46de25fac181451ee31e30b276554950f7d741397efea6212a206368e19e62d1",
+ "output_tail": "........................................................................ [ 6%]\n........................................................................ [ 12%]\n........................................................................ [ 19%]\n........................................................................ [ 25%]\n........................................................................ [ 31%]\n........................................................................ [ 38%]\n........................................................................ [ 44%]\n........................................................................ [ 50%]\n........................................................................ [ 57%]\n........................................................................ [ 63%]\n........................................................................ [ 70%]\n........................................................................ [ 76%]\n........................................................................ [ 82%]\n........................................................................ [ 89%]\n........................................................................ [ 95%]\n................................................... [100%]\n1131 passed in 305.98s (0:05:05)\n"
+ },
+ {
+ "check": "just-lint",
+ "command": [
+ "just",
+ "lint"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch120/verification/just-lint.log",
+ "log_sha256": "27ffa709ada7bdb942c6cc58699c51f5d6e0ccd31bc208a0659cd75afb6ca6c8",
+ "output_tail": "All checks passed!\nSuccess: no issues found in 49 source files\nuv run black --check src/ tests/ scripts/\nAll done! \u2728 \ud83c\udf70 \u2728\n373 files would be left unchanged.\nuv run ruff check src/ tests/ scripts/\nwarning: Invalid `# noqa` directive on scripts/gtdb_ground.py:74: expected code to consist of uppercase letters followed by digits only (e.g. `F401`)\nuv run mypy src/\n"
+ },
+ {
+ "check": "mypy-explicit-runtime",
+ "command": [
+ "/private/tmp/communitymech-batch100/lint-env/bin/mypy",
+ "--no-incremental",
+ "--python-executable",
+ "/private/tmp/communitymech-batch100/lint-env/bin/python",
+ "src/"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch120/verification/mypy-explicit-runtime.log",
+ "log_sha256": "b1fdd8413863455c6896d811c9ab42dc9256d679a668643bb18df2318c3bc875",
+ "output_tail": "Success: no issues found in 49 source files\n"
+ },
+ {
+ "check": "audit-snippets-all",
+ "command": [
+ "just",
+ "audit-snippets"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch120/verification/audit-snippets-all.log",
+ "log_sha256": "5a78ad3709557028016cccf1a8b2394dcc02405ecf33214ac7fa17139a417c8c",
+ "output_tail": "# 9059 evidence snippets scanned across 460 files\n MATCH 8914\n RENDERING 28\n ASSEMBLED 1\n WEAK 0\n MISMATCH 40\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 1 (1 hard) kb/communities/Shewanella_Geobacter_Exoelectrogenic_Biofilm_Community.yaml\n 1 (1 hard) kb/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml\nuv run python scripts/evidence_snippet_audit.py \n"
+ },
+ {
+ "check": "diff-check",
+ "command": [
+ "git",
+ "diff",
+ "--check"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch120/verification/diff-check.log",
+ "log_sha256": "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855",
+ "output_tail": ""
+ }
+ ],
+ "limitations": [
+ "Both-root baseline precedes primary research:460records,923caches,57existing warnings,zero structural defects. All four whole records and10existing nodes/four arrows reviewed. Retain10nodes/three arrows,remove one common-cause arrow,rename six nodes,no new topology.",
+ "All four fresh EuropePMC abstracts and Crossref identities checked. Biomethanation and tobacco complete main-body XML texts read including methods,results,discussion,table text and captions. No original figure pixels,separate supplementary files,raw data or analysis code audited. Figure alt text is not independent experimental evidence.",
+ "Arsenic and compost changes are abstract-bounded. Neither EuropePMC metadata exposed a PMC article; DOI searches found publisher pages whose opens returned403. No exhaustive full-text absence claim,access bypass or author contact. Existing caches retained; no article-body import. Tobacco source license is CC BY-NC-ND4.0,not unrestricted CC BY.",
+ "Arsenic retains direct NanoSIMS carbon transfer and reciprocal-growth mutualism. Supplemented heterotroph culture and genomic complementarity do not independently establish oxygen-source necessity,nitrogen transfer or the identity of exchanged carbon compounds. Existing culture-conditions discussion remains open.",
+ "Biomethanation preserves measured methane and VFA outcomes from a single sequential CSTR. External gas supply is not microbial cross-feeding. Taxon-specific routes and thermodynamic cooperation remain interpretations; qPCR counts are not activity or viability. Washout affects pools,phase1sampling wording is not assigned to phase4. Non-graph roles/viability claims remain1935.",
+ "Compost retains reported maturation,transient ARG rebound and later attenuation. KEGG and potential host-gene networks are not expression,actual motility or transfer-frequency measurements. Maturation-to-attenuation remains PARTIAL; no maturation-to-profile causation is inferred from shared inoculation. Non-graph overview/role/access wording remains1936.",
+ "Tobacco keeps positive strain-specific broth and combined field-treatment results,including the Y878 null enhancement. cheA positivity is potential,not measured root migration; authors call for non-chemotactic controls. Source species/strain rows,resource-count discrepancies and tomato caption wording remain1937. The graph does not certify the current merged two-row taxonomy.",
+ "Initial all-state1168issue titles/bodies searched; fresh pre-creation expanded alias/DOI search receipt records exact count and local paths. Matching1160/1162 bodies read and distinct. Local searches include hidden/ignored files,excluding.git,docs,site,references_cache,.env; not a historical PR-comment audit.",
+ "Four guarded writes preserve456otherrecords,all923caches,unrelated raw YAML blocks,all prior histories/decisions. Four append-only histories and curation events. Taxon identities unchanged; evidence aliases detached. No new experimental or optimization protocol.",
+ "Existing-graph repair with no new nodes/directions: no Edison run,provider submission or spend. Prior authorized Ruegeria1883 authentication blocker not retried unchanged; no credential inspected. Source-based self-adversarial review is not independent approval. Overall review,protected merge and branch deletion remain incomplete."
+ ],
+ "reference_validator_version": "0.1.7",
+ "snippet_counts_by_record": {
+ "kb/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml": {
+ "MATCH": 13,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml": {
+ "MATCH": 43,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml": {
+ "MATCH": 16,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Tobacco_Chemotactic_Biocontrol_SynCom.yaml": {
+ "MATCH": 17,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ }
+ },
+ "unchanged_record_files": 456,
+ "unchanged_cache_files": 923,
+ "unchanged_raw_blocks": 52,
+ "cache_changes": [],
+ "edison": {
+ "required_for_this_repair": false,
+ "provider_submissions": 0,
+ "credits_spent": 0,
+ "new_nodes_or_directions": 0,
+ "prior_extension_blocker": "Ruegeria1883: configured authentication unavailable in prior approved invocation; no unchanged-state retry."
+ },
+ "primary_artifacts": {
+ "/private/tmp/communitymech-batch120/arsenic-abstract.txt": "a909e837092f1da517e50c42ff313c20550b11cb582d166ddf59d8586ddc2d4c",
+ "/private/tmp/communitymech-batch120/arsenic-crossref.json": "3149d8a27a6c985fa051aa8f72f0d7e9e30973772db3b6ac6f0ce9e3fa1409a9",
+ "/private/tmp/communitymech-batch120/arsenic-metadata.json": "ac574c108980520414341685d5eb2e6799b923575355b1c78c2f63c1c33c41d8",
+ "/private/tmp/communitymech-batch120/baseline.json": "d42d40339f6ba33b43924bf90686d932911392d036e74948cee75f9c42ff72f0",
+ "/private/tmp/communitymech-batch120/biomethane-abstract.txt": "ad02f9b8ff0bae6cbb65b0f27897c15e0a811df73f4ede1b030b6d3f57c691c0",
+ "/private/tmp/communitymech-batch120/biomethane-crossref.json": "a746e5cb42ee04cae8c3570416db6e71a1bd77c0ac359edf3bd3c0a31af52da2",
+ "/private/tmp/communitymech-batch120/biomethane-metadata.json": "0825df418eecc1d99e9dd929f807a1543fbc41a3770b6f2fe7f970867d751289",
+ "/private/tmp/communitymech-batch120/biomethane-primary.txt": "118147cf4280579fd51de0a87a785cfc692c3a61d3744f3654a781f199d7c982",
+ "/private/tmp/communitymech-batch120/biomethane-primary.xml": "c2fa0a603345aa191a0c2b0baf002377049dbcf1314df2a03e1547e70e9738f3",
+ "/private/tmp/communitymech-batch120/compost-abstract.txt": "292153c2db3d6d378c131f0441260289cb918332db5e54710a14d7d118a81cf1",
+ "/private/tmp/communitymech-batch120/compost-crossref.json": "ac99461fc313a7938ec8c8575672e8e953347b1585e259f725a67c8caa51ef5d",
+ "/private/tmp/communitymech-batch120/compost-metadata.json": "2a7db350a825482366f272247bed219889838e1b7c1984052d07416bb472591e",
+ "/private/tmp/communitymech-batch120/issue-dedup-current.json": "3cc0aa058fb10c87f24a23b942fce47a8522f99da4cf25f90ca959c2f7bf0696",
+ "/private/tmp/communitymech-batch120/local-matches-expanded.txt": "5463acc4575050d5644d3bcd0626f449ec01ea39f106c78e6593731682138272",
+ "/private/tmp/communitymech-batch120/local-matches.txt": "8fae12d5cc5b383bf190840897389fcb1eb473d6ac069e04336505322a475f49",
+ "/private/tmp/communitymech-batch120/primary-manifest.json": "3153d33ec4b983c9f5cd4a61126ad4b67db94f70b22494f40cc6f644276dc04f",
+ "/private/tmp/communitymech-batch120/target-baseline.json": "b3e222155b610d5d68957d5f8310c10dee71335bbc658eecbad25cd55ff3c0bf",
+ "/private/tmp/communitymech-batch120/tobacco-abstract.txt": "d43a05eae6fa9d0482997ea6ee7ab9f0ed61b69a9bd6dfe46f4bae622da2c45f",
+ "/private/tmp/communitymech-batch120/tobacco-crossref.json": "81ebdc1512fe7f4f6223878ef206fef2e00b1d89746c5fbceb62d1f2a1a6a103",
+ "/private/tmp/communitymech-batch120/tobacco-metadata.json": "0cc228df759e084065a551f5c853db1b5611d778ea598ea31bf638eb43f5747c",
+ "/private/tmp/communitymech-batch120/tobacco-primary.txt": "aab21d91bbaccd305b39a0d53a598c013717825a2d7ed294892d7b1f9329693b",
+ "/private/tmp/communitymech-batch120/tobacco-primary.xml": "a5b94ad21ff186c3bd617fa9c5a3932dc898200789bbc686a1a577cafadcd5c7",
+ "references_cache/PMID_40670700.txt": "37ffd9320d083751cc694555dd3530044fa8b1fba07d4543242aa9545028f31a",
+ "references_cache/PMID_41839407.md": "f514018cde834bbe39601275e389eaacfd7b274f4422687e713f7852f7812929",
+ "references_cache/PMID_42293522.txt": "436160c020b6dea8acef0eeba5c9ff81d7b2ba18f5ed7b400445f6fdc29541b1",
+ "references_cache/PMID_42468699.txt": "79d5c2a3114b5d25e1bc789a2288ebf584858f799b995c40adb5bf4beca4a896"
+ },
+ "immutable_prior_history_and_decision_files": 889,
+ "primary_graph_snippet_proof": {
+ "graph_quotations": 27,
+ "discussion_quotations": 6,
+ "fresh_primary_literal_matches": 33,
+ "all_cached_literal_matches": 33,
+ "retained_nodes": 10,
+ "removed_nodes": 0,
+ "renamed_nodes": 6,
+ "retained_arrows": 3,
+ "removed_arrows": 1,
+ "new_nodes_or_directions": 0
+ },
+ "network_delta": {
+ "existing_findings_preserved": 57,
+ "added_findings": {},
+ "removed_findings": {},
+ "structural_defects": 0
+ },
+ "render_determinism": true,
+ "published_description_coverage": {
+ "pages": 456,
+ "nodes": 1361,
+ "arrows": 522
+ },
+ "render_scope": "Deterministic rendering and exact HTML description parsing, not screenshots; postcommit docs-current still required.",
+ "participant_census": {
+ "current": {
+ "records": 460,
+ "with_community_level": 414,
+ "mixed": 136,
+ "community_level_only": 278,
+ "taxa": 1568,
+ "credited_solely_by_the_rule": 1281
+ },
+ "delta_from_batch119": {
+ "records": 0,
+ "with_community_level": 0,
+ "mixed": 0,
+ "community_level_only": 0,
+ "taxa": 0,
+ "credited_solely_by_the_rule": 0
+ },
+ "explanation": "All participant lists and scopes are unchanged;299participant-list users. Scope credit is not certification of actual participant coverage. Connectivity logic and thresholds are unchanged."
+ },
+ "lint_environment": {
+ "path": "/private/tmp/communitymech-batch100/lint-env",
+ "scope": "Temporary established Python3.13 lint environment; project dependencies unchanged."
+ },
+ "full_corpus_snippet_counts": {
+ "records": 460,
+ "total": 9059,
+ "categories": {
+ "MATCH": 8914,
+ "RENDERING": 28,
+ "ASSEMBLED": 1,
+ "WEAK": 0,
+ "MISMATCH": 40,
+ "NOCONTENT": 76
+ }
+ },
+ "full_corpus_snippet_audit_caveat": "Informational audit exit0 is not clean-corpus or entailment certification.",
+ "corpus": {
+ "scope": "Every YAML under kb/communities and data/isolates; filesystem discovery includes hidden/ignored files.",
+ "records": 460,
+ "nodes": 1375,
+ "edges": 530,
+ "records_without_nodes": 10,
+ "records_without_edges": 189,
+ "review_status_counts": {
+ "needs_research": 54,
+ "pending": 18,
+ "reviewed": 388
+ },
+ "structural_defects": []
+ },
+ "tested_file_sha256": {
+ "reports/causal_graph_review/decisions/20261008-four-records-batch120.yaml": "02d8e5bcf94ac4a351a5c23517211f8dfe3d3545b73c3de784f53d23ddc6105b",
+ "tests/test_causal_review_batch120.py": "6f25ad6bbd01d3eb06b6bfd1b9f4b03372f2ccfafca2923d6f4ac9cbc7673aa4",
+ "tests/test_participating_taxa.py": "f438815b4a028c0f38a077df53c95f685f98b3c2b523593896a124b544269db1",
+ "tests/test_community_level_connectivity_credit.py": "996cc631423bfa7adc5d8e693d67d55b374a24379d119ab0fa8f1802f38f216a",
+ "tests/test_causal_review_batch109.py": "ff8e9e26771545e1ace22b3c1d42076789c99cc4bc83e588b6a4b9ad698d3d73",
+ "tests/test_datamodel.py": "f8d4750ad64eb4156857a86a8c6adf16dedefb09ca3c3da908f697e609a35f25",
+ "reports/causal_graph_review/cache-provenance-20261008-batch120.json": "151d0064a128baf905eba3e41ae9b2035d47b740eab7b134d091caf52f7a4290",
+ "kb/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml": "bc09df336e1e5a701bf24c3f47eed41c24829eb4618c8597840052a93d0f822c",
+ "kb/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml": "51357584e2099b2916e81f893f46fc0af8cede23e3b2616ca957adc5f7a4bf71",
+ "kb/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml": "9d6ab3706fb821b6231441efc4342728b21ede4ab1aad3e5962ba5dab5d79199",
+ "kb/communities/Tobacco_Chemotactic_Biocontrol_SynCom.yaml": "2d1851c88c385f813706b923eeb0754bf70bbac4dd94fb15369bf5e45317e371"
+ },
+ "pre_research_baseline": {
+ "base_commit": "0c53674faea0dcf72f3fb830f46ebb656811684a",
+ "base_tree": "000b678a6237ea7c28c562d153fa8f66cbcda2b2",
+ "research_worktree": "/private/tmp/communitymech-causal-batch120",
+ "checks": [
+ {
+ "name": "rank",
+ "command": [
+ "just",
+ "rank-causal-graphs"
+ ],
+ "exit_code": 0,
+ "expected_exit_code": 0,
+ "log": "/private/tmp/communitymech-batch120/baseline-rank.log",
+ "sha256": "c05a4807c6dcde02a74e0b08c380c94393c4304de973301f6f0ca7372ff118ec"
+ },
+ {
+ "name": "just-network",
+ "command": [
+ "just",
+ "audit-network-json"
+ ],
+ "exit_code": 2,
+ "expected_exit_code": 2,
+ "log": "/private/tmp/communitymech-batch120/baseline-just-network.log",
+ "sha256": "8595db43420d3f0a01c57acd6ad733a531a72e962486d20b4e1c2840dda55bff"
+ },
+ {
+ "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-batch120/baseline-network.log",
+ "sha256": "6a349ee70c3b3deb2e3171d0a85501f53c7faa0aca02351007a8296feed367e9"
+ },
+ {
+ "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-batch120/baseline-downstream.log",
+ "sha256": "a1e756640ecc13500cb7b6b7a2a80f5f278141356714599df2958e2247d8f320"
+ }
+ ],
+ "baseline_sha256": "d42d40339f6ba33b43924bf90686d932911392d036e74948cee75f9c42ff72f0"
+ },
+ "reference_validator_caveat": "Full-record local passes are macOS, not Linux certification. Literal matching does not establish entailment. Total checks in the reference CLI counts issues, not examined snippets.",
+ "status": "verified_existing_graph_repairs",
+ "total_recorded_gate_outputs": 41
+}
diff --git a/tests/test_causal_review_batch120.py b/tests/test_causal_review_batch120.py
new file mode 100644
index 000000000..c800f5d66
--- /dev/null
+++ b/tests/test_causal_review_batch120.py
@@ -0,0 +1,199 @@
+"""Keep positive outcomes distinct from unmeasured ecological mechanisms."""
+
+import hashlib
+from pathlib import Path
+
+import yaml
+
+ROOT = Path(__file__).resolve().parents[1]
+LEDGER = ROOT / "reports/causal_graph_review/decisions/20261008-four-records-batch120.yaml"
+
+
+def records():
+ ledger = yaml.safe_load(LEDGER.read_text())
+ rows = ledger["records"]
+ return ledger, rows, [yaml.safe_load((ROOT / row["path"]).read_text()) for row in rows]
+
+
+def test_arsenic_preserves_direct_carbon_cross_feeding():
+ _, _, docs = records()
+ node = docs[0]["ecological_interactions"][0]
+ assert node["interaction_type"] == "CROSS_FEEDING"
+ assert node["scope"] == "PAIRWISE"
+ assert node["source_taxon"]["preferred_term"] == "Thermoleptolyngbya sichuanensis XZ-Cy5"
+ assert node["target_taxon"]["preferred_term"] == "Chelatococcus sp. XZ-Ab1"
+ assert "direct evidence of photoautotroph-derived carbon" in node["evidence"][1]["snippet"]
+ assert "an identified secreted molecule" in node["description"]
+
+
+def test_arsenic_mutualism_keeps_actual_reciprocal_growth_evidence():
+ _, _, docs = records()
+ node = docs[0]["ecological_interactions"][1]
+ assert node["interaction_type"] == "MUTUALISM"
+ assert node["source_taxon"]["preferred_term"] == "Chelatococcus sp. XZ-Ab1"
+ assert "promoted growth" in node["evidence"][0]["snippet"]
+ assert node["evidence"][0]["supports"] == "SUPPORT"
+ assert "reciprocal heterotrophic benefit" in node["description"]
+
+
+def test_arsenic_genomic_routes_are_not_traced_oxygen_or_nitrogen():
+ _, _, docs = records()
+ doc = docs[0]
+ node = doc["ecological_interactions"][1]
+ assert node["evidence"][-1]["supports"] == "PARTIAL"
+ assert "not a demonstrated oxygen-source requirement" in node["evidence"][-1]["explanation"]
+ assert "No nitrogen transfer" in node["description"]
+ assert "not direct tracing" in node["description"]
+ assert len(doc["discussions"]) == 2
+ assert not any(n.get("downstream") for n in doc["ecological_interactions"])
+
+
+def test_biomethanation_external_gas_is_not_interspecies_cross_feeding():
+ _, _, docs = records()
+ node = docs[1]["ecological_interactions"][0]
+ assert "interaction_type" not in node
+ assert "pressurised gas cylinders" in node["evidence"][0]["snippet"]
+ assert "reaching 86% by day 69" in node["evidence"][1]["snippet"]
+ assert "exceeding 90% was proposed, not observed" in node["description"]
+ assert {m["term"]["id"] for m in node["metabolites"]} == {
+ "CHEBI:18276",
+ "CHEBI:16526",
+ "CHEBI:16183",
+ }
+
+
+def test_biomethanation_group_counts_are_not_taxon_specific_activity():
+ _, _, docs = records()
+ node = docs[1]["ecological_interactions"][0]
+ assert node["evidence"][2]["supports"] == "PARTIAL"
+ assert "not taxon-resolved flux measurements" in node["description"]
+ assert "overlapping taxonomic summaries" in node["description"]
+ assert "single proof-of-concept CSTR" in node["description"]
+ assert len(node["participating_taxa"]) == 3
+
+
+def test_biomethanation_vfa_pools_do_not_prove_thermodynamic_syntrophy():
+ _, _, docs = records()
+ node = docs[1]["ecological_interactions"][1]
+ assert "interaction_type" not in node
+ assert "73% acetate" in node["evidence"][0]["snippet"]
+ assert all(e["supports"] == "PARTIAL" for e in node["evidence"][1:4])
+ assert "phase-1" in node["evidence"][4]["explanation"]
+ assert "does not establish phase-4 sampling timing" in node["evidence"][4]["explanation"]
+ assert "Washout and substrate-pool changes remain alternatives" in node["description"]
+ assert "product-removal-dependent thermodynamic cooperation" in node["description"]
+ assert not node.get("downstream")
+
+
+def test_compost_maturation_is_not_demonstrated_member_mutualism():
+ _, _, docs = records()
+ node = docs[2]["ecological_interactions"][0]
+ assert "interaction_type" not in node
+ assert "enhanced humification" in node["evidence"][0]["snippet"]
+ assert node["evidence"][1]["evidence_source"] == "COMPUTATIONAL"
+ assert node["evidence"][1]["supports"] == "PARTIAL"
+ assert "Mantel correlation" in node["description"]
+
+
+def test_compost_preserves_rebound_and_later_reported_attenuation():
+ _, _, docs = records()
+ node = docs[2]["ecological_interactions"][1]
+ assert "interaction_type" not in node and "biological_processes" not in node
+ assert (
+ "transient ARG rebound followed by profound attenuation" in node["evidence"][1]["snippet"]
+ )
+ assert node["evidence"][1]["evidence_source"] == "COMPUTATIONAL"
+ assert "eliminating high-risk pathogens" in node["evidence"][0]["snippet"]
+ assert "every viable pathogen" in node["description"]
+ assert "not" in node["description"] or "without" in node["description"]
+
+
+def test_compost_hgt_is_potential_not_measured_transfer_frequency():
+ _, _, docs = records()
+ node = docs[2]["ecological_interactions"][2]
+ assert "interaction_type" not in node
+ assert all(e["evidence_source"] == "COMPUTATIONAL" for e in node["evidence"])
+ assert "potential host-gene associations by 26.6%" in node["evidence"][1]["snippet"]
+ assert node["evidence"][2]["supports"] == "PARTIAL"
+ assert "not measurements of conjugation frequency" in node["description"]
+ assert "not a directly measured transfer rate" in node["biological_processes"][0]["notes"]
+
+
+def test_compost_retains_partial_environmental_mediation_not_common_cause_arrow():
+ _, rows, docs = records()
+ maturation, attenuation, _ = docs[2]["ecological_interactions"]
+ assert len(maturation["downstream"]) == 1
+ assert maturation["downstream"][0]["target"] == attenuation["name"]
+ assert maturation["downstream"][0]["description"].startswith("PARTIAL:")
+ assert len(rows[2]["removed_edge_decisions"]) == 1
+ assert "Shared SynCom inoculation" in rows[2]["removed_edge_decisions"][0]["rationale"]
+
+
+def test_tobacco_prebiotic_results_are_isolate_specific_with_y878_null():
+ _, _, docs = records()
+ node = docs[3]["ecological_interactions"][0]
+ assert "interaction_type" not in node
+ assert "Vitamin C increased Y364" in node["description"]
+ assert "increased Y832" in node["description"]
+ assert "for Y878, none" in node["evidence"][1]["snippet"]
+ assert "tomato root exudates" in node["description"]
+
+
+def test_tobacco_chea_marker_and_compatibility_are_not_colonization_measurements():
+ _, _, docs = records()
+ node = docs[3]["ecological_interactions"][1]
+ assert "interaction_type" not in node and "biological_processes" not in node
+ assert "metabolites" not in node
+ assert "showed mutual compatibility" in node["evidence"][0]["snippet"]
+ assert (
+ "lacked cheA gene, still displayed strong antagonistic activity"
+ in node["evidence"][1]["snippet"]
+ )
+ assert "not directly measured root migration or colonization" in node["description"]
+
+
+def test_tobacco_positive_field_result_is_a_combined_treatment():
+ _, _, docs = records()
+ node = docs[3]["ecological_interactions"][2]
+ assert "interaction_type" not in node and "biological_processes" not in node
+ assert "nearly doubled crop yield" in node["evidence"][1]["snippet"]
+ assert all(e["evidence_source"] == "IN_VIVO" for e in node["evidence"])
+ assert "positive combined-treatment result" in node["description"]
+ assert "qPCR abundance is not a direct viable-cell count" in node["description"]
+
+
+def test_tobacco_existing_arrows_do_not_prove_the_unique_mediator():
+ _, _, docs = records()
+ a, b, c = docs[3]["ecological_interactions"]
+ assert a["downstream"][0]["target"] == b["name"]
+ assert b["downstream"][0]["target"] == c["name"]
+ assert "PARTIAL for growth as the mediator" in a["downstream"][0]["description"]
+ assert b["downstream"][0]["description"].startswith("PARTIAL:")
+ assert "cow-manure fertilization" in b["downstream"][0]["description"]
+ assert (
+ "future studies should include non-chemotactic"
+ in docs[3]["discussions"][-1]["evidence"][0]["snippet"]
+ )
+
+
+def test_review_accounts_for_all_nodes_arrows_and_preserves_caches():
+ ledger, rows, docs = records()
+ counts = ledger["reviewed_counts"]
+ assert counts["original_nodes"] == counts["retained_nodes"] == 10
+ assert counts["removed_nodes"] == 0 and counts["renamed_nodes"] == 6
+ assert (counts["original_arrows"], counts["retained_arrows"], counts["removed_arrows"]) == (
+ 4,
+ 3,
+ 1,
+ )
+ assert (counts["graph_quotations"], counts["discussion_quotations"]) == (27, 6)
+ assert ledger["cache_changes"] == [] and not ledger["independent_approval"]
+ assert ledger["edison"]["new_nodes_or_directions"] == 0
+ for row, doc in zip(rows, docs, strict=True):
+ assert hashlib.sha256((ROOT / row["path"]).read_bytes()).hexdigest() == row["record_sha256"]
+ names = [n["name"] for n in doc["ecological_interactions"]]
+ assert [r["node"] for r in row["node_decisions"]] == names
+ assert len(row["history_files"]) == 1 and doc["curation_history"][-1]["llm_assisted"]
+ for node in doc["ecological_interactions"]:
+ assert "downstream" not in node or node["downstream"]
+ assert all(e["target"] in names for e in node.get("downstream", []))