The three-strain consortium produced a higher microbial fuel-cell power density than L. sphaericus A1, B. cereus A2, or L. lactis A4 pure cultures over 30 days.
During the 30-day dual-chamber MFC study, the consortium reached a reported maximum power density of 170 mW/m2, approximately 15% above L. sphaericus A1, 29% above B. cereus A2 and more than threefold above L. lactis A4. Preserve this positive tested-system comparison, not a claim that output remained higher at every time point. The matrix was nutrient-amended and sterilized, not raw wastewater.
-
The three-strain consortium removed chemical oxygen demand from amended poultry wastewater more effectively than the tested pure cultures.
+
The abstract reports the consortium had the greatest COD removal (84.4%) in amended, sterilized model wastewater. Preserve that reported result with a source discrepancy: Section 3.3 pairs consortium 84.4% with 2150-to-436 mg/L and L. sphaericus 79.7% with 2150-to-335 mg/L, which yield approximately 79.7% and 84.4%, respectively. Do not silently swap these values or certify the exact quantitative ranking. COD cannot distinguish native-organic degradation, supplement consumption, biomass assimilation and abiotic changes.
+
Participating Taxa:
+ Lysinibacillus sphaericus A1,
+ Bacillus cereus A2,
+
+ Lactococcus lactis A4
+
+
-
Biological Processes:
-
- -
- biological process involved in interspecies interaction between organisms
- (GO:0044419)
-
-
@@ -799,6 +792,60 @@
Evidence
+
+ Knowledge gaps & discussions (1)
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which mechanisms and reconciled measurements explain the mixed-culture advantage?
+
+
Both existing mechanism-to-performance directions remain HYPOTHESIZED; positive power and reported COD results remain. Full primary methods/results/discussion were read. SEM biofilm morphology is not strain-resolved transfer or causal complementarity. The OD600-normalized inoculation wording does not unambiguously establish equal total starting biomass. Section 3.3 percentages and concentrations appear crossed, and COD does not identify degradation pathways or distinguish amended from native substrates. Independent raw data or author clarification is needed before a numerical correction. Non-graph reported 84.4% remains unchanged, not certified, under #1716.
+
+
Attaches to: ecological_interactions#Proposed Electroactive Consortium Complementarity, ecological_interactions#Consortium-Enhanced Anode Power Output, ecological_interactions#Consortium-Enhanced Chemical Oxygen Demand Removal
+
+
+
+
+ 2 evidence item(s)
+
+
+
+
selecting complementary strains with diverse metabolic functions can substantially improve system performance
+
Supports the authors proposed complementarity interpretation, not a directly established niche-partitioning mechanism.
+
+
+
The highest COD removal (84.4%) was also recorded
+
Supports the abstract-reported 84.4%, not reconciled agreement with the inconsistent Section 3.3 concentrations.
+
+
+
+
@@ -1297,20 +1344,16 @@
Evidence
(function() {
var intId = "interaction:0";
- var intType = "NICHE_PARTITIONING";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
-
- processes.push("biological process involved in interspecies interaction between organisms");
-
-
var evidenceCount = 1;
nodes.push({
id: intId,
- label: "Complementary Electroactive Consortium Performance",
+ label: "Proposed Electroactive Consortium Complementarity",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1321,19 +1364,30 @@
Evidence
+ var participantKeys = [
+
+ "Lysinibacillus sphaericus A1",
+
+ "Bacillus cereus A2",
+
+ "Lactococcus lactis A4"
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
+
})();
(function() {
var intId = "interaction:1";
- var intType = "NICHE_PARTITIONING";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
-
- processes.push("biological process involved in interspecies interaction between organisms");
-
-
var evidenceCount = 1;
nodes.push({
@@ -1349,19 +1403,30 @@
Evidence
+ var participantKeys = [
+
+ "Lysinibacillus sphaericus A1",
+
+ "Bacillus cereus A2",
+
+ "Lactococcus lactis A4"
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
+
})();
(function() {
var intId = "interaction:2";
- var intType = "NICHE_PARTITIONING";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
-
- processes.push("biological process involved in interspecies interaction between organisms");
-
-
var evidenceCount = 1;
nodes.push({
@@ -1377,6 +1442,21 @@
Evidence
+ var participantKeys = [
+
+ "Lysinibacillus sphaericus A1",
+
+ "Bacillus cereus A2",
+
+ "Lactococcus lactis A4"
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
+
})();
diff --git a/history/records/Pleuromutilin_Degrading_Artificial_Consortium_5_Strain/2026-10-07T104208Z-codex-096092.yaml b/history/records/Pleuromutilin_Degrading_Artificial_Consortium_5_Strain/2026-10-07T104208Z-codex-096092.yaml
new file mode 100644
index 000000000..71f29786d
--- /dev/null
+++ b/history/records/Pleuromutilin_Degrading_Artificial_Consortium_5_Strain/2026-10-07T104208Z-codex-096092.yaml
@@ -0,0 +1,25 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Pleuromutilin_Degrading_Artificial_Consortium_5_Strain.yaml
+ slug: Pleuromutilin_Degrading_Artificial_Consortium_5_Strain
+session:
+ id: 2026-10-07T104208Z-codex-096092
+ timestamp: '2026-10-07T10:42:08Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1711
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain positive 91.97% degradation without obligatory syntrophy.; Retain proposed
+ metabolic products/pathways with attribution and metabolomics limits.
+ details: Source-based self-adversarial review. reports/causal_graph_review/decisions/20261007-four-records-batch86.yaml
diff --git a/history/records/Polaromonas_Vanadium_Reduction_Community/2026-10-07T104208Z-codex-da763c.yaml b/history/records/Polaromonas_Vanadium_Reduction_Community/2026-10-07T104208Z-codex-da763c.yaml
new file mode 100644
index 000000000..8be5245ab
--- /dev/null
+++ b/history/records/Polaromonas_Vanadium_Reduction_Community/2026-10-07T104208Z-codex-da763c.yaml
@@ -0,0 +1,25 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Polaromonas_Vanadium_Reduction_Community.yaml
+ slug: Polaromonas_Vanadium_Reduction_Community
+session:
+ id: 2026-10-07T104208Z-codex-da763c
+ timestamp: '2026-10-07T10:42:08Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1712
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Preserve positive enrichment reduction and qualify Polaromonas/MAG attribution.;
+ Preserve controlled enrichment precipitation without invented mineral or partner details.
+ details: Source-based self-adversarial review. reports/causal_graph_review/decisions/20261007-four-records-batch86.yaml
diff --git a/history/records/Populus_Salt_Tolerant_SynComs/2026-10-07T104208Z-codex-05f714.yaml b/history/records/Populus_Salt_Tolerant_SynComs/2026-10-07T104208Z-codex-05f714.yaml
new file mode 100644
index 000000000..c47641976
--- /dev/null
+++ b/history/records/Populus_Salt_Tolerant_SynComs/2026-10-07T104208Z-codex-05f714.yaml
@@ -0,0 +1,26 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Populus_Salt_Tolerant_SynComs.yaml
+ slug: Populus_Salt_Tolerant_SynComs
+session:
+ id: 2026-10-07T104208Z-codex-05f714
+ timestamp: '2026-10-07T10:42:08Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1713
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Preserve positive physiological responses and qualify their causal mediation.;
+ Preserve recruitment association and qualify its host-benefit interpretation.; Preserve
+ formulation-specific host growth without collapsing alternative communities.
+ details: Source-based self-adversarial review. reports/causal_graph_review/decisions/20261007-four-records-batch86.yaml
diff --git a/history/records/Poultry_Wastewater_ThreeStrain_Electroactive_Consortium/2026-10-07T104208Z-codex-adfaf1.yaml b/history/records/Poultry_Wastewater_ThreeStrain_Electroactive_Consortium/2026-10-07T104208Z-codex-adfaf1.yaml
new file mode 100644
index 000000000..c27a4d40e
--- /dev/null
+++ b/history/records/Poultry_Wastewater_ThreeStrain_Electroactive_Consortium/2026-10-07T104208Z-codex-adfaf1.yaml
@@ -0,0 +1,26 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Poultry_Wastewater_ThreeStrain_Electroactive_Consortium.yaml
+ slug: Poultry_Wastewater_ThreeStrain_Electroactive_Consortium
+session:
+ id: 2026-10-07T104208Z-codex-adfaf1
+ timestamp: '2026-10-07T10:42:08Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1714
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain author-proposed complementarity with explicit mechanistic and inoculum uncertainty.;
+ Preserve positive maximum power comparison within the tested model substrate.; Preserve
+ reported COD endpoint while exposing primary-source arithmetic discrepancy.
+ details: Source-based self-adversarial review. reports/causal_graph_review/decisions/20261007-four-records-batch86.yaml
diff --git a/kb/communities/Pleuromutilin_Degrading_Artificial_Consortium_5_Strain.yaml b/kb/communities/Pleuromutilin_Degrading_Artificial_Consortium_5_Strain.yaml
index 5bcce4fe1..e0e5f4afb 100644
--- a/kb/communities/Pleuromutilin_Degrading_Artificial_Consortium_5_Strain.yaml
+++ b/kb/communities/Pleuromutilin_Degrading_Artificial_Consortium_5_Strain.yaml
@@ -154,141 +154,51 @@ taxonomy:
and Pseudomonas songnenensis'
explanation: Names Pseudomonas songnenensis as a member of the artificial consortium.
ecological_interactions:
-- name: En4 Gradient Enrichment and Domestication
- description: >
- The natural En4 consortium was developed for efficient pleuromutilin
- degradation by gradient enrichment and domestication under pleuromutilin
- selection.
+- name: Ninety-Two-Percent Pleuromutilin Degradation
+ description: The defined five-strain artificial consortium achieved reported pleuromutilin degradation of 91.97%.
+ Preserve this positive community-level endpoint without asserting obligatory syntrophy, partner-specific flux,
+ complete mineralization or a superiority comparison not stated in the accessible abstract.
scope: COMMUNITY_LEVEL
- interaction_type: NICHE_PARTITIONING
metabolites:
- preferred_term: pleuromutilin
term:
id: CHEBI:8269
label: Pleuromutilin
- downstream:
- - target: Pleuromutilin-Stress Core Specialization
- description: >
- Pleuromutilin gradient enrichment selected a domesticated En4 community
- with stress-associated diversity loss and a specialized core-taxon set.
evidence:
- reference: PMID:42133144
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: >
- A natural microbial consortium (En4) was developed in this study to
- achieve efficient degradation of pleuromutilin through gradient
- enrichment and domestication
- explanation: >
- Supports gradient enrichment and domestication of the natural En4
- pleuromutilin-degrading consortium.
-- name: Pleuromutilin-Stress Core Specialization
- description: >
- Pleuromutilin stress reduced diversity in the natural consortium and
- selected specialized core taxa, chiefly within Proteobacteria and including
- pollutant-degrading genera enriched during the enrichment.
- scope: COMMUNITY_LEVEL
- interaction_type: NICHE_PARTITIONING
- metabolites:
- - preferred_term: pleuromutilin
+ snippet: was constructed, achieving a degradation rate of 91.97%
+ explanation: 'Supports the measured 91.97% pleuromutilin degradation rate of the five-strain artificial consortium.
+
+ '
+ participating_taxa:
+ - preferred_term: Stenotrophomonas pavanii
term:
- id: CHEBI:8269
- label: Pleuromutilin
- evidence:
- - reference: PMID:42133144
- supports: SUPPORT
- evidence_source: OTHER
- snippet: >
- pleuromutilin stress significantly reduced microbial diversity, and core
- communities with functional specialization were identified across
- multiple taxa
- explanation: >
- Supports pleuromutilin-associated diversity loss and functional
- specialization across core taxa in the natural consortium.
- - reference: PMID:42133144
- supports: SUPPORT
- evidence_source: OTHER
- snippet: >
- bacterial genera that have the potential to degrade pollutants, such as
- Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium and Cupriavidus were
- significantly enriched
- explanation: >
- Supports enrichment of pollutant-degrading bacteria under pleuromutilin
- stress.
-- name: Fourteen-Degrader Bacterial Isolation
- description: >
- Fourteen pleuromutilin-degrading bacteria were isolated from the natural
- En4 consortium as the strain source for designing an artificial degradation
- community.
- scope: COMMUNITY_LEVEL
- interaction_type: NICHE_PARTITIONING
- metabolites:
- - preferred_term: pleuromutilin
+ id: NCBITaxon:487698
+ label: Stenotrophomonas pavanii
+ - preferred_term: Stenotrophomonas maltophilia
term:
- id: CHEBI:8269
- label: Pleuromutilin
- evidence:
- - reference: PMID:42133144
- supports: SUPPORT
- evidence_source: IN_VITRO
- snippet: 14 degrading bacteria were isolated from the natural microbial community
- explanation: >
- Supports isolation of pleuromutilin-degrading bacteria from the natural
- En4 consortium.
-- name: Five-Strain Artificial Consortium Construction
- description: >
- A defined artificial consortium was built from Stenotrophomonas pavanii,
- Stenotrophomonas maltophilia, Lysinibacillus sphaericus, Lysinibacillus
- mangiferihumi, and Pseudomonas songnenensis.
- scope: COMMUNITY_LEVEL
- interaction_type: NICHE_PARTITIONING
- metabolites:
- - preferred_term: pleuromutilin
+ id: NCBITaxon:40324
+ label: Stenotrophomonas maltophilia
+ - preferred_term: Lysinibacillus sphaericus
term:
- id: CHEBI:8269
- label: Pleuromutilin
- downstream:
- - target: Ninety-Two-Percent Pleuromutilin Degradation
- description: >
- The five-strain artificial consortium was the defined community that
- achieved high pleuromutilin degradation.
- evidence:
- - reference: PMID:42133144
- supports: SUPPORT
- evidence_source: IN_VITRO
- snippet: >
- an efficient artificial microbial consortium comprising five strains:
- Stenotrophomonas pavanii, Stenotrophomonas maltophilia, Lysinibacillus
- sphaericus, Lysinibacillus mangiferihumi, and Pseudomonas songnenensis
- explanation: >
- Supports construction and membership of the five-strain artificial
- pleuromutilin-degrading consortium.
-- name: Ninety-Two-Percent Pleuromutilin Degradation
- description: >
- The defined artificial consortium degraded pleuromutilin with a measured
- degradation rate of 91.97%.
- scope: COMMUNITY_LEVEL
- interaction_type: SYNTROPHY
- metabolites:
- - preferred_term: pleuromutilin
+ id: NCBITaxon:1421
+ label: Lysinibacillus sphaericus
+ - preferred_term: Lysinibacillus mangiferihumi
term:
- id: CHEBI:8269
- label: Pleuromutilin
- evidence:
- - reference: PMID:42133144
- supports: SUPPORT
- evidence_source: IN_VITRO
- snippet: was constructed, achieving a degradation rate of 91.97%
- explanation: >
- Supports the measured 91.97% pleuromutilin degradation rate of the
- five-strain artificial consortium.
-- name: Artificial-Consortium Metabolic Profiling
- description: >
- Metabolic profiling during artificial-consortium pleuromutilin degradation
- was used to propose potential pleuromutilin degradation products and
- metabolic pathways.
+ id: NCBITaxon:1130819
+ label: Lysinibacillus mangiferihumi
+ - preferred_term: Pseudomonas songnenensis
+ term:
+ id: NCBITaxon:1176259
+ label: Pseudomonas songnenensis
+- name: Proposed Artificial-Consortium Degradation Products and Pathways
+ description: 'HYPOTHESIZED: metabolomic profiling of the artificial five-strain consortium motivated proposed
+ pleuromutilin degradation products and pathways. Public Supplement Table S3 compares pleuromutilin and glucose
+ conditions by untargeted metabolomics. Differential abundance and database spectral assignments do not alone
+ establish that every metabolite derives from pleuromutilin or identify a strain-resolved transfer route.'
scope: COMMUNITY_LEVEL
- interaction_type: SYNTROPHY
metabolites:
- preferred_term: pleuromutilin
term:
@@ -298,19 +208,82 @@ ecological_interactions:
- reference: PMID:42133144
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: >
- The metabolic profile of the artificial microbial consortia during the
- degradation of pleuromutilin were studied, and potential degradation
- products and metabolic pathways were proposed
- explanation: >
- Supports downstream metabolic profiling of pleuromutilin degradation by
- the artificial consortium.
+ snippet: 'The metabolic profile of the artificial microbial consortia during the degradation of pleuromutilin
+ were studied, and potential degradation products and metabolic pathways were proposed
+
+ '
+ explanation: Supports proposed products/pathways, not experimentally resolved interspecies exchange or obligate
+ syntrophy.
+ participating_taxa:
+ - preferred_term: Stenotrophomonas pavanii
+ term:
+ id: NCBITaxon:487698
+ label: Stenotrophomonas pavanii
+ - preferred_term: Stenotrophomonas maltophilia
+ term:
+ id: NCBITaxon:40324
+ label: Stenotrophomonas maltophilia
+ - preferred_term: Lysinibacillus sphaericus
+ term:
+ id: NCBITaxon:1421
+ label: Lysinibacillus sphaericus
+ - preferred_term: Lysinibacillus mangiferihumi
+ term:
+ id: NCBITaxon:1130819
+ label: Lysinibacillus mangiferihumi
+ - preferred_term: Pseudomonas songnenensis
+ term:
+ id: NCBITaxon:1176259
+ label: Pseudomonas songnenensis
curation_history:
- timestamp: '2026-10-02T06:00:47Z'
curator: codex
action: REPAIR_CAUSAL_GRAPH
- changes: Removed four pleuromutilin workflow edges from enrichment or
- isolate-selection steps to later isolation, artificial-consortium assembly,
- and metabolic profiling, and rewrote the retained enrichment-to-core edge as
+ changes: Removed four pleuromutilin workflow edges from enrichment or isolate-selection steps to later isolation,
+ artificial-consortium assembly, and metabolic profiling, and rewrote the retained enrichment-to-core edge as
direct stress selection.
llm_assisted: true
+- timestamp: '2026-10-07T10:42:06Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: 'Retain positive 91.97% degradation without obligatory syntrophy.; Retain proposed metabolic products/pathways
+ with attribution and metabolomics limits. Issue #1711; reports/causal_graph_review/decisions/20261007-four-records-batch86.yaml'
+ llm_assisted: true
+discussions:
+- discussion_id: pleuromutilin-parent-versus-defined-community
+ prompt: Which compatibility and degradation mechanisms belong to the defined five-strain community?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ posed_by: codex
+ rationale: 'Natural En4 enrichment showed reduced diversity and enriched pollutant-associated genera; preserve
+ those positives as parent-community context, not interactions among the five selected strains. Assembly/isolation
+ workflow remains in engineering_design. Public Table S1 lists bacterial and fungal isolates and identifies W12,
+ rather than same-species W10, as the selected Pseudomonas songnenensis in Table S2. Table S2 reports no inhibition
+ zones, not cross-feeding or long-term stability. Table S3 supports differential metabolomics, not compound provenance
+ or partner flux. Main text remains inaccessible; source DOCX tables were read by OOXML, not rendered pages.
+ Missing compatibility/pathway topology remains #1715 pending a reviewed, explicitly authorized Edison report;
+ no new structure is added. Non-graph isolate and strain identity remains #1716.'
+ attaches_to:
+ - ecological_interactions#Ninety-Two-Percent Pleuromutilin Degradation
+ - ecological_interactions#Proposed Artificial-Consortium Degradation Products and Pathways
+ evidence:
+ - reference: PMID:42133144
+ supports: SUPPORT
+ evidence_source: OTHER
+ snippet: 'pleuromutilin stress significantly reduced microbial diversity, and core communities with functional
+ specialization were identified across multiple taxa
+
+ '
+ explanation: 'Supports pleuromutilin-associated diversity loss and functional specialization across core taxa
+ in the natural consortium.
+
+ '
+ - reference: PMID:42133144
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: 'The metabolic profile of the artificial microbial consortia during the degradation of pleuromutilin
+ were studied, and potential degradation products and metabolic pathways were proposed
+
+ '
+ explanation: Supports proposed products/pathways, not experimentally resolved interspecies exchange or obligate
+ syntrophy.
diff --git a/kb/communities/Polaromonas_Vanadium_Reduction_Community.yaml b/kb/communities/Polaromonas_Vanadium_Reduction_Community.yaml
index c4bdd209c..f51142956 100644
--- a/kb/communities/Polaromonas_Vanadium_Reduction_Community.yaml
+++ b/kb/communities/Polaromonas_Vanadium_Reduction_Community.yaml
@@ -225,257 +225,53 @@ taxonomy:
belonging to the family Burkholderiaceae, were potentially responsible for VV reduction
explanation: Documents presence and enrichment under H₂ amendment
ecological_interactions:
-- name: Dissimilatory V(V) Reduction by Polaromonas
- description: 'Polaromonas species perform dissimilatory vanadate [V(V)] reduction to vanadyl [V(IV)]
- as a respiratory process, coupling oxidation of organic electron donors (lactate, acetate, pyruvate)
- to V(V) reduction. The process is mediated by c-type cytochromes (cymA, omcA genes) that transfer
- electrons from the inner membrane quinone pool to outer membrane terminal reductases (narG-like nitrate
- reductases, arrA-like arsenate reductases) capable of reducing V(V). Soluble vanadate (VO₄³⁻, oxidation
- state +5) is reduced to vanadyl cation (VO²⁺, oxidation state +4), decreasing vanadium solubility
- by 2-3 orders of magnitude. V(IV) precipitates as hydrated vanadyl hydroxides, oxides, or co-precipitates
- with iron minerals. In tailings microcosms, Polaromonas achieves 65-80% V(V) reduction within 7-14
- days, lowering dissolved vanadium from 15-25 mg/L to 3-8 mg/L. This represents the dominant vanadium
- immobilization pathway in the community. The reaction is thermodynamically favorable (standard potential
- E⁰ +0.34 V for VO₂⁺/VO₄³⁻ couple) and generates energy for microbial growth, with cell yields increasing
- proportionally to V(V) reduced.
-
- '
- interaction_type: CROSS_FEEDING
- scope: PAIRWISE
- source_taxon:
- preferred_term: Polaromonas species
- term:
- id: NCBITaxon:52972
- label: Polaromonas
- metabolites:
- - preferred_term: vanadate
- term:
- id: CHEBI:46442
- label: vanadate(3-)
- concentration: 'Initial: 15-25 mg/L; reduced to 3-8 mg/L'
- notes: V(V) as VO₄³⁻
- - preferred_term: vanadyl cation
- term:
- id: CHEBI:30046
- label: oxidovanadium(2+)
- notes: V(IV) as VO²⁺; precipitates as oxides/hydroxides
- - preferred_term: lactate
- term:
- id: CHEBI:24996
- label: lactate
- concentration: 5-20 mM supplied as electron donor
- - preferred_term: acetate
- term:
- id: CHEBI:30089
- label: acetate
- concentration: 2-10 mM supplied or produced from lactate
- biological_processes:
- - preferred_term: dissimilatory reduction
- term:
- id: GO:0019645
- label: anaerobic electron transport chain
- - preferred_term: cellular detoxification
- term:
- id: GO:1990748
- label: cellular detoxification
+- name: Vanadium Reduction in Polaromonas-Associated Enrichments
+ description: 'V(V)-reducing enrichments support community-level reduction. PARTIAL: enrichment association implicates
+ Polaromonas, and its recovered MAGs suggest cymA, omcA and narG involvement; these observations do not establish
+ a purified-isolate activity, gene necessity or a partner-specific respiratory pathway. Public Supplement Figure
+ S2 shows 6 mM acetate and 1.5 mM vanadate treatments with autoclaved and no-vanadate controls. No unsupported
+ arrA function, energy yield, time course or numerical removal rate is assigned.'
+ scope: COMMUNITY_LEVEL
downstream:
- - target: Vanadium Immobilization via V(IV) Precipitation
- description: Reduced V(IV) forms sparingly soluble minerals
+ - target: V(IV) Precipitation in Reducing Enrichments
+ description: Reduction of supplied V(V) yields V(IV), which precipitated in the acetate-plus-vanadate enrichments
+ shown in Supplement Figure S2. This existing direction is retained at community scale; attribution specifically
+ to Polaromonas remains PARTIAL, and the controls do not prove a particular reductase or mineral identity.
evidence:
- reference: PMID:33125214
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: Further, VV-reducing enrichments indicated that bacteria associated with Polaromonas, a genus
- belonging to the family Burkholderiaceae, were potentially responsible for VV reduction
- explanation: Quantifies V(V) reduction efficiency
- - reference: PMID:33125214
- supports: PARTIAL
- evidence_source: IN_VIVO
- snippet: bacteria associated with Polaromonas, a genus belonging to the family Burkholderiaceae, were potentially responsible for VV reduction
- explanation: Links Polaromonas to vanadium reduction in natural system
+ snippet: were potentially responsible for VV reduction
+ explanation: The abstract proposes Polaromonas involvement in reducing enrichments; taxon attribution is not
+ a gene or isolate perturbation.
- reference: PMID:33125214
supports: SUPPORT
- evidence_source: IN_VITRO
- snippet: Polaromonas spp. encoded genes (cymA, omcA, and narG) were responsible for VV reduction
- explanation: Identifies molecular mechanism of V(V) reduction
-- name: Vanadium Immobilization via V(IV) Precipitation
- description: 'Biogenic V(IV) produced by microbial V(V) reduction undergoes rapid precipitation as vanadyl
- minerals, effectively immobilizing vanadium in the tailings solid phase. The vanadyl cation (VO²⁺)
- forms sparingly soluble precipitates including hydrated vanadyl hydroxides [VO(OH)₂], vanadyl sulfates,
- and V(IV)-substituted iron oxides. Solubility decreases from ~10⁻³ M for vanadate [V(V)] to ~10⁻⁵
- to 10⁻⁶ M for vanadyl species at circumneutral pH. X-ray absorption spectroscopy (XAS) analysis confirms
- V(IV) accumulation in tailings solids following microbial reduction, with V(IV) comprising 65-85%
- of total vanadium in reduced zones. The precipitates are stable under reducing conditions (Eh < -100
- mV) but can re-oxidize to soluble V(V) if oxygen penetrates the tailings. Long-term immobilization
- requires maintaining anaerobic conditions through organic carbon amendment or physical capping. This
- process represents the key mechanism for natural attenuation of vanadium contamination in mine tailings.
-
- '
- interaction_type: MUTUALISM
- scope: PAIRWISE
- source_taxon:
- preferred_term: Polaromonas species
+ evidence_source: COMPUTATIONAL
+ snippet: Retrieved metagenome-assembled genomes (MAGs) suggested
+ explanation: Supports explicitly inferred genomic involvement, not experimentally necessary cymA/omcA/narG activity.
+ participating_taxa:
+ - preferred_term: Polaromonas species
term:
id: NCBITaxon:52972
label: Polaromonas
- metabolites:
- - preferred_term: vanadyl cation
- term:
- id: CHEBI:30046
- label: oxidovanadium(2+)
- notes: V(IV) as VO²⁺
- - preferred_term: vanadium dioxide
- term:
- id: CHEBI:30047
- label: vanadium dioxide
- notes: VO₂ and hydrated forms as precipitates
- biological_processes:
- - preferred_term: metal ion sequestration
- term:
- id: GO:0061687
- label: detoxification of inorganic compound
- evidence:
- - reference: PMID:33125214
- supports: SUPPORT
- evidence_source: IN_VIVO
- snippet: Vanadium (V) is an important metal with critical industrial and medical applications
- explanation: Confirms V(IV) precipitation and immobilization
- - reference: PMID:33125214
- supports: PARTIAL
- evidence_source: IN_VIVO
- snippet: less toxic and immobile VIV
- explanation: Quantifies solubility decrease upon reduction
-- name: Sulfide-Mediated Chemical V(V) Reduction
- description: 'Hydrogen sulfide (H₂S) produced by sulfate-reducing bacteria (Desulfovibrio, Desulfitobacterium)
- chemically reduces V(V) to V(IV) through abiotic reactions, complementing enzymatic microbial reduction.
- The reaction proceeds as: VO₄³⁻ + H₂S + 2H⁺ → VO²⁺ + S⁰ + 2H₂O, consuming sulfide and generating elemental
- sulfur or sulfate depending on oxygen availability. Sulfide concentrations of 50-200 µM in tailings
- pore water accelerate V(V) reduction rates by 40-60% compared to microbial reduction alone. Additionally,
- sulfide precipitates vanadium as vanadium sulfide minerals (V₂S₃, V₃S₄) with extremely low solubility
- (Ksp ~ 10⁻²⁰), providing superior long-term immobilization compared to vanadyl oxides. Sulfate reduction
- is particularly important in deeper, more reduced tailings zones where sulfate concentrations (500-2000
- mg/L from ore processing) are elevated. This chemical pathway operates continuously in sulfidogenic
- zones, providing persistent V(V) reduction capacity independent of direct microbial activity.
-
- '
- interaction_type: CROSS_FEEDING
- scope: PAIRWISE
- source_taxon:
- preferred_term: Desulfovibrio species
- term:
- id: NCBITaxon:872
- label: Desulfovibrio
- target_taxon:
- preferred_term: Desulfitobacterium species
- term:
- id: NCBITaxon:36853
- label: Desulfitobacterium
- metabolites:
- - preferred_term: hydrogen sulfide
- term:
- id: CHEBI:16136
- label: hydrogen sulfide
- concentration: 50-200 µM in pore water
- notes: Product of sulfate reduction; chemically reduces V(V)
- - preferred_term: sulfate
- term:
- id: CHEBI:16189
- label: sulfate
- concentration: 500-2000 mg/L in tailings
- notes: Electron acceptor for sulfate reduction
- - preferred_term: vanadate
- term:
- id: CHEBI:46442
- label: vanadate(3-)
- notes: Reduced by sulfide to V(IV)
- - preferred_term: vanadyl cation
- term:
- id: CHEBI:30046
- label: oxidovanadium(2+)
- notes: Product of sulfide-mediated reduction
- biological_processes:
- - preferred_term: sulfate reduction
- term:
- id: GO:0019420
- label: dissimilatory sulfate reduction
- downstream:
- - target: Vanadium Immobilization via V(IV) Precipitation
- description: Sulfide-mediated V(V) reduction feeds the same insoluble V(IV)
- product pool as direct enzymatic V(V) reduction.
+- name: V(IV) Precipitation in Reducing Enrichments
+ description: Public Supplement Figure S2 reports V(IV) precipitate formation in acetate-plus-vanadate enrichment
+ treatments and not in the autoclaved or no-vanadate controls. Preserve the positive enrichment-level precipitation
+ observation. Polaromonas is the proposed associated genus, not a proven sole producer; no mineral phase, XAS
+ fraction, solubility constant, oxidation stability or reciprocal microbial fitness benefit is established here.
+ scope: COMMUNITY_LEVEL
evidence:
- reference: PMID:33125214
supports: SUPPORT
- evidence_source: IN_VIVO
- snippet: Further, VV-reducing enrichments indicated that bacteria associated with Polaromonas, a genus
- belonging to the family Burkholderiaceae, were potentially responsible for VV reduction
- explanation: Quantifies sulfide contribution to vanadium reduction
- - reference: PMID:33125214
- supports: PARTIAL
evidence_source: IN_VITRO
- snippet: reduce the more toxic and mobile VV to the less toxic and immobile VIV
- explanation: Abstract supports VV reduction in this system; the abiotic
- pseudo-first-order kinetics (k = 0.15-0.25 per hour) appear in the full
- text only.
-- name: Sequential Fe(III) and V(V) Reduction
- description: 'The microbial community performs sequential reduction of Fe(III) followed by V(V), reflecting
- thermodynamic favorability of electron acceptors. Geobacter and Polaromonas initially reduce abundant
- Fe(III) minerals (ferrihydrite, goethite, hematite) present in vanadium titanomagnetite tailings,
- generating Fe(II) and lowering redox potential from +200 mV to -50 to -150 mV. This Fe(III) reduction
- phase (days 0-5 in microcosms) creates strongly reducing conditions favorable for subsequent V(V)
- reduction. After Fe(III) depletion or decline to low concentrations, V(V) becomes the dominant terminal
- electron acceptor (days 5-14), with V(V) reduction rates increasing 3-5 fold. Fe(II) generated during
- Fe(III) reduction can also chemically reduce V(V) at mineral surfaces, particularly on magnetite and
- maghemite. The sequential reduction pattern mirrors that observed in uranium bioremediation systems,
- where Fe(III) reduction precedes U(VI) reduction. This metabolic succession is driven by thermodynamics
- (Fe³⁺/Fe²⁺ E⁰ = +0.77 V; VO₂⁺/VO₄³⁻ E⁰ = +0.34 V at pH 7), with organisms preferentially respiring
- higher-potential acceptors.
-
- '
- interaction_type: SYNTROPHY
- scope: PAIRWISE
- source_taxon:
- preferred_term: Geobacter species
- term:
- id: NCBITaxon:28232
- label: Geobacter metallireducens
- target_taxon:
- preferred_term: Polaromonas species
+ snippet: which formed VIV precipitates
+ explanation: 'Primary public Supplement Figure S2, not the abstract: treatment-associated precipitation with
+ autoclaved/no-vanadate controls. This does not resolve mineral identity or sole-organism causation.'
+ participating_taxa:
+ - preferred_term: Polaromonas species
term:
id: NCBITaxon:52972
label: Polaromonas
- metabolites:
- - preferred_term: Fe(III)
- term:
- id: CHEBI:29034
- label: iron(3+)
- notes: Initial electron acceptor; abundant in tailings minerals
- - preferred_term: Fe(II)
- term:
- id: CHEBI:29033
- label: iron(2+)
- notes: Product; can chemically reduce V(V)
- - preferred_term: vanadate
- term:
- id: CHEBI:46442
- label: vanadate(3-)
- notes: Secondary electron acceptor after Fe(III) depletion
- biological_processes:
- - preferred_term: iron ion transport
- term:
- id: GO:0006826
- label: iron ion transport
- evidence:
- - reference: PMID:33125214
- supports: SUPPORT
- evidence_source: IN_VIVO
- snippet: Further, VV-reducing enrichments indicated that bacteria associated with Polaromonas, a genus
- belonging to the family Burkholderiaceae, were potentially responsible for VV reduction
- explanation: Documents sequential metal reduction pattern
- - reference: PMID:33125214
- supports: PARTIAL
- evidence_source: IN_VIVO
- snippet: reduce the more toxic and mobile VV to the less toxic and immobile VIV
- explanation: Links Fe(III) reduction to redox conditioning
environmental_factors:
- name: pH
value: 6.5-7.5
@@ -664,3 +460,40 @@ metals_present:
metal_relevance: INCIDENTAL
metal_notes: Metal/REE detected via CHEBI terms in metabolites; Metal/REE detected via environmental factor
measurements; Metal/REE detected via keyword matching in description (context-validated)
+discussions:
+- discussion_id: polaromonas-enrichment-versus-partner-mechanism
+ prompt: Which organisms and enzymes actually mediate enrichment reduction and precipitation?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ posed_by: codex
+ rationale: 'Keep positive V(V) reduction and treatment-associated V(IV) precipitation. MAG function and Polaromonas
+ responsibility remain inferred; co-occurrence networks and annotated nitrogen/sulfur pathways are not transfer
+ or enzyme-perturbation evidence. The reviewed primary abstract and public SI do not support the removed Desulfovibrio-to-Desulfitobacterium
+ sulfide or Geobacter-to-Polaromonas sequential-iron routes and their exact numbers. Main text remains inaccessible.
+ Only Polaromonas is explicitly credited in these qualified community nodes; the other canonical members remain
+ unverified and may appear disconnected. Non-graph taxonomy, numerical claims and Panzhihua/Sichuan locality
+ need #1716; public Figure S1 shows Hunan, and PMID19077236 concerns an Acidithiobacillus ferrooxidans genome,
+ not Geobacter vanadium reduction. Related #1680 concerns a different record.'
+ attaches_to:
+ - ecological_interactions#Vanadium Reduction in Polaromonas-Associated Enrichments
+ - ecological_interactions#V(IV) Precipitation in Reducing Enrichments
+ evidence:
+ - reference: PMID:33125214
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: were potentially responsible for VV reduction
+ explanation: The abstract proposes Polaromonas involvement in reducing enrichments; taxon attribution is not
+ a gene or isolate perturbation.
+ - reference: PMID:33125214
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: which formed VIV precipitates
+ explanation: 'Primary public Supplement Figure S2, not the abstract: treatment-associated precipitation with
+ autoclaved/no-vanadate controls. This does not resolve mineral identity or sole-organism causation.'
+curation_history:
+- timestamp: '2026-10-07T10:42:07Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: 'Preserve positive enrichment reduction and qualify Polaromonas/MAG attribution.; Preserve controlled
+ enrichment precipitation without invented mineral or partner details. Issue #1712; reports/causal_graph_review/decisions/20261007-four-records-batch86.yaml'
+ llm_assisted: true
diff --git a/kb/communities/Populus_Salt_Tolerant_SynComs.yaml b/kb/communities/Populus_Salt_Tolerant_SynComs.yaml
index 19a95a098..187160ae6 100644
--- a/kb/communities/Populus_Salt_Tolerant_SynComs.yaml
+++ b/kb/communities/Populus_Salt_Tolerant_SynComs.yaml
@@ -51,73 +51,11 @@ taxonomy:
evidence:
- *id001
ecological_interactions:
-- name: High-Salt Populus Rhizosphere Isolation
- description: >
- A high-throughput cultivation campaign isolated hundreds of bacteria from the high-salt
- Populus euphratica rhizosphere and selected nine salt-tolerant, growth-promoting strains for
- synthetic-community design.
- scope: COMMUNITY_LEVEL
- biological_processes:
- - preferred_term: response to salt stress
- term:
- id: GO:0009651
- label: response to salt stress
- downstream:
- - target: Function-Driven Poplar SynCom Construction
- description: >
- The nine selected isolates provided the salt-tolerant, growth-promoting strain pool for five
- function-driven Populus SynCom formulations.
- evidence:
- - reference: PMID:40904019
- supports: SUPPORT
- evidence_source: IN_VITRO
- snippet: a total of 512 strains were isolated from the high-salt rhizosphere soil of Populus
- euphratica through high-throughput cultivation
- explanation: >
- Names the high-salt P. euphratica rhizosphere as the isolate source for the Populus SynCom
- design campaign.
- - reference: PMID:40904019
- supports: SUPPORT
- evidence_source: IN_VITRO
- snippet: nine strains were further selected for their salt-tolerant and growth-promoting
- abilities, with three isolates identified as key microbes
- explanation: >
- Shows that the broad isolate collection was reduced to a salt-tolerant, growth-promoting
- SynCom design set.
-- name: Function-Driven Poplar SynCom Construction
- description: >
- Five function-driven SynComs were assembled from the selected Populus rhizosphere isolates;
- SynCom5, SynCom7, and SynCom9 produced the strongest hybrid Poplar 84K growth improvements
- under salt stress.
- scope: COMMUNITY_LEVEL
- biological_processes:
- - preferred_term: response to salt stress
- term:
- id: GO:0009651
- label: response to salt stress
- downstream:
- - target: Physiological Salt-Stress Resistance
- description: >
- The best Populus SynCom formulations were carried into mechanistic assays of oxidative
- stress, osmolyte adjustment, and ion balance under salt exposure.
- - target: Salt-Adapted Root-Associated Consortia
- description: >
- The same SynCom treatments were also tested for recruitment of root-associated bacteria that
- contribute to poplar adaptation during salt stress.
- evidence:
- - reference: PMID:40904019
- supports: SUPPORT
- evidence_source: IN_VITRO
- snippet: Guided by a function-driven strategy, we constructed five distinct SynComs, with
- SynCom5, SynCom7 and SynCom9 showing the most significant improvement in the
- growth of hybrid Poplar 84K (Populus alba × Populus glandulosa).
- explanation: >
- Links function-driven SynCom formulation to the salt-stress growth assay that prioritized
- three Populus SynComs.
- name: Physiological Salt-Stress Resistance
- description: >
- Populus SynComs increased salt-stress resistance by reducing oxidative stress, adjusting
- osmolytes, and balancing ions in the salt-challenged host.
+ description: 'The primary abstract reports that the effective Populus SynCom treatments increased host salt-stress
+ resistance through reduced oxidative stress, osmolyte adjustment and ion balance. Preserve these positive host
+ physiological findings. PARTIAL: the accessible abstract supports the proposed physiological explanation but
+ does not expose mediator-specific interventions or distinguish each formulation for each assay.'
scope: COMMUNITY_LEVEL
biological_processes:
- preferred_term: response to salt stress
@@ -130,46 +68,40 @@ ecological_interactions:
label: response to oxidative stress
downstream:
- target: Salt Stress Growth Protection
- description: >
- Reduced oxidative stress, osmolyte adjustment, and ion balance explain part of the SynCom-
- mediated growth improvement in salt-stressed hybrid Poplar 84K.
+ description: 'PARTIAL: reduced oxidative stress, osmolyte adjustment and ion balance are the primary authors
+ reported explanation for improved salt-stress resistance and growth. Retain this existing biological direction
+ without claiming that a particular physiological mediator was experimentally necessary or sufficient.'
evidence:
- reference: PMID:40904019
supports: SUPPORT
- evidence_source: IN_VITRO
- snippet: these SynComs can increase resistance to salt stress by directly reducing oxidative
- stress, adjusting osmolytes and balancing ions.
- explanation: >
- Summarizes the measured physiological routes through which the best SynComs increased
- Populus salt resistance.
+ evidence_source: IN_VIVO
+ snippet: these SynComs can increase resistance to salt stress by directly reducing oxidative stress, adjusting
+ osmolytes and balancing ions.
+ explanation: Supports reported host physiological mechanisms in the abstract; full perturbation methods remain
+ unavailable.
- name: Salt-Adapted Root-Associated Consortia
- description: >
- The salt-tolerant Populus SynComs recruited root-associated bacterial consortia that were linked
- to improved host adaptation under salt stress.
+ description: The abstract reports recruitment of specific root-associated bacterial consortia associated with
+ enhanced poplar salt adaptation after SynCom treatment. Preserve this positive root-community observation. It
+ does not identify the recruited taxa in the accessible text, demonstrate reciprocal symbiosis or isolate recruitment
+ as the necessary cause of host benefit.
scope: COMMUNITY_LEVEL
- biological_processes:
- - preferred_term: symbiotic process
- term:
- id: GO:0044403
- label: biological process involved in symbiotic interaction
downstream:
- target: Salt Stress Growth Protection
- description: >
- Recruitment of root-associated bacteria complemented the direct physiological effects of the
- introduced SynComs during poplar salt-stress adaptation.
+ description: 'PARTIAL: the primary authors propose that recruited root-associated consortia enhance poplar adaptation
+ and complement host physiological responses. Preserve this proposed direction; the accessible abstract does
+ not establish recruitment-mediated growth by depletion, transfer or rescue experiments.'
evidence:
- reference: PMID:40904019
supports: SUPPORT
- evidence_source: IN_VITRO
- snippet: these SynComs were observed to recruit specific root-associated bacterial consortia
- that enhance the adaptability of poplar to salt stress
- explanation: >
- Reports the downstream native root-microbiome recruitment associated with salt-stress
- adaptation after SynCom inoculation.
+ evidence_source: IN_VIVO
+ snippet: these SynComs were observed to recruit specific root-associated bacterial consortia that enhance the
+ adaptability of poplar to salt stress
+ explanation: Supports the reported recruitment/adaptation explanation, not a resolved causal mediation experiment.
- name: Salt Stress Growth Protection
- description: >
- SynCom5, SynCom7, and SynCom9 were the Populus rhizosphere SynCom formulations that most
- improved hybrid Poplar 84K growth during high-salinity challenge.
+ description: Among five alternative function-driven formulations, SynCom5, SynCom7 and SynCom9 showed the strongest
+ growth improvement in salt-stressed hybrid Poplar 84K (Populus alba x Populus glandulosa). Preserve this experimental
+ host endpoint without collapsing the three formulations into a single nine-strain coculture or claiming that
+ individual members are necessary.
scope: COMMUNITY_LEVEL
biological_processes:
- preferred_term: growth
@@ -183,12 +115,13 @@ ecological_interactions:
evidence:
- reference: PMID:40904019
supports: SUPPORT
- evidence_source: IN_VITRO
- snippet: SynCom5, SynCom7 and SynCom9 showing the most significant improvement in the growth
- of hybrid Poplar 84K (Populus alba × Populus glandulosa)
- explanation: >
- Identifies the three SynCom formulations with the strongest measured growth protection under
- salt stress.
+ evidence_source: IN_VIVO
+ snippet: SynCom5, SynCom7 and SynCom9 showing the most significant improvement in the growth of hybrid Poplar
+ 84K (Populus alba × Populus glandulosa)
+ explanation: 'Identifies the three SynCom formulations with the strongest measured growth protection under salt
+ stress.
+
+ '
environmental_factors:
- name: defined synthetic community design
value: Isolate-select-construct workflow from 512 high-salt rhizosphere isolates, with nine growth-promoting
@@ -212,3 +145,41 @@ related_ingredients:
euphratica through high-throughput cultivation
explanation: Identifies high-salt rhizosphere as the source environment and NaCl as the abiotic
stressor the SynComs are engineered to mitigate.
+discussions:
+- discussion_id: populus-physiology-recruitment-and-formulation-scope
+ prompt: Which physiological and recruited-community mediators are necessary for each formulation?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ posed_by: codex
+ rationale: 'The abstract positively supports growth, physiological responses and recruitment, so both existing
+ biological directions remain explicitly PARTIAL. Isolation, selection and construction are workflow already
+ represented in engineering_design, not biological interactions. Main text and the linked supplement download
+ remain unavailable (403); a publisher supplement caption mentions pot experiments but is not a read supplement.
+ Host outcomes are IN_VIVO. Domain-level Bacteria is not strain-resolved composition, and SynCom5/7/9 are alternative
+ formulations. Exact membership and non-graph evidence contexts need #1716. No new node or arrow was added.'
+ attaches_to:
+ - ecological_interactions#Physiological Salt-Stress Resistance
+ - ecological_interactions#Salt-Adapted Root-Associated Consortia
+ - ecological_interactions#Salt Stress Growth Protection
+ evidence:
+ - reference: PMID:40904019
+ supports: SUPPORT
+ evidence_source: IN_VIVO
+ snippet: these SynComs can increase resistance to salt stress by directly reducing oxidative stress, adjusting
+ osmolytes and balancing ions.
+ explanation: Supports reported host physiological mechanisms in the abstract; full perturbation methods remain
+ unavailable.
+ - reference: PMID:40904019
+ supports: SUPPORT
+ evidence_source: IN_VIVO
+ snippet: these SynComs were observed to recruit specific root-associated bacterial consortia that enhance the
+ adaptability of poplar to salt stress
+ explanation: Supports the reported recruitment/adaptation explanation, not a resolved causal mediation experiment.
+curation_history:
+- timestamp: '2026-10-07T10:42:07Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: 'Preserve positive physiological responses and qualify their causal mediation.; Preserve recruitment
+ association and qualify its host-benefit interpretation.; Preserve formulation-specific host growth without
+ collapsing alternative communities. Issue #1713; reports/causal_graph_review/decisions/20261007-four-records-batch86.yaml'
+ llm_assisted: true
diff --git a/kb/communities/Poultry_Wastewater_ThreeStrain_Electroactive_Consortium.yaml b/kb/communities/Poultry_Wastewater_ThreeStrain_Electroactive_Consortium.yaml
index 557dd8b79..ac5f984a7 100644
--- a/kb/communities/Poultry_Wastewater_ThreeStrain_Electroactive_Consortium.yaml
+++ b/kb/communities/Poultry_Wastewater_ThreeStrain_Electroactive_Consortium.yaml
@@ -138,63 +138,95 @@ taxonomy:
A4.
explanation: Identifies strain A4 as an electroactive member of the exact consortium.
ecological_interactions:
-- name: Complementary Electroactive Consortium Performance
- description: >
- Combining Lysinibacillus sphaericus A1, Bacillus cereus A2, and
- Lactococcus lactis A4 in equal volumes supplied a complementary
- electroactive inoculum for the poultry-wastewater microbial fuel cell.
- interaction_type: NICHE_PARTITIONING
+- name: Proposed Electroactive Consortium Complementarity
+ description: 'HYPOTHESIZED: metabolic complementarity and biofilm organization among Lysinibacillus sphaericus
+ A1, Bacillus cereus A2 and Lactococcus lactis A4 may explain improved mixed-inoculum performance. The three-strain
+ versus pure-culture comparison demonstrates a treatment difference, not measured resource partitioning, interspecies
+ electron transfer or the individual necessity of a strain. Section 2.1.1 standardizes culture OD600 but leaves
+ total mixed-versus-single inoculum volume ambiguous.'
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
downstream:
- target: Consortium-Enhanced Anode Power Output
- description: The mixed electroactive inoculum increased the microbial fuel cell's power-density
- output beyond the power densities produced by each strain in pure culture.
+ description: 'HYPOTHESIZED: complementary microbial metabolism and biofilm organization may increase electron
+ delivery and thus power output. Retain the authors proposed mechanism for the positive mixed-versus-pure comparison;
+ no strain-resolved electron-transfer or complementarity perturbation isolates this mechanism.'
- target: Consortium-Enhanced Chemical Oxygen Demand Removal
- description: The mixed electroactive inoculum also improved organic-wastewater removal, producing
- the highest chemical oxygen demand removal among the tested inocula.
+ description: 'HYPOTHESIZED: complementary metabolism may improve utilization of oxidizable substrates and hence
+ COD reduction. COD is an aggregate assay in amended, sterilized wastewater, not proof of native-wastewater
+ mineralization; Section 3.3 inconsistencies prevent certifying the exact reported ranking from concentrations.'
evidence:
- reference: PMID:41594859
supports: SUPPORT
evidence_source: IN_VITRO
snippet: selecting complementary strains with diverse metabolic functions can substantially improve system performance
- explanation: Supports metabolic complementarity as the proposed basis for the consortium-level improvement.
+ explanation: Supports the authors proposed complementarity interpretation, not a directly established niche-partitioning
+ mechanism.
+ participating_taxa:
+ - preferred_term: Lysinibacillus sphaericus A1
+ term:
+ id: NCBITaxon:1421
+ label: Lysinibacillus sphaericus
+ - preferred_term: Bacillus cereus A2
+ term:
+ id: NCBITaxon:1396
+ label: Bacillus cereus
+ - preferred_term: Lactococcus lactis A4
+ term:
+ id: NCBITaxon:1358
+ label: Lactococcus lactis
- name: Consortium-Enhanced Anode Power Output
- description: The three-strain consortium produced a higher microbial fuel-cell power density than
- L. sphaericus A1, B. cereus A2, or L. lactis A4 pure cultures over 30 days.
- interaction_type: NICHE_PARTITIONING
+ description: During the 30-day dual-chamber MFC study, the consortium reached a reported maximum power density
+ of 170 mW/m2, approximately 15% above L. sphaericus A1, 29% above B. cereus A2 and more than threefold above
+ L. lactis A4. Preserve this positive tested-system comparison, not a claim that output remained higher at every
+ time point. The matrix was nutrient-amended and sterilized, not raw wastewater.
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:41594859
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: Compared with single cultures, the consortium produced approximately 15% higher power density than L. sphericus A1, about 29% higher than B. cereus A2, and more than threefold higher than L. lactis A4.
+ snippet: Compared with single cultures, the consortium produced approximately 15% higher power density than
+ L. sphericus A1, about 29% higher than B. cereus A2, and more than threefold higher than L. lactis A4.
explanation: Quantifies the emergent power-density improvement over each pure culture.
+ participating_taxa:
+ - preferred_term: Lysinibacillus sphaericus A1
+ term:
+ id: NCBITaxon:1421
+ label: Lysinibacillus sphaericus
+ - preferred_term: Bacillus cereus A2
+ term:
+ id: NCBITaxon:1396
+ label: Bacillus cereus
+ - preferred_term: Lactococcus lactis A4
+ term:
+ id: NCBITaxon:1358
+ label: Lactococcus lactis
- name: Consortium-Enhanced Chemical Oxygen Demand Removal
- description: The three-strain consortium removed chemical oxygen demand from amended poultry wastewater
- more effectively than the tested pure cultures.
- interaction_type: NICHE_PARTITIONING
+ description: 'The abstract reports the consortium had the greatest COD removal (84.4%) in amended, sterilized
+ model wastewater. Preserve that reported result with a source discrepancy: Section 3.3 pairs consortium 84.4%
+ with 2150-to-436 mg/L and L. sphaericus 79.7% with 2150-to-335 mg/L, which yield approximately 79.7% and 84.4%,
+ respectively. Do not silently swap these values or certify the exact quantitative ranking. COD cannot distinguish
+ native-organic degradation, supplement consumption, biomass assimilation and abiotic changes.'
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:41594859
supports: SUPPORT
evidence_source: IN_VITRO
snippet: The highest COD removal (84.4%) was also recorded
- explanation: Supports the consortium's maximum reported chemical oxygen demand removal.
+ explanation: Supports the abstract-reported 84.4%, not reconciled agreement with the inconsistent Section 3.3
+ concentrations.
+ participating_taxa:
+ - preferred_term: Lysinibacillus sphaericus A1
+ term:
+ id: NCBITaxon:1421
+ label: Lysinibacillus sphaericus
+ - preferred_term: Bacillus cereus A2
+ term:
+ id: NCBITaxon:1396
+ label: Bacillus cereus
+ - preferred_term: Lactococcus lactis A4
+ term:
+ id: NCBITaxon:1358
+ label: Lactococcus lactis
environmental_factors:
- name: Operation duration
value: '30'
@@ -317,3 +349,40 @@ external_resources:
explanation: Links the publication to the exact three-strain composition despite the abstract's epithet spelling.
metal_relevance: NOT_APPLICABLE
metal_notes: No metal or rare-earth processing role is reported for this wastewater microbial fuel-cell consortium.
+discussions:
+- discussion_id: poultry-complementarity-and-cod-source-discrepancy
+ prompt: Which mechanisms and reconciled measurements explain the mixed-culture advantage?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ posed_by: codex
+ rationale: 'Both existing mechanism-to-performance directions remain HYPOTHESIZED; positive power and reported
+ COD results remain. Full primary methods/results/discussion were read. SEM biofilm morphology is not strain-resolved
+ transfer or causal complementarity. The OD600-normalized inoculation wording does not unambiguously establish
+ equal total starting biomass. Section 3.3 percentages and concentrations appear crossed, and COD does not identify
+ degradation pathways or distinguish amended from native substrates. Independent raw data or author clarification
+ is needed before a numerical correction. Non-graph reported 84.4% remains unchanged, not certified, under #1716.'
+ attaches_to:
+ - ecological_interactions#Proposed Electroactive Consortium Complementarity
+ - ecological_interactions#Consortium-Enhanced Anode Power Output
+ - ecological_interactions#Consortium-Enhanced Chemical Oxygen Demand Removal
+ evidence:
+ - reference: PMID:41594859
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: selecting complementary strains with diverse metabolic functions can substantially improve system performance
+ explanation: Supports the authors proposed complementarity interpretation, not a directly established niche-partitioning
+ mechanism.
+ - reference: PMID:41594859
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: The highest COD removal (84.4%) was also recorded
+ explanation: Supports the abstract-reported 84.4%, not reconciled agreement with the inconsistent Section 3.3
+ concentrations.
+curation_history:
+- timestamp: '2026-10-07T10:42:07Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: 'Retain author-proposed complementarity with explicit mechanistic and inoculum uncertainty.; Preserve
+ positive maximum power comparison within the tested model substrate.; Preserve reported COD endpoint while exposing
+ primary-source arithmetic discrepancy. Issue #1714; reports/causal_graph_review/decisions/20261007-four-records-batch86.yaml'
+ llm_assisted: true
diff --git a/references_cache/PMID_33125214.md b/references_cache/PMID_33125214.md
index af6fbb2f4..62aaf9c71 100644
--- a/references_cache/PMID_33125214.md
+++ b/references_cache/PMID_33125214.md
@@ -75,4 +75,16 @@ donors. The metabolic versatility of Polaromonas spp. may be important for its
ability to flourish in the V tailings.
DOI: 10.1021/acs.est.0c05328
-PMID: 33125214 [Indexed for MEDLINE]
\ No newline at end of file
+PMID: 33125214 [Indexed for MEDLINE]
+
+## Public Supplement Figure S2 (not main-article full text)
+
+Source: https://acs.figshare.com/articles/journal_contribution/V_sup_V_sup_Reduction_by_i_Polaromonas_i_spp_in_Vanadium_Mine_Tailings/13171776
+Public file: https://ndownloader.figshare.com/files/25328205
+Archive license: CC BY-NC 4.0, https://creativecommons.org/licenses/by-nc/4.0/
+Original PDF SHA256: 195ad74c09de6c9925cb71e573f4988b91939214e59084b1979498048a20e85f
+
+Figure S2, verbatim fragment: "which formed VIV precipitates"
+
+Caption context (curator paraphrase): the fragment describes the acetate/vanadate
+treatments. Precipitation was absent from the autoclaved and vanadate-free controls.
diff --git a/reports/causal_graph_review/README.md b/reports/causal_graph_review/README.md
index 31ec933b8..e49990a49 100644
--- a/reports/causal_graph_review/README.md
+++ b/reports/causal_graph_review/README.md
@@ -879,3 +879,20 @@ live commensalism or that stronger phototroph growth improves biofertilization.
No new causal structure or provider spend. Non-graph metadata remains #1586,
coordinated with #1580 and #573. Canonical taxonomy and caches are preserved,
not recertified; self-review is not independent approval or corpus completion.
+
+## Batch86: Enrichment And Host-Response Boundaries
+
+[Decisions](decisions/20261007-four-records-batch86.yaml),
+[validation](validation-20261007-batch86.json) and
+[self-adversarial review](adversarial-review-20261007-batch86.yaml) review all
+18 original nodes and 11 arrows in four records. Ten nodes and five qualified
+directions remain. Positive pleuromutilin degradation, vanadium reduction and
+precipitation, Populus host responses and poultry MFC power are preserved.
+Workflow, parent-community scope leakage and unsupported partner mechanisms
+are removed. Populus mediation stays PARTIAL; poultry complementarity stays
+HYPOTHESIZED, with an explicit primary-source COD arithmetic discrepancy.
+The vanadium cache gains a source-labeled public Figure S2 caption, not a
+claim of main-text access. Canonical taxonomy and other non-graph fields are
+preserved, not certified; missing participant support is exposed rather than
+silently credited. Repairs #1711-#1714 await protected-main merge; research
+#1715 and metadata #1716 remain open. One Edison dry run, no paid submission.
diff --git a/reports/causal_graph_review/adversarial-review-20261007-batch86.yaml b/reports/causal_graph_review/adversarial-review-20261007-batch86.yaml
new file mode 100644
index 000000000..4ebf72904
--- /dev/null
+++ b/reports/causal_graph_review/adversarial-review-20261007-batch86.yaml
@@ -0,0 +1,745 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: a815f01634f6b8a316434226d99e86cff58095c7
+scope:
+- kb/communities/Pleuromutilin_Degrading_Artificial_Consortium_5_Strain.yaml
+- kb/communities/Polaromonas_Vanadium_Reduction_Community.yaml
+- kb/communities/Populus_Salt_Tolerant_SynComs.yaml
+- kb/communities/Poultry_Wastewater_ThreeStrain_Electroactive_Consortium.yaml
+decision_ledger: reports/causal_graph_review/decisions/20261007-four-records-batch86.yaml
+validation_report: reports/causal_graph_review/validation-20261007-batch86.json
+findings:
+- issue: 1711
+ severity: P2
+ status: addressed_in_this_change
+ finding: Separate pleuromutilin parent enrichment and assembly workflow from five-strain graph
+ disposition: Close only after protected-main merge.
+- issue: 1712
+ severity: P1
+ status: addressed_in_this_change
+ finding: Bound Polaromonas vanadium graph to enrichment evidence and inferred genes
+ disposition: Close only after protected-main merge.
+- issue: 1713
+ severity: P2
+ status: addressed_in_this_change
+ finding: Repair Populus workflow arrows and qualify salt-resistance mediation
+ disposition: Close only after protected-main merge.
+- issue: 1714
+ severity: P2
+ status: addressed_in_this_change
+ finding: Qualify poultry consortium complementarity and COD endpoint interpretation
+ disposition: Close only after protected-main merge.
+- issue: 1715
+ severity: P2
+ status: unresolved_research
+ finding: Research missing compatibility and pathway structure for five-strain pleuromutilin consortium
+ disposition: Keep OPEN after graph repair.
+- issue: 1716
+ severity: P1
+ status: unresolved_non_graph
+ finding: Reconcile batch86 non-graph identity and numerical-source contradictions
+ disposition: Keep OPEN after graph repair.
+adversarial_checks:
+- Fresh two-root baseline preceded papers; whole four records and all18nodes11arrows reviewed. Retain10nodes5existing
+ directions, remove8nodes6directions, add no topology. Every original node/arrow has a disposition.
+- Pleuromutilin91.97%degradation remains positive. Natural En4 diversity/enrichment is preserved as parent context
+ rather than assigned to five selected strains. Isolation/assembly are workflow, not niche partitioning. Proposed
+ products remain HYPOTHESIZED without obligatory syntrophy or metabolite provenance assumptions.
+- Pleuromutilin public TableS2 no-inhibition assay is not cross-feeding/stable coexistence. TableS1 distinguishes
+ W12 from same-species W10 and bacterial/fungal pool from abstract14bacteria. No unreviewed new compatibility/pathway
+ topology;1715remains needs_research and1716identity follow-up staysopen.
+- Vanadium public FigureS2 supplies positive controlled precipitation evidence, so reduction-to-precipitation survives
+ at enrichment scale. Polaromonas and MAG reductase attribution remain PARTIAL, not isolate/gene necessity. No
+ invented exact kinetics, mineral phase, reciprocal mutualism or arrA function.
+- Desulfovibrio/Desulfitobacterium sulfide and Geobacter sequential-iron nodes lack reviewed exact-system support
+ and are removed. Only Polaromonas receives explicit community credit. Three disconnected canonical taxa are exposed,
+ not silenced;51warnings includes three new DISCONNECTED entries, zero structural defects. Source Hunan locality
+ and Acidithiobacillus citation mismatch remain non-graph1716.
+- Populus retains positive host physiology, root recruitment and growth plus two PARTIAL biological explanations.
+ Three workflow arrows removed. Host evidence IN_VIVO, alternative SynCom5/7/9 formulations not one combined culture.
+ No claim of mediator intervention or inaccessible full-text/supplement review.
+- Poultry maximum170mW/m2positive comparison survives, not every-time-point superiority. Both complementarity arrows
+ remain HYPOTHESIZED and niche-partitioning labels are removed. SEM morphology does not establish interspecies
+ electron transfer. OD-normalized source wording leaves total inoculum-volume ambiguity.
+- Poultry reported84.4%COD remains with explicit primary arithmetic conflict:2150to436is79.7%,2150to335is84.4%.
+ No silent swap, exact ranking certification, native-wastewater mineralization or scale-up claim. Amended/sterilized
+ matrix and aggregate COD limits retained; non-graph1716staysopen.
+- Source access distinguishes three abstracts without main text, one full poultry main text, read-only DOCX tables/method
+ note, structured XLSX parsing and ten visually inspected vanadium PDF pages. No paywall bypass or claim that all
+ annotation/metabolomics rows were manually reviewed. Public SI source URLs and original hashes preserved.
+- 456otherrecords,920othercaches and raw non-graph blocks preserved; one provenance-labeled public FigureS2 caption
+ appended, abstract-only main-source metadata unchanged. Four append-only histories, concrete curation events and
+ ten focused tests. Required local gates and deterministic HTML-description checks actually executed, not browser
+ screenshots.
+- Dedup984issues and65ignored/hidden local matches with declared exclusions;1680read, comments/PRs not exhaustive.
+ One scoped Edison dry run11100characters, no paid job. Repair1711-1714close after protected-main merge;1715/1716remainOPEN.
+ Exact-head self-comment is not independent approval; corpus and loader1703remain unfinished.
+verification:
+ combined_regressions: 776 passed in 260.37s (0:04:20)
+ new_regression_tests: 10
+ primary_graph_snippet_proof:
+ primary_graph_quotations: 11
+ primary_discussion_quotations: 8
+ retained_nodes: 10
+ removed_nodes: 8
+ retained_arrows: 5
+ removed_arrows: 6
+ new_topology: 0
+ original_vanadium_pdf_pages_visually_inspected:
+ - 3
+ - 4
+ - 5
+ - 6
+ - 7
+ - 8
+ - 9
+ - 10
+ - 11
+ - 12
+ primary_main_texts_read: 1
+ missing_main_texts: 3
+ cache_append: Four-word public FigureS2 fragment with paraphrased context and archive/download/license links;
+ original abstract-only metadata preserved.
+ references: Four full-record reference validators exit0. CLI Total checks counts issues, not executed checks.
+ Eleven graph and eight discussion quotations independently match primary sources and cache text; matching is
+ not scientific entailment. Vanadium FigureS2 is a separately labeled public supplement, not main-text access.
+ Other source limits remain explicit.
+ snippet_counts_by_record:
+ kb/communities/Pleuromutilin_Degrading_Artificial_Consortium_5_Strain.yaml:
+ MATCH: 9
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Polaromonas_Vanadium_Reduction_Community.yaml:
+ MATCH: 24
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Populus_Salt_Tolerant_SynComs.yaml:
+ MATCH: 9
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Poultry_Wastewater_ThreeStrain_Electroactive_Consortium.yaml:
+ MATCH: 22
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ full_corpus_snippet_audit:
+ caveat: Both-root recipe actually executed. Exit0 is informational, not clean-corpus certification; four focused
+ snippet gates separately pass.
+ output: "# 8902 evidence snippets scanned across 460 files\n MATCH 8767\n RENDERING 20\n ASSEMBLED\
+ \ 1\n WEAK 0\n MISMATCH 38\n NOCONTENT 76\n\n# Files with MISMATCH/WEAK (content present but\
+ \ snippet absent) \u2014 fabrication suspects\n 19 (19 hard) kb/communities/DCPP_DBS4_DCP4_DCP11d_Degradation_SynCom.yaml\n\
+ \ 15 (15 hard) kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml\n 3 (3 hard) kb/communities/Coscinodiscus_Synthetic_Community.yaml\n\
+ \ 1 (1 hard) kb/communities/Altered_Schaedler_Flora_Gnotobiotic_Mouse_Community.yaml\nuv run python scripts/evidence_snippet_audit.py\
+ \ \n"
+ network:
+ existing_findings_preserved: 48
+ added_findings:
+ Polaromonas_Vanadium_Reduction_Community:
+ - type: DISCONNECTED
+ taxon: Desulfitobacterium species
+ taxon_id: NCBITaxon:36853
+ taxon_data:
+ taxon_term:
+ preferred_term: Desulfitobacterium species
+ term:
+ id: NCBITaxon:36853
+ label: Desulfitobacterium
+ gtdb_grounding_status: GROUNDED
+ gtdb_classification:
+ gtdb_id: GTDB:g__Desulfitobacterium
+ gtdb_taxon: Desulfitobacterium
+ gtdb_lineage: d__Bacteria;p__Bacillota_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfitobacterium
+ ncbi_source_id: NCBITaxon:36853
+ majority_fraction: 0.939
+ support_genomes: 46
+ total_genomes: 49
+ is_reclassified: false
+ mapping_source: kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-07-25) [grounded at g__
+ rank; 2 GTDB taxa under the NCBI taxon]
+ notes: 'Gram-positive, spore-forming bacteria (Firmicutes phylum) capable of organohalide respiration
+ and metal reduction. Desulfitobacterium species comprise 3-6% of the tailings community and perform
+ dissimilatory reduction of V(V), Cr(VI), and arsenate using respiratory reductases. This genus couples
+ oxidation of hydrogen, formate, lactate, and pyruvate to reduction of electron acceptors including
+ V(V) and sulfite. Desulfitobacterium exhibits greater tolerance to acidic pH (5.5-7.0) and high metal
+ concentrations compared to many deltaproteobacteria, enabling activity in variable tailings microenvironments.
+ Spore formation provides resilience during desiccation or oxidative episodes in surface tailings.
+ The organism expresses reductive dehalogenase homologs (rdhA genes) that reduce V(V) as an alternative
+ electron acceptor. Desulfitobacterium contributes to vanadium reduction particularly in hydrogen-rich
+ microniches generated by fermentative bacteria.
+
+ '
+ functional_role:
+ - SECONDARY_FERMENTER
+ abundance_level: COMMON
+ abundance_value: 3-6% in tailings
+ evidence:
+ - reference: PMID:33125214
+ supports: SUPPORT
+ evidence_source: IN_VIVO
+ snippet: Further, VV-reducing enrichments indicated that bacteria associated with Polaromonas, a genus
+ belonging to the family Burkholderiaceae, were potentially responsible for VV reduction
+ explanation: "Documents presence and enrichment under H\u2082 amendment"
+ message: Taxon 'Desulfitobacterium species' has no interactions
+ - type: DISCONNECTED
+ taxon: Desulfovibrio species
+ taxon_id: NCBITaxon:872
+ taxon_data:
+ taxon_term:
+ preferred_term: Desulfovibrio species
+ term:
+ id: NCBITaxon:872
+ label: Desulfovibrio
+ gtdb_grounding_status: GROUNDED
+ gtdb_classification:
+ gtdb_id: GTDB:g__Desulfovibrio
+ gtdb_taxon: Desulfovibrio
+ gtdb_lineage: d__Bacteria;p__Desulfobacterota;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio
+ ncbi_source_id: NCBITaxon:872
+ majority_fraction: 0.931
+ support_genomes: 551
+ total_genomes: 592
+ is_reclassified: false
+ mapping_source: kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-07-25) [grounded at g__
+ rank; 9 GTDB taxa under the NCBI taxon]
+ notes: "Gram-negative deltaproteobacteria performing dissimilatory sulfate reduction in the vanadium\
+ \ tailings. Desulfovibrio oxidizes organic acids (lactate, pyruvate, formate) and hydrogen coupled\
+ \ to sulfate reduction, producing hydrogen sulfide (H\u2082S) that chemically reduces V(V) to V(IV)\
+ \ and precipitates vanadium as sulfide minerals. Additionally, Desulfovibrio can enzymatically reduce\
+ \ V(V) through periplasmic and cytoplasmic reductases. The organism comprises 8-12% of the tailings\
+ \ community and increases under sulfate-rich, organic-amended conditions. Hydrogen sulfide generated\
+ \ by Desulfovibrio (concentrations reaching 50-200 \xB5M) creates strongly reducing microenvironments\
+ \ (Eh < -200 mV) that favor vanadium immobilization. Desulfovibrio species are known to reduce multiple\
+ \ toxic metals including uranium, chromium, and technetium, contributing to polymetallic remediation\
+ \ in this system.\n"
+ functional_role:
+ - SECONDARY_FERMENTER
+ - SYNTROPHIC_PARTNER
+ abundance_level: COMMON
+ abundance_value: 8-12% in tailings; enriched under sulfate amendment
+ evidence:
+ - reference: PMID:33125214
+ supports: SUPPORT
+ evidence_source: IN_VIVO
+ snippet: Microorganisms can reduce the more toxic and mobile VV to the less toxic and immobile VIV,
+ which could be a detoxification and energy metabolism strategy adopted by V-reducing bacteria (VRB)
+ explanation: Documents Desulfovibrio presence in vanadium tailings
+ - reference: PMID:33125214
+ supports: PARTIAL
+ evidence_source: IN_VIVO
+ snippet: bacteria associated with Polaromonas
+ explanation: Links sulfate reduction to vanadium immobilization
+ - reference: PMID:33125214
+ supports: PARTIAL
+ evidence_source: IN_VITRO
+ snippet: VV-reducing enrichments
+ explanation: Establishes dual mechanisms for vanadium reduction
+ message: Taxon 'Desulfovibrio species' has no interactions
+ - type: DISCONNECTED
+ taxon: Geobacter species
+ taxon_id: NCBITaxon:28232
+ taxon_data:
+ taxon_term:
+ preferred_term: Geobacter species
+ term:
+ id: NCBITaxon:28232
+ label: Geobacter metallireducens
+ gtdb_grounding_status: GROUNDED
+ gtdb_classification:
+ gtdb_id: GTDB:s__Geobacter_metallireducens
+ gtdb_taxon: Geobacter metallireducens
+ gtdb_lineage: d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geobacter;s__Geobacter
+ metallireducens
+ ncbi_source_id: NCBITaxon:28232
+ majority_fraction: 1.0
+ total_genomes: 4
+ is_reclassified: false
+ mapping_source: "kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-07-25) [mapped via NCBI\
+ \ species name \u2014 no species-level NCBI id in table]"
+ notes: 'Deltaproteobacteria specialized in dissimilatory metal reduction, present at 5-8% relative abundance
+ in vanadium tailings. Geobacter oxidizes acetate and other organic acids coupled to reduction of Fe(III),
+ Mn(IV), and V(V). This genus possesses extensive arrays of c-type cytochromes enabling extracellular
+ electron transfer to metal oxides and soluble metal ions. In vanadium tailings, Geobacter reduces
+ co-occurring Fe(III) minerals, creating reducing conditions that facilitate V(V) reduction by other
+ community members. Geobacter can directly reduce V(V) through outer membrane cytochromes (OmcB, OmcS,
+ OmcZ) and periplasmic reductases. The organism is particularly important in zones with high Fe(III)
+ content (common in vanadium titanomagnetite tailings), where Fe(III) reduction precedes and enhances
+ V(V) reduction. Geobacter forms syntrophic relationships with Polaromonas, potentially exchanging
+ electrons or metabolites.
+
+ '
+ functional_role:
+ - PRIMARY_DEGRADER
+ - SYNTROPHIC_PARTNER
+ abundance_level: COMMON
+ abundance_value: 5-8% in tailings; enriched in Fe(III)-rich zones
+ evidence:
+ - reference: PMID:33125214
+ supports: SUPPORT
+ evidence_source: IN_VIVO
+ snippet: Further, VV-reducing enrichments indicated that bacteria associated with Polaromonas, a genus
+ belonging to the family Burkholderiaceae, were potentially responsible for VV reduction
+ explanation: Documents Geobacter presence in Fe/V-contaminated tailings
+ - reference: PMID:33125214
+ supports: PARTIAL
+ evidence_source: IN_VIVO
+ snippet: reduce the more toxic and mobile VV to the less toxic and immobile VIV
+ explanation: Describes role in sequential metal reduction processes
+ - reference: PMID:19077236
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: It is a chemolithoautrophic, gamma-proteobacterium using energy from the oxidation of iron-
+ and sulfur-containing minerals for growth
+ explanation: Confirms V(V) reduction capability
+ message: Taxon 'Geobacter species' has no interactions
+ removed_findings: {}
+ interpretation: Existing warning entries preserved. Three newly exposed disconnected Polaromonas-record taxa
+ lack exact-system support; metadata1716 remains open. No structural defects, taxonomy edits or auditor-rule
+ changes.
+ tested_file_sha256:
+ reports/causal_graph_review/decisions/20261007-four-records-batch86.yaml: 52c9010cc9daba2e08129e016e0c9122925fcf1f038d1545e756dbc855683669
+ tests/test_causal_review_batch86.py: 534b320feedd82080c833b468b877478361dcf80536e838123004d4acab908e7
+ tests/test_participating_taxa.py: 43e2c183cf12a3b977b0a6b93ea4180050515a310bdba664be5e3d7375f6ae74
+ kb/communities/Pleuromutilin_Degrading_Artificial_Consortium_5_Strain.yaml: 4ad5e08b3c65011a09783c45c8504e32f33817ec3edbef10ea88a70597530b38
+ kb/communities/Polaromonas_Vanadium_Reduction_Community.yaml: bdb14ed3d33c4a9adc05479849201bf3530bd23d9867a2bc5ddb635b9507a3a5
+ kb/communities/Populus_Salt_Tolerant_SynComs.yaml: c96458a84a7951d477b792d0a23164f263c4dee76dae2593656d4b39699b10bd
+ kb/communities/Poultry_Wastewater_ThreeStrain_Electroactive_Consortium.yaml: 932b57ad58aa3a1f58b9ad9be0163d2210a7cfa593964b37abc6d3a83d7f3ebb
+ reports/causal_graph_review/README.md: 21fc6d57b86eaa845d2cff6678a0d5e3f43af49b44a0b14ec1c2914c42534328
+ references_cache/PMID_33125214.md: b651cbb4bd68a39f4621770bb9c0c557e689fe46cdfb28fb7f5a8af705a21ceb
+ unchanged_records: 456
+ unchanged_caches: 920
+ cache_changes:
+ - path: references_cache/PMID_33125214.md
+ original_sha256: e3b46b9a3b6e1844aa13f336c6a77b708a3ebb94456a482bc5e10407e8964f6e
+ sha256: b651cbb4bd68a39f4621770bb9c0c557e689fe46cdfb28fb7f5a8af705a21ceb
+ reason: Append four-word public Figure S2 fragment, curator-paraphrased context, exact archive/download/license
+ links and original PDF hash; not main-text access.
+ edison:
+ required_for_this_repair: false
+ required_for_unresolved_extensions: true
+ provider_submissions: 0
+ credits_spent: 0
+ dry_runs:
+ - community_id: CommunityMech:000300
+ query_chars: 11100
+ query_sha256: a75cf4410df5e354aebb8f9fac360f50141f9aae47e84d499b7266d31e5c98bc
+ meta_path: /private/tmp/communitymech-batch86/edison-pleuromutilin/Pleuromutilin_Degrading_Artificial_Consortium_5_Strain-edison-literature-causal-meta.yaml
+ authorization: Scoped paid question unanswered; no submission.
+ post_commit_docs_current: Separate publication gate, not preasserted.
+ superseded_checks:
+ - check: Polaromonas_Vanadium_Reduction_Community-references
+ command:
+ - /Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator
+ - validate
+ - data
+ - kb/communities/Polaromonas_Vanadium_Reduction_Community.yaml
+ - -s
+ - src/communitymech/schema/communitymech.yaml
+ - --config
+ - conf/reference_validator.yaml
+ exit_code: 0
+ expected_exit_codes:
+ - 0
+ log: /private/tmp/communitymech-batch86/Polaromonas_Vanadium_Reduction_Community-references-initial.log
+ log_sha256: 88d1d7259ad27dc7a30da6c48ed918330b9cec2ade00f8f4e1f54bad952c74dc
+ output_tail: "Validating kb/communities/Polaromonas_Vanadium_Reduction_Community.yaml against schema src/communitymech/schema/communitymech.yaml\n\
+ Cache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n"
+ explained_output_tail: "Validating kb/communities/Polaromonas_Vanadium_Reduction_Community.yaml against schema\
+ \ src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n\
+ \ Total checks: 0\n All validations passed!\n"
+ disposition: Superseded after whitespace/source-cache citation cleanup; original graph records and all scientific
+ decisions unchanged.
+ - check: Polaromonas_Vanadium_Reduction_Community-snippets
+ command:
+ - /Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3
+ - scripts/evidence_snippet_audit.py
+ - kb/communities/Polaromonas_Vanadium_Reduction_Community.yaml
+ - --list-mismatch
+ - --list-nocontent
+ - --list-rendering
+ - --list-assembled
+ exit_code: 0
+ expected_exit_codes:
+ - 0
+ log: /private/tmp/communitymech-batch86/Polaromonas_Vanadium_Reduction_Community-snippets-initial.log
+ log_sha256: 2ffa6e242265b4c1c2eb555bd8bd14abb6cc63ed4d5a8a818da9b515db44daff
+ output_tail: "# 24 evidence snippets scanned across 1 files\n MATCH 24\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"
+ disposition: Superseded after whitespace/source-cache citation cleanup; original graph records and all scientific
+ decisions unchanged.
+ - 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-batch86/render-initial.log
+ log_sha256: 3abc64114ef228075275f79b1c88c558a6565dac011d087a077cb7654e7a6fcc
+ output_tail: "sm.html\n \u2713 Synechococcus_Bacillus_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Synechococcus_Bacillus_SPC.html\n\
+ \ \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Synechococcus_Ecoli_SPC.html\n\
+ \ \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n\
+ \ \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n\
+ \ \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Synechococcus_Saccharomyces_SPC.html\n\
+ \ \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n\
+ \ \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n\
+ \ \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n\
+ \ \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n\
+ \ \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n\
+ \ \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n\
+ \ \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n\
+ \ \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n\
+ \ \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Syntrophus_Benzoate_Degrader.html\n\
+ \ \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n\
+ \ \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n\
+ \ \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/THOR_Rhizosphere_Model_Community.html\n\
+ \ \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n\
+ \ \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n\
+ \ \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n\
+ \ \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n\
+ \ \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n\
+ \ \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n\
+ \ \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n\
+ \ \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n\
+ \ \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n\
+ \ \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n\
+ \ \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n\
+ \ \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Tinto_River_Iron_Cycling_Community.html\n\
+ \ \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n\
+ \ \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Tomato_Oxylipin_SynCom3.html\n\
+ \ \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n\
+ \ \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n\
+ \ \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n\
+ \ \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Trichoderma_Lactate_Platform.html\n\
+ \ \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n\
+ \ \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n\
+ \ \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n\
+ \ \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Urine_Nitrification_SynCom.html\n\
+ \ \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n\
+ \ \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n\
+ \ \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n\
+ \ \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n\
+ \ \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n\
+ \ \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Wheat_Consortium_C1.html\n\
+ \ \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Wheat_Consortium_C6.html\n\
+ \ \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n\
+ \ \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n\
+ \ \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n\
+ \ \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n\
+ \ \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n\
+ \ \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n\
+ \ \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n\
+ \ \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n\
+ \ \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n\
+ \ \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n\
+ \ \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n\
+ \ \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n\
+ \ \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/hCom2_Complex_Gut_Microbiome.html\n\
+ \ \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/mCAFEs_Brachypodium_RCC.html\n\
+ \n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch86/docs/communities\n \u2713\
+ \ Generated browser at /private/tmp/communitymech-causal-batch86/docs/browser.html\n \u2713 Generated landing\
+ \ at /private/tmp/communitymech-causal-batch86/docs/index.html\n"
+ disposition: Superseded after whitespace/source-cache citation cleanup; original graph records and all scientific
+ decisions unchanged.
+ - 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-batch86/render-repeat-initial.log
+ log_sha256: 3abc64114ef228075275f79b1c88c558a6565dac011d087a077cb7654e7a6fcc
+ output_tail: "sm.html\n \u2713 Synechococcus_Bacillus_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Synechococcus_Bacillus_SPC.html\n\
+ \ \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Synechococcus_Ecoli_SPC.html\n\
+ \ \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n\
+ \ \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n\
+ \ \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Synechococcus_Saccharomyces_SPC.html\n\
+ \ \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n\
+ \ \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n\
+ \ \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n\
+ \ \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n\
+ \ \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n\
+ \ \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n\
+ \ \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n\
+ \ \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n\
+ \ \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Syntrophus_Benzoate_Degrader.html\n\
+ \ \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n\
+ \ \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n\
+ \ \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/THOR_Rhizosphere_Model_Community.html\n\
+ \ \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n\
+ \ \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n\
+ \ \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n\
+ \ \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n\
+ \ \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n\
+ \ \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n\
+ \ \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n\
+ \ \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n\
+ \ \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n\
+ \ \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n\
+ \ \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n\
+ \ \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Tinto_River_Iron_Cycling_Community.html\n\
+ \ \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n\
+ \ \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Tomato_Oxylipin_SynCom3.html\n\
+ \ \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n\
+ \ \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n\
+ \ \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n\
+ \ \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Trichoderma_Lactate_Platform.html\n\
+ \ \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n\
+ \ \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n\
+ \ \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n\
+ \ \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Urine_Nitrification_SynCom.html\n\
+ \ \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n\
+ \ \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n\
+ \ \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n\
+ \ \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n\
+ \ \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n\
+ \ \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Wheat_Consortium_C1.html\n\
+ \ \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Wheat_Consortium_C6.html\n\
+ \ \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n\
+ \ \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n\
+ \ \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n\
+ \ \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n\
+ \ \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n\
+ \ \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n\
+ \ \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n\
+ \ \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n\
+ \ \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n\
+ \ \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n\
+ \ \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n\
+ \ \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n\
+ \ \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/hCom2_Complex_Gut_Microbiome.html\n\
+ \ \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/mCAFEs_Brachypodium_RCC.html\n\
+ \n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch86/docs/communities\n \u2713\
+ \ Generated browser at /private/tmp/communitymech-causal-batch86/docs/browser.html\n \u2713 Generated landing\
+ \ at /private/tmp/communitymech-causal-batch86/docs/index.html\n"
+ disposition: Superseded after whitespace/source-cache citation cleanup; original graph records and all scientific
+ decisions unchanged.
+ - check: regressions
+ command:
+ - /Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3
+ - -m
+ - pytest
+ - -q
+ - tests/test_causal_review_batch10.py
+ - tests/test_causal_review_batch11.py
+ - tests/test_causal_review_batch12.py
+ - tests/test_causal_review_batch13.py
+ - tests/test_causal_review_batch14.py
+ - tests/test_causal_review_batch15.py
+ - tests/test_causal_review_batch16.py
+ - tests/test_causal_review_batch17.py
+ - tests/test_causal_review_batch18.py
+ - tests/test_causal_review_batch19.py
+ - tests/test_causal_review_batch20.py
+ - tests/test_causal_review_batch21.py
+ - tests/test_causal_review_batch22.py
+ - tests/test_causal_review_batch23.py
+ - tests/test_causal_review_batch24.py
+ - tests/test_causal_review_batch25.py
+ - tests/test_causal_review_batch27.py
+ - tests/test_causal_review_batch28.py
+ - tests/test_causal_review_batch29.py
+ - tests/test_causal_review_batch30.py
+ - tests/test_causal_review_batch31.py
+ - tests/test_causal_review_batch32.py
+ - tests/test_causal_review_batch33.py
+ - tests/test_causal_review_batch34.py
+ - tests/test_causal_review_batch35.py
+ - tests/test_causal_review_batch36.py
+ - tests/test_causal_review_batch37.py
+ - tests/test_causal_review_batch38.py
+ - tests/test_causal_review_batch39.py
+ - tests/test_causal_review_batch40.py
+ - tests/test_causal_review_batch41.py
+ - tests/test_causal_review_batch42.py
+ - tests/test_causal_review_batch43.py
+ - tests/test_causal_review_batch44.py
+ - tests/test_causal_review_batch45.py
+ - tests/test_causal_review_batch46.py
+ - tests/test_causal_review_batch47.py
+ - tests/test_causal_review_batch48.py
+ - tests/test_causal_review_batch49.py
+ - tests/test_causal_review_batch5.py
+ - tests/test_causal_review_batch50.py
+ - tests/test_causal_review_batch51.py
+ - tests/test_causal_review_batch52.py
+ - tests/test_causal_review_batch53.py
+ - tests/test_causal_review_batch54.py
+ - tests/test_causal_review_batch55.py
+ - tests/test_causal_review_batch56.py
+ - tests/test_causal_review_batch57.py
+ - tests/test_causal_review_batch58.py
+ - tests/test_causal_review_batch59.py
+ - tests/test_causal_review_batch6.py
+ - tests/test_causal_review_batch60.py
+ - tests/test_causal_review_batch61.py
+ - tests/test_causal_review_batch62.py
+ - tests/test_causal_review_batch63.py
+ - tests/test_causal_review_batch64.py
+ - tests/test_causal_review_batch65.py
+ - tests/test_causal_review_batch66.py
+ - tests/test_causal_review_batch67.py
+ - tests/test_causal_review_batch68.py
+ - tests/test_causal_review_batch69.py
+ - tests/test_causal_review_batch7.py
+ - tests/test_causal_review_batch70.py
+ - tests/test_causal_review_batch71.py
+ - tests/test_causal_review_batch72.py
+ - tests/test_causal_review_batch73.py
+ - tests/test_causal_review_batch74.py
+ - tests/test_causal_review_batch75.py
+ - tests/test_causal_review_batch76.py
+ - tests/test_causal_review_batch77.py
+ - tests/test_causal_review_batch78.py
+ - tests/test_causal_review_batch79.py
+ - tests/test_causal_review_batch8.py
+ - tests/test_causal_review_batch80.py
+ - tests/test_causal_review_batch81.py
+ - tests/test_causal_review_batch82.py
+ - tests/test_causal_review_batch83.py
+ - tests/test_causal_review_batch84.py
+ - tests/test_causal_review_batch85.py
+ - tests/test_causal_review_batch86.py
+ - tests/test_causal_review_batch9.py
+ - tests/test_site_audit_fixes.py
+ - tests/test_causal_review_inventory.py
+ - tests/test_rank_causal_graph_readiness.py
+ - tests/test_network_auditor.py
+ - tests/test_participating_taxa.py
+ - tests/test_causal_descriptions_are_published.py
+ - tests/test_published_pages_name_real_records.py
+ - tests/test_reference_validator_actually_validates.py
+ - tests/test_snippet_audit_artefact_classes.py
+ - tests/test_reference_error_annotation.py
+ - tests/test_community_level_connectivity_credit.py
+ - tests/test_no_paywalled_text_in_repo.py
+ exit_code: 0
+ expected_exit_codes:
+ - 0
+ log: /private/tmp/communitymech-batch86/regressions-initial.log
+ log_sha256: 31320acac0f5bfd3801bea9831b952a379cf9bcda020ed9059f3a33624fb11fa
+ output_tail: '........................................................................ [ 9%]
+
+ ........................................................................ [ 18%]
+
+ ........................................................................ [ 27%]
+
+ ........................................................................ [ 37%]
+
+ ........................................................................ [ 46%]
+
+ ........................................................................ [ 55%]
+
+ ........................................................................ [ 64%]
+
+ ........................................................................ [ 74%]
+
+ ........................................................................ [ 83%]
+
+ ........................................................................ [ 92%]
+
+ ........................................................ [100%]
+
+ 776 passed in 223.94s (0:03:43)
+
+ '
+ disposition: Superseded after whitespace/source-cache citation cleanup; original graph records and all scientific
+ decisions unchanged.
+ - check: diff-check
+ command:
+ - git
+ - diff
+ - --check
+ exit_code: 2
+ expected_exit_codes:
+ - 0
+ log: /private/tmp/communitymech-batch86/diff-check-initial.log
+ log_sha256: 2d9b69337d0a2b4cbfb3d42708125cb955ad897df710ac86e7f3ff2c2c9a8d7a
+ output_tail: "references_cache/PMID_33125214.md:86: trailing whitespace.\n+Figure S2. Enrichment culture experiment\
+ \ setup. The colors represent the different treatments and \nreferences_cache/PMID_33125214.md:87: trailing\
+ \ whitespace.\n+controls. The blue ones are the actual color of the treatments with acetate and vanadate addition,\
+ \ \nreferences_cache/PMID_33125214.md:88: trailing whitespace.\n+which formed VIV precipitates. The pink ones\
+ \ are the actual colors of the autoclaved and no \n"
+ disposition: Superseded after whitespace/source-cache citation cleanup; original graph records and all scientific
+ decisions unchanged.
+ cleanup: Initial broad regressions passed, but diff check found caption-extraction trailing whitespace. Source-cache
+ citation/fragment cleanup left graph records unchanged; affected gates and complete broad regressions rerun.
+ Original six outputs retained.
+participant_census:
+ measurements:
+ baseline:
+ records: 460
+ with_community_level: 394
+ mixed: 126
+ community_level_only: 268
+ taxa: 1517
+ credited_solely_by_the_rule: 1243
+ current:
+ records: 460
+ with_community_level: 395
+ mixed: 126
+ community_level_only: 269
+ taxa: 1521
+ credited_solely_by_the_rule: 1247
+ delta:
+ records: 0
+ with_community_level: 1
+ mixed: 0
+ community_level_only: 1
+ taxa: 4
+ credited_solely_by_the_rule: 4
+ interpretation: Polaromonas becomes community-level-only. Legacy census counts all four canonical members, but
+ explicit participant credit names only Polaromonas and three others are disconnected. No canonical taxon or
+ auditor-rule change.
+corpus:
+ records: 460
+ nodes: 1425
+ edges: 586
+ review_status_counts:
+ needs_research: 48
+ pending: 148
+ reviewed: 264
+limitations:
+- Fresh before-paper baseline includes both roots:460records921caches,1433nodes592arrows,48warning entries and zero
+ structural defects. All18originalnodes11arrows reviewed;10nodes5arrows remain without new topology.
+- Preserve positive91.97%pleuromutilin degradation and proposed products. En4 parent findings retained as context;
+ workflow and unsupported syntrophy removed. Compatibility/pathway expansion1715remains needs_research.
+- Public vanadium FigureS2 supports reduction-to-precipitation at enrichment scale. Only Polaromonas explicitly
+ credited; genomic attribution is partial, other partner claims removed. Newly exposed disconnected canonical taxa
+ are a metadata gap1716, not silently credited by community scope.
+- Populus physiological and recruitment explanations retain two PARTIAL biological arrows, with IN_VIVO host evidence
+ and alternative formulations distinguished. Full mediator methods unavailable.
+- Poultry retains two HYPOTHESIZED complementarity arrows and positive maximum power, with model-matrix limits and
+ source COD arithmetic/inoculum ambiguity exposed. Reported84.4%is not silently corrected or certified.
+- One cache gains a clearly labeled public Supplement FigureS2 excerpt with source/PDF hash; main-article abstract-only
+ status remains accurate. Other920caches,456otherrecords and raw non-graph blocks preserved. No taxonomy or auditor-rule
+ changes.
+- Four primary abstracts inspected; poultry main text read. Source access scopes distinguish abstracts, main text,
+ extracted tables and visual PDF pages. No full-text claim for paywalled sources; no access bypass.
+- Dedup984all-state issue titles/bodies and65ignored/hidden local matches with explicit .git/docs/site/references_cache
+ exclusions. Related1680read; comments/PRs not exhaustive.
+- One-community Edison causal dry run11100characters; scoped paid question unanswered, zero provider jobs/credits.
+ Earlier pending/denied scopes unchanged. Repair1711-1714close only after protected-main merge;1715/1716remainOPEN.
+- Validation and rendering are separate actual gates, not preasserted. Self-adversarial review is not independent
+ approval, whole-record certification or corpus completion. Generated-model loading defect1703remains unresolved.
+- Final diff check caught trailing whitespace in the original supplemental caption extraction. Cache appendix was
+ shortened to a four-word fragment plus paraphrased context and explicit archive/download/license links. Graph
+ records/history unchanged; affected checks and broad regressions rerun, with original outputs retained as superseded.
diff --git a/reports/causal_graph_review/decisions/20261007-four-records-batch86.yaml b/reports/causal_graph_review/decisions/20261007-four-records-batch86.yaml
new file mode 100644
index 000000000..52cecd06c
--- /dev/null
+++ b/reports/causal_graph_review/decisions/20261007-four-records-batch86.yaml
@@ -0,0 +1,631 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+source_access:
+- reference: PMID:42133144
+ url: https://doi.org/10.1007/s11274-026-05013-w
+ accessed_scope: Abstract and subscription preview. Public DOCX Tables S1/S2 and S3 methods note read via OOXML;
+ no rendered-page QA because soffice/LibreOffice not on PATH. Main text unavailable.
+- reference: PMID:33125214
+ url: https://doi.org/10.1021/acs.est.0c05328
+ accessed_scope: Abstract plus public ACS SI. All PDF text extracted/read; pages3-12 visually inspected. Both XLSX
+ files parsed as structured cells; focused gene/taxon matches inspected, not all annotation rows manually read.
+ Main text unavailable.
+- reference: PMID:40904019
+ url: https://doi.org/10.1111/pce.70160
+ accessed_scope: Primary abstract and publisher preview; main text unavailable and linked supplement returned403.
+ No supplement read.
+- reference: PMID:41594859
+ url: https://doi.org/10.3390/biology15020124
+ accessed_scope: Open main text methods/results/discussion read. No figure-pixel audit. Primary and cached abstract
+ excerpts inspected; fresh XML is independent verification.
+- reference: PMID:19077236
+ url: https://doi.org/10.1186/1471-2164-9-597
+ accessed_scope: Title, abstract and opening sections inspected to resolve taxon/citation mismatch. Not a full-paper
+ review.
+base_commit: a815f01634f6b8a316434226d99e86cff58095c7
+baseline_commit: a815f01634f6b8a316434226d99e86cff58095c7
+base_tree: f5387cc2ae8f8868c7a51091b89e562e54abdb82
+pre_source_baseline_sha256: 3ab1fbc81fa5b01477051e2316dcac36fd68d6f9b41d9700bd8b8be39757f7ec
+issues:
+- 1711
+- 1712
+- 1713
+- 1714
+unresolved_research_issues:
+- 1715
+unresolved_non_graph_issues:
+- 1716
+issue_deduplication:
+ all_state_issue_titles_and_bodies: 984
+ ignored_hidden_local_search: true
+ matching_issues:
+ - 1680
+primary_artifacts:
+ /private/tmp/communitymech-batch86/acs-13171776.json: 13b1e5c6b3d2fa187e6d0e953727b4a1ad70c19bc050d4d8eb070d50a78564d6
+ /private/tmp/communitymech-batch86/acs-13171779.json: 8c934a046aef3d0180652a33171901bdf1895935a32286ddc34a0c014078ff83
+ /private/tmp/communitymech-batch86/acs-13171782.json: 7a1ff32b2b2910e7a2c8674b460ef609d24c66cdca52161a91f35aeeddb780e2
+ /private/tmp/communitymech-batch86/acs-supplement-manifest.json: 103bae81d402de6ad58db089df47f69998df9412cbbecfa7900bac081f4bdd94
+ /private/tmp/communitymech-batch86/baseline.json: 3ab1fbc81fa5b01477051e2316dcac36fd68d6f9b41d9700bd8b8be39757f7ec
+ /private/tmp/communitymech-batch86/created-issues.json: 350f78abfa6b96706cfc781727f44209f7f4bb38928dd32e9588ae6fc8cc07cc
+ ? /private/tmp/communitymech-batch86/edison-pleuromutilin/Pleuromutilin_Degrading_Artificial_Consortium_5_Strain-edison-literature-causal-meta.yaml
+ : d89ee294851c893e61ab93e26c10597bde30b5d36528e659cb28d3276f93a674
+ /private/tmp/communitymech-batch86/es0c05328_si_001.pdf: 195ad74c09de6c9925cb71e573f4988b91939214e59084b1979498048a20e85f
+ /private/tmp/communitymech-batch86/es0c05328_si_002-cells.json: 8dc9195f281cd7669afae0f3135899e25e6b4fe4aa2ed6b23da97aba3482b683
+ /private/tmp/communitymech-batch86/es0c05328_si_002-matches.json: 72af7c01b531ccb1570ed46a09812874ff7a277ff36ea07a48af706effd3612f
+ /private/tmp/communitymech-batch86/es0c05328_si_002.xlsx: 49bad9ba78decb67d7661ad26eb966b27262f28c7d2d3a5011ff3007b011381f
+ /private/tmp/communitymech-batch86/es0c05328_si_003-cells.json: a12e46ba3837ce416d2d99fa7d66259b47755ed59935273d6ab57398b275191c
+ /private/tmp/communitymech-batch86/es0c05328_si_003-matches.json: 37517e5f3dc66819f61f5a7bb8ace1921282415f10551d2defa5c3eb0985b570
+ /private/tmp/communitymech-batch86/es0c05328_si_003.xlsx: b66bbbb6f22ea6a2445213a45c6944810c8d470ee387f69bf9709b877f78c4c9
+ /private/tmp/communitymech-batch86/issue-matches-current.json: b5413432f855caed8ed53afe334565ea3a32c078702525dea26ab36962c84afe
+ /private/tmp/communitymech-batch86/issue-matches.json: b5413432f855caed8ed53afe334565ea3a32c078702525dea26ab36962c84afe
+ /private/tmp/communitymech-batch86/issues-current.json: d2070bb063e9203170ac5ba63a9a13b6ee7210ea9428a4eb774894a3b3115bc7
+ /private/tmp/communitymech-batch86/issues.json: ace9c2ab652df69ef1726af0ecc5d37d0fc0840fecfae4651b065e578cbeffd9
+ /private/tmp/communitymech-batch86/local-matches-current.txt: bc85fc1d7c079e58c76aa1ba07ea67fd5acb5dce7fe6fdf73b42b2e5983b092d
+ /private/tmp/communitymech-batch86/local-matches.txt: cee4fd899c56d0ff9a39ebe379ae23901977d97c1b3a3d88c2bb71d85cf54ab0
+ /private/tmp/communitymech-batch86/pleuromutilin-metadata.json: 31186032c1fa4c474ab634e27b9a92414bad6df0a09f6dd1df9d6e3a8c666a10
+ /private/tmp/communitymech-batch86/pleuromutilin-primary.txt: 9e03c24ff8f6bf5a898e2aa4ef0f3b56ab74e11eaa2bf2a68ede5a6816fc4d3c
+ /private/tmp/communitymech-batch86/pleuromutilin-supplement-image29.png: 5b04bde1a09ec8f10ed8a2c5c9962f960f98ab4795d44a81f3229f68fa86590e
+ /private/tmp/communitymech-batch86/pleuromutilin-supplement-text.txt: b0adcb59b59a61fea74de471dc5119ac9a44b54541165a8ad990503f64d356c7
+ /private/tmp/communitymech-batch86/pleuromutilin-supplement.docx: e7b74f47b25af37ee16c16ffabcb1ef477430ccc809c4c7d496b6bfe1533fdf8
+ /private/tmp/communitymech-batch86/populus-metadata.json: 68b07543809f6a903632e1b495fd0d13c7e4276d4683ffe3deb6d3d29ddf6721
+ /private/tmp/communitymech-batch86/populus-primary.txt: 764ef05b70ab51c5c59aedb6fe5a31fec981f8d4dd091d67e850221a0b1729d1
+ /private/tmp/communitymech-batch86/poultry-metadata.json: 23dac4bb57b8fb445eb074adf8d84aecb454676ea8751a2a83bf0881781b74e3
+ /private/tmp/communitymech-batch86/poultry-primary.txt: de5bebb3a9eaf178410ae940d51ccfcdb6668af14be7fc50fe90a986a82fa901
+ /private/tmp/communitymech-batch86/poultry-primary.xml: d89341e3b190e6fde78d702fdbea7a6f60edc2696f7ca5fb9ce97d74553f198f
+ /private/tmp/communitymech-batch86/poultry-tables.txt: 6251c21a6eedc434ab9646eb20c7241189e1975594b197182e24d39d926a76f8
+ /private/tmp/communitymech-batch86/primary-manifest.json: 1dd18265718d893b806745c552e48bd875cffeaa0305bf5069799fc3ae5fe079
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+primary_graph_snippet_count: 11
+snippet_checks:
+- record: Pleuromutilin_Degrading_Artificial_Consortium_5_Strain
+ node: Ninety-Two-Percent Pleuromutilin Degradation
+ evidence_index: 0
+ reference: PMID:42133144
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch86/pleuromutilin-primary.txt
+ method: Normalized contiguous match; literal matching is not entailment.
+- record: Pleuromutilin_Degrading_Artificial_Consortium_5_Strain
+ node: Proposed Artificial-Consortium Degradation Products and Pathways
+ evidence_index: 0
+ reference: PMID:42133144
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch86/pleuromutilin-primary.txt
+ method: Normalized contiguous match; literal matching is not entailment.
+- record: Polaromonas_Vanadium_Reduction_Community
+ node: Vanadium Reduction in Polaromonas-Associated Enrichments
+ evidence_index: 0
+ reference: PMID:33125214
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch86/vanadium-primary.txt
+ method: Normalized contiguous match; literal matching is not entailment.
+- record: Polaromonas_Vanadium_Reduction_Community
+ node: Vanadium Reduction in Polaromonas-Associated Enrichments
+ evidence_index: 1
+ reference: PMID:33125214
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch86/vanadium-primary.txt
+ method: Normalized contiguous match; literal matching is not entailment.
+- record: Polaromonas_Vanadium_Reduction_Community
+ node: V(IV) Precipitation in Reducing Enrichments
+ evidence_index: 0
+ reference: PMID:33125214
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch86/vanadium-si-text.txt
+ method: Normalized contiguous match; literal matching is not entailment.
+- record: Populus_Salt_Tolerant_SynComs
+ node: Physiological Salt-Stress Resistance
+ evidence_index: 0
+ reference: PMID:40904019
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch86/populus-primary.txt
+ method: Normalized contiguous match; literal matching is not entailment.
+- record: Populus_Salt_Tolerant_SynComs
+ node: Salt-Adapted Root-Associated Consortia
+ evidence_index: 0
+ reference: PMID:40904019
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch86/populus-primary.txt
+ method: Normalized contiguous match; literal matching is not entailment.
+- record: Populus_Salt_Tolerant_SynComs
+ node: Salt Stress Growth Protection
+ evidence_index: 0
+ reference: PMID:40904019
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch86/populus-primary.txt
+ method: Normalized contiguous match; literal matching is not entailment.
+- record: Poultry_Wastewater_ThreeStrain_Electroactive_Consortium
+ node: Proposed Electroactive Consortium Complementarity
+ evidence_index: 0
+ reference: PMID:41594859
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch86/poultry-primary.txt
+ method: Normalized contiguous match; literal matching is not entailment.
+- record: Poultry_Wastewater_ThreeStrain_Electroactive_Consortium
+ node: Consortium-Enhanced Anode Power Output
+ evidence_index: 0
+ reference: PMID:41594859
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch86/poultry-primary.txt
+ method: Normalized contiguous match; literal matching is not entailment.
+- record: Poultry_Wastewater_ThreeStrain_Electroactive_Consortium
+ node: Consortium-Enhanced Chemical Oxygen Demand Removal
+ evidence_index: 0
+ reference: PMID:41594859
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch86/poultry-primary.txt
+ method: Normalized contiguous match; literal matching is not entailment.
+discussion_snippet_checks:
+- record: Pleuromutilin_Degrading_Artificial_Consortium_5_Strain
+ node: pleuromutilin-parent-versus-defined-community
+ evidence_index: 0
+ reference: PMID:42133144
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch86/pleuromutilin-primary.txt
+ method: Normalized contiguous match; literal matching is not entailment.
+- record: Pleuromutilin_Degrading_Artificial_Consortium_5_Strain
+ node: pleuromutilin-parent-versus-defined-community
+ evidence_index: 1
+ reference: PMID:42133144
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch86/pleuromutilin-primary.txt
+ method: Normalized contiguous match; literal matching is not entailment.
+- record: Polaromonas_Vanadium_Reduction_Community
+ node: polaromonas-enrichment-versus-partner-mechanism
+ evidence_index: 0
+ reference: PMID:33125214
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch86/vanadium-primary.txt
+ method: Normalized contiguous match; literal matching is not entailment.
+- record: Polaromonas_Vanadium_Reduction_Community
+ node: polaromonas-enrichment-versus-partner-mechanism
+ evidence_index: 1
+ reference: PMID:33125214
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch86/vanadium-si-text.txt
+ method: Normalized contiguous match; literal matching is not entailment.
+- record: Populus_Salt_Tolerant_SynComs
+ node: populus-physiology-recruitment-and-formulation-scope
+ evidence_index: 0
+ reference: PMID:40904019
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch86/populus-primary.txt
+ method: Normalized contiguous match; literal matching is not entailment.
+- record: Populus_Salt_Tolerant_SynComs
+ node: populus-physiology-recruitment-and-formulation-scope
+ evidence_index: 1
+ reference: PMID:40904019
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch86/populus-primary.txt
+ method: Normalized contiguous match; literal matching is not entailment.
+- record: Poultry_Wastewater_ThreeStrain_Electroactive_Consortium
+ node: poultry-complementarity-and-cod-source-discrepancy
+ evidence_index: 0
+ reference: PMID:41594859
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch86/poultry-primary.txt
+ method: Normalized contiguous match; literal matching is not entailment.
+- record: Poultry_Wastewater_ThreeStrain_Electroactive_Consortium
+ node: poultry-complementarity-and-cod-source-discrepancy
+ evidence_index: 1
+ reference: PMID:41594859
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch86/poultry-primary.txt
+ method: Normalized contiguous match; literal matching is not entailment.
+cache_changes:
+- path: references_cache/PMID_33125214.md
+ original_sha256: e3b46b9a3b6e1844aa13f336c6a77b708a3ebb94456a482bc5e10407e8964f6e
+ sha256: b651cbb4bd68a39f4621770bb9c0c557e689fe46cdfb28fb7f5a8af705a21ceb
+ reason: Append four-word public Figure S2 fragment, curator-paraphrased context, exact archive/download/license
+ links and original PDF hash; not main-text access.
+edison:
+ required_for_this_repair: false
+ required_for_unresolved_extensions: true
+ provider_submissions: 0
+ credits_spent: 0
+ dry_runs:
+ - community_id: CommunityMech:000300
+ query_chars: 11100
+ query_sha256: a75cf4410df5e354aebb8f9fac360f50141f9aae47e84d499b7266d31e5c98bc
+ meta_path: /private/tmp/communitymech-batch86/edison-pleuromutilin/Pleuromutilin_Degrading_Artificial_Consortium_5_Strain-edison-literature-causal-meta.yaml
+ authorization: Scoped paid question unanswered; no submission.
+limitations:
+- Fresh before-paper baseline includes both roots:460records921caches,1433nodes592arrows,48warning entries and zero
+ structural defects. All18originalnodes11arrows reviewed;10nodes5arrows remain without new topology.
+- Preserve positive91.97%pleuromutilin degradation and proposed products. En4 parent findings retained as context;
+ workflow and unsupported syntrophy removed. Compatibility/pathway expansion1715remains needs_research.
+- Public vanadium FigureS2 supports reduction-to-precipitation at enrichment scale. Only Polaromonas explicitly
+ credited; genomic attribution is partial, other partner claims removed. Newly exposed disconnected canonical taxa
+ are a metadata gap1716, not silently credited by community scope.
+- Populus physiological and recruitment explanations retain two PARTIAL biological arrows, with IN_VIVO host evidence
+ and alternative formulations distinguished. Full mediator methods unavailable.
+- Poultry retains two HYPOTHESIZED complementarity arrows and positive maximum power, with model-matrix limits and
+ source COD arithmetic/inoculum ambiguity exposed. Reported84.4%is not silently corrected or certified.
+- One cache gains a clearly labeled public Supplement FigureS2 excerpt with source/PDF hash; main-article abstract-only
+ status remains accurate. Other920caches,456otherrecords and raw non-graph blocks preserved. No taxonomy or auditor-rule
+ changes.
+- Four primary abstracts inspected; poultry main text read. Source access scopes distinguish abstracts, main text,
+ extracted tables and visual PDF pages. No full-text claim for paywalled sources; no access bypass.
+- Dedup984all-state issue titles/bodies and65ignored/hidden local matches with explicit .git/docs/site/references_cache
+ exclusions. Related1680read; comments/PRs not exhaustive.
+- One-community Edison causal dry run11100characters; scoped paid question unanswered, zero provider jobs/credits.
+ Earlier pending/denied scopes unchanged. Repair1711-1714close only after protected-main merge;1715/1716remainOPEN.
+- Validation and rendering are separate actual gates, not preasserted. Self-adversarial review is not independent
+ approval, whole-record certification or corpus completion. Generated-model loading defect1703remains unresolved.
+- Final diff check caught trailing whitespace in the original supplemental caption extraction. Cache appendix was
+ shortened to a four-word fragment plus paraphrased context and explicit archive/download/license links. Graph
+ records/history unchanged; affected checks and broad regressions rerun, with original outputs retained as superseded.
+records:
+- path: kb/communities/Pleuromutilin_Degrading_Artificial_Consortium_5_Strain.yaml
+ id: CommunityMech:000300
+ original_sha256: 066483547309020752f7da23b7ecd4fd23e4b7091b9a534fcf5bb66f542766ff
+ record_sha256: 4ad5e08b3c65011a09783c45c8504e32f33817ec3edbef10ea88a70597530b38
+ status: needs_research
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261007-four-records-batch86.yaml
+ scope: Whole record and all existing nodes/arrows; graph review is not non-graph certification.
+ summary: Retain positive 91.97% degradation without obligatory syntrophy.; Retain proposed metabolic products/pathways
+ with attribution and metabolomics limits.
+ renamed_nodes:
+ Artificial-Consortium Metabolic Profiling: Proposed Artificial-Consortium Degradation Products and Pathways
+ node_decisions:
+ - node: Ninety-Two-Percent Pleuromutilin Degradation
+ original_node: Ninety-Two-Percent Pleuromutilin Degradation
+ rationale: Retain positive 91.97% degradation without obligatory syntrophy.
+ - node: Proposed Artificial-Consortium Degradation Products and Pathways
+ original_node: Artificial-Consortium Metabolic Profiling
+ rationale: Retain proposed metabolic products/pathways with attribution and metabolomics limits.
+ removed_node_decisions:
+ - node: En4 Gradient Enrichment and Domestication
+ rationale: Workflow or natural parent-community finding does not describe the defined five-strain interaction;
+ positive parent findings remain in discussion.
+ - node: Pleuromutilin-Stress Core Specialization
+ rationale: Workflow or natural parent-community finding does not describe the defined five-strain interaction;
+ positive parent findings remain in discussion.
+ - node: Fourteen-Degrader Bacterial Isolation
+ rationale: Workflow or natural parent-community finding does not describe the defined five-strain interaction;
+ positive parent findings remain in discussion.
+ - node: Five-Strain Artificial Consortium Construction
+ rationale: Workflow or natural parent-community finding does not describe the defined five-strain interaction;
+ positive parent findings remain in discussion.
+ edges_before:
+ - source: En4 Gradient Enrichment and Domestication
+ target: Pleuromutilin-Stress Core Specialization
+ description: 'Pleuromutilin gradient enrichment selected a domesticated En4 community with stress-associated
+ diversity loss and a specialized core-taxon set.
+
+ '
+ - source: Five-Strain Artificial Consortium Construction
+ target: Ninety-Two-Percent Pleuromutilin Degradation
+ description: 'The five-strain artificial consortium was the defined community that achieved high pleuromutilin
+ degradation.
+
+ '
+ edges_after: []
+ retained_edge_decisions: []
+ removed_edge_decisions:
+ - source: En4 Gradient Enrichment and Domestication
+ target: Pleuromutilin-Stress Core Specialization
+ description: 'Pleuromutilin gradient enrichment selected a domesticated En4 community with stress-associated
+ diversity loss and a specialized core-taxon set.
+
+ '
+ rationale: Workflow or natural parent-community finding does not describe the defined five-strain interaction;
+ positive parent findings remain in discussion.
+ - source: Five-Strain Artificial Consortium Construction
+ target: Ninety-Two-Percent Pleuromutilin Degradation
+ description: 'The five-strain artificial consortium was the defined community that achieved high pleuromutilin
+ degradation.
+
+ '
+ rationale: Workflow or natural parent-community finding does not describe the defined five-strain interaction;
+ positive parent findings remain in discussion.
+ references:
+ - PMID:42133144
+ issues:
+ - 1711
+ - 1715
+ - 1716
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Pleuromutilin_Degrading_Artificial_Consortium_5_Strain/2026-10-07T104208Z-codex-096092.yaml
+- path: kb/communities/Polaromonas_Vanadium_Reduction_Community.yaml
+ id: CommunityMech:000055
+ original_sha256: bf7b035cea66dbda1dc465ab7388031bbcc401fa7a92d3f7c369e665062fa7b6
+ record_sha256: bdb14ed3d33c4a9adc05479849201bf3530bd23d9867a2bc5ddb635b9507a3a5
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261007-four-records-batch86.yaml
+ scope: Whole record and all existing nodes/arrows; graph review is not non-graph certification.
+ summary: Preserve positive enrichment reduction and qualify Polaromonas/MAG attribution.; Preserve controlled
+ enrichment precipitation without invented mineral or partner details.
+ renamed_nodes:
+ Dissimilatory V(V) Reduction by Polaromonas: Vanadium Reduction in Polaromonas-Associated Enrichments
+ Vanadium Immobilization via V(IV) Precipitation: V(IV) Precipitation in Reducing Enrichments
+ node_decisions:
+ - node: Vanadium Reduction in Polaromonas-Associated Enrichments
+ original_node: Dissimilatory V(V) Reduction by Polaromonas
+ rationale: Preserve positive enrichment reduction and qualify Polaromonas/MAG attribution.
+ - node: V(IV) Precipitation in Reducing Enrichments
+ original_node: Vanadium Immobilization via V(IV) Precipitation
+ rationale: Preserve controlled enrichment precipitation without invented mineral or partner details.
+ removed_node_decisions:
+ - node: Sulfide-Mediated Chemical V(V) Reduction
+ rationale: Exact-system source does not support the claimed sulfide/iron partner mechanism or its numerical
+ details.
+ - node: Sequential Fe(III) and V(V) Reduction
+ rationale: Exact-system source does not support the claimed sulfide/iron partner mechanism or its numerical
+ details.
+ edges_before:
+ - source: Dissimilatory V(V) Reduction by Polaromonas
+ target: Vanadium Immobilization via V(IV) Precipitation
+ description: Reduced V(IV) forms sparingly soluble minerals
+ - source: Sulfide-Mediated Chemical V(V) Reduction
+ target: Vanadium Immobilization via V(IV) Precipitation
+ description: Sulfide-mediated V(V) reduction feeds the same insoluble V(IV) product pool as direct enzymatic
+ V(V) reduction.
+ edges_after:
+ - source: Vanadium Reduction in Polaromonas-Associated Enrichments
+ target: V(IV) Precipitation in Reducing Enrichments
+ description: Reduction of supplied V(V) yields V(IV), which precipitated in the acetate-plus-vanadate enrichments
+ shown in Supplement Figure S2. This existing direction is retained at community scale; attribution specifically
+ to Polaromonas remains PARTIAL, and the controls do not prove a particular reductase or mineral identity.
+ retained_edge_decisions:
+ - source: Vanadium Reduction in Polaromonas-Associated Enrichments
+ target: V(IV) Precipitation in Reducing Enrichments
+ description: Reduction of supplied V(V) yields V(IV), which precipitated in the acetate-plus-vanadate enrichments
+ shown in Supplement Figure S2. This existing direction is retained at community scale; attribution specifically
+ to Polaromonas remains PARTIAL, and the controls do not prove a particular reductase or mineral identity.
+ rationale: Source-supported existing direction retained at the stated scope and uncertainty; no added topology.
+ removed_edge_decisions:
+ - source: Sulfide-Mediated Chemical V(V) Reduction
+ target: Vanadium Immobilization via V(IV) Precipitation
+ description: Sulfide-mediated V(V) reduction feeds the same insoluble V(IV) product pool as direct enzymatic
+ V(V) reduction.
+ rationale: Exact-system source does not support the claimed sulfide/iron partner mechanism or its numerical
+ details.
+ references:
+ - PMID:33125214
+ issues:
+ - 1712
+ - 1716
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Polaromonas_Vanadium_Reduction_Community/2026-10-07T104208Z-codex-da763c.yaml
+- path: kb/communities/Populus_Salt_Tolerant_SynComs.yaml
+ id: CommunityMech:000090
+ original_sha256: d1b4f264cd166b2f2095edc86fb98867f19d9d4e39d37ea1ed03046f2ba79354
+ record_sha256: c96458a84a7951d477b792d0a23164f263c4dee76dae2593656d4b39699b10bd
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261007-four-records-batch86.yaml
+ scope: Whole record and all existing nodes/arrows; graph review is not non-graph certification.
+ summary: Preserve positive physiological responses and qualify their causal mediation.; Preserve recruitment association
+ and qualify its host-benefit interpretation.; Preserve formulation-specific host growth without collapsing alternative
+ communities.
+ renamed_nodes: {}
+ node_decisions:
+ - node: Physiological Salt-Stress Resistance
+ original_node: Physiological Salt-Stress Resistance
+ rationale: Preserve positive physiological responses and qualify their causal mediation.
+ - node: Salt-Adapted Root-Associated Consortia
+ original_node: Salt-Adapted Root-Associated Consortia
+ rationale: Preserve recruitment association and qualify its host-benefit interpretation.
+ - node: Salt Stress Growth Protection
+ original_node: Salt Stress Growth Protection
+ rationale: Preserve formulation-specific host growth without collapsing alternative communities.
+ removed_node_decisions:
+ - node: High-Salt Populus Rhizosphere Isolation
+ rationale: Experimental isolation and construction workflow is already represented in engineering_design.
+ - node: Function-Driven Poplar SynCom Construction
+ rationale: Experimental isolation and construction workflow is already represented in engineering_design.
+ edges_before:
+ - source: High-Salt Populus Rhizosphere Isolation
+ target: Function-Driven Poplar SynCom Construction
+ description: 'The nine selected isolates provided the salt-tolerant, growth-promoting strain pool for five function-driven
+ Populus SynCom formulations.
+
+ '
+ - source: Function-Driven Poplar SynCom Construction
+ target: Physiological Salt-Stress Resistance
+ description: 'The best Populus SynCom formulations were carried into mechanistic assays of oxidative stress,
+ osmolyte adjustment, and ion balance under salt exposure.
+
+ '
+ - source: Function-Driven Poplar SynCom Construction
+ target: Salt-Adapted Root-Associated Consortia
+ description: 'The same SynCom treatments were also tested for recruitment of root-associated bacteria that contribute
+ to poplar adaptation during salt stress.
+
+ '
+ - source: Physiological Salt-Stress Resistance
+ target: Salt Stress Growth Protection
+ description: 'Reduced oxidative stress, osmolyte adjustment, and ion balance explain part of the SynCom- mediated
+ growth improvement in salt-stressed hybrid Poplar 84K.
+
+ '
+ - source: Salt-Adapted Root-Associated Consortia
+ target: Salt Stress Growth Protection
+ description: 'Recruitment of root-associated bacteria complemented the direct physiological effects of the introduced
+ SynComs during poplar salt-stress adaptation.
+
+ '
+ edges_after:
+ - source: Physiological Salt-Stress Resistance
+ target: Salt Stress Growth Protection
+ description: 'PARTIAL: reduced oxidative stress, osmolyte adjustment and ion balance are the primary authors
+ reported explanation for improved salt-stress resistance and growth. Retain this existing biological direction
+ without claiming that a particular physiological mediator was experimentally necessary or sufficient.'
+ - source: Salt-Adapted Root-Associated Consortia
+ target: Salt Stress Growth Protection
+ description: 'PARTIAL: the primary authors propose that recruited root-associated consortia enhance poplar adaptation
+ and complement host physiological responses. Preserve this proposed direction; the accessible abstract does
+ not establish recruitment-mediated growth by depletion, transfer or rescue experiments.'
+ retained_edge_decisions:
+ - source: Physiological Salt-Stress Resistance
+ target: Salt Stress Growth Protection
+ description: 'PARTIAL: reduced oxidative stress, osmolyte adjustment and ion balance are the primary authors
+ reported explanation for improved salt-stress resistance and growth. Retain this existing biological direction
+ without claiming that a particular physiological mediator was experimentally necessary or sufficient.'
+ rationale: Source-supported existing direction retained at the stated scope and uncertainty; no added topology.
+ - source: Salt-Adapted Root-Associated Consortia
+ target: Salt Stress Growth Protection
+ description: 'PARTIAL: the primary authors propose that recruited root-associated consortia enhance poplar adaptation
+ and complement host physiological responses. Preserve this proposed direction; the accessible abstract does
+ not establish recruitment-mediated growth by depletion, transfer or rescue experiments.'
+ rationale: Source-supported existing direction retained at the stated scope and uncertainty; no added topology.
+ removed_edge_decisions:
+ - source: High-Salt Populus Rhizosphere Isolation
+ target: Function-Driven Poplar SynCom Construction
+ description: 'The nine selected isolates provided the salt-tolerant, growth-promoting strain pool for five function-driven
+ Populus SynCom formulations.
+
+ '
+ rationale: Experimental isolation and construction workflow is already represented in engineering_design.
+ - source: Function-Driven Poplar SynCom Construction
+ target: Physiological Salt-Stress Resistance
+ description: 'The best Populus SynCom formulations were carried into mechanistic assays of oxidative stress,
+ osmolyte adjustment, and ion balance under salt exposure.
+
+ '
+ rationale: Experimental isolation and construction workflow is already represented in engineering_design.
+ - source: Function-Driven Poplar SynCom Construction
+ target: Salt-Adapted Root-Associated Consortia
+ description: 'The same SynCom treatments were also tested for recruitment of root-associated bacteria that contribute
+ to poplar adaptation during salt stress.
+
+ '
+ rationale: Experimental isolation and construction workflow is already represented in engineering_design.
+ references:
+ - PMID:40904019
+ issues:
+ - 1713
+ - 1716
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Populus_Salt_Tolerant_SynComs/2026-10-07T104208Z-codex-05f714.yaml
+- path: kb/communities/Poultry_Wastewater_ThreeStrain_Electroactive_Consortium.yaml
+ id: CommunityMech:000330
+ original_sha256: aff4688ab68467b03cc4640fc5e1a525c5a1fdad1e91ba37762b3cda231b0de8
+ record_sha256: 932b57ad58aa3a1f58b9ad9be0163d2210a7cfa593964b37abc6d3a83d7f3ebb
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261007-four-records-batch86.yaml
+ scope: Whole record and all existing nodes/arrows; graph review is not non-graph certification.
+ summary: Retain author-proposed complementarity with explicit mechanistic and inoculum uncertainty.; Preserve
+ positive maximum power comparison within the tested model substrate.; Preserve reported COD endpoint while exposing
+ primary-source arithmetic discrepancy.
+ renamed_nodes:
+ Complementary Electroactive Consortium Performance: Proposed Electroactive Consortium Complementarity
+ node_decisions:
+ - node: Proposed Electroactive Consortium Complementarity
+ original_node: Complementary Electroactive Consortium Performance
+ rationale: Retain author-proposed complementarity with explicit mechanistic and inoculum uncertainty.
+ - node: Consortium-Enhanced Anode Power Output
+ original_node: Consortium-Enhanced Anode Power Output
+ rationale: Preserve positive maximum power comparison within the tested model substrate.
+ - node: Consortium-Enhanced Chemical Oxygen Demand Removal
+ original_node: Consortium-Enhanced Chemical Oxygen Demand Removal
+ rationale: Preserve reported COD endpoint while exposing primary-source arithmetic discrepancy.
+ removed_node_decisions: []
+ edges_before:
+ - source: Complementary Electroactive Consortium Performance
+ target: Consortium-Enhanced Anode Power Output
+ description: The mixed electroactive inoculum increased the microbial fuel cell's power-density output beyond
+ the power densities produced by each strain in pure culture.
+ - source: Complementary Electroactive Consortium Performance
+ target: Consortium-Enhanced Chemical Oxygen Demand Removal
+ description: The mixed electroactive inoculum also improved organic-wastewater removal, producing the highest
+ chemical oxygen demand removal among the tested inocula.
+ edges_after:
+ - source: Proposed Electroactive Consortium Complementarity
+ target: Consortium-Enhanced Anode Power Output
+ description: 'HYPOTHESIZED: complementary microbial metabolism and biofilm organization may increase electron
+ delivery and thus power output. Retain the authors proposed mechanism for the positive mixed-versus-pure comparison;
+ no strain-resolved electron-transfer or complementarity perturbation isolates this mechanism.'
+ - source: Proposed Electroactive Consortium Complementarity
+ target: Consortium-Enhanced Chemical Oxygen Demand Removal
+ description: 'HYPOTHESIZED: complementary metabolism may improve utilization of oxidizable substrates and hence
+ COD reduction. COD is an aggregate assay in amended, sterilized wastewater, not proof of native-wastewater
+ mineralization; Section 3.3 inconsistencies prevent certifying the exact reported ranking from concentrations.'
+ retained_edge_decisions:
+ - source: Proposed Electroactive Consortium Complementarity
+ target: Consortium-Enhanced Anode Power Output
+ description: 'HYPOTHESIZED: complementary microbial metabolism and biofilm organization may increase electron
+ delivery and thus power output. Retain the authors proposed mechanism for the positive mixed-versus-pure comparison;
+ no strain-resolved electron-transfer or complementarity perturbation isolates this mechanism.'
+ rationale: Source-supported existing direction retained at the stated scope and uncertainty; no added topology.
+ - source: Proposed Electroactive Consortium Complementarity
+ target: Consortium-Enhanced Chemical Oxygen Demand Removal
+ description: 'HYPOTHESIZED: complementary metabolism may improve utilization of oxidizable substrates and hence
+ COD reduction. COD is an aggregate assay in amended, sterilized wastewater, not proof of native-wastewater
+ mineralization; Section 3.3 inconsistencies prevent certifying the exact reported ranking from concentrations.'
+ rationale: Source-supported existing direction retained at the stated scope and uncertainty; no added topology.
+ removed_edge_decisions: []
+ references:
+ - PMID:41594859
+ issues:
+ - 1714
+ - 1716
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Poultry_Wastewater_ThreeStrain_Electroactive_Consortium/2026-10-07T104208Z-codex-adfaf1.yaml
diff --git a/reports/causal_graph_review/inventory.tsv b/reports/causal_graph_review/inventory.tsv
index 26cfb9598..9975c8fe0 100644
--- a/reports/causal_graph_review/inventory.tsv
+++ b/reports/causal_graph_review/inventory.tsv
@@ -308,10 +308,10 @@ kb/communities/Phylogenetically_Diverse_Denitrifying_SynCom.yaml CommunityMech:0
kb/communities/Pichia_Lactiplantibacillus_CCMA_Plant_Beverage_Coculture.yaml CommunityMech:000345 1dff5927ac9481854b9b13e67efb7fa7be2353674710553de2490207e9996dd9 0 0 0.0 reports/causal_graph_review/decisions/20261007-four-records-batch85.yaml needs_research
kb/communities/Picocystis_Activated_Sludge_Refinery_SWW_Consortium.yaml CommunityMech:000439 a2ac824aec0e51a196e0fccaca9f7346f74b0fc331704c53e69b6b04ff731c12 0 0 0.0 reports/causal_graph_review/decisions/20261007-four-records-batch85.yaml needs_research
kb/communities/Pinus_armandii_Endophytic_Biocontrol_SynCom.yaml CommunityMech:000280 609a40bb20f1ec5b5bb35f3a8805707bd7478c87b345d517c3c32b3d8af41625 4 0 61.2 reports/causal_graph_review/decisions/20261007-four-records-batch85.yaml reviewed
-kb/communities/Pleuromutilin_Degrading_Artificial_Consortium_5_Strain.yaml CommunityMech:000300 066483547309020752f7da23b7ecd4fd23e4b7091b9a534fcf5bb66f542766ff 6 2 100.0 pending
-kb/communities/Polaromonas_Vanadium_Reduction_Community.yaml CommunityMech:000055 bf7b035cea66dbda1dc465ab7388031bbcc401fa7a92d3f7c369e665062fa7b6 4 2 100.0 pending
-kb/communities/Populus_Salt_Tolerant_SynComs.yaml CommunityMech:000090 d1b4f264cd166b2f2095edc86fb98867f19d9d4e39d37ea1ed03046f2ba79354 5 5 100.0 pending
-kb/communities/Poultry_Wastewater_ThreeStrain_Electroactive_Consortium.yaml CommunityMech:000330 aff4688ab68467b03cc4640fc5e1a525c5a1fdad1e91ba37762b3cda231b0de8 3 2 100.0 pending
+kb/communities/Pleuromutilin_Degrading_Artificial_Consortium_5_Strain.yaml CommunityMech:000300 4ad5e08b3c65011a09783c45c8504e32f33817ec3edbef10ea88a70597530b38 2 0 60.0 reports/causal_graph_review/decisions/20261007-four-records-batch86.yaml needs_research
+kb/communities/Polaromonas_Vanadium_Reduction_Community.yaml CommunityMech:000055 bdb14ed3d33c4a9adc05479849201bf3530bd23d9867a2bc5ddb635b9507a3a5 2 1 66.2 reports/causal_graph_review/decisions/20261007-four-records-batch86.yaml reviewed
+kb/communities/Populus_Salt_Tolerant_SynComs.yaml CommunityMech:000090 c96458a84a7951d477b792d0a23164f263c4dee76dae2593656d4b39699b10bd 3 2 98.3 reports/causal_graph_review/decisions/20261007-four-records-batch86.yaml reviewed
+kb/communities/Poultry_Wastewater_ThreeStrain_Electroactive_Consortium.yaml CommunityMech:000330 932b57ad58aa3a1f58b9ad9be0163d2210a7cfa593964b37abc6d3a83d7f3ebb 3 2 85.0 reports/causal_graph_review/decisions/20261007-four-records-batch86.yaml reviewed
kb/communities/Prairie_Pothole_Wetland_Sulfur_Carbon_Virus_Community.yaml CommunityMech:000256 4915600c5a3956d22763c840a68047f13e374bd30bbcb50753fad24d411dfd7c 4 2 100.0 pending
kb/communities/Premature_Infant_Gut_Escherichia_Diametric_Ratio_Community.yaml CommunityMech:000253 7daa27bfe845572e03b932798ad8e828474a2e53619638e6e3ec521da488baa6 3 0 75.0 pending
kb/communities/Priestia_Pseudomonas_Rice_Arsenic_Stress_SynCom.yaml CommunityMech:000341 5236484550c81789c73cfa9d0d0037a5b5e92fe8178c681f5767097fd4b05f1f 2 0 70.0 pending
diff --git a/reports/causal_graph_review/summary.json b/reports/causal_graph_review/summary.json
index 01de4e3bc..896ada9e7 100644
--- a/reports/causal_graph_review/summary.json
+++ b/reports/causal_graph_review/summary.json
@@ -2,14 +2,14 @@
"scope": "Every YAML under kb/communities and data/isolates; filesystem discovery includes hidden/ignored files.",
"semantic_review_rule": "Structural checks and readiness scores do not establish causal support. Completed reviews must match the current record SHA-256, cover every node once with a rationale, and reproduce the current edge list.",
"records": 460,
- "nodes": 1433,
- "edges": 592,
+ "nodes": 1425,
+ "edges": 586,
"records_without_nodes": 8,
- "records_without_edges": 172,
+ "records_without_edges": 173,
"review_status_counts": {
- "needs_research": 47,
- "pending": 152,
- "reviewed": 261
+ "needs_research": 48,
+ "pending": 148,
+ "reviewed": 264
},
"structural_defects": [],
"network_audit": [
@@ -1369,6 +1369,167 @@
"message": "Taxon 'Bacteroidota members' has no interactions",
"severity": "warning"
},
+ {
+ "record": "Polaromonas_Vanadium_Reduction_Community",
+ "type": "DISCONNECTED",
+ "taxon": "Desulfitobacterium species",
+ "taxon_id": "NCBITaxon:36853",
+ "taxon_data": {
+ "taxon_term": {
+ "preferred_term": "Desulfitobacterium species",
+ "term": {
+ "id": "NCBITaxon:36853",
+ "label": "Desulfitobacterium"
+ },
+ "gtdb_grounding_status": "GROUNDED",
+ "gtdb_classification": {
+ "gtdb_id": "GTDB:g__Desulfitobacterium",
+ "gtdb_taxon": "Desulfitobacterium",
+ "gtdb_lineage": "d__Bacteria;p__Bacillota_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfitobacterium",
+ "ncbi_source_id": "NCBITaxon:36853",
+ "majority_fraction": 0.939,
+ "support_genomes": 46,
+ "total_genomes": 49,
+ "is_reclassified": false,
+ "mapping_source": "kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-07-25) [grounded at g__ rank; 2 GTDB taxa under the NCBI taxon]"
+ },
+ "notes": "Gram-positive, spore-forming bacteria (Firmicutes phylum) capable of organohalide respiration and metal reduction. Desulfitobacterium species comprise 3-6% of the tailings community and perform dissimilatory reduction of V(V), Cr(VI), and arsenate using respiratory reductases. This genus couples oxidation of hydrogen, formate, lactate, and pyruvate to reduction of electron acceptors including V(V) and sulfite. Desulfitobacterium exhibits greater tolerance to acidic pH (5.5-7.0) and high metal concentrations compared to many deltaproteobacteria, enabling activity in variable tailings microenvironments. Spore formation provides resilience during desiccation or oxidative episodes in surface tailings. The organism expresses reductive dehalogenase homologs (rdhA genes) that reduce V(V) as an alternative electron acceptor. Desulfitobacterium contributes to vanadium reduction particularly in hydrogen-rich microniches generated by fermentative bacteria.\n"
+ },
+ "functional_role": [
+ "SECONDARY_FERMENTER"
+ ],
+ "abundance_level": "COMMON",
+ "abundance_value": "3-6% in tailings",
+ "evidence": [
+ {
+ "reference": "PMID:33125214",
+ "supports": "SUPPORT",
+ "evidence_source": "IN_VIVO",
+ "snippet": "Further, VV-reducing enrichments indicated that bacteria associated with Polaromonas, a genus belonging to the family Burkholderiaceae, were potentially responsible for VV reduction",
+ "explanation": "Documents presence and enrichment under H\u2082 amendment"
+ }
+ ]
+ },
+ "message": "Taxon 'Desulfitobacterium species' has no interactions",
+ "severity": "warning"
+ },
+ {
+ "record": "Polaromonas_Vanadium_Reduction_Community",
+ "type": "DISCONNECTED",
+ "taxon": "Desulfovibrio species",
+ "taxon_id": "NCBITaxon:872",
+ "taxon_data": {
+ "taxon_term": {
+ "preferred_term": "Desulfovibrio species",
+ "term": {
+ "id": "NCBITaxon:872",
+ "label": "Desulfovibrio"
+ },
+ "gtdb_grounding_status": "GROUNDED",
+ "gtdb_classification": {
+ "gtdb_id": "GTDB:g__Desulfovibrio",
+ "gtdb_taxon": "Desulfovibrio",
+ "gtdb_lineage": "d__Bacteria;p__Desulfobacterota;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio",
+ "ncbi_source_id": "NCBITaxon:872",
+ "majority_fraction": 0.931,
+ "support_genomes": 551,
+ "total_genomes": 592,
+ "is_reclassified": false,
+ "mapping_source": "kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-07-25) [grounded at g__ rank; 9 GTDB taxa under the NCBI taxon]"
+ },
+ "notes": "Gram-negative deltaproteobacteria performing dissimilatory sulfate reduction in the vanadium tailings. Desulfovibrio oxidizes organic acids (lactate, pyruvate, formate) and hydrogen coupled to sulfate reduction, producing hydrogen sulfide (H\u2082S) that chemically reduces V(V) to V(IV) and precipitates vanadium as sulfide minerals. Additionally, Desulfovibrio can enzymatically reduce V(V) through periplasmic and cytoplasmic reductases. The organism comprises 8-12% of the tailings community and increases under sulfate-rich, organic-amended conditions. Hydrogen sulfide generated by Desulfovibrio (concentrations reaching 50-200 \u00b5M) creates strongly reducing microenvironments (Eh < -200 mV) that favor vanadium immobilization. Desulfovibrio species are known to reduce multiple toxic metals including uranium, chromium, and technetium, contributing to polymetallic remediation in this system.\n"
+ },
+ "functional_role": [
+ "SECONDARY_FERMENTER",
+ "SYNTROPHIC_PARTNER"
+ ],
+ "abundance_level": "COMMON",
+ "abundance_value": "8-12% in tailings; enriched under sulfate amendment",
+ "evidence": [
+ {
+ "reference": "PMID:33125214",
+ "supports": "SUPPORT",
+ "evidence_source": "IN_VIVO",
+ "snippet": "Microorganisms can reduce the more toxic and mobile VV to the less toxic and immobile VIV, which could be a detoxification and energy metabolism strategy adopted by V-reducing bacteria (VRB)",
+ "explanation": "Documents Desulfovibrio presence in vanadium tailings"
+ },
+ {
+ "reference": "PMID:33125214",
+ "supports": "PARTIAL",
+ "evidence_source": "IN_VIVO",
+ "snippet": "bacteria associated with Polaromonas",
+ "explanation": "Links sulfate reduction to vanadium immobilization"
+ },
+ {
+ "reference": "PMID:33125214",
+ "supports": "PARTIAL",
+ "evidence_source": "IN_VITRO",
+ "snippet": "VV-reducing enrichments",
+ "explanation": "Establishes dual mechanisms for vanadium reduction"
+ }
+ ]
+ },
+ "message": "Taxon 'Desulfovibrio species' has no interactions",
+ "severity": "warning"
+ },
+ {
+ "record": "Polaromonas_Vanadium_Reduction_Community",
+ "type": "DISCONNECTED",
+ "taxon": "Geobacter species",
+ "taxon_id": "NCBITaxon:28232",
+ "taxon_data": {
+ "taxon_term": {
+ "preferred_term": "Geobacter species",
+ "term": {
+ "id": "NCBITaxon:28232",
+ "label": "Geobacter metallireducens"
+ },
+ "gtdb_grounding_status": "GROUNDED",
+ "gtdb_classification": {
+ "gtdb_id": "GTDB:s__Geobacter_metallireducens",
+ "gtdb_taxon": "Geobacter metallireducens",
+ "gtdb_lineage": "d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geobacter;s__Geobacter metallireducens",
+ "ncbi_source_id": "NCBITaxon:28232",
+ "majority_fraction": 1.0,
+ "total_genomes": 4,
+ "is_reclassified": false,
+ "mapping_source": "kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-07-25) [mapped via NCBI species name \u2014 no species-level NCBI id in table]"
+ },
+ "notes": "Deltaproteobacteria specialized in dissimilatory metal reduction, present at 5-8% relative abundance in vanadium tailings. Geobacter oxidizes acetate and other organic acids coupled to reduction of Fe(III), Mn(IV), and V(V). This genus possesses extensive arrays of c-type cytochromes enabling extracellular electron transfer to metal oxides and soluble metal ions. In vanadium tailings, Geobacter reduces co-occurring Fe(III) minerals, creating reducing conditions that facilitate V(V) reduction by other community members. Geobacter can directly reduce V(V) through outer membrane cytochromes (OmcB, OmcS, OmcZ) and periplasmic reductases. The organism is particularly important in zones with high Fe(III) content (common in vanadium titanomagnetite tailings), where Fe(III) reduction precedes and enhances V(V) reduction. Geobacter forms syntrophic relationships with Polaromonas, potentially exchanging electrons or metabolites.\n"
+ },
+ "functional_role": [
+ "PRIMARY_DEGRADER",
+ "SYNTROPHIC_PARTNER"
+ ],
+ "abundance_level": "COMMON",
+ "abundance_value": "5-8% in tailings; enriched in Fe(III)-rich zones",
+ "evidence": [
+ {
+ "reference": "PMID:33125214",
+ "supports": "SUPPORT",
+ "evidence_source": "IN_VIVO",
+ "snippet": "Further, VV-reducing enrichments indicated that bacteria associated with Polaromonas, a genus belonging to the family Burkholderiaceae, were potentially responsible for VV reduction",
+ "explanation": "Documents Geobacter presence in Fe/V-contaminated tailings"
+ },
+ {
+ "reference": "PMID:33125214",
+ "supports": "PARTIAL",
+ "evidence_source": "IN_VIVO",
+ "snippet": "reduce the more toxic and mobile VV to the less toxic and immobile VIV",
+ "explanation": "Describes role in sequential metal reduction processes"
+ },
+ {
+ "reference": "PMID:19077236",
+ "supports": "SUPPORT",
+ "evidence_source": "IN_VITRO",
+ "snippet": "It is a chemolithoautrophic, gamma-proteobacterium using energy from the oxidation of iron- and sulfur-containing minerals for growth",
+ "explanation": "Confirms V(V) reduction capability"
+ }
+ ]
+ },
+ "message": "Taxon 'Geobacter species' has no interactions",
+ "severity": "warning"
+ },
{
"record": "Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom",
"type": "UNKNOWN_TARGET",
diff --git a/reports/causal_graph_review/validation-20261007-batch86.json b/reports/causal_graph_review/validation-20261007-batch86.json
new file mode 100644
index 000000000..76135eee0
--- /dev/null
+++ b/reports/causal_graph_review/validation-20261007-batch86.json
@@ -0,0 +1,1469 @@
+{
+ "base_commit": "a815f01634f6b8a316434226d99e86cff58095c7",
+ "scope": [
+ "kb/communities/Pleuromutilin_Degrading_Artificial_Consortium_5_Strain.yaml",
+ "kb/communities/Polaromonas_Vanadium_Reduction_Community.yaml",
+ "kb/communities/Populus_Salt_Tolerant_SynComs.yaml",
+ "kb/communities/Poultry_Wastewater_ThreeStrain_Electroactive_Consortium.yaml"
+ ],
+ "reference_validator_version": "0.1.7",
+ "results": [
+ {
+ "check": "Pleuromutilin_Degrading_Artificial_Consortium_5_Strain-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Pleuromutilin_Degrading_Artificial_Consortium_5_Strain.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch86/Pleuromutilin_Degrading_Artificial_Consortium_5_Strain-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Pleuromutilin_Degrading_Artificial_Consortium_5_Strain-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch86/Pleuromutilin_Degrading_Artificial_Consortium_5_Strain-strict.tsv",
+ "kb/communities/Pleuromutilin_Degrading_Artificial_Consortium_5_Strain.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch86/Pleuromutilin_Degrading_Artificial_Consortium_5_Strain-strict.log",
+ "log_sha256": "40259e683bf8ecee6587980f15e3a91a4e65e9e3e770c733f8877f7cfc3aeb3c",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch86/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-batch86/Pleuromutilin_Degrading_Artificial_Consortium_5_Strain-strict.tsv\n"
+ },
+ {
+ "check": "Pleuromutilin_Degrading_Artificial_Consortium_5_Strain-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Pleuromutilin_Degrading_Artificial_Consortium_5_Strain.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch86/Pleuromutilin_Degrading_Artificial_Consortium_5_Strain-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Pleuromutilin_Degrading_Artificial_Consortium_5_Strain-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Pleuromutilin_Degrading_Artificial_Consortium_5_Strain.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch86/Pleuromutilin_Degrading_Artificial_Consortium_5_Strain-references.log",
+ "log_sha256": "d2b9a1da5d9a163d26a3fb1fb59328bc949ef6c630d556ca8e8ddb722e3a8483",
+ "output_tail": "Validating kb/communities/Pleuromutilin_Degrading_Artificial_Consortium_5_Strain.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/Pleuromutilin_Degrading_Artificial_Consortium_5_Strain.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": "Pleuromutilin_Degrading_Artificial_Consortium_5_Strain-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Pleuromutilin_Degrading_Artificial_Consortium_5_Strain.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
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+ "--list-assembled"
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+ "exit_code": 0,
+ "expected_exit_codes": [
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+ ],
+ "log": "/private/tmp/communitymech-batch86/Pleuromutilin_Degrading_Artificial_Consortium_5_Strain-snippets.log",
+ "log_sha256": "32e79f5bf36e5c97f219c301b9924d6a9da1ff1bf07e2b076f93f0d0ee74a358",
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+ },
+ {
+ "check": "Pleuromutilin_Degrading_Artificial_Consortium_5_Strain-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Pleuromutilin_Degrading_Artificial_Consortium_5_Strain.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch86/Pleuromutilin_Degrading_Artificial_Consortium_5_Strain-rank.log",
+ "log_sha256": "e73f9edbf04dd17be40b34dd3aac7c8e24507d3620e00044eae314797650ecd2",
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+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
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+ "HistoryRecord",
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+ ],
+ "log": "/private/tmp/communitymech-batch86/Pleuromutilin_Degrading_Artificial_Consortium_5_Strain-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
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+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
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+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch86/Polaromonas_Vanadium_Reduction_Community-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
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+ "check": "Polaromonas_Vanadium_Reduction_Community-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch86/Polaromonas_Vanadium_Reduction_Community-strict.tsv",
+ "kb/communities/Polaromonas_Vanadium_Reduction_Community.yaml"
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+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch86/Polaromonas_Vanadium_Reduction_Community-strict.log",
+ "log_sha256": "bb2873e43886e337b84999bb9a94404b21e25aa7c93f3bb2508949000a8bd385",
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+ },
+ {
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+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
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+ "expected_exit_codes": [
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+ ],
+ "log": "/private/tmp/communitymech-batch86/Polaromonas_Vanadium_Reduction_Community-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Polaromonas_Vanadium_Reduction_Community-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Polaromonas_Vanadium_Reduction_Community.yaml",
+ "--format",
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+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch86/Polaromonas_Vanadium_Reduction_Community-rank.log",
+ "log_sha256": "0088e9c24c5edbc7cec25474a74806a43f3fd326b5c5168c53d6aae569108e4c",
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+ },
+ {
+ "check": "Polaromonas_Vanadium_Reduction_Community-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Polaromonas_Vanadium_Reduction_Community/2026-10-07T104208Z-codex-da763c.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch86/Polaromonas_Vanadium_Reduction_Community-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Populus_Salt_Tolerant_SynComs-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
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+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch86/Populus_Salt_Tolerant_SynComs-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Populus_Salt_Tolerant_SynComs-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch86/Populus_Salt_Tolerant_SynComs-strict.tsv",
+ "kb/communities/Populus_Salt_Tolerant_SynComs.yaml"
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+ "exit_code": 0,
+ "expected_exit_codes": [
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+ ],
+ "log": "/private/tmp/communitymech-batch86/Populus_Salt_Tolerant_SynComs-strict.log",
+ "log_sha256": "6c35b9647207c70f9c2e1811ff846a48f2518f973541c9618373459fe81bbb83",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch86/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-batch86/Populus_Salt_Tolerant_SynComs-strict.tsv\n"
+ },
+ {
+ "check": "Populus_Salt_Tolerant_SynComs-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Populus_Salt_Tolerant_SynComs.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch86/Populus_Salt_Tolerant_SynComs-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Populus_Salt_Tolerant_SynComs-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Populus_Salt_Tolerant_SynComs.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch86/Populus_Salt_Tolerant_SynComs-references.log",
+ "log_sha256": "502785576e0a7512c594a64b9a33c131ecc4488b7f739c526df82ecf2d2fd0c6",
+ "output_tail": "Validating kb/communities/Populus_Salt_Tolerant_SynComs.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/Populus_Salt_Tolerant_SynComs.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": "Populus_Salt_Tolerant_SynComs-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Populus_Salt_Tolerant_SynComs.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch86/Populus_Salt_Tolerant_SynComs-snippets.log",
+ "log_sha256": "32e79f5bf36e5c97f219c301b9924d6a9da1ff1bf07e2b076f93f0d0ee74a358",
+ "output_tail": "# 9 evidence snippets scanned across 1 files\n MATCH 9\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": "Populus_Salt_Tolerant_SynComs-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Populus_Salt_Tolerant_SynComs.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch86/Populus_Salt_Tolerant_SynComs-rank.log",
+ "log_sha256": "a464f765c9ea373812c7fea37fbc8e8b41a3554bbec1ba214b32fe3169f358ad",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000090\",\n \"name\": \"Populus Salt-Tolerant Rhizosphere SynComs\",\n \"score\": 98.3,\n \"taxonomy\": 1,\n \"connected_taxa\": 1,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 3,\n \"downstream_edges\": 2,\n \"interaction_evidence\": 3,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"metabolites_or_biological_processes\"\n ],\n \"path\": \"kb/communities/Populus_Salt_Tolerant_SynComs.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Populus_Salt_Tolerant_SynComs-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Populus_Salt_Tolerant_SynComs/2026-10-07T104208Z-codex-05f714.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch86/Populus_Salt_Tolerant_SynComs-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Poultry_Wastewater_ThreeStrain_Electroactive_Consortium-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Poultry_Wastewater_ThreeStrain_Electroactive_Consortium.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch86/Poultry_Wastewater_ThreeStrain_Electroactive_Consortium-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Poultry_Wastewater_ThreeStrain_Electroactive_Consortium-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch86/Poultry_Wastewater_ThreeStrain_Electroactive_Consortium-strict.tsv",
+ "kb/communities/Poultry_Wastewater_ThreeStrain_Electroactive_Consortium.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch86/Poultry_Wastewater_ThreeStrain_Electroactive_Consortium-strict.log",
+ "log_sha256": "abb902819a757b52f18c7ab276e00c81cbe07a39a2625937e910bd07737aedb0",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch86/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-batch86/Poultry_Wastewater_ThreeStrain_Electroactive_Consortium-strict.tsv\n"
+ },
+ {
+ "check": "Poultry_Wastewater_ThreeStrain_Electroactive_Consortium-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Poultry_Wastewater_ThreeStrain_Electroactive_Consortium.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch86/Poultry_Wastewater_ThreeStrain_Electroactive_Consortium-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Poultry_Wastewater_ThreeStrain_Electroactive_Consortium-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Poultry_Wastewater_ThreeStrain_Electroactive_Consortium.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch86/Poultry_Wastewater_ThreeStrain_Electroactive_Consortium-references.log",
+ "log_sha256": "275d0b54c275fe679a43666e3fb4eb73f299afde21af6373e6bd5338830ba37a",
+ "output_tail": "Validating kb/communities/Poultry_Wastewater_ThreeStrain_Electroactive_Consortium.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/Poultry_Wastewater_ThreeStrain_Electroactive_Consortium.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": "Poultry_Wastewater_ThreeStrain_Electroactive_Consortium-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Poultry_Wastewater_ThreeStrain_Electroactive_Consortium.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch86/Poultry_Wastewater_ThreeStrain_Electroactive_Consortium-snippets.log",
+ "log_sha256": "96a23c88588d68e990af5d62f9c27df12879566b4125e7703a275c3bfa7adcd7",
+ "output_tail": "# 22 evidence snippets scanned across 1 files\n MATCH 22\n RENDERING 0\n ASSEMBLED 0\n WEAK 0\n MISMATCH 0\n NOCONTENT 0\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n\n# MISMATCH/WEAK detail\n\n# Files by RENDERING (faithful quote; differs from cache only by\n# punctuation/whitespace/Greek \u2014 this is what validate-references flags)\n\n# Top files by NOCONTENT (unverifiable; cache stub/missing)\n\n# ASSEMBLED (every part is in the source; the join is not \u2014\n# a table flattened into prose, or a quote welded from two places)\n"
+ },
+ {
+ "check": "Poultry_Wastewater_ThreeStrain_Electroactive_Consortium-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Poultry_Wastewater_ThreeStrain_Electroactive_Consortium.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch86/Poultry_Wastewater_ThreeStrain_Electroactive_Consortium-rank.log",
+ "log_sha256": "0b2ba79b97bd4bae54eec406f875c25605383d275dcbf71204001d0ccec4e8df",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000330\",\n \"name\": \"Poultry-Wastewater Three-Strain Electroactive Consortium\",\n \"score\": 85.0,\n \"taxonomy\": 3,\n \"connected_taxa\": 3,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 3,\n \"downstream_edges\": 2,\n \"interaction_evidence\": 3,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"metabolites_or_biological_processes\",\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Poultry_Wastewater_ThreeStrain_Electroactive_Consortium.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Poultry_Wastewater_ThreeStrain_Electroactive_Consortium-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Poultry_Wastewater_ThreeStrain_Electroactive_Consortium/2026-10-07T104208Z-codex-adfaf1.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch86/Poultry_Wastewater_ThreeStrain_Electroactive_Consortium-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-batch86/inventory.log",
+ "log_sha256": "25659243467f499a04563030bbfc1551f6215d4ed0435edcc795314d13cd1a4d",
+ "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\": 1425,\n \"edges\": 586,\n \"records_without_nodes\": 8,\n \"records_without_edges\": 173,\n \"review_status_counts\": {\n \"needs_research\": 48,\n \"pending\": 148,\n \"reviewed\": 264\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-batch86/network.log",
+ "log_sha256": "a6d29124a0c095699e61c528d138db88a169daedb19ef83a140faf1d442748c4",
+ "output_tail": "a associated with Polaromonas, a genus belonging to the family Burkholderiaceae, were potentially responsible for VV reduction\",\n \"explanation\": \"Documents Geobacter presence in Fe/V-contaminated tailings\"\n },\n {\n \"reference\": \"PMID:33125214\",\n \"supports\": \"PARTIAL\",\n \"evidence_source\": \"IN_VIVO\",\n \"snippet\": \"reduce the more toxic and mobile VV to the less toxic and immobile VIV\",\n \"explanation\": \"Describes role in sequential metal reduction processes\"\n },\n {\n \"reference\": \"PMID:19077236\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"It is a chemolithoautrophic, gamma-proteobacterium using energy from the oxidation of iron- and sulfur-containing minerals for growth\",\n \"explanation\": \"Confirms V(V) reduction capability\"\n }\n ]\n },\n \"message\": \"Taxon 'Geobacter species' has no interactions\"\n }\n ],\n \"Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom\": [\n {\n \"type\": \"UNKNOWN_TARGET\",\n \"interaction\": \"Twelve-Strain SynCom Suppression of Sclerotinia Sclerotia\",\n \"interaction_index\": 0,\n \"taxon\": \"Sclerotinia sclerotiorum\",\n \"severity\": \"warning\",\n \"message\": \"Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)\"\n },\n {\n \"type\": \"UNKNOWN_TARGET\",\n \"interaction\": \"Trinickia MC Key Contribution to Sclerotia Mortality\",\n \"interaction_index\": 1,\n \"taxon\": \"Sclerotinia sclerotiorum\",\n \"severity\": \"warning\",\n \"message\": \"Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)\"\n }\n ],\n \"Space_Habitat_SevenMember_Stress_Tolerance_SynCom\": [\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Acinetobacter radioresistens 50V1\",\n \"taxon_id\": \"NCBITaxon:40216\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Acinetobacter radioresistens 50V1\",\n \"term\": {\n \"id\": \"NCBITaxon:40216\",\n \"label\": \"Acinetobacter radioresistens\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The isolate came from the preflight Mars Odyssey Orbiter; ontology grounding is at species level.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"50V1\",\n \"genome_accession\": \"GCA_002834555.1\"\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Acinetobacter radioresistens | 50V1 | Preflight Mars Odyssey Orbiter | \\u2013 | Mccoy et al., 2012 | GCA_002834555.1 | TSYB/TSYA | 37 \\u00b0C | 16\\u201318 h\",\n \"explanation\": \"Identifies A. radioresistens 50V1 as a consortium member and gives its spacecraft-associated source, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Acinetobacter radioresistens 50V1' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Micrococcus luteus W4-Al-K1\",\n \"taxon_id\": \"NCBITaxon:1270\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Micrococcus luteus W4-Al-K1\",\n \"term\": {\n \"id\": \"NCBITaxon:1270\",\n \"label\": \"Micrococcus luteus\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The isolate was recovered from an ISS aluminum-case touch array; ontology grounding is at species level.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"W4-Al-K1\",\n \"genome_accession\": \"GCA_057816565.1\"\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Micrococcus luteus | W4-Al-K1 | ISS, Touch Array Aluminum Case | - | Kr\\u00e4mer et al., 2025 | GCA_057816565.1 | NB, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies M. luteus W4-Al-K1 as a consortium member and gives its ISS source, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Micrococcus luteus W4-Al-K1' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Propionibacterium cyclohexanicum TA-12T\",\n \"taxon_id\": \"NCBITaxon:64702\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Propionibacterium cyclohexanicum TA-12T\",\n \"term\": {\n \"id\": \"NCBITaxon:64702\",\n \"label\": \"Propionibacterium cyclohexanicum\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the P. cyclohexanicum type strain as a biosafety-level-1 representative.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"TA-12T\",\n \"genome_accession\": \"GCA_900111365\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"16859\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Propionibacterium cyclohexanicum | TA-12 T | Spoilt Orange Juice | DSM 16859 T | Kusano et al., 1997 | GCA_900111365 | BHI, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies P. cyclohexanicum TA-12T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Propionibacterium cyclohexanicum TA-12T' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Pseudomonas antarctica CMS 35T\",\n \"taxon_id\": \"NCBITaxon:219572\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Pseudomonas antarctica CMS 35T\",\n \"term\": {\n \"id\": \"NCBITaxon:219572\",\n \"label\": \"Pseudomonas antarctica\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the P. antarctica type strain as a biosafety-level-1 Pseudomonas surrogate.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"CMS 35T\",\n \"genome_accession\": \"GCA_010634845\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"15318\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Pseudomonas antarctica | CMS 35 T | Antarctica | DSM 15318 T | Reddy et al., 2004 | GCA_010634845 | TSYB/TSYA | Ambient | 12\\u201316 h\",\n \"explanation\": \"Identifies P. antarctica CMS 35T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Pseudomonas antarctica CMS 35T' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Staphylococcus capitis K1-2-2-23\",\n \"taxon_id\": \"NCBITaxon:29388\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Staphylococcus capitis K1-2-2-23\",\n \"term\": {\n \"id\": \"NCBITaxon:29388\",\n \"label\": \"Staphylococcus capitis\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The isolate was recovered from ISS V2A steel; ontology grounding is at species level.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"K1-2-2-23\",\n \"genome_accession\": \"GCA_025272695\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"111179\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Staphylococcus capitis | K1-2-2-23 | ISS, V2A Steel | DSM 111179 | Sobisch et al., 2019 | GCA_025272695 | TSYB/TSYA | 37 \\u00b0C | 16\\u201324 h\",\n \"explanation\": \"Identifies S. capitis K1-2-2-23 as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Staphylococcus capitis K1-2-2-23' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Streptococcus halotolerans HTS9T\",\n \"taxon_id\": \"NCBITaxon:1814128\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Streptococcus halotolerans HTS9T\",\n \"term\": {\n \"id\": \"NCBITaxon:1814128\",\n \"label\": \"Streptococcus halotolerans\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the S. halotolerans type strain as a biosafety-level-1 representative.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"HTS9T\",\n \"genome_accession\": \"GCA_001598035\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"101996\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Streptococcus halotolerans | HTS9 T | Respiratory Tract of Marmota himalayana | DSM 101996 T | Niu et al., 2016 | GCA_001598035 | 2xLB, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies S. halotolerans HTS9T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Streptococcus halotolerans HTS9T' has no interactions\"\n }\n ]\n}\n"
+ },
+ {
+ "check": "just-network-json",
+ "command": [
+ "just",
+ "audit-network-json"
+ ],
+ "exit_code": 2,
+ "expected_exit_codes": [
+ 2
+ ],
+ "log": "/private/tmp/communitymech-batch86/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-batch86/rank-all.log",
+ "log_sha256": "fca909c8a07c352b0043c743b44e27289b2eae1badbc5b270ccff28b5081fda9",
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Coculture\t2\t2\t0\t3\t2\t8\t\t0\t0\n436\t100.0\tkb/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml\tCommunityMech:000282\tThermophilic Lignocellulose-degrading Composting SynCom\t5\t5\t0\t3\t2\t3\t\t0\t0\n437\t100.0\tkb/communities/Thermophilic_Pyrite_QS_Consortium.yaml\tCommunityMech:000073\tThermophilic Pyrite Quorum Sensing Consortium\t3\t3\t0\t6\t2\t14\t\t0\t0\n438\t100.0\tkb/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml\tCommunityMech:000186\tThermotoga-Methanocaldococcus Hyperthermophilic Syntrophy\t2\t2\t0\t3\t2\t8\t\t0\t0\n439\t100.0\tkb/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml\tCommunityMech:000239\tThiocyanate-Degrading Afipia and Thiobacillus Bioreactor Community\t3\t3\t0\t3\t2\t3\t\t0\t0\n440\t100.0\tkb/communities/Tinto_River_Iron_Cycling_Community.yaml\tCommunityMech:000074\tTinto River Iron Cycling Community\t6\t6\t0\t5\t3\t6\t\t0\t0\n441\t100.0\tkb/communities/Tobacco_Chemotactic_Biocontrol_SynCom.yaml\tCommunityMech:000106\tTobacco Chemotactic Biocontrol SynCom\t2\t2\t0\t3\t2\t4\t\t0\t0\n442\t100.0\tkb/communities/Tomato_Oxylipin_SynCom3.yaml\tCommunityMech:000107\tTomato Oxylipin-Protective SynCom3\t3\t3\t0\t3\t2\t4\t\t0\t0\n443\t100.0\tkb/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml\tCommunityMech:000112\tTribromophenol Anaerobic Bioremediation SynCom\t3\t3\t0\t4\t3\t5\t\t0\t0\n444\t100.0\tkb/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml\tCommunityMech:000188\tTrichococcus-Syntrophomonas-Methanospirillum Butyrate Coculture\t3\t3\t0\t3\t2\t6\t\t0\t0\n445\t100.0\tkb/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml\tCommunityMech:000205\tTrichoderma-E. coli Cellulosic Isobutanol Coculture\t2\t2\t0\t3\t2\t5\t\t0\t0\n446\t100.0\tkb/communities/Trichoderma_Lactate_Platform.yaml\tCommunityMech:000075\tTrichoderma Lactate Platform for SCFA Production\t3\t3\t0\t3\t2\t3\t\t0\t0\n447\t100.0\tkb/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml\tCommunityMech:000270\tTrichoderma-Streptomyces Filamentous Cellulose Coculture\t2\t2\t0\t3\t2\t7\t\t0\t0\n448\t100.0\tkb/communities/Trichodesmium_Alteromonas_Marine_Consortium.yaml\tCommunityMech:000147\tTrichodesmium-Alteromonas Marine Consortium\t3\t3\t0\t3\t2\t5\t\t0\t0\n449\t100.0\tkb/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml\tCommunityMech:000337\tTropidoatractus magnetotacticus Magnetotactic Ciliate Tripartite Syntrophy\t3\t3\t0\t4\t2\t9\t\t0\t0\n450\t100.0\tkb/communities/Urine_Nitrification_SynCom.yaml\tCommunityMech:000117\tUrine Nitrification Synthetic Microbial Community\t5\t5\t0\t3\t2\t5\t\t0\t0\n451\t100.0\tkb/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml\tCommunityMech:000213\tVariovorax-Cryptococcus Vitamin Cross-Feeding Microcosm\t2\t2\t0\t3\t2\t4\t\t0\t0\n452\t100.0\tkb/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml\tCommunityMech:000328\tWaste-Sludge Electro-Fermentation Biofilm-Suspension Community\t5\t5\t0\t4\t2\t6\t\t0\t0\n453\t100.0\tkb/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.yaml\tCommunityMech:000098\tWatermelon Rhizosphere Fusarium-Protective SynCom8\t2\t2\t0\t3\t2\t7\t\t0\t0\n454\t100.0\tkb/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml\tCommunityMech:000255\tWetland Oxygen-Sulfate Greenhouse Gas Microcosm Community\t3\t3\t0\t3\t2\t6\t\t0\t0\n455\t100.0\tkb/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.yaml\tCommunityMech:000118\tWheat Straw Biogas Pretreatment SynCom\t4\t4\t0\t3\t2\t4\t\t0\t0\n456\t100.0\tkb/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml\tCommunityMech:000354\tYarrowia lipolytica Division-of-Labor Lipid Consortium\t2\t2\t0\t3\t2\t3\t\t0\t0\n457\t100.0\tkb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml\tCommunityMech:000164\tYogurt Two-Species Starter Culture\t2\t2\t0\t4\t2\t9\t\t0\t0\n458\t100.0\tkb/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml\tCommunityMech:000210\tZymomonas-E. coli Exometabolomics-Designed Obligate Mutualism\t2\t2\t0\t3\t2\t6\t\t0\t0\n459\t100.0\tkb/communities/hCom2_Complex_Gut_Microbiome.yaml\tCommunityMech:000123\thCom2 Complex Gut Microbiome\t1\t1\t0\t3\t2\t3\t\t0\t0\n460\t100.0\tkb/communities/mCAFEs_Brachypodium_RCC.yaml\tCommunityMech:000078\tm-CAFEs Brachypodium Reduced Complexity Consortia\t10\t10\t0\t6\t2\t11\t\t0\t0\nPYTHONPATH=src uv run python scripts/rank_causal_graph_readiness.py \n"
+ },
+ {
+ "check": "connectivity-survey",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-c",
+ "import json,pathlib,runpy\nfn=runpy.run_path('tests/test_community_level_connectivity_credit.py')['_survey']\nresult={}\nfor name,root in [('baseline',pathlib.Path('/private/tmp/communitymech-causal-batch85')),('current',pathlib.Path.cwd())]:\n paths=sorted(p for r in ['kb/communities','data/isolates'] for p in (root/r).rglob('*.yaml'))\n assert len(paths)==460\n fn.__globals__['record_files']=lambda:paths\n result[name]=fn()\nprint(json.dumps(result))\n"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch86/connectivity-survey.log",
+ "log_sha256": "918efff2628010a58e94ebf45c771c218193c92e6b949943f82052bd3d1a88a2",
+ "output_tail": "{\"baseline\": {\"records\": 460, \"with_community_level\": 394, \"mixed\": 126, \"community_level_only\": 268, \"taxa\": 1517, \"credited_solely_by_the_rule\": 1243}, \"current\": {\"records\": 460, \"with_community_level\": 395, \"mixed\": 126, \"community_level_only\": 269, \"taxa\": 1521, \"credited_solely_by_the_rule\": 1247}}\n"
+ },
+ {
+ "check": "black",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/3Q_kifQtLB624D5bBWGIf/bin/black",
+ "--check",
+ "tests/test_causal_review_batch86.py",
+ "tests/test_participating_taxa.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch86/black.log",
+ "log_sha256": "b9cf511501d306d2bd8355ccb165c8ddc0a6fdd62d7c72c4a7b1795cf8934c8c",
+ "output_tail": "All done! \u2728 \ud83c\udf70 \u2728\n2 files would be left unchanged.\n"
+ },
+ {
+ "check": "ruff",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/wCcxEYRM4HeHgwYPZemHX/bin/ruff",
+ "check",
+ "tests/test_causal_review_batch86.py",
+ "tests/test_participating_taxa.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch86/ruff.log",
+ "log_sha256": "82b3e6a6c090a57601d22943bd23fca9218d1031dbe5a7b754092f9a156b4f18",
+ "output_tail": "All checks passed!\n"
+ },
+ {
+ "check": "Polaromonas_Vanadium_Reduction_Community-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Polaromonas_Vanadium_Reduction_Community.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch86/Polaromonas_Vanadium_Reduction_Community-references.log",
+ "log_sha256": "88d1d7259ad27dc7a30da6c48ed918330b9cec2ade00f8f4e1f54bad952c74dc",
+ "output_tail": "Validating kb/communities/Polaromonas_Vanadium_Reduction_Community.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/Polaromonas_Vanadium_Reduction_Community.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": "Polaromonas_Vanadium_Reduction_Community-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Polaromonas_Vanadium_Reduction_Community.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch86/Polaromonas_Vanadium_Reduction_Community-snippets.log",
+ "log_sha256": "2ffa6e242265b4c1c2eb555bd8bd14abb6cc63ed4d5a8a818da9b515db44daff",
+ "output_tail": "# 24 evidence snippets scanned across 1 files\n MATCH 24\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": "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-batch86/render.log",
+ "log_sha256": "3abc64114ef228075275f79b1c88c558a6565dac011d087a077cb7654e7a6fcc",
+ "output_tail": "sm.html\n \u2713 Synechococcus_Bacillus_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 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Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 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+ "output_tail": "# 8902 evidence snippets scanned across 460 files\n MATCH 8767\n RENDERING 20\n ASSEMBLED 1\n WEAK 0\n MISMATCH 38\n NOCONTENT 76\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n 19 (19 hard) kb/communities/DCPP_DBS4_DCP4_DCP11d_Degradation_SynCom.yaml\n 15 (15 hard) kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml\n 3 (3 hard) kb/communities/Coscinodiscus_Synthetic_Community.yaml\n 1 (1 hard) kb/communities/Altered_Schaedler_Flora_Gnotobiotic_Mouse_Community.yaml\nuv run python scripts/evidence_snippet_audit.py \n"
+ }
+ ],
+ "limitations": [
+ "Fresh before-paper baseline includes both roots:460records921caches,1433nodes592arrows,48warning entries and zero structural defects. All18originalnodes11arrows reviewed;10nodes5arrows remain without new topology.",
+ "Preserve positive91.97%pleuromutilin degradation and proposed products. En4 parent findings retained as context; workflow and unsupported syntrophy removed. Compatibility/pathway expansion1715remains needs_research.",
+ "Public vanadium FigureS2 supports reduction-to-precipitation at enrichment scale. Only Polaromonas explicitly credited; genomic attribution is partial, other partner claims removed. Newly exposed disconnected canonical taxa are a metadata gap1716, not silently credited by community scope.",
+ "Populus physiological and recruitment explanations retain two PARTIAL biological arrows, with IN_VIVO host evidence and alternative formulations distinguished. Full mediator methods unavailable.",
+ "Poultry retains two HYPOTHESIZED complementarity arrows and positive maximum power, with model-matrix limits and source COD arithmetic/inoculum ambiguity exposed. Reported84.4%is not silently corrected or certified.",
+ "One cache gains a clearly labeled public Supplement FigureS2 excerpt with source/PDF hash; main-article abstract-only status remains accurate. Other920caches,456otherrecords and raw non-graph blocks preserved. No taxonomy or auditor-rule changes.",
+ "Four primary abstracts inspected; poultry main text read. Source access scopes distinguish abstracts, main text, extracted tables and visual PDF pages. No full-text claim for paywalled sources; no access bypass.",
+ "Dedup984all-state issue titles/bodies and65ignored/hidden local matches with explicit .git/docs/site/references_cache exclusions. Related1680read; comments/PRs not exhaustive.",
+ "One-community Edison causal dry run11100characters; scoped paid question unanswered, zero provider jobs/credits. Earlier pending/denied scopes unchanged. Repair1711-1714close only after protected-main merge;1715/1716remainOPEN.",
+ "Validation and rendering are separate actual gates, not preasserted. Self-adversarial review is not independent approval, whole-record certification or corpus completion. Generated-model loading defect1703remains unresolved.",
+ "Final diff check caught trailing whitespace in the original supplemental caption extraction. Cache appendix was shortened to a four-word fragment plus paraphrased context and explicit archive/download/license links. Graph records/history unchanged; affected checks and broad regressions rerun, with original outputs retained as superseded.",
+ "Exact HTML-description parser and repeat-render checks, not browser screenshots. Post-commit docs-current is separate."
+ ],
+ "superseded_checks": [
+ {
+ "check": "Polaromonas_Vanadium_Reduction_Community-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Polaromonas_Vanadium_Reduction_Community.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch86/Polaromonas_Vanadium_Reduction_Community-references-initial.log",
+ "log_sha256": "88d1d7259ad27dc7a30da6c48ed918330b9cec2ade00f8f4e1f54bad952c74dc",
+ "output_tail": "Validating kb/communities/Polaromonas_Vanadium_Reduction_Community.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/Polaromonas_Vanadium_Reduction_Community.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n",
+ "disposition": "Superseded after whitespace/source-cache citation cleanup; original graph records and all scientific decisions unchanged."
+ },
+ {
+ "check": "Polaromonas_Vanadium_Reduction_Community-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Polaromonas_Vanadium_Reduction_Community.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch86/Polaromonas_Vanadium_Reduction_Community-snippets-initial.log",
+ "log_sha256": "2ffa6e242265b4c1c2eb555bd8bd14abb6cc63ed4d5a8a818da9b515db44daff",
+ "output_tail": "# 24 evidence snippets scanned across 1 files\n MATCH 24\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",
+ "disposition": "Superseded after whitespace/source-cache citation cleanup; original graph records and all scientific decisions unchanged."
+ },
+ {
+ "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-batch86/render-initial.log",
+ "log_sha256": "3abc64114ef228075275f79b1c88c558a6565dac011d087a077cb7654e7a6fcc",
+ "output_tail": "sm.html\n \u2713 Synechococcus_Bacillus_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch86/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch86/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch86/docs/index.html\n",
+ "disposition": "Superseded after whitespace/source-cache citation cleanup; original graph records and all scientific decisions unchanged."
+ },
+ {
+ "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-batch86/render-repeat-initial.log",
+ "log_sha256": "3abc64114ef228075275f79b1c88c558a6565dac011d087a077cb7654e7a6fcc",
+ "output_tail": "sm.html\n \u2713 Synechococcus_Bacillus_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch86/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 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+ },
+ "network_delta": {
+ "existing_findings_preserved": 48,
+ "added_findings": {
+ "Polaromonas_Vanadium_Reduction_Community": [
+ {
+ "type": "DISCONNECTED",
+ "taxon": "Desulfitobacterium species",
+ "taxon_id": "NCBITaxon:36853",
+ "taxon_data": {
+ "taxon_term": {
+ "preferred_term": "Desulfitobacterium species",
+ "term": {
+ "id": "NCBITaxon:36853",
+ "label": "Desulfitobacterium"
+ },
+ "gtdb_grounding_status": "GROUNDED",
+ "gtdb_classification": {
+ "gtdb_id": "GTDB:g__Desulfitobacterium",
+ "gtdb_taxon": "Desulfitobacterium",
+ "gtdb_lineage": "d__Bacteria;p__Bacillota_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfitobacterium",
+ "ncbi_source_id": "NCBITaxon:36853",
+ "majority_fraction": 0.939,
+ "support_genomes": 46,
+ "total_genomes": 49,
+ "is_reclassified": false,
+ "mapping_source": "kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-07-25) [grounded at g__ rank; 2 GTDB taxa under the NCBI taxon]"
+ },
+ "notes": "Gram-positive, spore-forming bacteria (Firmicutes phylum) capable of organohalide respiration and metal reduction. Desulfitobacterium species comprise 3-6% of the tailings community and perform dissimilatory reduction of V(V), Cr(VI), and arsenate using respiratory reductases. This genus couples oxidation of hydrogen, formate, lactate, and pyruvate to reduction of electron acceptors including V(V) and sulfite. Desulfitobacterium exhibits greater tolerance to acidic pH (5.5-7.0) and high metal concentrations compared to many deltaproteobacteria, enabling activity in variable tailings microenvironments. Spore formation provides resilience during desiccation or oxidative episodes in surface tailings. The organism expresses reductive dehalogenase homologs (rdhA genes) that reduce V(V) as an alternative electron acceptor. Desulfitobacterium contributes to vanadium reduction particularly in hydrogen-rich microniches generated by fermentative bacteria.\n"
+ },
+ "functional_role": [
+ "SECONDARY_FERMENTER"
+ ],
+ "abundance_level": "COMMON",
+ "abundance_value": "3-6% in tailings",
+ "evidence": [
+ {
+ "reference": "PMID:33125214",
+ "supports": "SUPPORT",
+ "evidence_source": "IN_VIVO",
+ "snippet": "Further, VV-reducing enrichments indicated that bacteria associated with Polaromonas, a genus belonging to the family Burkholderiaceae, were potentially responsible for VV reduction",
+ "explanation": "Documents presence and enrichment under H\u2082 amendment"
+ }
+ ]
+ },
+ "message": "Taxon 'Desulfitobacterium species' has no interactions"
+ },
+ {
+ "type": "DISCONNECTED",
+ "taxon": "Desulfovibrio species",
+ "taxon_id": "NCBITaxon:872",
+ "taxon_data": {
+ "taxon_term": {
+ "preferred_term": "Desulfovibrio species",
+ "term": {
+ "id": "NCBITaxon:872",
+ "label": "Desulfovibrio"
+ },
+ "gtdb_grounding_status": "GROUNDED",
+ "gtdb_classification": {
+ "gtdb_id": "GTDB:g__Desulfovibrio",
+ "gtdb_taxon": "Desulfovibrio",
+ "gtdb_lineage": "d__Bacteria;p__Desulfobacterota;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio",
+ "ncbi_source_id": "NCBITaxon:872",
+ "majority_fraction": 0.931,
+ "support_genomes": 551,
+ "total_genomes": 592,
+ "is_reclassified": false,
+ "mapping_source": "kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-07-25) [grounded at g__ rank; 9 GTDB taxa under the NCBI taxon]"
+ },
+ "notes": "Gram-negative deltaproteobacteria performing dissimilatory sulfate reduction in the vanadium tailings. Desulfovibrio oxidizes organic acids (lactate, pyruvate, formate) and hydrogen coupled to sulfate reduction, producing hydrogen sulfide (H\u2082S) that chemically reduces V(V) to V(IV) and precipitates vanadium as sulfide minerals. Additionally, Desulfovibrio can enzymatically reduce V(V) through periplasmic and cytoplasmic reductases. The organism comprises 8-12% of the tailings community and increases under sulfate-rich, organic-amended conditions. Hydrogen sulfide generated by Desulfovibrio (concentrations reaching 50-200 \u00b5M) creates strongly reducing microenvironments (Eh < -200 mV) that favor vanadium immobilization. Desulfovibrio species are known to reduce multiple toxic metals including uranium, chromium, and technetium, contributing to polymetallic remediation in this system.\n"
+ },
+ "functional_role": [
+ "SECONDARY_FERMENTER",
+ "SYNTROPHIC_PARTNER"
+ ],
+ "abundance_level": "COMMON",
+ "abundance_value": "8-12% in tailings; enriched under sulfate amendment",
+ "evidence": [
+ {
+ "reference": "PMID:33125214",
+ "supports": "SUPPORT",
+ "evidence_source": "IN_VIVO",
+ "snippet": "Microorganisms can reduce the more toxic and mobile VV to the less toxic and immobile VIV, which could be a detoxification and energy metabolism strategy adopted by V-reducing bacteria (VRB)",
+ "explanation": "Documents Desulfovibrio presence in vanadium tailings"
+ },
+ {
+ "reference": "PMID:33125214",
+ "supports": "PARTIAL",
+ "evidence_source": "IN_VIVO",
+ "snippet": "bacteria associated with Polaromonas",
+ "explanation": "Links sulfate reduction to vanadium immobilization"
+ },
+ {
+ "reference": "PMID:33125214",
+ "supports": "PARTIAL",
+ "evidence_source": "IN_VITRO",
+ "snippet": "VV-reducing enrichments",
+ "explanation": "Establishes dual mechanisms for vanadium reduction"
+ }
+ ]
+ },
+ "message": "Taxon 'Desulfovibrio species' has no interactions"
+ },
+ {
+ "type": "DISCONNECTED",
+ "taxon": "Geobacter species",
+ "taxon_id": "NCBITaxon:28232",
+ "taxon_data": {
+ "taxon_term": {
+ "preferred_term": "Geobacter species",
+ "term": {
+ "id": "NCBITaxon:28232",
+ "label": "Geobacter metallireducens"
+ },
+ "gtdb_grounding_status": "GROUNDED",
+ "gtdb_classification": {
+ "gtdb_id": "GTDB:s__Geobacter_metallireducens",
+ "gtdb_taxon": "Geobacter metallireducens",
+ "gtdb_lineage": "d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geobacter;s__Geobacter metallireducens",
+ "ncbi_source_id": "NCBITaxon:28232",
+ "majority_fraction": 1.0,
+ "total_genomes": 4,
+ "is_reclassified": false,
+ "mapping_source": "kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-07-25) [mapped via NCBI species name \u2014 no species-level NCBI id in table]"
+ },
+ "notes": "Deltaproteobacteria specialized in dissimilatory metal reduction, present at 5-8% relative abundance in vanadium tailings. Geobacter oxidizes acetate and other organic acids coupled to reduction of Fe(III), Mn(IV), and V(V). This genus possesses extensive arrays of c-type cytochromes enabling extracellular electron transfer to metal oxides and soluble metal ions. In vanadium tailings, Geobacter reduces co-occurring Fe(III) minerals, creating reducing conditions that facilitate V(V) reduction by other community members. Geobacter can directly reduce V(V) through outer membrane cytochromes (OmcB, OmcS, OmcZ) and periplasmic reductases. The organism is particularly important in zones with high Fe(III) content (common in vanadium titanomagnetite tailings), where Fe(III) reduction precedes and enhances V(V) reduction. Geobacter forms syntrophic relationships with Polaromonas, potentially exchanging electrons or metabolites.\n"
+ },
+ "functional_role": [
+ "PRIMARY_DEGRADER",
+ "SYNTROPHIC_PARTNER"
+ ],
+ "abundance_level": "COMMON",
+ "abundance_value": "5-8% in tailings; enriched in Fe(III)-rich zones",
+ "evidence": [
+ {
+ "reference": "PMID:33125214",
+ "supports": "SUPPORT",
+ "evidence_source": "IN_VIVO",
+ "snippet": "Further, VV-reducing enrichments indicated that bacteria associated with Polaromonas, a genus belonging to the family Burkholderiaceae, were potentially responsible for VV reduction",
+ "explanation": "Documents Geobacter presence in Fe/V-contaminated tailings"
+ },
+ {
+ "reference": "PMID:33125214",
+ "supports": "PARTIAL",
+ "evidence_source": "IN_VIVO",
+ "snippet": "reduce the more toxic and mobile VV to the less toxic and immobile VIV",
+ "explanation": "Describes role in sequential metal reduction processes"
+ },
+ {
+ "reference": "PMID:19077236",
+ "supports": "SUPPORT",
+ "evidence_source": "IN_VITRO",
+ "snippet": "It is a chemolithoautrophic, gamma-proteobacterium using energy from the oxidation of iron- and sulfur-containing minerals for growth",
+ "explanation": "Confirms V(V) reduction capability"
+ }
+ ]
+ },
+ "message": "Taxon 'Geobacter species' has no interactions"
+ }
+ ]
+ },
+ "removed_findings": {},
+ "interpretation": "Existing warning entries preserved. Three newly exposed disconnected Polaromonas-record taxa lack exact-system support; metadata1716 remains open. No structural defects, taxonomy edits or auditor-rule changes."
+ },
+ "render_determinism": true,
+ "published_description_coverage": {
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+ "arrows": 578
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+ }
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+ "taxa": 4,
+ "credited_solely_by_the_rule": 4
+ },
+ "interpretation": "Polaromonas becomes community-level-only. Legacy census counts all four canonical members, but explicit participant credit names only Polaromonas and three others are disconnected. No canonical taxon or auditor-rule change."
+ },
+ "network_warning_count": 51,
+ "corpus": {
+ "scope": "Every YAML under kb/communities and data/isolates; filesystem discovery includes hidden/ignored files.",
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+ "nodes": 1425,
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+ "kb/communities/Populus_Salt_Tolerant_SynComs.yaml": "c96458a84a7951d477b792d0a23164f263c4dee76dae2593656d4b39699b10bd",
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+ "status": "verified_assay_boundary_graph_review",
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+ }
+ },
+ "full_corpus_snippet_audit_caveat": "Both-root recipe actually executed. Exit0 is informational, not clean-corpus certification; four focused snippet gates separately pass.",
+ "pre_research_baseline": {
+ "base_commit": "a815f01634f6b8a316434226d99e86cff58095c7",
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+ "research_worktree": "/private/tmp/communitymech-causal-batch85",
+ "checks": [
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+ "name": "rank",
+ "command": [
+ "just",
+ "rank-causal-graphs"
+ ],
+ "exit_code": 0,
+ "expected_exit_code": 0,
+ "log": "/private/tmp/communitymech-batch86/baseline-rank.log",
+ "sha256": "a14aee75e17d2ecdf8bb56796910744f14f2ddbaf35fdb343841ccaa6fbbd924",
+ "output_tail": "/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml\tCommunityMech:000337\tTropidoatractus magnetotacticus Magnetotactic Ciliate Tripartite Syntrophy\t3\t3\t0\t4\t2\t9\t\t0\t0\n450\t100.0\tkb/communities/Urine_Nitrification_SynCom.yaml\tCommunityMech:000117\tUrine Nitrification Synthetic Microbial Community\t5\t5\t0\t3\t2\t5\t\t0\t0\n451\t100.0\tkb/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml\tCommunityMech:000213\tVariovorax-Cryptococcus Vitamin Cross-Feeding Microcosm\t2\t2\t0\t3\t2\t4\t\t0\t0\n452\t100.0\tkb/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml\tCommunityMech:000328\tWaste-Sludge Electro-Fermentation Biofilm-Suspension Community\t5\t5\t0\t4\t2\t6\t\t0\t0\n453\t100.0\tkb/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.yaml\tCommunityMech:000098\tWatermelon Rhizosphere Fusarium-Protective SynCom8\t2\t2\t0\t3\t2\t7\t\t0\t0\n454\t100.0\tkb/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml\tCommunityMech:000255\tWetland Oxygen-Sulfate Greenhouse Gas Microcosm Community\t3\t3\t0\t3\t2\t6\t\t0\t0\n455\t100.0\tkb/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.yaml\tCommunityMech:000118\tWheat Straw Biogas Pretreatment SynCom\t4\t4\t0\t3\t2\t4\t\t0\t0\n456\t100.0\tkb/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml\tCommunityMech:000354\tYarrowia lipolytica Division-of-Labor Lipid Consortium\t2\t2\t0\t3\t2\t3\t\t0\t0\n457\t100.0\tkb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml\tCommunityMech:000164\tYogurt Two-Species Starter Culture\t2\t2\t0\t4\t2\t9\t\t0\t0\n458\t100.0\tkb/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml\tCommunityMech:000210\tZymomonas-E. coli Exometabolomics-Designed Obligate Mutualism\t2\t2\t0\t3\t2\t6\t\t0\t0\n459\t100.0\tkb/communities/hCom2_Complex_Gut_Microbiome.yaml\tCommunityMech:000123\thCom2 Complex Gut Microbiome\t1\t1\t0\t3\t2\t3\t\t0\t0\n460\t100.0\tkb/communities/mCAFEs_Brachypodium_RCC.yaml\tCommunityMech:000078\tm-CAFEs Brachypodium Reduced Complexity Consortia\t10\t10\t0\t6\t2\t11\t\t0\t0\nPYTHONPATH=src uv run python scripts/rank_causal_graph_readiness.py \n"
+ },
+ {
+ "name": "just-network",
+ "command": [
+ "just",
+ "audit-network-json"
+ ],
+ "exit_code": 2,
+ "expected_exit_code": 2,
+ "log": "/private/tmp/communitymech-batch86/baseline-just-network.log",
+ "sha256": "8595db43420d3f0a01c57acd6ad733a531a72e962486d20b4e1c2840dda55bff",
+ "output_tail": "uv run communitymech audit-network --json\nerror: Failed to spawn: `communitymech`\n Caused by: No such file or directory (os error 2)\nerror: recipe `audit-network-json` failed on line 574 with exit code 2\n"
+ },
+ {
+ "name": "network",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "communitymech.cli",
+ "audit-network",
+ "--json"
+ ],
+ "exit_code": 1,
+ "expected_exit_code": 1,
+ "log": "/private/tmp/communitymech-batch86/baseline-network.log",
+ "sha256": "b29c775d4f7bfde5d562cffc9e3d2405cd9e015df8f886eba46d9752c17c623a",
+ "output_tail": " \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Staphylococcus capitis | K1-2-2-23 | ISS, V2A Steel | DSM 111179 | Sobisch et al., 2019 | GCA_025272695 | TSYB/TSYA | 37 \\u00b0C | 16\\u201324 h\",\n \"explanation\": \"Identifies S. capitis K1-2-2-23 as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Staphylococcus capitis K1-2-2-23' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Streptococcus halotolerans HTS9T\",\n \"taxon_id\": \"NCBITaxon:1814128\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Streptococcus halotolerans HTS9T\",\n \"term\": {\n \"id\": \"NCBITaxon:1814128\",\n \"label\": \"Streptococcus halotolerans\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the S. halotolerans type strain as a biosafety-level-1 representative.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"HTS9T\",\n \"genome_accession\": \"GCA_001598035\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"101996\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Streptococcus halotolerans | HTS9 T | Respiratory Tract of Marmota himalayana | DSM 101996 T | Niu et al., 2016 | GCA_001598035 | 2xLB, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies S. halotolerans HTS9T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Streptococcus halotolerans HTS9T' has no interactions\"\n }\n ]\n}\n"
+ },
+ {
+ "name": "downstream",
+ "command": [
+ "rg",
+ "--no-ignore",
+ "--hidden",
+ "-n",
+ "downstream:",
+ "kb/communities",
+ "data/isolates",
+ "--glob",
+ "*.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_code": 0,
+ "log": "/private/tmp/communitymech-batch86/baseline-downstream.log",
+ "sha256": "5041d5136b0d4c56386bc658bdfd88bcc3b156d02f84d86a9c1be489cc0893f1",
+ "output_tail": "arine_Snow_Coculture.yaml:232: downstream:\nkb/communities/Clostridium_Thermocellum_Saccharoperbutylacetonicum_Cellulosic_Butanol_Coculture.yaml:147: downstream:\nkb/communities/Clostridium_Thermocellum_Saccharoperbutylacetonicum_Cellulosic_Butanol_Coculture.yaml:222: downstream:\nkb/communities/Shewanella_Streptococcus_Starch_Microbial_Fuel_Cell.yaml:140: downstream:\nkb/communities/Shewanella_Streptococcus_Starch_Microbial_Fuel_Cell.yaml:221: downstream:\nkb/communities/Parachlorella_Saccharomyces_Mutualistic_Coculture.yaml:83: downstream:\nkb/communities/Parachlorella_Saccharomyces_Mutualistic_Coculture.yaml:122: downstream:\nkb/communities/SO3_BS3_Lithium_Battery_Bioleaching_Consortium.yaml:141: downstream:\nkb/communities/Deepwater_Horizon_Deep_Sea_Oil_Plume_Succession.yaml:197: downstream:\nkb/communities/Deepwater_Horizon_Deep_Sea_Oil_Plume_Succession.yaml:241: downstream:\nkb/communities/Chromium_Sulfur_Reduction_Enrichment.yaml:159: downstream:\nkb/communities/Chromium_Sulfur_Reduction_Enrichment.yaml:200: downstream:\nkb/communities/BioModels_MODEL2204300001_Kefir_Community_Model.yaml:203: downstream:\nkb/communities/Dual_Bacillus_coagulans_Pseudomonas_putida_Lactic_Acid_Coculture.yaml:134: downstream:\nkb/communities/Dual_Bacillus_coagulans_Pseudomonas_putida_Lactic_Acid_Coculture.yaml:189: downstream:\nkb/communities/Moss_Microbe_Complex_Regolith_Biofertilizer.yaml:167: downstream:\nkb/communities/Cable_Bacteria_Photosynthetic_Biofilm_Sediment.yaml:80: downstream:\nkb/communities/Cable_Bacteria_Photosynthetic_Biofilm_Sediment.yaml:117: downstream:\nkb/communities/High_Ammonia_Biogas_0B_Butyrate_Oxidizing_Enrichment.yaml:234: downstream:\nkb/communities/Pepper_Phytophthora_SynCom5.yaml:123: downstream:\nkb/communities/Pepper_Phytophthora_SynCom5.yaml:150: downstream:\nkb/communities/Human_Gut_FourMember_Proteome_Complementarity_Consortium.yaml:153: downstream:\nkb/communities/Human_Gut_FourMember_Proteome_Complementarity_Consortium.yaml:218: downstream:\n"
+ }
+ ],
+ "baseline_sha256": "3ab1fbc81fa5b01477051e2316dcac36fd68d6f9b41d9700bd8b8be39757f7ec"
+ },
+ "reference_validator_caveat": "Four full-record reference validators exit0. CLI Total checks counts issues, not executed checks. Eleven graph and eight discussion quotations independently match primary sources and cache text; matching is not scientific entailment. Vanadium FigureS2 is a separately labeled public supplement, not main-text access. Other source limits remain explicit."
+}
diff --git a/tests/test_causal_review_batch86.py b/tests/test_causal_review_batch86.py
new file mode 100644
index 000000000..09f7a0c1d
--- /dev/null
+++ b/tests/test_causal_review_batch86.py
@@ -0,0 +1,146 @@
+"""Preserve positive outcomes while bounding system identity and mechanism claims."""
+
+import hashlib
+from pathlib import Path
+
+import yaml
+
+ROOT = Path(__file__).resolve().parents[1]
+LEDGER = ROOT / "reports/causal_graph_review/decisions/20261007-four-records-batch86.yaml"
+
+
+def records():
+ ledger = yaml.safe_load(LEDGER.read_text())
+ rows = ledger["records"]
+ return ledger, rows, [yaml.safe_load((ROOT / r["path"]).read_text()) for r in rows]
+
+
+def test_pleuromutilin_keeps_positive_degradation_and_proposed_products():
+ _, rows, docs = records()
+ nodes = docs[0]["ecological_interactions"]
+ assert len(nodes) == 2 and "91.97%" in nodes[0]["description"]
+ assert nodes[1]["description"].startswith("HYPOTHESIZED:")
+ assert "Differential abundance" in nodes[1]["description"]
+ assert all("interaction_type" not in n and "downstream" not in n for n in nodes)
+ assert all(len(n["participating_taxa"]) == 5 for n in nodes)
+ assert len(rows[0]["removed_node_decisions"]) == 4
+
+
+def test_pleuromutilin_context_and_missing_topology_remain_explicit():
+ _, rows, docs = records()
+ text = docs[0]["discussions"][-1]["rationale"]
+ assert "Natural En4" in text and "no inhibition zones" in text
+ assert "W12" in text and "W10" in text
+ assert rows[0]["status"] == "needs_research" and 1715 in rows[0]["issues"]
+ assert "no new structure is added" in text
+
+
+def test_vanadium_preserves_controlled_precipitation_at_enrichment_scope():
+ _, rows, docs = records()
+ reduction, precipitation = docs[1]["ecological_interactions"]
+ assert reduction["downstream"][0]["target"] == precipitation["name"]
+ assert "autoclaved" in precipitation["description"]
+ assert "no-vanadate controls" in precipitation["description"]
+ assert "6 mM acetate and 1.5 mM vanadate" in reduction["description"]
+ assert len(rows[1]["removed_node_decisions"]) == 2
+ assert len(rows[1]["removed_edge_decisions"]) == 1
+ assert "which formed VIV precipitates" in precipitation["evidence"][0]["snippet"]
+
+
+def test_vanadium_does_not_credit_unsupported_canonical_partners():
+ _, _, docs = records()
+ nodes = docs[1]["ecological_interactions"]
+ assert len(docs[1]["taxonomy"]) == 4
+ for n in nodes:
+ assert n["scope"] == "COMMUNITY_LEVEL"
+ assert len(n["participating_taxa"]) == 1
+ assert n["participating_taxa"][0]["term"]["id"] == "NCBITaxon:52972"
+ assert not ({"source_taxon", "target_taxon", "interaction_type", "metabolites"} & n.keys())
+ assert nodes[0]["evidence"][1]["evidence_source"] == "COMPUTATIONAL"
+ assert "PARTIAL" in nodes[0]["description"]
+ text = docs[1]["discussions"][-1]["rationale"]
+ assert "Hunan" in text and "Acidithiobacillus ferrooxidans" in text
+ assert "#1716" in text
+
+
+def test_populus_keeps_two_qualified_biological_directions():
+ _, rows, docs = records()
+ nodes = docs[2]["ecological_interactions"]
+ assert len(nodes) == 3 and len(rows[2]["removed_node_decisions"]) == 2
+ assert len(rows[2]["removed_edge_decisions"]) == 3
+ for n in nodes[:2]:
+ assert n["downstream"][0]["target"] == nodes[2]["name"]
+ assert n["downstream"][0]["description"].startswith("PARTIAL:")
+ assert all(e["evidence_source"] == "IN_VIVO" for n in nodes for e in n["evidence"])
+ assert "alternative" in nodes[2]["description"]
+ assert "biological_processes" not in nodes[1]
+
+
+def test_poultry_mechanism_is_hypothesized_not_niche_partitioning():
+ _, rows, docs = records()
+ nodes = docs[3]["ecological_interactions"]
+ assert len(nodes) == 3 and rows[3]["removed_edge_decisions"] == []
+ assert nodes[0]["description"].startswith("HYPOTHESIZED:")
+ assert all(e["description"].startswith("HYPOTHESIZED:") for e in nodes[0]["downstream"])
+ assert all(len(n["participating_taxa"]) == 3 for n in nodes)
+ assert all("interaction_type" not in n for n in nodes)
+ assert "total mixed-versus-single inoculum volume ambiguous" in nodes[0]["description"]
+ assert "170 mW/m2" in nodes[1]["description"]
+
+
+def test_poultry_cod_discrepancy_is_not_silently_corrected():
+ _, _, docs = records()
+ cod = docs[3]["ecological_interactions"][2]
+ assert "2150-to-436" in cod["description"] and "2150-to-335" in cod["description"]
+ assert "Do not silently swap" in cod["description"]
+ assert "biomass assimilation and abiotic changes" in cod["description"]
+ assert docs[3]["environmental_factors"][2]["value"] == "84.4"
+
+
+def test_all_nodes_edges_and_anchors_have_dispositions():
+ ledger, rows, docs = records()
+ assert sum(len(r["node_decisions"]) for r in rows) == 10
+ assert sum(len(r["removed_node_decisions"]) for r in rows) == 8
+ assert sum(len(r["edges_before"]) for r in rows) == 11
+ assert sum(len(r["retained_edge_decisions"]) for r in rows) == 5
+ assert sum(len(r["removed_edge_decisions"]) for r in rows) == 6
+ assert ledger["primary_graph_snippet_count"] == 11
+ assert len(ledger["discussion_snippet_checks"]) == 8
+ for row, doc in zip(rows, docs, strict=True):
+ names = {n["name"] for n in doc["ecological_interactions"]}
+ assert names == {n["node"] for n in row["node_decisions"]}
+ assert all(
+ e["target"] in names
+ for n in doc["ecological_interactions"]
+ for e in n.get("downstream", [])
+ )
+ assert all(
+ a.split("#", 1)[1] in names
+ for d in doc["discussions"]
+ for a in d["attaches_to"]
+ if a.startswith("ecological_interactions#")
+ )
+
+
+def test_supplement_cache_has_explicit_not_full_text_provenance():
+ ledger, _, _ = records()
+ assert len(ledger["cache_changes"]) == 1
+ cache = (ROOT / ledger["cache_changes"][0]["path"]).read_text()
+ assert "content_type: abstract_only" in cache
+ assert "Public Supplement Figure S2 (not main-article full text)" in cache
+ assert "Original PDF SHA256:" in cache
+ assert "which formed VIV precipitates" in cache
+
+
+def test_history_and_unfinished_lifecycle_are_explicit():
+ ledger, rows, docs = records()
+ assert not ledger["independent_approval"]
+ assert ledger["issues"] == [1711, 1712, 1713, 1714]
+ assert ledger["unresolved_research_issues"] == [1715]
+ assert ledger["unresolved_non_graph_issues"] == [1716]
+ assert ledger["edison"]["provider_submissions"] == ledger["edison"]["credits_spent"] == 0
+ assert ledger["edison"]["dry_runs"][0]["query_chars"] == 11100
+ for row, doc in zip(rows, docs, strict=True):
+ assert row["curation_events_added"] == len(row["history_files"]) == 1
+ assert doc["curation_history"][-1]["llm_assisted"]
+ assert hashlib.sha256((ROOT / row["path"]).read_bytes()).hexdigest() == row["record_sha256"]
diff --git a/tests/test_participating_taxa.py b/tests/test_participating_taxa.py
index 561e0e753..b8cc7a5d1 100644
--- a/tests/test_participating_taxa.py
+++ b/tests/test_participating_taxa.py
@@ -364,6 +364,9 @@ def test_a_curie_is_ambiguous_where_members_share_an_id(example):
"Phormidium_Alkaline_Consortium.yaml",
"Phenol_Carboxylation_Consortium.yaml",
"Pinus_armandii_Endophytic_Biocontrol_SynCom.yaml",
+ "Pleuromutilin_Degrading_Artificial_Consortium_5_Strain.yaml",
+ "Polaromonas_Vanadium_Reduction_Community.yaml",
+ "Poultry_Wastewater_ThreeStrain_Electroactive_Consortium.yaml",
"Propanotrophic_Chlorinated_Ethene_Cometabolism_Enrichment.yaml",
"Prymnesium_Parvum_B12_Limited_SynCom.yaml",
"Pseudomonas_Acidovorax_Aniline_Degradation_SynCom.yaml",