- Niche partitioning
+ aria-hidden="true" data-symbol="symbolTriangle2"
+ data-color="#929caa"> Other
@@ -718,41 +713,33 @@
Ecological Interactions
Conserved Methane-Cycling Genera Across Wetlands
- NICHE_PARTITIONING
-
MUCC v2.0.0 integrates wetland microbiome and flux datasets to identify conserved methane-cycling genera shared across multiple wetland types.
+
MUCC combines nine wetland sites; five high-emitting marsh and swamp sites share five methanogen and three methanotroph genera under the authors occupancy definition. Core means present in at least one sample at every site in this subset, not present in every sample or a demonstrated stable mutualistic consortium. The canonical whole-community aggregate and Archaea/Bacteria guild participants are contextual placeholders, not all eight resolved genera. Genus occupancy and relative abundance do not establish niche partitioning or metabolic dependence.
PMID:39843444
- - SUPPORT (COMPUTATIONAL)
+ - PARTIAL (COMPUTATIONAL)
"Microorganisms drive methane cycling"
@@ -793,17 +780,20 @@
Evidence
-
Marsh Metabolic Interaction Networks
- NICHE_PARTITIONING
+
Wetland Methanogen Co-occurrence Networks
-
Marsh wetland networks show wetland-specific metabolic interactions, including low methanogen-methanotroph connectivity in high-emitting wetlands.
+
Positive Spearman genus co-occurrence networks used 12 late-season samples per site, four per depth category, at JLA, LA2, OWC, PPR P7 and PPR P8. JLA is a swamp despite shorthand marsh wording. Fewer methanogen-associated nodes and methanogen-methanotroph connections were associated with greater methane flux; whole-community network structure did not show the same relationship. MAG-derived metabolic categories were matched at genus level, providing potential cross-feeding interpretations rather than direct exchange measurements. Shared environmental responses, relative-abundance effects and incomplete genome coverage remain alternatives. Broad canonical guilds do not identify every network member or a directed donor-recipient pair.
PMID:39843444
- - SUPPORT (COMPUTATIONAL)
+ - PARTIAL (COMPUTATIONAL)
"wetland-specific metabolic interactions in marshes"
@@ -854,7 +833,7 @@
Evidence
PMID:39843444
- - SUPPORT (COMPUTATIONAL)
+ - PARTIAL (COMPUTATIONAL)
"low connections between methanogens and methanotrophs in high-emitting wetlands"
@@ -868,14 +847,17 @@
Evidence
Methanoregula Hub Methanogen And Flux Predictor
- SYNTROPHY
-
Methanoregula is identified as a network hub and predictor of methane flux, linking methanogen network structure to wetland methane emissions.
+
Methanoregula was a core network member, and its fraction within methanogens predicted methane flux across nine sites; temperature plus this dominance measure improved the reported fit. These are cross-site associations, not evidence that removing or adding Methanoregula changes flux or that it is an obligate syntrophic hub. OWC MAG/genus transcription supplies an activity proxy, not methane-production flux. Methods describe 2018 transcriptomes and production estimates using 2015 flux/porewater inputs; temporal alignment needs reconciliation before treating the VIP analysis as a matched contemporaneous test. The single canonical participant identifies the focal genus, not its partners.
In the MUCC wetlands, Methanoregula shows functional potential for methylotrophic methanogenesis, highlighting a methane production pathway that can contribute to wetland emissions.
+
Some of 107 dereplicated Methanoregula MAGs encoded candidate methylotrophic machinery for methylated sulfides and methoxylated compounds alongside broadly conserved hydrogenotrophic potential. Genomic annotation, phylogenetic placement and synteny support metabolic potential, not confirmed substrate use, enzyme activity or pathway-specific methane flux in these wetlands. This does not establish methanol use by the curated genus or experimentally demonstrated niche partitioning. Physiological validation is needed to assign the proposed expanded substrate range.
PMID:39843444
- - SUPPORT (COMPUTATIONAL)
+ - PARTIAL (COMPUTATIONAL)
"functional potential for methylotrophic methanogenesis"
@@ -1002,7 +961,7 @@
Evidence
PMID:39843444
- - SUPPORT (COMPUTATIONAL)
+ - PARTIAL (COMPUTATIONAL)
"highlighting the importance of this pathway"
@@ -1117,6 +1076,25 @@
Associated Datasets
+
+
Knowledge gaps & discussions (1)
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which wetland associations correspond to causal metabolic exchange?
+
+
Retain four observations and zero arrows, preserving the prior three workflow-edge removals. Genus co-occurrence and MAG potential do not establish pairwise transfer or obligate syntrophy; flux prediction does not establish a perturbed driver. Validate candidate methylated-sulfide/methoxylated-compound use rather than substituting methanol. Temporal alignment of 2018 expression and 2015 modeled production, transcriptome counts and roster/metadata ambiguities remain under #1574. Complete primary main text read, not original figure pixels, separate supplements, raw data or executable models.
+
+
Attaches to: ecological_interactions#Conserved Methane-Cycling Genera Across Wetlands, ecological_interactions#Wetland Methanogen Co-occurrence Networks, ecological_interactions#Methanoregula Hub Methanogen And Flux Predictor, ecological_interactions#Methylotrophic Methanogenesis Potential
+
+
+
+
+
+
+
@@ -1427,7 +1405,7 @@
Environmental Factors
(function() {
var intId = "interaction:0";
- var intType = "NICHE_PARTITIONING";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1436,12 +1414,6 @@
Niche partitioning
+ aria-hidden="true" data-symbol="symbolTriangle2"
+ data-color="#929caa"> Other
@@ -643,11 +643,23 @@
Ecological Interactions
Cross-fed metabolic byproduct partitioning
CROSS_FEEDING
-
The four MWF001 strains coexisted because they generated and partitioned metabolic byproducts that supported cross-feeding beyond the externally supplied carbon source.
+
PARTIAL - partner spent-media growth and persistence of primary-carbon-source nonusers support byproduct cross-feeding in MWF001. All four strains grew better in partner spent medium than their own, but exact exchanged compounds and donor-recipient fluxes were not chemically resolved. Unchanged stationary OD does not establish complete primary-substrate depletion; the greater-than-10-percent residual-resource exclusion described in Methods applies to simulations, not an equivalent experimental chemical assay. Generic consumer-resource models support coexistence through byproduct availability and differential resource affinities, not exact four-strain pathways. Fresh-medium pair effects were positive or negative depending on partner and condition, so reciprocal benefit is not universal.
PMID:42752228
- - SUPPORT (IN_VITRO)
+ - PARTIAL (IN_VITRO)
"experimental assays and consumer-resource modeling showed that the coexistence was explained by cross-feeding and niche partitioning of metabolic byproducts"
@@ -692,12 +704,23 @@
Evidence
Robust coexistence across simple nutrient environments
- NICHE_PARTITIONING
-
All four members survived eight serial batch transfers across the first 31 single- or paired-resource M9 media tested, despite several media supplying only one carbon source.
+
All four strains remained detectable through eight 72-hour growth-and-dilution cycles in 31 carbon-supplied conditions, including 16 single-resource environments. These finite observations support broad conditional persistence, not asymptotic stability or a measured niche-partitioning mechanism. Additional 5X-malate conditions lost Comamonas after the first transfer; Microbacterium did not persist without carbon. The initial batch panel used 1/100 transfers except 1/10 for citrate and inosine, with the first citrate transfer at 1/100. Separate four-day chemostats on four single carbon sources also retained all four strains. The canonical participants preserve the source roster and prior unresolved taxonomic mappings, not independently recertified identities.
+ KNOWLEDGE_GAP
+ OPEN
+ How strongly does byproduct partitioning support the observed coexistence?
+
+
The complete primary text supports considering a PARTIAL arrow from cross-feeding/byproduct partitioning to coexistence, with generic-model, residual-substrate and exact-metabolite limits. This new causal structure is tracked in #1575: the free one-community Edison causal dry run passed, but the paid run and report review are not complete. Keep needs_research rather than calling the sparse graph complete. Preserve the existing exact-byproduct gap and #1127/#1128 safeguards. Protocol and source inconsistencies remain under #1574. Original figure pixels, separate supplements, raw data and executable models were not audited.
+
+
Attaches to: ecological_interactions#Cross-fed metabolic byproduct partitioning, ecological_interactions#Robust coexistence across simple nutrient environments
Syntrophy
+ aria-hidden="true" data-symbol="symbolTriangle2"
+ data-color="#929caa"> Other
@@ -771,13 +771,23 @@
Ecological Interactions
Magnetite-enhanced methanogenesis under sulfate stress
- SYNTROPHY
-
Adding 10 g/L magnetite to the 0.6 g/L sulfate condition relieved the sulfate-associated methane-production penalty, reduced sulfide stress through precipitation, and increased CH4 production by 19% relative to the sulfate-only treatment without eliminating sulfate-reducer activity.
-
+
At 0.6 g/L sulfate, 10 g/L magnetite increased cumulative methane by 19% relative to the sulfate-only treatment in five-day batch assays, without reducing sulfate consumption. This is partial improvement, not full sulfate-free recovery or rescue at 1.2 g/L sulfate. Separate abiotic tests showed sulfide removal and sulfur retained on magnetite, but elemental analysis did not resolve sulfur species and no abiotic hydrogen accumulation was detected. These results support toxicity mitigation as a contributing interpretation; they do not isolate its mediation of the methane response or demonstrate syntrophy or direct interspecies electron transfer. The four guilds identify an incomplete community context, not all organisms contributing to the bulk endpoints.
Genome-scale metabolic models for the representative methanogen, SRB, homoacetogen, and SAOB MAGs supported acetate turnover in which the homoacetogen consumes H2 and CO2 to secrete acetate, and acetate is then oxidized back to H2 and CO2 by SAOB or used by SRB as an electron donor for sulfate reduction.
-
+
HYPOTHESIZED - condition-specific four-member GEMs predict acetate-centered exchange: a homoacetogen uses H2/CO2 and secretes acetate, a syntrophic acetate oxidizer returns H2/CO2, and a putative sulfate reducer oxidizes acetate while reducing sulfate, with the shared pool supporting hydrogenotrophic methanogenesis. Representatives are Methanoculleus DTU8, Halopseudomonas DTU25, Limnochordia DTU38 and Dethiobacteria DTU36, not every MAG in the four canonical guild placeholders. Models were gap-filled and curated for expected roles, constrained by measured reactor outputs, and analyzed using MICOM cooperative trade-off 0.7 and flux-space sampling. Agreement is stoichiometric feasibility under assumptions, not independent validation, measured partner flux or demonstrated DIET. One biological replicate per sequenced condition and relative MAG abundances cannot establish replicated absolute guild growth.
@@ -967,8 +976,7 @@
Evidence
Model-predicted amino-acid and organic-acid exchange
CROSS_FEEDING
-
Flux-space sampling of the community GEMs predicted exchange of glucogenic amino acids and short-chain organic acids among the four modeled guilds, with the homoacetogen, SAOB, and methanogen acting as major exchange hubs and the SRB predicted to import several amino acids.
-
+
HYPOTHESIZED - flux-space sampling of the four representative GEMs predicts exchange of amino acids and organic acids, with the homoacetogen, acetate oxidizer and methanogen serving as modeled hubs and the putative sulfate reducer importing multiple amino acids. The reported heatmaps select mean exchange fluxes above 0.1 mmol/gDW/hour from feasible solutions; these are model summaries, not extracellular metabolomics or traced donor-recipient rates. Multiple solutions satisfy the imposed constraints, and regulation, protein capacity and kinetics are not resolved. These exchanges could support alternative metabolic routes, but actual necessity, universal mutualism and specific partner transfers remain untested.
@@ -1075,7 +1083,7 @@
Associated Datasets
-
Knowledge gaps & discussions (1)
+
Knowledge gaps & discussions (2)
@@ -1114,6 +1122,21 @@
+
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which processes mediate magnetite-associated methane improvement?
+
+
Keep zero arrows and preserve #914 backward-edge removal. Separate abiotic sulfide removal, replicated bulk methane response and single-replicate compositional metagenomics. Feasibility of role-curated and output-constrained GEMs does not independently verify partner flux. Retain the existing direct-DIET knowledge gap, #913 putative-SRB caveats and #915 restriction to MAGN_0.6. Myxococcota DTU51 lacks sulfate-reduction genes; do not silently promote it to a validated reducer. Source metadata and identity limits remain under #1574. Complete primary main text and figure captions read, not original figure pixels, separate supplements, raw data or executable models.
+
+
Attaches to: ecological_interactions#Magnetite-enhanced methanogenesis under sulfate stress, ecological_interactions#Acetate-centered four-guild redox cycling, ecological_interactions#Model-predicted amino-acid and organic-acid exchange
+
+
+
+
@@ -1508,7 +1531,7 @@
Evidence
(function() {
var intId = "interaction:0";
- var intType = "SYNTROPHY";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1542,6 +1565,23 @@
Evidence
+ var participantKeys = [
+
+ "Methanoculleus methanogenic MAGs",
+
+ "putative sulfate-reducing MAGs",
+
+ "Limnochordia homoacetogenic MAGs",
+
+ "Dethiobacteria syntrophic acetate-oxidizing MAGs"
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
+
})();
(function() {
diff --git a/history/records/MUCC_Freshwater_Wetland_Methane_Network_Community/2026-10-06T230847Z-codex-95d09c.yaml b/history/records/MUCC_Freshwater_Wetland_Methane_Network_Community/2026-10-06T230847Z-codex-95d09c.yaml
new file mode 100644
index 000000000..7fef384fd
--- /dev/null
+++ b/history/records/MUCC_Freshwater_Wetland_Methane_Network_Community/2026-10-06T230847Z-codex-95d09c.yaml
@@ -0,0 +1,25 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/MUCC_Freshwater_Wetland_Methane_Network_Community.yaml
+ slug: MUCC_Freshwater_Wetland_Methane_Network_Community
+session:
+ id: 2026-10-06T230847Z-codex-95d09c
+ timestamp: '2026-10-06T23:08:47Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1571
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Bound wetland co-occurrence and Methanoregula predictions to observational and
+ genomic evidence.
+ details: Source-based self-adversarial review. reports/causal_graph_review/decisions/20261006-wetland-crossfeeding-batch66.yaml
diff --git a/history/records/MWF001_FourSpecies_CrossFeeding_Consortium/2026-10-06T230847Z-codex-73e39c.yaml b/history/records/MWF001_FourSpecies_CrossFeeding_Consortium/2026-10-06T230847Z-codex-73e39c.yaml
new file mode 100644
index 000000000..9d10935b7
--- /dev/null
+++ b/history/records/MWF001_FourSpecies_CrossFeeding_Consortium/2026-10-06T230847Z-codex-73e39c.yaml
@@ -0,0 +1,25 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/MWF001_FourSpecies_CrossFeeding_Consortium.yaml
+ slug: MWF001_FourSpecies_CrossFeeding_Consortium
+session:
+ id: 2026-10-06T230847Z-codex-73e39c
+ timestamp: '2026-10-06T23:08:47Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1572
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Qualify MWF001 cross-feeding and finite coexistence; keep causal extension research
+ open.
+ details: Source-based self-adversarial review. reports/causal_graph_review/decisions/20261006-wetland-crossfeeding-batch66.yaml
diff --git a/history/records/Magnetite_Sulfate_Stress_Anaerobic_Microbiome/2026-10-06T230847Z-codex-cac4a6.yaml b/history/records/Magnetite_Sulfate_Stress_Anaerobic_Microbiome/2026-10-06T230847Z-codex-cac4a6.yaml
new file mode 100644
index 000000000..c4630b122
--- /dev/null
+++ b/history/records/Magnetite_Sulfate_Stress_Anaerobic_Microbiome/2026-10-06T230847Z-codex-cac4a6.yaml
@@ -0,0 +1,25 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Magnetite_Sulfate_Stress_Anaerobic_Microbiome.yaml
+ slug: Magnetite_Sulfate_Stress_Anaerobic_Microbiome
+session:
+ id: 2026-10-06T230847Z-codex-cac4a6
+ timestamp: '2026-10-06T23:08:47Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1573
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Separate magnetite methane response from unvalidated DIET and constrained model
+ flux.
+ details: Source-based self-adversarial review. reports/causal_graph_review/decisions/20261006-wetland-crossfeeding-batch66.yaml
diff --git a/kb/communities/MUCC_Freshwater_Wetland_Methane_Network_Community.yaml b/kb/communities/MUCC_Freshwater_Wetland_Methane_Network_Community.yaml
index 42b1028ff..9d60fa37b 100644
--- a/kb/communities/MUCC_Freshwater_Wetland_Methane_Network_Community.yaml
+++ b/kb/communities/MUCC_Freshwater_Wetland_Methane_Network_Community.yaml
@@ -148,141 +148,147 @@ taxonomy:
explanation: Supports methanotrophs as a network-resolved guild.
ecological_interactions:
- name: Conserved Methane-Cycling Genera Across Wetlands
- description: MUCC v2.0.0 integrates wetland microbiome and flux datasets to
- identify conserved methane-cycling genera shared across multiple wetland
- types.
- interaction_type: NICHE_PARTITIONING
+ description: MUCC combines nine wetland sites; five high-emitting marsh and swamp sites share five methanogen
+ and three methanotroph genera under the authors occupancy definition. Core means present in at least one sample
+ at every site in this subset, not present in every sample or a demonstrated stable mutualistic consortium. The
+ canonical whole-community aggregate and Archaea/Bacteria guild participants are contextual placeholders, not
+ all eight resolved genera. Genus occupancy and relative abundance do not establish niche partitioning or metabolic
+ dependence.
scope: COMMUNITY_LEVEL
metabolites:
- preferred_term: methane
term:
id: CHEBI:16183
label: methane
- biological_processes:
- - preferred_term: methanogenesis
- term:
- id: GO:0015948
- label: methanogenesis
- - preferred_term: methane metabolic process
- term:
- id: GO:0015947
- label: methane metabolic process
+ notes: Methane-cycle context, not measured partner-to-partner exchange or taxon-specific production flux.
evidence:
- reference: PMID:39843444
supports: SUPPORT
evidence_source: COMPUTATIONAL
snippet: identify eight methane-cycling genera shared across wetlands
- explanation: Supports conserved methane-cycling genera across the wetland synthesis.
+ explanation: Supports the eight core genera; the primary Results locate this core analysis in five marsh/swamp
+ sites, not universal occupancy across every sample or all nine sites.
- reference: PMID:39843444
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: COMPUTATIONAL
snippet: Microorganisms drive methane cycling
- explanation: Supports the microbial basis of wetland methane cycling.
-- name: Marsh Metabolic Interaction Networks
- description: Marsh wetland networks show wetland-specific metabolic
- interactions, including low methanogen-methanotroph connectivity in
- high-emitting wetlands.
- interaction_type: NICHE_PARTITIONING
- scope: COMMUNITY_LEVEL
- source_taxon:
- preferred_term: MUCC wetland methanogens
+ explanation: General methane-cycle context only; this short statement does not establish a particular interaction
+ mechanism.
+ participating_taxa:
+ - preferred_term: MUCC freshwater wetland microbial community
+ term:
+ id: NCBITaxon:131567
+ label: cellular organisms
+ - preferred_term: MUCC wetland methanogens
term:
id: NCBITaxon:2157
label: Archaea
- target_taxon:
- preferred_term: MUCC wetland methanotrophs
+ - preferred_term: MUCC wetland methanotrophs
term:
id: NCBITaxon:2
label: Bacteria
+- name: Wetland Methanogen Co-occurrence Networks
+ description: Positive Spearman genus co-occurrence networks used 12 late-season samples per site, four per depth
+ category, at JLA, LA2, OWC, PPR P7 and PPR P8. JLA is a swamp despite shorthand marsh wording. Fewer methanogen-associated
+ nodes and methanogen-methanotroph connections were associated with greater methane flux; whole-community network
+ structure did not show the same relationship. MAG-derived metabolic categories were matched at genus level,
+ providing potential cross-feeding interpretations rather than direct exchange measurements. Shared environmental
+ responses, relative-abundance effects and incomplete genome coverage remain alternatives. Broad canonical guilds
+ do not identify every network member or a directed donor-recipient pair.
+ scope: COMMUNITY_LEVEL
metabolites:
- preferred_term: methane
term:
id: CHEBI:16183
label: methane
- biological_processes:
- - preferred_term: methane metabolic process
- term:
- id: GO:0015947
- label: methane metabolic process
+ notes: Methane-cycle context, not measured partner-to-partner exchange or taxon-specific production flux.
evidence:
- reference: PMID:39843444
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: COMPUTATIONAL
snippet: wetland-specific metabolic interactions in marshes
- explanation: Supports marsh-specific metabolic interaction networks.
+ explanation: Supports computed co-occurrence patterns and the authors metabolic interpretation, not perturbed
+ pairwise causality or directly observed substrate transfer.
- reference: PMID:39843444
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: COMPUTATIONAL
snippet: low connections between methanogens and methanotrophs in high-emitting wetlands
- explanation: Supports reduced methanogen-methanotroph connectivity in high-emitting wetlands.
+ explanation: Supports computed co-occurrence patterns and the authors metabolic interpretation, not perturbed
+ pairwise causality or directly observed substrate transfer.
+ participating_taxa:
+ - preferred_term: MUCC wetland methanogens
+ term:
+ id: NCBITaxon:2157
+ label: Archaea
+ - preferred_term: MUCC wetland methanotrophs
+ term:
+ id: NCBITaxon:2
+ label: Bacteria
- name: Methanoregula Hub Methanogen And Flux Predictor
- description: Methanoregula is identified as a network hub and predictor of
- methane flux, linking methanogen network structure to wetland methane
- emissions.
- interaction_type: SYNTROPHY
+ description: Methanoregula was a core network member, and its fraction within methanogens predicted methane flux
+ across nine sites; temperature plus this dominance measure improved the reported fit. These are cross-site associations,
+ not evidence that removing or adding Methanoregula changes flux or that it is an obligate syntrophic hub. OWC
+ MAG/genus transcription supplies an activity proxy, not methane-production flux. Methods describe 2018 transcriptomes
+ and production estimates using 2015 flux/porewater inputs; temporal alignment needs reconciliation before treating
+ the VIP analysis as a matched contemporaneous test. The single canonical participant identifies the focal genus,
+ not its partners.
scope: COMMUNITY_LEVEL
- source_taxon:
- preferred_term: Methanoregula
- term:
- id: NCBITaxon:395331
- label: Methanoregula
metabolites:
- preferred_term: methane
term:
id: CHEBI:16183
label: methane
- biological_processes:
- - preferred_term: methanogenesis
- term:
- id: GO:0015948
- label: methanogenesis
+ notes: Methane-cycle context, not measured partner-to-partner exchange or taxon-specific production flux.
evidence:
- reference: PMID:39843444
supports: SUPPORT
evidence_source: COMPUTATIONAL
snippet: Methanoregula emerged as a hub methanogen across networks
- explanation: Supports Methanoregula as a hub methanogen.
+ explanation: Supports a network/predictor association, not demonstrated keystone necessity, syntrophy or a selectively
+ established contribution to methane flux.
- reference: PMID:39843444
supports: SUPPORT
evidence_source: COMPUTATIONAL
snippet: strong predictor of methane flux
- explanation: Supports the Methanoregula-methane flux relationship.
-- name: Methylotrophic Methanogenesis Potential
- description: In the MUCC wetlands, Methanoregula shows functional potential
- for methylotrophic methanogenesis, highlighting a methane production
- pathway that can contribute to wetland emissions.
- interaction_type: NICHE_PARTITIONING
- scope: COMMUNITY_LEVEL
- source_taxon:
- preferred_term: Methanoregula
+ explanation: Supports a network/predictor association, not demonstrated keystone necessity, syntrophy or a selectively
+ established contribution to methane flux.
+ participating_taxa:
+ - preferred_term: Methanoregula
term:
id: NCBITaxon:395331
label: Methanoregula
+- name: Methylotrophic Methanogenesis Potential
+ description: Some of 107 dereplicated Methanoregula MAGs encoded candidate methylotrophic machinery for methylated
+ sulfides and methoxylated compounds alongside broadly conserved hydrogenotrophic potential. Genomic annotation,
+ phylogenetic placement and synteny support metabolic potential, not confirmed substrate use, enzyme activity
+ or pathway-specific methane flux in these wetlands. This does not establish methanol use by the curated genus
+ or experimentally demonstrated niche partitioning. Physiological validation is needed to assign the proposed
+ expanded substrate range.
+ scope: COMMUNITY_LEVEL
metabolites:
- preferred_term: methane
term:
id: CHEBI:16183
label: methane
- - preferred_term: methanol
- term:
- id: CHEBI:17790
- label: methanol
- biological_processes:
- - preferred_term: methanogenesis
- term:
- id: GO:0015948
- label: methanogenesis
+ notes: Methane-cycle context, not measured partner-to-partner exchange or taxon-specific production flux.
evidence:
- reference: PMID:39843444
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: COMPUTATIONAL
snippet: functional potential for methylotrophic methanogenesis
- explanation: Supports methylotrophic methanogenesis potential in Methanoregula.
+ explanation: Supports candidate genomic methylotrophic potential, not measured methanol use or a quantified
+ contribution to methane production.
- reference: PMID:39843444
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: COMPUTATIONAL
snippet: highlighting the importance of this pathway
- explanation: Supports the pathway relevance for these wetlands.
+ explanation: Supports candidate genomic methylotrophic potential, not measured methanol use or a quantified
+ contribution to methane production.
+ participating_taxa:
+ - preferred_term: Methanoregula
+ term:
+ id: NCBITaxon:395331
+ label: Methanoregula
environmental_factors:
- name: Wetland type
value: marsh, swamp, fen, and bog
@@ -426,7 +432,30 @@ curation_history:
- timestamp: '2026-10-02T06:10:22Z'
curator: codex
action: REVIEW_CAUSAL_GRAPH
- changes: Removed three downstream edges that linked conserved-genera, network,
- Methanoregula hub, and methylotrophic-potential findings as analysis
- provenance instead of ecological causal steps.
+ changes: Removed three downstream edges that linked conserved-genera, network, Methanoregula hub, and methylotrophic-potential
+ findings as analysis provenance instead of ecological causal steps.
+ llm_assisted: true
+- timestamp: '2026-10-06T23:08:45Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: 'Bound wetland co-occurrence and Methanoregula predictions to observational and genomic evidence. Issue
+ #1571; reports/causal_graph_review/decisions/20261006-wetland-crossfeeding-batch66.yaml'
llm_assisted: true
+discussions:
+- discussion_id: mucc_association_and_substrate_limits
+ prompt: Which wetland associations correspond to causal metabolic exchange?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Conserved Methane-Cycling Genera Across Wetlands
+ - ecological_interactions#Wetland Methanogen Co-occurrence Networks
+ - ecological_interactions#Methanoregula Hub Methanogen And Flux Predictor
+ - ecological_interactions#Methylotrophic Methanogenesis Potential
+ rationale: 'Retain four observations and zero arrows, preserving the prior three workflow-edge removals. Genus
+ co-occurrence and MAG potential do not establish pairwise transfer or obligate syntrophy; flux prediction does
+ not establish a perturbed driver. Validate candidate methylated-sulfide/methoxylated-compound use rather than
+ substituting methanol. Temporal alignment of 2018 expression and 2015 modeled production, transcriptome counts
+ and roster/metadata ambiguities remain under #1574. Complete primary main text read, not original figure pixels,
+ separate supplements, raw data or executable models.'
+ posed_by: codex
+ posed_date: '2026-10-06'
diff --git a/kb/communities/MWF001_FourSpecies_CrossFeeding_Consortium.yaml b/kb/communities/MWF001_FourSpecies_CrossFeeding_Consortium.yaml
index 2f39345c6..a6aad2caa 100644
--- a/kb/communities/MWF001_FourSpecies_CrossFeeding_Consortium.yaml
+++ b/kb/communities/MWF001_FourSpecies_CrossFeeding_Consortium.yaml
@@ -125,36 +125,83 @@ taxonomy:
explanation: Names Ochrobactrum anthropi MWF001 as one of the four MWF001 consortium members.
ecological_interactions:
- name: Cross-fed metabolic byproduct partitioning
- description: The four MWF001 strains coexisted because they generated and partitioned metabolic byproducts that supported
- cross-feeding beyond the externally supplied carbon source.
- interaction_type: CROSS_FEEDING
+ description: PARTIAL - partner spent-media growth and persistence of primary-carbon-source nonusers support byproduct
+ cross-feeding in MWF001. All four strains grew better in partner spent medium than their own, but exact exchanged
+ compounds and donor-recipient fluxes were not chemically resolved. Unchanged stationary OD does not establish
+ complete primary-substrate depletion; the greater-than-10-percent residual-resource exclusion described in Methods
+ applies to simulations, not an equivalent experimental chemical assay. Generic consumer-resource models support
+ coexistence through byproduct availability and differential resource affinities, not exact four-strain pathways.
+ Fresh-medium pair effects were positive or negative depending on partner and condition, so reciprocal benefit
+ is not universal.
scope: COMMUNITY_LEVEL
evidence:
- reference: PMID:42752228
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: IN_VITRO
snippet: experimental assays and consumer-resource modeling showed that the coexistence was explained by cross-feeding
and niche partitioning of metabolic byproducts
- explanation: Supports cross-feeding of metabolic byproducts and niche partitioning as the mechanistic explanation for
- coexistence.
+ explanation: Supports the integrated cross-feeding interpretation, with experimental spent-media growth and
+ generic-model evidence; it does not identify exact compounds or selectively isolate the mechanism in all conditions.
- reference: PMID:42752228
supports: SUPPORT
evidence_source: COMPUTATIONAL
- snippet: Our CRM simulates growth, resource depletion, and byproduct accumulation as a function of species' resource affinities,
- maximum uptake rates, and metabolite release profiles and thus captures both resource competition and cross-feeding
- explanation: Supports the consumer-resource modeling component used to interpret byproduct cross-feeding and niche partitioning.
+ snippet: Our CRM simulates growth, resource depletion, and byproduct accumulation as a function of species'
+ resource affinities, maximum uptake rates, and metabolite release profiles and thus captures both resource
+ competition and cross-feeding
+ explanation: Supports the generic consumer-resource model components, not a genome-resolved model or measured
+ resource affinities for the four exact strains.
+ participating_taxa:
+ - preferred_term: Agrobacterium tumefaciens MWF001
+ term:
+ id: NCBITaxon:358
+ label: Agrobacterium tumefaciens
+ - preferred_term: Comamonas testosteroni MWF001
+ term:
+ id: NCBITaxon:285
+ label: Comamonas testosteroni
+ - preferred_term: Microbacterium liquefaciens MWF001
+ term:
+ id: NCBITaxon:33918
+ label: Microbacterium maritypicum
+ - preferred_term: Ochrobactrum anthropi MWF001
+ term:
+ id: NCBITaxon:529
+ label: Brucella anthropi
+ interaction_type: CROSS_FEEDING
- name: Robust coexistence across simple nutrient environments
- description: All four members survived eight serial batch transfers across the first 31 single- or paired-resource M9 media
- tested, despite several media supplying only one carbon source.
- interaction_type: NICHE_PARTITIONING
+ description: All four strains remained detectable through eight 72-hour growth-and-dilution cycles in 31 carbon-supplied
+ conditions, including 16 single-resource environments. These finite observations support broad conditional persistence,
+ not asymptotic stability or a measured niche-partitioning mechanism. Additional 5X-malate conditions lost Comamonas
+ after the first transfer; Microbacterium did not persist without carbon. The initial batch panel used 1/100
+ transfers except 1/10 for citrate and inosine, with the first citrate transfer at 1/100. Separate four-day chemostats
+ on four single carbon sources also retained all four strains. The canonical participants preserve the source
+ roster and prior unresolved taxonomic mappings, not independently recertified identities.
scope: COMMUNITY_LEVEL
evidence:
- reference: PMID:42752228
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: Across 31 simple nutrient conditions, including 16 single-resource environments, all four species survived and
- coexisted over eight growth-and-dilution cycles.
- explanation: Supports robust persistence of all four strains through serial batch assembly.
+ snippet: Across 31 simple nutrient conditions, including 16 single-resource environments, all four species survived
+ and coexisted over eight growth-and-dilution cycles.
+ explanation: Supports finite persistence in the initial 31 carbon-supplied conditions; no-carbon and additional
+ high-malate exceptions prevent a universal coexistence claim.
+ participating_taxa:
+ - preferred_term: Agrobacterium tumefaciens MWF001
+ term:
+ id: NCBITaxon:358
+ label: Agrobacterium tumefaciens
+ - preferred_term: Comamonas testosteroni MWF001
+ term:
+ id: NCBITaxon:285
+ label: Comamonas testosteroni
+ - preferred_term: Microbacterium liquefaciens MWF001
+ term:
+ id: NCBITaxon:33918
+ label: Microbacterium maritypicum
+ - preferred_term: Ochrobactrum anthropi MWF001
+ term:
+ id: NCBITaxon:529
+ label: Brucella anthropi
environmental_factors:
- name: Normalized carbon supply
value: '90'
@@ -303,11 +350,27 @@ discussions:
status: OPEN
attaches_to:
- ecological_interactions#Cross-fed metabolic byproduct partitioning
- rationale: The paper supports cross-feeding of partner-derived spent-media metabolites and uses a consumer-resource model
- to interpret the four-species coexistence, but it explicitly notes the technical challenge of quantifying resource affinities
- for cross-fed metabolites in vitro. No exact exchanged metabolite was therefore asserted in the record.
+ rationale: The paper supports cross-feeding of partner-derived spent-media metabolites and uses a consumer-resource
+ model to interpret the four-species coexistence, but it explicitly notes the technical challenge of quantifying
+ resource affinities for cross-fed metabolites in vitro. No exact exchanged metabolite was therefore asserted
+ in the record.
posed_by: codex
posed_date: '2026-09-26'
+- discussion_id: mwf001_causal_extension_pending
+ prompt: How strongly does byproduct partitioning support the observed coexistence?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Cross-fed metabolic byproduct partitioning
+ - ecological_interactions#Robust coexistence across simple nutrient environments
+ rationale: 'The complete primary text supports considering a PARTIAL arrow from cross-feeding/byproduct partitioning
+ to coexistence, with generic-model, residual-substrate and exact-metabolite limits. This new causal structure
+ is tracked in #1575: the free one-community Edison causal dry run passed, but the paid run and report review
+ are not complete. Keep needs_research rather than calling the sparse graph complete. Preserve the existing exact-byproduct
+ gap and #1127/#1128 safeguards. Protocol and source inconsistencies remain under #1574. Original figure pixels,
+ separate supplements, raw data and executable models were not audited.'
+ posed_by: codex
+ posed_date: '2026-10-06'
metal_relevance: NOT_APPLICABLE
metal_notes: The source strains were isolated from toxic metal-working fluids, but the curated PNAS experiment probed carbon-source
coexistence rather than metal or rare-earth processing.
@@ -315,13 +378,19 @@ curation_history:
- timestamp: '2026-09-26T23:42:21Z'
curator: codex
action: ADD_COMMUNITY_RECORD
- changes: Created CommunityMech:000443 from PMID:42752228 and DOI 10.1073/pnas.2607664123 for the four-member MWF001 synthetic
- bacterial consortium, including exact strain membership, M9 serial batch passaging, chemostat confirmation, cross-feeding
- and niche-partitioning evidence, and a knowledge gap for exact byproduct resolution.
+ changes: Created CommunityMech:000443 from PMID:42752228 and DOI 10.1073/pnas.2607664123 for the four-member MWF001
+ synthetic bacterial consortium, including exact strain membership, M9 serial batch passaging, chemostat confirmation,
+ cross-feeding and niche-partitioning evidence, and a knowledge gap for exact byproduct resolution.
llm_assisted: true
- timestamp: '2026-09-26T23:45:55Z'
curator: codex
action: TIGHTEN_EVIDENCE
- changes: Tightened Zenodo external-resource evidence to quote the exact 10.5281/zenodo.20789145 reference-list DOI after
- adversarial PR review in https://github.com/CultureBotAI/CommunityMech/issues/1127.
+ changes: Tightened Zenodo external-resource evidence to quote the exact 10.5281/zenodo.20789145 reference-list
+ DOI after adversarial PR review in https://github.com/CultureBotAI/CommunityMech/issues/1127.
+ llm_assisted: true
+- timestamp: '2026-10-06T23:08:46Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: 'Qualify MWF001 cross-feeding and finite coexistence; keep causal extension research open. Issue #1572;
+ reports/causal_graph_review/decisions/20261006-wetland-crossfeeding-batch66.yaml'
llm_assisted: true
diff --git a/kb/communities/Magnetite_Sulfate_Stress_Anaerobic_Microbiome.yaml b/kb/communities/Magnetite_Sulfate_Stress_Anaerobic_Microbiome.yaml
index d32797928..8f8d9a4a0 100644
--- a/kb/communities/Magnetite_Sulfate_Stress_Anaerobic_Microbiome.yaml
+++ b/kb/communities/Magnetite_Sulfate_Stress_Anaerobic_Microbiome.yaml
@@ -268,12 +268,13 @@ taxonomy:
measured acetate-oxidation phenotype.
ecological_interactions:
- name: Magnetite-enhanced methanogenesis under sulfate stress
- description: >
- Adding 10 g/L magnetite to the 0.6 g/L sulfate condition relieved the
- sulfate-associated methane-production penalty, reduced sulfide stress
- through precipitation, and increased CH4 production by 19% relative to the
- sulfate-only treatment without eliminating sulfate-reducer activity.
- interaction_type: SYNTROPHY
+ description: At 0.6 g/L sulfate, 10 g/L magnetite increased cumulative methane by 19% relative to the sulfate-only
+ treatment in five-day batch assays, without reducing sulfate consumption. This is partial improvement, not full
+ sulfate-free recovery or rescue at 1.2 g/L sulfate. Separate abiotic tests showed sulfide removal and sulfur
+ retained on magnetite, but elemental analysis did not resolve sulfur species and no abiotic hydrogen accumulation
+ was detected. These results support toxicity mitigation as a contributing interpretation; they do not isolate
+ its mediation of the methane response or demonstrate syntrophy or direct interspecies electron transfer. The
+ four guilds identify an incomplete community context, not all organisms contributing to the bulk endpoints.
scope: COMMUNITY_LEVEL
metabolites:
- preferred_term: sulfate
@@ -301,30 +302,48 @@ ecological_interactions:
- reference: PMID:42231497
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: >
- the presence of magnetite reversed the sulfate-induced inhibition at 0.6
- g/L sulfate, resulting in a 19% increase in CH4 production in MAGN_0.6
- compared to SULF_0.6
- explanation: >
- Supports the 19% methane-production rescue by magnetite at moderate
- sulfate stress.
+ snippet: 'the presence of magnetite reversed the sulfate-induced inhibition at 0.6 g/L sulfate, resulting in
+ a 19% increase in CH4 production in MAGN_0.6 compared to SULF_0.6
+
+ '
+ explanation: Supports the moderate-sulfate methane improvement and sulfide-removal interpretation, not complete
+ rescue, high-sulfate efficacy, demonstrated DIET or selectively established biotic mediation.
- reference: PMID:42231497
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: >
- Magnetite reduced dissolved sulfide species accumulation via
- precipitation and increased methane production by 19% at 0.6 g/L sulfate
- addition without limiting sulfate utilization.
- explanation: >
- Supports the combined sulfide-scavenging and methane-enhancing outcome.
+ snippet: 'Magnetite reduced dissolved sulfide species accumulation via precipitation and increased methane production
+ by 19% at 0.6 g/L sulfate addition without limiting sulfate utilization.
+
+ '
+ explanation: Supports the moderate-sulfate methane improvement and sulfide-removal interpretation, not complete
+ rescue, high-sulfate efficacy, demonstrated DIET or selectively established biotic mediation.
+ participating_taxa:
+ - preferred_term: Methanoculleus methanogenic MAGs
+ term:
+ id: NCBITaxon:45989
+ label: Methanoculleus
+ - preferred_term: putative sulfate-reducing MAGs
+ term:
+ id: NCBITaxon:2
+ label: Bacteria
+ - preferred_term: Limnochordia homoacetogenic MAGs
+ term:
+ id: NCBITaxon:2
+ label: Bacteria
+ - preferred_term: Dethiobacteria syntrophic acetate-oxidizing MAGs
+ term:
+ id: NCBITaxon:2
+ label: Bacteria
- name: Acetate-centered four-guild redox cycling
- description: >
- Genome-scale metabolic models for the representative methanogen, SRB,
- homoacetogen, and SAOB MAGs supported acetate turnover in which the
- homoacetogen consumes H2 and CO2 to secrete acetate, and acetate is then
- oxidized back to H2 and CO2 by SAOB or used by SRB as an electron donor for
- sulfate reduction.
- interaction_type: CROSS_FEEDING
+ description: 'HYPOTHESIZED - condition-specific four-member GEMs predict acetate-centered exchange: a homoacetogen
+ uses H2/CO2 and secretes acetate, a syntrophic acetate oxidizer returns H2/CO2, and a putative sulfate reducer
+ oxidizes acetate while reducing sulfate, with the shared pool supporting hydrogenotrophic methanogenesis. Representatives
+ are Methanoculleus DTU8, Halopseudomonas DTU25, Limnochordia DTU38 and Dethiobacteria DTU36, not every MAG in
+ the four canonical guild placeholders. Models were gap-filled and curated for expected roles, constrained by
+ measured reactor outputs, and analyzed using MICOM cooperative trade-off 0.7 and flux-space sampling. Agreement
+ is stoichiometric feasibility under assumptions, not independent validation, measured partner flux or demonstrated
+ DIET. One biological replicate per sequenced condition and relative MAG abundances cannot establish replicated
+ absolute guild growth.'
scope: COMMUNITY_LEVEL
participating_taxa:
- preferred_term: Methanoculleus methanogenic MAGs
@@ -348,22 +367,32 @@ ecological_interactions:
term:
id: CHEBI:18276
label: dihydrogen
+ notes: Modeled exchange context, not experimentally assigned donor-recipient flux. Computational evidence and
+ model assumptions qualify this annotation.
- preferred_term: carbon dioxide
term:
id: CHEBI:16526
label: carbon dioxide
+ notes: Modeled exchange context, not experimentally assigned donor-recipient flux. Computational evidence and
+ model assumptions qualify this annotation.
- preferred_term: acetate
term:
id: CHEBI:30089
label: acetate
+ notes: Modeled exchange context, not experimentally assigned donor-recipient flux. Computational evidence and
+ model assumptions qualify this annotation.
- preferred_term: sulfate
term:
id: CHEBI:16189
label: sulfate
+ notes: Modeled exchange context, not experimentally assigned donor-recipient flux. Computational evidence and
+ model assumptions qualify this annotation.
- preferred_term: methane
term:
id: CHEBI:16183
label: methane
+ notes: Modeled exchange context, not experimentally assigned donor-recipient flux. Computational evidence and
+ model assumptions qualify this annotation.
biological_processes:
- preferred_term: methanogenesis
term:
@@ -377,31 +406,31 @@ ecological_interactions:
- reference: PMID:42231497
supports: SUPPORT
evidence_source: COMPUTATIONAL
- snippet: >
- The curated GEMs of the individual species were then integrated into
- multispecies community networks, one per condition, i.e., for CTRL,
- SULF_0.6, and MAGN_0.6.
- explanation: >
- Identifies the condition-specific four-member community GEMs behind the
- flux predictions.
+ snippet: 'The curated GEMs of the individual species were then integrated into multispecies community networks,
+ one per condition, i.e., for CTRL, SULF_0.6, and MAGN_0.6.
+
+ '
+ explanation: Supports constrained model feasibility of acetate-centered exchanges, not direct transfer measurements
+ or independent validation of roles assigned during model curation.
- reference: PMID:42231497
supports: SUPPORT
evidence_source: COMPUTATIONAL
- snippet: >
- Solution-space sampling further identified acetate as a central
- intermediate, produced and consumed by multiple guilds, with its turnover
- redistributing carbon and reducing equivalents across the community and
- thereby influencing methane formation.
- explanation: >
- Supports acetate as the shared intermediate in the modeled four-guild
- redox cycle.
-- name: Model-predicted amino-acid and organic-acid exchange
- description: >
- Flux-space sampling of the community GEMs predicted exchange of glucogenic
- amino acids and short-chain organic acids among the four modeled guilds,
- with the homoacetogen, SAOB, and methanogen acting as major exchange hubs
- and the SRB predicted to import several amino acids.
+ snippet: 'Solution-space sampling further identified acetate as a central intermediate, produced and consumed
+ by multiple guilds, with its turnover redistributing carbon and reducing equivalents across the community
+ and thereby influencing methane formation.
+
+ '
+ explanation: Supports constrained model feasibility of acetate-centered exchanges, not direct transfer measurements
+ or independent validation of roles assigned during model curation.
interaction_type: CROSS_FEEDING
+- name: Model-predicted amino-acid and organic-acid exchange
+ description: HYPOTHESIZED - flux-space sampling of the four representative GEMs predicts exchange of amino acids
+ and organic acids, with the homoacetogen, acetate oxidizer and methanogen serving as modeled hubs and the putative
+ sulfate reducer importing multiple amino acids. The reported heatmaps select mean exchange fluxes above 0.1
+ mmol/gDW/hour from feasible solutions; these are model summaries, not extracellular metabolomics or traced donor-recipient
+ rates. Multiple solutions satisfy the imposed constraints, and regulation, protein capacity and kinetics are
+ not resolved. These exchanges could support alternative metabolic routes, but actual necessity, universal mutualism
+ and specific partner transfers remain untested.
scope: COMMUNITY_LEVEL
participating_taxa:
- preferred_term: Methanoculleus methanogenic MAGs
@@ -425,6 +454,8 @@ ecological_interactions:
term:
id: CHEBI:33709
label: amino acid
+ notes: Modeled exchange context, not experimentally assigned donor-recipient flux. Computational evidence and
+ model assumptions qualify this annotation.
biological_processes:
- preferred_term: biological process involved in interspecies interaction between organisms
term:
@@ -434,15 +465,14 @@ ecological_interactions:
- reference: PMID:42231497
supports: SUPPORT
evidence_source: COMPUTATIONAL
- snippet: >
- Flux-space sampling of the community model further provided a
- comprehensive view of feasible interspecies exchange patterns, not easily
- measurable in vivo (Supplementary material 3), suggesting extensive
- exchange of amino acids and short-chain organic acids among the four
- functional groups
- explanation: >
- Supports predicted amino-acid and organic-acid exchange among the modeled
- methanogen, SRB, homoacetogen, and SAOB guilds.
+ snippet: 'Flux-space sampling of the community model further provided a comprehensive view of feasible interspecies
+ exchange patterns, not easily measurable in vivo (Supplementary material 3), suggesting extensive exchange
+ of amino acids and short-chain organic acids among the four functional groups
+
+ '
+ explanation: Supports computationally feasible exchange candidates and their modeled hubs, not experimentally
+ measured amino-acid transfer or obligate dependence.
+ interaction_type: CROSS_FEEDING
environmental_factors:
- name: moderate sulfate stress
value: 0.6
@@ -633,59 +663,82 @@ metal_notes: >
was not cultivated for iron recovery or biomining.
discussions:
- discussion_id: kg-magnetite-sulfate-diet-validation
- prompt: >
- Which members directly exchange electrons through magnetite or biological
- conductive structures in the sulfate-stressed anaerobic microbiome?
+ prompt: 'Which members directly exchange electrons through magnetite or biological conductive structures in the
+ sulfate-stressed anaerobic microbiome?
+
+ '
kind: KNOWLEDGE_GAP
status: OPEN
attaches_to:
- ecological_interactions#Acetate-centered four-guild redox cycling
- rationale: >
- The Microbiome study links magnetite addition to a cooperative four-guild
- network and model-feasible metabolite exchange, but direct DIET validation
- was outside the experiment.
+ rationale: 'The Microbiome study links magnetite addition to a cooperative four-guild network and model-feasible
+ metabolite exchange, but direct DIET validation was outside the experiment.
+
+ '
evidence:
- reference: PMID:42231497
supports: PARTIAL
evidence_source: IN_VITRO
- snippet: >
- Direct validation of DIET requires additional targeted experimental
- approaches beyond the scope of this study.
- explanation: >
- Records the source paper's own boundary around direct electron-transfer
- validation.
+ snippet: 'Direct validation of DIET requires additional targeted experimental approaches beyond the scope of
+ this study.
+
+ '
+ explanation: 'Records the source paper''s own boundary around direct electron-transfer validation.
+
+ '
+- discussion_id: magnetite_assay_and_model_limits
+ prompt: Which processes mediate magnetite-associated methane improvement?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Magnetite-enhanced methanogenesis under sulfate stress
+ - ecological_interactions#Acetate-centered four-guild redox cycling
+ - ecological_interactions#Model-predicted amino-acid and organic-acid exchange
+ rationale: 'Keep zero arrows and preserve #914 backward-edge removal. Separate abiotic sulfide removal, replicated
+ bulk methane response and single-replicate compositional metagenomics. Feasibility of role-curated and output-constrained
+ GEMs does not independently verify partner flux. Retain the existing direct-DIET knowledge gap, #913 putative-SRB
+ caveats and #915 restriction to MAGN_0.6. Myxococcota DTU51 lacks sulfate-reduction genes; do not silently promote
+ it to a validated reducer. Source metadata and identity limits remain under #1574. Complete primary main text
+ and figure captions read, not original figure pixels, separate supplements, raw data or executable models.'
+ posed_by: codex
+ posed_date: '2026-10-06'
curation_history:
- timestamp: '2026-09-15T02:41:25Z'
curator: codex
action: CREATE_MAGNETITE_SULFATE_STRESS_ANAEROBIC_MICROBIOME
- changes: >
- Added the magnetite-amended sulfate-stressed anaerobic microbiome from
- PMID:42231497 with four genome-resolved guilds, H2/CO2-fed serum-bottle
- batch cultivation, the PRJNA1242289 metagenomic BioProject, and
- evidence-backed experimental and GEM-supported interactions.
+ changes: 'Added the magnetite-amended sulfate-stressed anaerobic microbiome from PMID:42231497 with four genome-resolved
+ guilds, H2/CO2-fed serum-bottle batch cultivation, the PRJNA1242289 metagenomic BioProject, and evidence-backed
+ experimental and GEM-supported interactions.
+
+ '
llm_assisted: true
- timestamp: '2026-09-15T02:53:10Z'
curator: codex
action: ADDRESS_MAGNETITE_SULFATE_STRESS_REVIEW
- changes: >
- Addressed adversarial review issues #913, #914, and #915 by backing the
- Myxococcota putative SRB inclusion with direct evidence, limiting the
- curated medium composition to the MAGN_0.6 bottle condition, and removing a
- backward causal edge from the methane-rescue observation to the modeled
- acetate cycle.
+ changes: 'Addressed adversarial review issues #913, #914, and #915 by backing the Myxococcota putative SRB inclusion
+ with direct evidence, limiting the curated medium composition to the MAGN_0.6 bottle condition, and removing
+ a backward causal edge from the methane-rescue observation to the modeled acetate cycle.
+
+ '
llm_assisted: true
- timestamp: '2026-09-15T03:03:06Z'
curator: codex
action: FIX_MAGNETITE_SULFATE_STRESS_PARTICIPANT_TERMS
- changes: >
- Added required term identifiers to the two computed interaction participant
- lists so their guild references remain closed-schema-valid.
+ changes: 'Added required term identifiers to the two computed interaction participant lists so their guild references
+ remain closed-schema-valid.
+
+ '
llm_assisted: true
- timestamp: '2026-09-15T03:31:05Z'
curator: codex
action: FIX_MAGNETITE_SULFATE_STRESS_PYTEST_GATES
- changes: >
- Replaced two citation-marker-bearing snippets with bracket-free exact
- spans from the same source sentence and kept the Myxococcota caveat as a
- separate evidence item.
+ changes: 'Replaced two citation-marker-bearing snippets with bracket-free exact spans from the same source sentence
+ and kept the Myxococcota caveat as a separate evidence item.
+
+ '
+ llm_assisted: true
+- timestamp: '2026-10-06T23:08:46Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: 'Separate magnetite methane response from unvalidated DIET and constrained model flux. Issue #1573; reports/causal_graph_review/decisions/20261006-wetland-crossfeeding-batch66.yaml'
llm_assisted: true
diff --git a/reports/causal_graph_review/README.md b/reports/causal_graph_review/README.md
index 101031472..42c47edfd 100644
--- a/reports/causal_graph_review/README.md
+++ b/reports/causal_graph_review/README.md
@@ -428,3 +428,17 @@ and expose ORT's gapfilled nitrogen-gas reaction. Nine existing nodes and three
qualified arrows remain; no new graph structure or provider spend.
Non-graph identity/model metadata and cached-abstract provenance remain open
under #1526-#1528. Exact cache matching is not independent provenance approval.
+
+## Batch66: Wetlands, MWF001 And Magnetite
+
+[Decisions](decisions/20261006-wetland-crossfeeding-batch66.yaml),
+[validation](validation-20261006-batch66.json) and
+[self-adversarial review](adversarial-review-20261006-batch66.yaml) qualify nine
+existing nodes without adding arrows. MUCC associations and genomic potential
+are not demonstrated exchange; magnetite bulk outcomes and constrained model
+fluxes are distinct. MWF001 cross-feeding remains supported with assay limits,
+but its candidate coexistence link remains `needs_research` under #1575 pending
+the paid Edison workflow. A free dry run is not a completed research report.
+Non-graph metadata/source ambiguities remain #1574. Canonical taxonomy and all
+caches are preserved, not independently recertified. No independent approval
+or corpus completion is claimed.
diff --git a/reports/causal_graph_review/adversarial-review-20261006-batch66.yaml b/reports/causal_graph_review/adversarial-review-20261006-batch66.yaml
new file mode 100644
index 000000000..6ef08225b
--- /dev/null
+++ b/reports/causal_graph_review/adversarial-review-20261006-batch66.yaml
@@ -0,0 +1,204 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: e788ade71f030cd1c482ac279b5a6c554aa1f467
+scope:
+- kb/communities/MUCC_Freshwater_Wetland_Methane_Network_Community.yaml
+- kb/communities/MWF001_FourSpecies_CrossFeeding_Consortium.yaml
+- kb/communities/Magnetite_Sulfate_Stress_Anaerobic_Microbiome.yaml
+decision_ledger: reports/causal_graph_review/decisions/20261006-wetland-crossfeeding-batch66.yaml
+validation_report: reports/causal_graph_review/validation-20261006-batch66.json
+findings:
+- issue: 1571
+ severity: P2
+ status: addressed_in_this_change
+ finding: Wetland core/network and Methanoregula claims exceed observational and genomic evidence.
+ disposition: Close only after protected-main merge.
+- issue: 1572
+ severity: P2
+ status: addressed_in_this_change
+ finding: MWF001 claims omit finite coexistence, generic-model and spent-media assay limits.
+ disposition: Close only after protected-main merge.
+- issue: 1573
+ severity: P2
+ status: addressed_in_this_change
+ finding: Magnetite outcomes and constrained model fluxes overstate independently demonstrated mechanisms.
+ disposition: Close only after protected-main merge.
+- issue: 1574
+ severity: P2
+ status: unresolved_non_graph
+ finding: Identity, role/protocol metadata and source reporting inconsistencies.
+ disposition: Keep OPEN after graph repair merge.
+- issue: 1575
+ severity: P2
+ status: unresolved_research
+ finding: MWF001 candidate causal extension requires authorized paid Edison report review.
+ disposition: Keep OPEN and record needs_research until completed.
+adversarial_checks:
+- Read all three whole records and every original node. Nine nodes and zero original arrows retained,
+ with one MUCC rename and intact discussion anchors. Earlier MUCC workflow and magnetite backward-edge
+ deletions preserved. All three primary main texts and captions read; no original figure-pixel, separate-supplement,
+ raw-data or executable-model audit. Extracted table artifacts contain no main-table cells.
+- 'MUCC: eight core genera concern five marsh/swamp sites, not occupancy in every sample or all nine wetland
+ sites. JLA is a swamp despite marsh shorthand. Canonical whole-community and Archaea/Bacteria guild
+ entries are contextual placeholders, not a resolved eight-genus roster.'
+- 'MUCC: 12 samples/site, positive Spearman genus associations, environmental covariates and genus-matched
+ MAG potential do not demonstrate exchange, niche partitioning or syntrophy. Whole-community network
+ structure did not have the methanogen-network association. Preserve observations, not a causal network
+ from analytic workflow.'
+- 'MUCC: Methanoregula relative dominance and transcription are not selectively tested drivers or methane
+ flux. Methods describe 2018 expression and 2015 modeled production; temporal alignment and source counts
+ need reconciliation. Candidate methylated-sulfide/methoxylated-substrate machinery is not demonstrated
+ methanol use; graph methanol grounding removed while genomic potential remains.'
+- 'MWF001: retain experimentally supported cross-feeding interpretation and explicit four source strains.
+ Spent-medium growth plus carbon-source nonusers support the interpretation, but stationary OD does not
+ chemically establish complete resource depletion. The residual-resource exclusion applies to simulated
+ spent medium. Generic CRM species/resources and unequal affinities are not exact-strain pathways or
+ measured exchanged compounds.'
+- 'MWF001: finite eight-cycle persistence in 31 carbon-supplied conditions is not universal stability.
+ Preserve the additional 5X-malate Ct loss, no-carbon Ml loss, citrate/inosine dilution exceptions and
+ separate four-day chemostats. Pair effects are condition dependent, not universal reciprocity. Existing
+ exact-byproduct gap and #1127/#1128 corrections preserved.'
+- 'MWF001: the candidate PARTIAL cross-feeding-to-coexistence arrow is scientifically plausible and remains
+ explicitly unfinished under #1575. Free one-target Edison dry run passed; no paid run/report was completed
+ and no new structure added. needs_research prevents falsely declaring this sparse graph complete.'
+- 'Magnetite: the 19% effect is relative to SULF_0.6, not full CTRL recovery or rescue at 1.2 g/L. Separate
+ abiotic sulfide removal, unresolved sulfur species and no detected abiotic H2 do not selectively establish
+ the biotic mediator or DIET. Keep the supported bulk outcome without an unsupported syntrophy type.'
+- 'Magnetite: only one biological replicate per condition was sequenced. Relative abundance cannot establish
+ replicated absolute growth. Four representative GEMs are not every MAG in four broad guilds; putative
+ SRB status and #913 caveats remain. Gap filling, expected-role curation, reactor-output constraints,
+ trade-off0.7 and nonunique solution sampling mean feasibility, not independent validation.'
+- 'Magnetite: keep computational CROSS_FEEDING on acetate and amino-acid/organic-acid model nodes, explicitly
+ HYPOTHESIZED. Mean sampled fluxes are not measured extracellular exchange or necessary mutualism. Existing
+ direct-DIET gap, #914 arrow removal and #915 MAGN_0.6 medium restriction remain intact.'
+- Review full biological diff and eight focused tests. Canonical taxonomy, pre-existing discussions and
+ append-only curation events preserved semantically.457 other records,920 caches and all raw non-graph
+ blocks unchanged. Coarse participant census unchanged; this does not verify identity or exact partner
+ flux.46 baseline network findings retained exactly; no structural errors or audit-rule changes.
+- Actual schema, strict, term, reference, snippet, history, network, deterministic render and regression
+ outputs recorded. Exact descriptions parsed over456 pages, not browser screenshots. One primary match
+ requires straight/curly apostrophe equivalence; no cache rewrite. Post-commit docs-current is a separate
+ publication gate.
+- 'Dedup865 all-state issue titles/bodies and24 scoped ignored/hidden local matches; five relevant full
+ issue bodies and prior graph histories read, not every PR/comment/artifact. #1571-#1573 addressed but
+ OPEN until protected-main merge; #1574 metadata and #1575 research stay OPEN. Exact-head COMMENT self-review
+ is not independent approval; corpus work remains unfinished.'
+verification:
+ combined_regressions: 603 passed in 214.64s (0:03:34)
+ new_regression_tests: 8
+ schema_strict_terms_history: Passed with actual outputs/digests
+ references: 'CLI Total checks counts reported issues, not executed checks. MATCH is not scientific entailment
+ or historical provenance certification. All920 caches unchanged;16 graph excerpts match fresh primary
+ text (15 whitespace-only,1 apostrophe rendering equivalence). #1574 remains unresolved; broader #476/#1091/#1095
+ limitations persist.'
+ snippet_counts_by_record:
+ kb/communities/MUCC_Freshwater_Wetland_Methane_Network_Community.yaml:
+ MATCH: 23
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/MWF001_FourSpecies_CrossFeeding_Consortium.yaml:
+ MATCH: 19
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Magnetite_Sulfate_Stress_Anaerobic_Microbiome.yaml:
+ MATCH: 27
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ primary_graph_snippet_proof:
+ primary_matched_graph_snippets: 16
+ whitespace_only_matches: 15
+ apostrophe_rendering_matches: 1
+ primary_main_texts: 3
+ paid_submissions: 0
+ new_nodes_or_arrows: 0
+ separate_supplements_inspected: false
+ original_figure_pixels_inspected: false
+ network:
+ existing_findings_preserved: 46
+ added_findings: {}
+ removed_findings: {}
+ interpretation: All46 baseline network findings preserved exactly; no auditor-rule changes or invented
+ links. Explicit participant lists identify tested panels/inoculants, not missing hosts or background
+ communities.
+ black_ruff_diff: passed
+ tested_file_sha256:
+ reports/causal_graph_review/decisions/20261006-wetland-crossfeeding-batch66.yaml: 25c1e04567419365da0bd38688918032decf12122cc83ab7c994b73d42a484f3
+ tests/test_causal_review_batch66.py: 225c29cd014b09e296d9f0ebf98c787d7cc88061d3e25f4f2c939c5b1e715f3b
+ tests/test_participating_taxa.py: f48d81d715605137dc9cb1951228142035ba8b242bf812489475294102ddaeb2
+ kb/communities/MUCC_Freshwater_Wetland_Methane_Network_Community.yaml: 7d4a55d47676c9d86d07bed817918b120fb80464e39212ef2cd4491c70c45abb
+ kb/communities/MWF001_FourSpecies_CrossFeeding_Consortium.yaml: e74f02ca9923e5df126fe571d3f6edc28a59451d385df9b89276f6a68882253b
+ kb/communities/Magnetite_Sulfate_Stress_Anaerobic_Microbiome.yaml: 1947b775f1ff0266347513042955d0502cae65b6fcfefc89264a35c2382217ca
+ reports/causal_graph_review/README.md: 16cb3f4925ca4a93dfdb19237bdfbfde11826ba388f62c5764406affe8274fba
+ unchanged_caches: 920
+ edison:
+ required_for_this_repair: false
+ required_for_pending_extension: true
+ provider_submissions: 0
+ credits_spent: 0
+ dry_run_receipt_sha256: 70eb5ca0534841446adb8e9e8ddad7a4ae7f0947a977d39795b91fd67b42c41b
+ reason: 'Existing-node repair only; MWF001 extension remains #1575, pending authorized paid run and
+ source-reviewed report.'
+ post_commit_docs_current: Separate publication gate, not asserted before commit.
+participant_census:
+ measurements:
+ baseline:
+ records: 460
+ with_community_level: 391
+ mixed: 124
+ community_level_only: 267
+ taxa: 1507
+ credited_solely_by_the_rule: 1238
+ current:
+ records: 460
+ with_community_level: 391
+ mixed: 124
+ community_level_only: 267
+ taxa: 1507
+ credited_solely_by_the_rule: 1238
+ interpretation: Canonical roster/scope census unchanged. Explicit participants identify MUCC aggregate/guild
+ context and focal genus, MWF001 input strains and four magnetite guild placeholders. This coarse census
+ does not certify exact identities, final abundance or partner flux.
+corpus:
+ records: 460
+ nodes: 1452
+ edges: 638
+ review_status_counts:
+ needs_research: 22
+ pending: 227
+ reviewed: 211
+limitations:
+- 'All9 original nodes retained;zero original arrows. No new causal structure. MWF001 candidate link remains
+ #1575 and needs_research, not complete.'
+- Three complete fresh primary main texts and captions read. Extracted main-table artifacts contain no
+ table cells. Original figure pixels, separate supplements, raw data and executable models not audited;
+ numerical summaries not independently recomputed.
+- MUCC core occupancy and genus networks are observational; MAG annotations are potential. Cross-site
+ flux prediction and transcription do not establish causal syntrophy. Methanol specificity removed from
+ graph; temporal input alignment remains unresolved.
+- MWF001 retains supported cross-feeding with exact-metabolite and residual-resource limits. Generic models
+ do not resolve exact strains; finite persistence has no-carbon/high-malate exceptions. Candidate causal
+ structure remains unfinished, not denied.
+- Magnetite bulk methane response is partial moderate-sulfate improvement. Abiotic sulfide removal does
+ not isolate biotic mediation or DIET. Single-replicate relative MAG abundance is not replicated absolute
+ growth; role-curated output-constrained GEMs provide feasible, nonunique flux hypotheses.
+- 'Canonical taxonomy and raw non-graph blocks preserved, not recertified. #1574 remains OPEN for metadata/source
+ ambiguities. Prior #1127/#1128/#913/#914/#915 corrections and existing knowledge gaps preserved.'
+- All920 caches unchanged;16 retained graph excerpts independently match fresh primary text after whitespace
+ normalization and a straight/curly apostrophe equivalence in one MWF001 excerpt. This does not certify
+ historical full-cache/non-graph provenance. Public OA XML used without access bypass; two sources are
+ CC-BY-NC-ND, not all CC-BY.
+- Deduplication covered865 all-state issue titles/bodies and24 scoped ignored/hidden local files;5 relevant
+ full issue bodies and prior graph histories read, not every PR/comment/local match. Self-review is not
+ independent approval; repair issues stay OPEN until protected-main merge.
+- One free MWF001 Edison dry run passed with zero provider submissions/credits. Specific paid-run authorization
+ was requested but the paid report and causal extension are not complete.
diff --git a/reports/causal_graph_review/decisions/20261006-wetland-crossfeeding-batch66.yaml b/reports/causal_graph_review/decisions/20261006-wetland-crossfeeding-batch66.yaml
new file mode 100644
index 000000000..da4c0216a
--- /dev/null
+++ b/reports/causal_graph_review/decisions/20261006-wetland-crossfeeding-batch66.yaml
@@ -0,0 +1,205 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: e788ade71f030cd1c482ac279b5a6c554aa1f467
+baseline_commit: e788ade71f030cd1c482ac279b5a6c554aa1f467
+base_tree: 783500cc8f3dad4f51a8fff0251273482facdf2b
+pre_source_baseline_sha256: 363385086dc5c5759fd08645be2e6770ad6c146bcf05219c69d693b58bbb6da2
+issues:
+- 1571
+- 1572
+- 1573
+unresolved_non_graph_issues:
+- 1574
+unresolved_research_issues:
+- 1575
+issue_deduplication:
+ all_state_issue_titles_and_bodies: 865
+ ignored_hidden_local_search: true
+ matching_local_files: 24
+ matching_issues:
+ - 1127
+ - 1128
+ - 913
+ - 914
+ - 915
+reference_cache_original_hashes:
+ references_cache/PMID_42231497.txt: 5cb9b900e10173576f5dce33643a018f70b32300c9fefdc9d29b8e025815edd6
+ references_cache/PMID_39843444.md: f4747a8774782a5e10516d079849c242462f41953de4f57e0a2198a624e9dbf6
+ references_cache/PMID_42752228.txt: ae2ac814391efb9b40bf9fa5cbe8d20286f3dc23f517081f5c370132abaa0852
+primary_artifacts:
+ /private/tmp/communitymech-batch66/mucc-primary.xml: 5528281c9aae58dc203046011826cba2b071236dea24e85ae1637543a2f87592
+ /private/tmp/communitymech-batch66/mucc-primary.txt: 02bf8c43266acc1702d23163c363b3e0dc3fcb9658cdc958f916ba3ff7259ea9
+ /private/tmp/communitymech-batch66/mucc-tables.txt: 01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b
+ /private/tmp/communitymech-batch66/mwf-primary.xml: 8ab6d89a9b95cddc91f088816ba4d5be229e43a0b31463e706067f203dbc97a6
+ /private/tmp/communitymech-batch66/mwf-primary.txt: 27520be0ae8c540433a25ef8a632147a9da9342ad68a66a7ef497a41f9472f94
+ /private/tmp/communitymech-batch66/mwf-tables.txt: 01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b
+ /private/tmp/communitymech-batch66/magnetite-primary.xml: 1ef9bcb9de73d6349c4994b56e4fb34199e4b7bea103b1d28df4e9db6daa0405
+ /private/tmp/communitymech-batch66/magnetite-primary.txt: 81679f92038d44b01e7ec5f53baa5b5cf3329c030fa07f14776bfdde5e157d8b
+ /private/tmp/communitymech-batch66/magnetite-tables.txt: 01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b
+primary_urls:
+- https://www.ebi.ac.uk/europepmc/webservices/rest/PMC11754854/fullTextXML
+- https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13598246/fullTextXML
+- https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13445774/fullTextXML
+primary_graph_snippet_count: 16
+edison:
+ required_for_this_repair: false
+ required_for_pending_extension: true
+ provider_submissions: 0
+ credits_spent: 0
+ dry_run_receipt_sha256: 70eb5ca0534841446adb8e9e8ddad7a4ae7f0947a977d39795b91fd67b42c41b
+ reason: 'Existing-node repair only; MWF001 extension remains #1575, pending authorized paid run and source-reviewed
+ report.'
+limitations:
+- 'All9 original nodes retained;zero original arrows. No new causal structure. MWF001 candidate link remains #1575
+ and needs_research, not complete.'
+- Three complete fresh primary main texts and captions read. Extracted main-table artifacts contain no table cells.
+ Original figure pixels, separate supplements, raw data and executable models not audited; numerical summaries
+ not independently recomputed.
+- MUCC core occupancy and genus networks are observational; MAG annotations are potential. Cross-site flux prediction
+ and transcription do not establish causal syntrophy. Methanol specificity removed from graph; temporal input alignment
+ remains unresolved.
+- MWF001 retains supported cross-feeding with exact-metabolite and residual-resource limits. Generic models do not
+ resolve exact strains; finite persistence has no-carbon/high-malate exceptions. Candidate causal structure remains
+ unfinished, not denied.
+- Magnetite bulk methane response is partial moderate-sulfate improvement. Abiotic sulfide removal does not isolate
+ biotic mediation or DIET. Single-replicate relative MAG abundance is not replicated absolute growth; role-curated
+ output-constrained GEMs provide feasible, nonunique flux hypotheses.
+- 'Canonical taxonomy and raw non-graph blocks preserved, not recertified. #1574 remains OPEN for metadata/source
+ ambiguities. Prior #1127/#1128/#913/#914/#915 corrections and existing knowledge gaps preserved.'
+- All920 caches unchanged;16 retained graph excerpts independently match fresh primary text after whitespace normalization
+ and a straight/curly apostrophe equivalence in one MWF001 excerpt. This does not certify historical full-cache/non-graph
+ provenance. Public OA XML used without access bypass; two sources are CC-BY-NC-ND, not all CC-BY.
+- Deduplication covered865 all-state issue titles/bodies and24 scoped ignored/hidden local files;5 relevant full
+ issue bodies and prior graph histories read, not every PR/comment/local match. Self-review is not independent
+ approval; repair issues stay OPEN until protected-main merge.
+- One free MWF001 Edison dry run passed with zero provider submissions/credits. Specific paid-run authorization
+ was requested but the paid report and causal extension are not complete.
+records:
+- path: kb/communities/MUCC_Freshwater_Wetland_Methane_Network_Community.yaml
+ id: CommunityMech:000257
+ original_sha256: f8d6d735d77518d955b0240996f5379f3844c87b33c90effb13a1ca74a3d8735
+ record_sha256: 7d4a55d47676c9d86d07bed817918b120fb80464e39212ef2cd4491c70c45abb
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261006-wetland-crossfeeding-batch66.yaml
+ scope: Whole record and all original nodes; each graph has zero original arrows.
+ summary: Bound wetland co-occurrence and Methanoregula predictions to observational and genomic evidence.
+ renamed_nodes:
+ Marsh Metabolic Interaction Networks: Wetland Methanogen Co-occurrence Networks
+ node_decisions:
+ - node: Conserved Methane-Cycling Genera Across Wetlands
+ rationale: Retain core occupancy without stable-consortium or niche-partitioning claims.
+ - node: Wetland Methanogen Co-occurrence Networks
+ rationale: Represent genus co-occurrence as association, not demonstrated metabolic exchange.
+ - node: Methanoregula Hub Methanogen And Flux Predictor
+ rationale: Retain Methanoregula flux prediction without syntrophic or causal-hub inference.
+ - node: Methylotrophic Methanogenesis Potential
+ rationale: Retain genomic methylotrophic potential and remove unsupported methanol specificity.
+ removed_node_decisions: []
+ edges_before: []
+ edges_after: []
+ retained_edge_decisions: []
+ removed_edge_decisions: []
+ references:
+ - PMID:39843444
+ issues:
+ - 1571
+ - 1574
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/MUCC_Freshwater_Wetland_Methane_Network_Community/2026-10-06T230847Z-codex-95d09c.yaml
+ source_review:
+ PMID:39843444:
+ url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC11754854/fullTextXML
+ scope: Complete primary XML main body, abstract, embedded table text and captions; original figure pixels,
+ separate supplements and raw data require separate inspection.
+ all_retained_graph_snippets_primary_matched: true
+ cache_provenance_certified: false
+- path: kb/communities/MWF001_FourSpecies_CrossFeeding_Consortium.yaml
+ id: CommunityMech:000443
+ original_sha256: d857232408f6b7c54e23cb8fb32466080bb6c0a149bfb76914f514965c4b5ddf
+ record_sha256: e74f02ca9923e5df126fe571d3f6edc28a59451d385df9b89276f6a68882253b
+ status: needs_research
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261006-wetland-crossfeeding-batch66.yaml
+ scope: Whole record and all original nodes; each graph has zero original arrows.
+ summary: Qualify MWF001 cross-feeding and finite coexistence; keep causal extension research open.
+ renamed_nodes: {}
+ node_decisions:
+ - node: Cross-fed metabolic byproduct partitioning
+ rationale: Retain supported cross-feeding with exact-compound, residual-resource and generic-model limits.
+ - node: Robust coexistence across simple nutrient environments
+ rationale: Retain finite coexistence observations and explicit exceptions; track the candidate causal arrow
+ as unfinished research.
+ removed_node_decisions: []
+ edges_before: []
+ edges_after: []
+ retained_edge_decisions: []
+ removed_edge_decisions: []
+ references:
+ - PMID:42752228
+ issues:
+ - 1572
+ - 1574
+ - 1575
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/MWF001_FourSpecies_CrossFeeding_Consortium/2026-10-06T230847Z-codex-73e39c.yaml
+ source_review:
+ PMID:42752228:
+ url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13598246/fullTextXML
+ scope: Complete primary XML main body, abstract, embedded table text and captions; original figure pixels,
+ separate supplements and raw data require separate inspection.
+ all_retained_graph_snippets_primary_matched: true
+ cache_provenance_certified: false
+- path: kb/communities/Magnetite_Sulfate_Stress_Anaerobic_Microbiome.yaml
+ id: CommunityMech:000380
+ original_sha256: d353aabbfd3e6316ec9d270b1a46e53da73db2e69b5ab0d864f4a3cbcb8fa14c
+ record_sha256: 1947b775f1ff0266347513042955d0502cae65b6fcfefc89264a35c2382217ca
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261006-wetland-crossfeeding-batch66.yaml
+ scope: Whole record and all original nodes; each graph has zero original arrows.
+ summary: Separate magnetite methane response from unvalidated DIET and constrained model flux.
+ renamed_nodes: {}
+ node_decisions:
+ - node: Magnetite-enhanced methanogenesis under sulfate stress
+ rationale: Retain moderate-sulfate methane improvement without full rescue or demonstrated DIET.
+ - node: Acetate-centered four-guild redox cycling
+ rationale: Retain computational acetate exchange as a constrained model hypothesis with representative-guild
+ limits.
+ - node: Model-predicted amino-acid and organic-acid exchange
+ rationale: Retain modeled amino-acid/organic-acid exchange without measured flux or dependency claims.
+ removed_node_decisions: []
+ edges_before: []
+ edges_after: []
+ retained_edge_decisions: []
+ removed_edge_decisions: []
+ references:
+ - PMID:42231497
+ issues:
+ - 1573
+ - 1574
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Magnetite_Sulfate_Stress_Anaerobic_Microbiome/2026-10-06T230847Z-codex-cac4a6.yaml
+ source_review:
+ PMID:42231497:
+ url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13445774/fullTextXML
+ scope: Complete primary XML main body, abstract, embedded table text and captions; original figure pixels,
+ separate supplements and raw data require separate inspection.
+ all_retained_graph_snippets_primary_matched: true
+ cache_provenance_certified: false
diff --git a/reports/causal_graph_review/inventory.tsv b/reports/causal_graph_review/inventory.tsv
index 94285f430..7fc55bbe9 100644
--- a/reports/causal_graph_review/inventory.tsv
+++ b/reports/causal_graph_review/inventory.tsv
@@ -229,9 +229,9 @@ kb/communities/MAMC_M48_Lignocellulose.yaml CommunityMech:000041 d877e4431871627
kb/communities/MSC1_Dominant_Core.yaml CommunityMech:000042 479f6594e26ce8439b24c947798594f7e1a28c6deedf918911ed5d342885d540 3 0 63.3 reports/causal_graph_review/decisions/20261006-soil-mucin-batch65.yaml reviewed
kb/communities/MSC2_Model_Soil_Consortium.yaml CommunityMech:000086 2145f5d6484f30023f834b708ccb23d3625375ab32dcf1a2e8a9fc3c4083271d 3 2 90.0 reports/causal_graph_review/decisions/20261006-soil-mucin-batch65.yaml reviewed
kb/communities/MUC2_Human_Gut_Commensal_Defined_Consortium.yaml CommunityMech:000351 01cb4512723915154b17fa1676382c9807fda7f733fc62efb63afabdad3e3742 2 0 57.5 reports/causal_graph_review/decisions/20261006-soil-mucin-batch65.yaml reviewed
-kb/communities/MUCC_Freshwater_Wetland_Methane_Network_Community.yaml CommunityMech:000257 f8d6d735d77518d955b0240996f5379f3844c87b33c90effb13a1ca74a3d8735 4 0 75.0 pending
-kb/communities/MWF001_FourSpecies_CrossFeeding_Consortium.yaml CommunityMech:000443 d857232408f6b7c54e23cb8fb32466080bb6c0a149bfb76914f514965c4b5ddf 2 0 65.0 pending
-kb/communities/Magnetite_Sulfate_Stress_Anaerobic_Microbiome.yaml CommunityMech:000380 d353aabbfd3e6316ec9d270b1a46e53da73db2e69b5ab0d864f4a3cbcb8fa14c 3 0 75.0 pending
+kb/communities/MUCC_Freshwater_Wetland_Methane_Network_Community.yaml CommunityMech:000257 7d4a55d47676c9d86d07bed817918b120fb80464e39212ef2cd4491c70c45abb 4 0 65.0 reports/causal_graph_review/decisions/20261006-wetland-crossfeeding-batch66.yaml reviewed
+kb/communities/MWF001_FourSpecies_CrossFeeding_Consortium.yaml CommunityMech:000443 e74f02ca9923e5df126fe571d3f6edc28a59451d385df9b89276f6a68882253b 2 0 60.0 reports/causal_graph_review/decisions/20261006-wetland-crossfeeding-batch66.yaml needs_research
+kb/communities/Magnetite_Sulfate_Stress_Anaerobic_Microbiome.yaml CommunityMech:000380 1947b775f1ff0266347513042955d0502cae65b6fcfefc89264a35c2382217ca 3 0 71.7 reports/causal_graph_review/decisions/20261006-wetland-crossfeeding-batch66.yaml reviewed
kb/communities/Maize_Benzoxazinoid_Metabolizing_SynComs.yaml CommunityMech:000101 a437ba2cb52c000bb10666abe37421a44acec6945b64a68ec944f09568979382 3 2 100.0 pending
kb/communities/Maize_Drought_Response_SynCom.yaml CommunityMech:000103 0b6b320adeb8f137a14dfd3e33f3dd9cf028cfb9d2c024ebcfe05f4864ec64ed 7 9 100.0 pending
kb/communities/Maize_Root_Simplified_Community.yaml CommunityMech:000043 c0a2c4e2cb8cd0dc56c40ec237b262f200700f1cff7f38a90911f2b1ac30977b 3 0 75.0 pending
diff --git a/reports/causal_graph_review/summary.json b/reports/causal_graph_review/summary.json
index af83a6659..a9dff773f 100644
--- a/reports/causal_graph_review/summary.json
+++ b/reports/causal_graph_review/summary.json
@@ -7,9 +7,9 @@
"records_without_nodes": 8,
"records_without_edges": 162,
"review_status_counts": {
- "needs_research": 21,
- "pending": 230,
- "reviewed": 209
+ "needs_research": 22,
+ "pending": 227,
+ "reviewed": 211
},
"structural_defects": [],
"network_audit": [
diff --git a/reports/causal_graph_review/validation-20261006-batch66.json b/reports/causal_graph_review/validation-20261006-batch66.json
new file mode 100644
index 000000000..bf0b41c01
--- /dev/null
+++ b/reports/causal_graph_review/validation-20261006-batch66.json
@@ -0,0 +1,821 @@
+{
+ "base_commit": "e788ade71f030cd1c482ac279b5a6c554aa1f467",
+ "scope": [
+ "kb/communities/MUCC_Freshwater_Wetland_Methane_Network_Community.yaml",
+ "kb/communities/MWF001_FourSpecies_CrossFeeding_Consortium.yaml",
+ "kb/communities/Magnetite_Sulfate_Stress_Anaerobic_Microbiome.yaml"
+ ],
+ "reference_validator_version": "0.1.7",
+ "results": [
+ {
+ "check": "MUCC_Freshwater_Wetland_Methane_Network_Community-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/MUCC_Freshwater_Wetland_Methane_Network_Community.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch66/MUCC_Freshwater_Wetland_Methane_Network_Community-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "MUCC_Freshwater_Wetland_Methane_Network_Community-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch66/MUCC_Freshwater_Wetland_Methane_Network_Community-strict.tsv",
+ "kb/communities/MUCC_Freshwater_Wetland_Methane_Network_Community.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch66/MUCC_Freshwater_Wetland_Methane_Network_Community-strict.log",
+ "log_sha256": "0ef864b9644df8383bc8ac4803d0984e39586e30d9b05e4a6b8255eabd7dac44",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch66/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-batch66/MUCC_Freshwater_Wetland_Methane_Network_Community-strict.tsv\n"
+ },
+ {
+ "check": "MUCC_Freshwater_Wetland_Methane_Network_Community-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/MUCC_Freshwater_Wetland_Methane_Network_Community.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch66/MUCC_Freshwater_Wetland_Methane_Network_Community-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "MUCC_Freshwater_Wetland_Methane_Network_Community-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/MUCC_Freshwater_Wetland_Methane_Network_Community.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch66/MUCC_Freshwater_Wetland_Methane_Network_Community-references.log",
+ "log_sha256": "33f42100bde80ebee83f31daceac27f73fadaaf09146473be942d88b95c3a51b",
+ "output_tail": "Validating kb/communities/MUCC_Freshwater_Wetland_Methane_Network_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/MUCC_Freshwater_Wetland_Methane_Network_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": "MUCC_Freshwater_Wetland_Methane_Network_Community-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/MUCC_Freshwater_Wetland_Methane_Network_Community.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch66/MUCC_Freshwater_Wetland_Methane_Network_Community-snippets.log",
+ "log_sha256": "06a536479395cd60c7eab504952fd1ebaea7cd4609924c29d687dbc4183c3686",
+ "output_tail": "# 23 evidence snippets scanned across 1 files\n MATCH 23\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": "MUCC_Freshwater_Wetland_Methane_Network_Community-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/MUCC_Freshwater_Wetland_Methane_Network_Community.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch66/MUCC_Freshwater_Wetland_Methane_Network_Community-rank.log",
+ "log_sha256": "634c77891e05b8ae24058000782f1e37aaf00659c41f48582e8d7f8b87ab4f64",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000257\",\n \"name\": \"MUCC Freshwater Wetland Methane-Cycling Network Community\",\n \"score\": 65.0,\n \"taxonomy\": 4,\n \"connected_taxa\": 4,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 4,\n \"downstream_edges\": 0,\n \"interaction_evidence\": 8,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"downstream\",\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/MUCC_Freshwater_Wetland_Methane_Network_Community.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "MUCC_Freshwater_Wetland_Methane_Network_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/MUCC_Freshwater_Wetland_Methane_Network_Community/2026-10-06T230847Z-codex-95d09c.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch66/MUCC_Freshwater_Wetland_Methane_Network_Community-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "MWF001_FourSpecies_CrossFeeding_Consortium-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/MWF001_FourSpecies_CrossFeeding_Consortium.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch66/MWF001_FourSpecies_CrossFeeding_Consortium-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "MWF001_FourSpecies_CrossFeeding_Consortium-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch66/MWF001_FourSpecies_CrossFeeding_Consortium-strict.tsv",
+ "kb/communities/MWF001_FourSpecies_CrossFeeding_Consortium.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch66/MWF001_FourSpecies_CrossFeeding_Consortium-strict.log",
+ "log_sha256": "2ce05a575acb4e767024ed6bbb5ad0db59e979c2698533999c600c45ad72ca12",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch66/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-batch66/MWF001_FourSpecies_CrossFeeding_Consortium-strict.tsv\n"
+ },
+ {
+ "check": "MWF001_FourSpecies_CrossFeeding_Consortium-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/MWF001_FourSpecies_CrossFeeding_Consortium.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch66/MWF001_FourSpecies_CrossFeeding_Consortium-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "MWF001_FourSpecies_CrossFeeding_Consortium-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/MWF001_FourSpecies_CrossFeeding_Consortium.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch66/MWF001_FourSpecies_CrossFeeding_Consortium-references.log",
+ "log_sha256": "42499a0eadacb3d5275dc2455bc37fd72a807b843cc16c40bd9e50e221370e62",
+ "output_tail": "Validating kb/communities/MWF001_FourSpecies_CrossFeeding_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/MWF001_FourSpecies_CrossFeeding_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": "MWF001_FourSpecies_CrossFeeding_Consortium-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/MWF001_FourSpecies_CrossFeeding_Consortium.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch66/MWF001_FourSpecies_CrossFeeding_Consortium-snippets.log",
+ "log_sha256": "8084678f5cf248d78dd90bd74538a6320ef0dcc9940ae3e5b5f759e13588ade6",
+ "output_tail": "# 19 evidence snippets scanned across 1 files\n MATCH 19\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": "MWF001_FourSpecies_CrossFeeding_Consortium-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/MWF001_FourSpecies_CrossFeeding_Consortium.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch66/MWF001_FourSpecies_CrossFeeding_Consortium-rank.log",
+ "log_sha256": "e358cd10d1cc05a2052395597172ab17f989f8bc0e1d292dd7be30756bf82520",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000443\",\n \"name\": \"MWF001 Four-Species Cross-Feeding Consortium\",\n \"score\": 60.0,\n \"taxonomy\": 4,\n \"connected_taxa\": 4,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 2,\n \"downstream_edges\": 0,\n \"interaction_evidence\": 3,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"additional_interactions\",\n \"downstream\",\n \"metabolites_or_biological_processes\",\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/MWF001_FourSpecies_CrossFeeding_Consortium.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "MWF001_FourSpecies_CrossFeeding_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/MWF001_FourSpecies_CrossFeeding_Consortium/2026-10-06T230847Z-codex-73e39c.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch66/MWF001_FourSpecies_CrossFeeding_Consortium-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Magnetite_Sulfate_Stress_Anaerobic_Microbiome-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Magnetite_Sulfate_Stress_Anaerobic_Microbiome.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch66/Magnetite_Sulfate_Stress_Anaerobic_Microbiome-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Magnetite_Sulfate_Stress_Anaerobic_Microbiome-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch66/Magnetite_Sulfate_Stress_Anaerobic_Microbiome-strict.tsv",
+ "kb/communities/Magnetite_Sulfate_Stress_Anaerobic_Microbiome.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch66/Magnetite_Sulfate_Stress_Anaerobic_Microbiome-strict.log",
+ "log_sha256": "3ead6046719bfbd06fa615b9410bd7987c7eee0bd2e8c7391a430b3d54ad69d8",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch66/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-batch66/Magnetite_Sulfate_Stress_Anaerobic_Microbiome-strict.tsv\n"
+ },
+ {
+ "check": "Magnetite_Sulfate_Stress_Anaerobic_Microbiome-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Magnetite_Sulfate_Stress_Anaerobic_Microbiome.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch66/Magnetite_Sulfate_Stress_Anaerobic_Microbiome-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Magnetite_Sulfate_Stress_Anaerobic_Microbiome-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Magnetite_Sulfate_Stress_Anaerobic_Microbiome.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch66/Magnetite_Sulfate_Stress_Anaerobic_Microbiome-references.log",
+ "log_sha256": "f4e756f043fca4b2e4f91ffa73ddfe2efe593f96a3b61e0ac167c6092ed206f8",
+ "output_tail": "Validating kb/communities/Magnetite_Sulfate_Stress_Anaerobic_Microbiome.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/Magnetite_Sulfate_Stress_Anaerobic_Microbiome.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": "Magnetite_Sulfate_Stress_Anaerobic_Microbiome-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Magnetite_Sulfate_Stress_Anaerobic_Microbiome.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch66/Magnetite_Sulfate_Stress_Anaerobic_Microbiome-snippets.log",
+ "log_sha256": "c72869c3cfa80d3275b80461e8b721727d9e301213f59836200303704b4482a6",
+ "output_tail": "# 27 evidence snippets scanned across 1 files\n MATCH 27\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": "Magnetite_Sulfate_Stress_Anaerobic_Microbiome-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Magnetite_Sulfate_Stress_Anaerobic_Microbiome.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch66/Magnetite_Sulfate_Stress_Anaerobic_Microbiome-rank.log",
+ "log_sha256": "3ec660b0a5ad264855a2cdcc442d20be9fe51a57e29298a4992095d43b83fe87",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000380\",\n \"name\": \"Magnetite Sulfate-Stress Anaerobic Microbiome\",\n \"score\": 71.7,\n \"taxonomy\": 4,\n \"connected_taxa\": 4,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 3,\n \"downstream_edges\": 0,\n \"interaction_evidence\": 5,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"downstream\",\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Magnetite_Sulfate_Stress_Anaerobic_Microbiome.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Magnetite_Sulfate_Stress_Anaerobic_Microbiome-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Magnetite_Sulfate_Stress_Anaerobic_Microbiome/2026-10-06T230847Z-codex-cac4a6.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch66/Magnetite_Sulfate_Stress_Anaerobic_Microbiome-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-batch66/inventory.log",
+ "log_sha256": "b0fdd2a0c2194135fba5f1532f074ff51af14700348bbe057002f4b81fd122ad",
+ "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\": 1452,\n \"edges\": 638,\n \"records_without_nodes\": 8,\n \"records_without_edges\": 162,\n \"review_status_counts\": {\n \"needs_research\": 22,\n \"pending\": 227,\n \"reviewed\": 211\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-batch66/network.log",
+ "log_sha256": "3a156d88a5b27b6a726e91303cf9249745ee46d4e53a0ac73d58779dc1041a7d",
+ "output_tail": "{\n \"preferred_term\": \"Legionella MAGs\",\n \"term\": {\n \"id\": \"NCBITaxon:445\",\n \"label\": \"Legionella\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The study detected Legionella-affiliated MAGs and used them in a virulence-gene risk assessment; the source did not assert pathogenicity for a cultured Legionella isolate.\\n\"\n },\n \"abundance_value\": \"Lower-abundance Legionella-affiliated MAGs detected during metagenomic risk assessment.\\n\",\n \"evidence\": [\n {\n \"reference\": \"PMID:41457319\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"COMPUTATIONAL\",\n \"snippet\": \"detection of waterborne pathogens from the Legionella genus\",\n \"explanation\": \"Supports Legionella-affiliated lower-abundance bins as monitored biosafety-relevant members of the consortium.\\n\"\n }\n ]\n },\n \"message\": \"Taxon 'Legionella MAGs' has no interactions\"\n }\n ],\n \"Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom\": [\n {\n \"type\": \"UNKNOWN_TARGET\",\n \"interaction\": \"Twelve-Strain SynCom Suppression of Sclerotinia Sclerotia\",\n \"interaction_index\": 0,\n \"taxon\": \"Sclerotinia sclerotiorum\",\n \"severity\": \"warning\",\n \"message\": \"Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)\"\n },\n {\n \"type\": \"UNKNOWN_TARGET\",\n \"interaction\": \"Trinickia MC Key Contribution to Sclerotia Mortality\",\n \"interaction_index\": 1,\n \"taxon\": \"Sclerotinia sclerotiorum\",\n \"severity\": \"warning\",\n \"message\": \"Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)\"\n }\n ],\n \"Space_Habitat_SevenMember_Stress_Tolerance_SynCom\": [\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Acinetobacter radioresistens 50V1\",\n \"taxon_id\": \"NCBITaxon:40216\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Acinetobacter radioresistens 50V1\",\n \"term\": {\n \"id\": \"NCBITaxon:40216\",\n \"label\": \"Acinetobacter radioresistens\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The isolate came from the preflight Mars Odyssey Orbiter; ontology grounding is at species level.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"50V1\",\n \"genome_accession\": \"GCA_002834555.1\"\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Acinetobacter radioresistens | 50V1 | Preflight Mars Odyssey Orbiter | \\u2013 | Mccoy et al., 2012 | GCA_002834555.1 | TSYB/TSYA | 37 \\u00b0C | 16\\u201318 h\",\n \"explanation\": \"Identifies A. radioresistens 50V1 as a consortium member and gives its spacecraft-associated source, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Acinetobacter radioresistens 50V1' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Micrococcus luteus W4-Al-K1\",\n \"taxon_id\": \"NCBITaxon:1270\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Micrococcus luteus W4-Al-K1\",\n \"term\": {\n \"id\": \"NCBITaxon:1270\",\n \"label\": \"Micrococcus luteus\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The isolate was recovered from an ISS aluminum-case touch array; ontology grounding is at species level.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"W4-Al-K1\",\n \"genome_accession\": \"GCA_057816565.1\"\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Micrococcus luteus | W4-Al-K1 | ISS, Touch Array Aluminum Case | - | Kr\\u00e4mer et al., 2025 | GCA_057816565.1 | NB, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies M. luteus W4-Al-K1 as a consortium member and gives its ISS source, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Micrococcus luteus W4-Al-K1' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Propionibacterium cyclohexanicum TA-12T\",\n \"taxon_id\": \"NCBITaxon:64702\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Propionibacterium cyclohexanicum TA-12T\",\n \"term\": {\n \"id\": \"NCBITaxon:64702\",\n \"label\": \"Propionibacterium cyclohexanicum\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the P. cyclohexanicum type strain as a biosafety-level-1 representative.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"TA-12T\",\n \"genome_accession\": \"GCA_900111365\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"16859\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Propionibacterium cyclohexanicum | TA-12 T | Spoilt Orange Juice | DSM 16859 T | Kusano et al., 1997 | GCA_900111365 | BHI, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies P. cyclohexanicum TA-12T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Propionibacterium cyclohexanicum TA-12T' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Pseudomonas antarctica CMS 35T\",\n \"taxon_id\": \"NCBITaxon:219572\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Pseudomonas antarctica CMS 35T\",\n \"term\": {\n \"id\": \"NCBITaxon:219572\",\n \"label\": \"Pseudomonas antarctica\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the P. antarctica type strain as a biosafety-level-1 Pseudomonas surrogate.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"CMS 35T\",\n \"genome_accession\": \"GCA_010634845\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"15318\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Pseudomonas antarctica | CMS 35 T | Antarctica | DSM 15318 T | Reddy et al., 2004 | GCA_010634845 | TSYB/TSYA | Ambient | 12\\u201316 h\",\n \"explanation\": \"Identifies P. antarctica CMS 35T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Pseudomonas antarctica CMS 35T' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Staphylococcus capitis K1-2-2-23\",\n \"taxon_id\": \"NCBITaxon:29388\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Staphylococcus capitis K1-2-2-23\",\n \"term\": {\n \"id\": \"NCBITaxon:29388\",\n \"label\": \"Staphylococcus capitis\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The isolate was recovered from ISS V2A steel; ontology grounding is at species level.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"K1-2-2-23\",\n \"genome_accession\": \"GCA_025272695\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"111179\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Staphylococcus capitis | K1-2-2-23 | ISS, V2A Steel | DSM 111179 | Sobisch et al., 2019 | GCA_025272695 | TSYB/TSYA | 37 \\u00b0C | 16\\u201324 h\",\n \"explanation\": \"Identifies S. capitis K1-2-2-23 as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Staphylococcus capitis K1-2-2-23' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Streptococcus halotolerans HTS9T\",\n \"taxon_id\": \"NCBITaxon:1814128\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Streptococcus halotolerans HTS9T\",\n \"term\": {\n \"id\": \"NCBITaxon:1814128\",\n \"label\": \"Streptococcus halotolerans\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the S. halotolerans type strain as a biosafety-level-1 representative.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"HTS9T\",\n \"genome_accession\": \"GCA_001598035\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"101996\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Streptococcus halotolerans | HTS9 T | Respiratory Tract of Marmota himalayana | DSM 101996 T | Niu et al., 2016 | GCA_001598035 | 2xLB, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies S. halotolerans HTS9T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Streptococcus halotolerans HTS9T' has no interactions\"\n }\n ]\n}\n"
+ },
+ {
+ "check": "rank-all",
+ "command": [
+ "just",
+ "rank-causal-graphs"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
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+ ],
+ "log": "/private/tmp/communitymech-batch66/rank-all.log",
+ "log_sha256": "c16e401b3c4129a244b804b685f38c7f592f1184648330762e5b3aafe55aef00",
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Community\t5\t5\t0\t3\t2\t5\t\t0\t0\n451\t100.0\tkb/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml\tCommunityMech:000213\tVariovorax-Cryptococcus Vitamin Cross-Feeding Microcosm\t2\t2\t0\t3\t2\t4\t\t0\t0\n452\t100.0\tkb/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml\tCommunityMech:000328\tWaste-Sludge Electro-Fermentation Biofilm-Suspension Community\t5\t5\t0\t4\t2\t6\t\t0\t0\n453\t100.0\tkb/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.yaml\tCommunityMech:000098\tWatermelon Rhizosphere Fusarium-Protective SynCom8\t2\t2\t0\t3\t2\t7\t\t0\t0\n454\t100.0\tkb/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml\tCommunityMech:000255\tWetland Oxygen-Sulfate Greenhouse Gas Microcosm Community\t3\t3\t0\t3\t2\t6\t\t0\t0\n455\t100.0\tkb/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.yaml\tCommunityMech:000118\tWheat Straw Biogas Pretreatment SynCom\t4\t4\t0\t3\t2\t4\t\t0\t0\n456\t100.0\tkb/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml\tCommunityMech:000354\tYarrowia lipolytica Division-of-Labor Lipid Consortium\t2\t2\t0\t3\t2\t3\t\t0\t0\n457\t100.0\tkb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml\tCommunityMech:000164\tYogurt Two-Species Starter Culture\t2\t2\t0\t4\t2\t9\t\t0\t0\n458\t100.0\tkb/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml\tCommunityMech:000210\tZymomonas-E. coli Exometabolomics-Designed Obligate Mutualism\t2\t2\t0\t3\t2\t6\t\t0\t0\n459\t100.0\tkb/communities/hCom2_Complex_Gut_Microbiome.yaml\tCommunityMech:000123\thCom2 Complex Gut Microbiome\t1\t1\t0\t3\t2\t3\t\t0\t0\n460\t100.0\tkb/communities/mCAFEs_Brachypodium_RCC.yaml\tCommunityMech:000078\tm-CAFEs Brachypodium Reduced Complexity Consortia\t10\t10\t0\t6\t2\t11\t\t0\t0\nPYTHONPATH=src uv run python scripts/rank_causal_graph_readiness.py \n"
+ },
+ {
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+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
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+ "communitymech.render"
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+ "output_tail": "sm.html\n \u2713 Synechococcus_Bacillus_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 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/private/tmp/communitymech-causal-batch66/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch66/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch66/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch66/docs/index.html\n"
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+ "output_tail": "sm.html\n \u2713 Synechococcus_Bacillus_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch66/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch66/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch66/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch66/docs/index.html\n"
+ },
+ {
+ "check": "connectivity-survey",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-c",
+ "import json,pathlib,runpy\nfn=runpy.run_path('tests/test_community_level_connectivity_credit.py')['_survey']\nresult={}\nfor name,root in [('baseline',pathlib.Path('/private/tmp/communitymech-causal-batch65')),('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-batch66/connectivity-survey.log",
+ "log_sha256": "2dcbda64d4b5530059ac8ad2c76a801bffcf051d557341927f6c204fb4d3f7e5",
+ "output_tail": "{\"baseline\": {\"records\": 460, \"with_community_level\": 391, \"mixed\": 124, \"community_level_only\": 267, \"taxa\": 1507, \"credited_solely_by_the_rule\": 1238}, \"current\": {\"records\": 460, \"with_community_level\": 391, \"mixed\": 124, \"community_level_only\": 267, \"taxa\": 1507, \"credited_solely_by_the_rule\": 1238}}\n"
+ },
+ {
+ "check": "regressions",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "pytest",
+ "-q",
+ "tests/test_causal_review_batch10.py",
+ "tests/test_causal_review_batch11.py",
+ "tests/test_causal_review_batch12.py",
+ "tests/test_causal_review_batch13.py",
+ "tests/test_causal_review_batch14.py",
+ "tests/test_causal_review_batch15.py",
+ "tests/test_causal_review_batch16.py",
+ "tests/test_causal_review_batch17.py",
+ "tests/test_causal_review_batch18.py",
+ "tests/test_causal_review_batch19.py",
+ "tests/test_causal_review_batch20.py",
+ "tests/test_causal_review_batch21.py",
+ "tests/test_causal_review_batch22.py",
+ "tests/test_causal_review_batch23.py",
+ "tests/test_causal_review_batch24.py",
+ "tests/test_causal_review_batch25.py",
+ "tests/test_causal_review_batch27.py",
+ "tests/test_causal_review_batch28.py",
+ "tests/test_causal_review_batch29.py",
+ "tests/test_causal_review_batch30.py",
+ "tests/test_causal_review_batch31.py",
+ "tests/test_causal_review_batch32.py",
+ "tests/test_causal_review_batch33.py",
+ "tests/test_causal_review_batch34.py",
+ "tests/test_causal_review_batch35.py",
+ "tests/test_causal_review_batch36.py",
+ "tests/test_causal_review_batch37.py",
+ "tests/test_causal_review_batch38.py",
+ "tests/test_causal_review_batch39.py",
+ "tests/test_causal_review_batch40.py",
+ "tests/test_causal_review_batch41.py",
+ "tests/test_causal_review_batch42.py",
+ "tests/test_causal_review_batch43.py",
+ "tests/test_causal_review_batch44.py",
+ "tests/test_causal_review_batch45.py",
+ "tests/test_causal_review_batch46.py",
+ "tests/test_causal_review_batch47.py",
+ "tests/test_causal_review_batch48.py",
+ "tests/test_causal_review_batch49.py",
+ "tests/test_causal_review_batch5.py",
+ "tests/test_causal_review_batch50.py",
+ "tests/test_causal_review_batch51.py",
+ "tests/test_causal_review_batch52.py",
+ "tests/test_causal_review_batch53.py",
+ "tests/test_causal_review_batch54.py",
+ "tests/test_causal_review_batch55.py",
+ "tests/test_causal_review_batch56.py",
+ "tests/test_causal_review_batch57.py",
+ "tests/test_causal_review_batch58.py",
+ "tests/test_causal_review_batch59.py",
+ "tests/test_causal_review_batch6.py",
+ "tests/test_causal_review_batch60.py",
+ "tests/test_causal_review_batch61.py",
+ "tests/test_causal_review_batch62.py",
+ "tests/test_causal_review_batch63.py",
+ "tests/test_causal_review_batch64.py",
+ "tests/test_causal_review_batch65.py",
+ "tests/test_causal_review_batch66.py",
+ "tests/test_causal_review_batch7.py",
+ "tests/test_causal_review_batch8.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-batch66/regressions.log",
+ "log_sha256": "c089bc597cfde0915b175b3a887b745ca3f07a7ee79983ab9eca4b0b9c3488e5",
+ "output_tail": "........................................................................ [ 11%]\n........................................................................ [ 23%]\n........................................................................ [ 35%]\n........................................................................ [ 47%]\n........................................................................ [ 59%]\n........................................................................ [ 71%]\n........................................................................ [ 83%]\n........................................................................ [ 95%]\n........................... [100%]\n603 passed in 214.64s (0:03:34)\n"
+ },
+ {
+ "check": "black",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/3Q_kifQtLB624D5bBWGIf/bin/black",
+ "--check",
+ "tests/test_causal_review_batch66.py",
+ "tests/test_participating_taxa.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch66/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_batch66.py",
+ "tests/test_participating_taxa.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch66/ruff.log",
+ "log_sha256": "82b3e6a6c090a57601d22943bd23fca9218d1031dbe5a7b754092f9a156b4f18",
+ "output_tail": "All checks passed!\n"
+ },
+ {
+ "check": "diff-check",
+ "command": [
+ "git",
+ "diff",
+ "--check"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch66/diff-check.log",
+ "log_sha256": "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855",
+ "output_tail": ""
+ },
+ {
+ "check": "primary-graph-proof",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-c",
+ "import hashlib,json,pathlib,yaml\nP=pathlib.Path\nledger=yaml.safe_load(P('reports/causal_graph_review/decisions/20261006-wetland-crossfeeding-batch66.yaml').read_text())\nmanifest=json.loads(P('/private/tmp/communitymech-batch66/primary-manifest.json').read_text())\nprimary={'PMID:'+v['pmid']:''.join(P(v['extracted_body']).read_text().split()) for v in manifest.values()}\nfor path,digest in ledger['primary_artifacts'].items():\n assert hashlib.sha256(P(path).read_bytes()).hexdigest()==digest\nexact=rendering=0\nfor row in ledger['records']:\n doc=yaml.safe_load(P(row['path']).read_text())\n for node in doc['ecological_interactions']:\n for ev in node['evidence']:\n snippet=''.join(ev['snippet'].split())\n body=primary[ev['reference']]\n if snippet in body: exact+=1\n else:\n assert ev['reference']=='PMID:42752228' and snippet in body.replace(chr(8217),chr(39))\n rendering+=1\nassert exact==15 and rendering==1 and exact+rendering==ledger['primary_graph_snippet_count']\nassert ledger['edison']['provider_submissions']==ledger['edison']['credits_spent']==0\nassert [r['status'] for r in ledger['records']]==['reviewed','needs_research','reviewed']\nassert ledger['unresolved_research_issues']==[1575]\nprint(json.dumps({'primary_matched_graph_snippets':exact+rendering,'whitespace_only_matches':exact,'apostrophe_rendering_matches':rendering,'primary_main_texts':3,'paid_submissions':0,'new_nodes_or_arrows':0,'separate_supplements_inspected':False,'original_figure_pixels_inspected':False}))\n"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch66/primary-graph-proof.log",
+ "log_sha256": "a7d6de5607a4945ae6d46b2466036ab5b5c628f994d99208a0ffe7c299d2655e",
+ "output_tail": "{\"primary_matched_graph_snippets\": 16, \"whitespace_only_matches\": 15, \"apostrophe_rendering_matches\": 1, \"primary_main_texts\": 3, \"paid_submissions\": 0, \"new_nodes_or_arrows\": 0, \"separate_supplements_inspected\": false, \"original_figure_pixels_inspected\": false}\n"
+ }
+ ],
+ "limitations": [
+ "All9 original nodes retained;zero original arrows. No new causal structure. MWF001 candidate link remains #1575 and needs_research, not complete.",
+ "Three complete fresh primary main texts and captions read. Extracted main-table artifacts contain no table cells. Original figure pixels, separate supplements, raw data and executable models not audited; numerical summaries not independently recomputed.",
+ "MUCC core occupancy and genus networks are observational; MAG annotations are potential. Cross-site flux prediction and transcription do not establish causal syntrophy. Methanol specificity removed from graph; temporal input alignment remains unresolved.",
+ "MWF001 retains supported cross-feeding with exact-metabolite and residual-resource limits. Generic models do not resolve exact strains; finite persistence has no-carbon/high-malate exceptions. Candidate causal structure remains unfinished, not denied.",
+ "Magnetite bulk methane response is partial moderate-sulfate improvement. Abiotic sulfide removal does not isolate biotic mediation or DIET. Single-replicate relative MAG abundance is not replicated absolute growth; role-curated output-constrained GEMs provide feasible, nonunique flux hypotheses.",
+ "Canonical taxonomy and raw non-graph blocks preserved, not recertified. #1574 remains OPEN for metadata/source ambiguities. Prior #1127/#1128/#913/#914/#915 corrections and existing knowledge gaps preserved.",
+ "All920 caches unchanged;16 retained graph excerpts independently match fresh primary text after whitespace normalization and a straight/curly apostrophe equivalence in one MWF001 excerpt. This does not certify historical full-cache/non-graph provenance. Public OA XML used without access bypass; two sources are CC-BY-NC-ND, not all CC-BY.",
+ "Deduplication covered865 all-state issue titles/bodies and24 scoped ignored/hidden local files;5 relevant full issue bodies and prior graph histories read, not every PR/comment/local match. Self-review is not independent approval; repair issues stay OPEN until protected-main merge.",
+ "One free MWF001 Edison dry run passed with zero provider submissions/credits. Specific paid-run authorization was requested but the paid report and causal extension are not complete.",
+ "Exact HTML-description parser and repeat-render checks, not browser screenshots. Post-commit docs-current is separate."
+ ],
+ "snippet_counts_by_record": {
+ "kb/communities/MUCC_Freshwater_Wetland_Methane_Network_Community.yaml": {
+ "MATCH": 23,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/MWF001_FourSpecies_CrossFeeding_Consortium.yaml": {
+ "MATCH": 19,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Magnetite_Sulfate_Stress_Anaerobic_Microbiome.yaml": {
+ "MATCH": 27,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ }
+ },
+ "unchanged_raw_blocks": 53,
+ "unchanged_record_files": 457,
+ "unchanged_cache_files": 920,
+ "edison": {
+ "required_for_this_repair": false,
+ "required_for_pending_extension": true,
+ "provider_submissions": 0,
+ "credits_spent": 0,
+ "dry_run_receipt_sha256": "70eb5ca0534841446adb8e9e8ddad7a4ae7f0947a977d39795b91fd67b42c41b",
+ "reason": "Existing-node repair only; MWF001 extension remains #1575, pending authorized paid run and source-reviewed report."
+ },
+ "primary_artifacts": {
+ "/private/tmp/communitymech-batch66/mucc-primary.xml": "5528281c9aae58dc203046011826cba2b071236dea24e85ae1637543a2f87592",
+ "/private/tmp/communitymech-batch66/mucc-primary.txt": "02bf8c43266acc1702d23163c363b3e0dc3fcb9658cdc958f916ba3ff7259ea9",
+ "/private/tmp/communitymech-batch66/mucc-tables.txt": "01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b",
+ "/private/tmp/communitymech-batch66/mwf-primary.xml": "8ab6d89a9b95cddc91f088816ba4d5be229e43a0b31463e706067f203dbc97a6",
+ "/private/tmp/communitymech-batch66/mwf-primary.txt": "27520be0ae8c540433a25ef8a632147a9da9342ad68a66a7ef497a41f9472f94",
+ "/private/tmp/communitymech-batch66/mwf-tables.txt": "01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b",
+ "/private/tmp/communitymech-batch66/magnetite-primary.xml": "1ef9bcb9de73d6349c4994b56e4fb34199e4b7bea103b1d28df4e9db6daa0405",
+ "/private/tmp/communitymech-batch66/magnetite-primary.txt": "81679f92038d44b01e7ec5f53baa5b5cf3329c030fa07f14776bfdde5e157d8b",
+ "/private/tmp/communitymech-batch66/magnetite-tables.txt": "01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
+ },
+ "network_delta": {
+ "existing_findings_preserved": 46,
+ "added_findings": {},
+ "removed_findings": {},
+ "interpretation": "All46 baseline network findings preserved exactly; no auditor-rule changes or invented links. Explicit participant lists identify tested panels/inoculants, not missing hosts or background communities."
+ },
+ "render_determinism": true,
+ "published_description_coverage": {
+ "pages": 456,
+ "nodes": 1438,
+ "arrows": 630
+ },
+ "participant_census": {
+ "measurements": {
+ "baseline": {
+ "records": 460,
+ "with_community_level": 391,
+ "mixed": 124,
+ "community_level_only": 267,
+ "taxa": 1507,
+ "credited_solely_by_the_rule": 1238
+ },
+ "current": {
+ "records": 460,
+ "with_community_level": 391,
+ "mixed": 124,
+ "community_level_only": 267,
+ "taxa": 1507,
+ "credited_solely_by_the_rule": 1238
+ }
+ },
+ "interpretation": "Canonical roster/scope census unchanged. Explicit participants identify MUCC aggregate/guild context and focal genus, MWF001 input strains and four magnetite guild placeholders. This coarse census does not certify exact identities, final abundance or partner flux."
+ },
+ "network_warning_count": 46,
+ "corpus": {
+ "scope": "Every YAML under kb/communities and data/isolates; filesystem discovery includes hidden/ignored files.",
+ "records": 460,
+ "nodes": 1452,
+ "edges": 638,
+ "records_without_nodes": 8,
+ "records_without_edges": 162,
+ "review_status_counts": {
+ "needs_research": 22,
+ "pending": 227,
+ "reviewed": 211
+ },
+ "structural_defects": []
+ },
+ "tested_file_sha256": {
+ "reports/causal_graph_review/decisions/20261006-wetland-crossfeeding-batch66.yaml": "25c1e04567419365da0bd38688918032decf12122cc83ab7c994b73d42a484f3",
+ "tests/test_causal_review_batch66.py": "225c29cd014b09e296d9f0ebf98c787d7cc88061d3e25f4f2c939c5b1e715f3b",
+ "tests/test_participating_taxa.py": "f48d81d715605137dc9cb1951228142035ba8b242bf812489475294102ddaeb2",
+ "kb/communities/MUCC_Freshwater_Wetland_Methane_Network_Community.yaml": "7d4a55d47676c9d86d07bed817918b120fb80464e39212ef2cd4491c70c45abb",
+ "kb/communities/MWF001_FourSpecies_CrossFeeding_Consortium.yaml": "e74f02ca9923e5df126fe571d3f6edc28a59451d385df9b89276f6a68882253b",
+ "kb/communities/Magnetite_Sulfate_Stress_Anaerobic_Microbiome.yaml": "1947b775f1ff0266347513042955d0502cae65b6fcfefc89264a35c2382217ca",
+ "reports/causal_graph_review/README.md": "16cb3f4925ca4a93dfdb19237bdfbfde11826ba388f62c5764406affe8274fba"
+ },
+ "status": "verified_assay_boundary_graph_review",
+ "pre_research_baseline": {
+ "base_commit": "e788ade71f030cd1c482ac279b5a6c554aa1f467",
+ "base_tree": "783500cc8f3dad4f51a8fff0251273482facdf2b",
+ "research_worktree": "/private/tmp/communitymech-causal-batch65",
+ "checks": [
+ {
+ "name": "rank",
+ "command": [
+ "just",
+ "rank-causal-graphs"
+ ],
+ "exit_code": 0,
+ "expected_exit_code": 0,
+ "log": "/private/tmp/communitymech-batch66/baseline-rank.log",
+ "sha256": "2a9d5b9cc978c3498874171080178455e371bd6644858798a48d848ffdd8c603",
+ "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-batch66/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-batch66/baseline-network.log",
+ "sha256": "3a156d88a5b27b6a726e91303cf9249745ee46d4e53a0ac73d58779dc1041a7d",
+ "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-batch66/baseline-downstream.log",
+ "sha256": "591bed59bbb19b25b79636435a4e08d33132892ba3ebef17bf8ba8e3c2b8c56b",
+ "output_tail": "Coculture.yaml:344: downstream:\nkb/communities/Chlamydomonas_Bacterial_H2_Consortium.yaml:311: downstream:\nkb/communities/Chlamydomonas_Bacterial_H2_Consortium.yaml:365: downstream:\nkb/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml:135: downstream:\nkb/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml:177: downstream:\nkb/communities/Geobacter_Pseudomonas_Formate_Fumarate_Electroactive_Coculture.yaml:191: downstream:\nkb/communities/Methylacidiphilum_Galdieria_Thermoacidophilic_Coculture.yaml:268: downstream:\nkb/communities/Methylacidiphilum_Galdieria_Thermoacidophilic_Coculture.yaml:315: downstream:\nkb/communities/Human_Gut_FourMember_Proteome_Complementarity_Consortium.yaml:153: downstream:\nkb/communities/Human_Gut_FourMember_Proteome_Complementarity_Consortium.yaml:218: downstream:\nkb/communities/Soybean_Chlorophyll_Selected_Biofertilizer_SynCom.yaml:98: downstream:\nkb/communities/Soybean_Chlorophyll_Selected_Biofertilizer_SynCom.yaml:155: 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/Clostridium_Autoethanogenum_Kluyveri_Syngas_Coculture.yaml:147: downstream:\nkb/communities/Clostridium_Autoethanogenum_Kluyveri_Syngas_Coculture.yaml:247: downstream:\nkb/communities/Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom.yaml:332: downstream:\nkb/communities/SMutans_VParvula_ASC_Biofilm.yaml:131: downstream:\nkb/communities/SMutans_VParvula_ASC_Biofilm.yaml:179: 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/Rice_P_Uptake_Intercropping_SynCom4.yaml:121: downstream:\nkb/communities/Rice_P_Uptake_Intercropping_SynCom4.yaml:149: downstream:\n"
+ }
+ ],
+ "baseline_sha256": "363385086dc5c5759fd08645be2e6770ad6c146bcf05219c69d693b58bbb6da2"
+ },
+ "reference_validator_caveat": "CLI Total checks counts reported issues, not executed checks. MATCH is not scientific entailment or historical provenance certification. All920 caches unchanged;16 graph excerpts match fresh primary text (15 whitespace-only,1 apostrophe rendering equivalence). #1574 remains unresolved; broader #476/#1091/#1095 limitations persist."
+}
diff --git a/tests/test_causal_review_batch66.py b/tests/test_causal_review_batch66.py
new file mode 100644
index 000000000..fb2311a30
--- /dev/null
+++ b/tests/test_causal_review_batch66.py
@@ -0,0 +1,128 @@
+"""Preserve observations without promoting association or feasible flux to proof."""
+
+import hashlib
+from pathlib import Path
+
+import yaml
+
+ROOT = Path(__file__).resolve().parents[1]
+LEDGER = ROOT / "reports/causal_graph_review/decisions/20261006-wetland-crossfeeding-batch66.yaml"
+A = "MUCC_Freshwater_Wetland_Methane_Network_Community"
+B = "MWF001_FourSpecies_CrossFeeding_Consortium"
+C = "Magnetite_Sulfate_Stress_Anaerobic_Microbiome"
+
+
+def records():
+ ledger = yaml.safe_load(LEDGER.read_text())
+ rows = {Path(r["path"]).stem: r for r in ledger["records"]}
+ docs = {name: yaml.safe_load((ROOT / r["path"]).read_text()) for name, r in rows.items()}
+ return ledger, rows, docs
+
+
+def test_mucc_occupancy_and_network_are_not_demonstrated_interactions():
+ _, rows, docs = records()
+ core, network, _, _ = docs[A]["ecological_interactions"]
+ for phrase in ["five high-emitting", "at least one sample", "contextual placeholders"]:
+ assert phrase in core["description"]
+ for phrase in ["12 late-season samples", "JLA is a swamp", "genus level", "environmental"]:
+ assert phrase in network["description"]
+ assert rows[A]["edges_before"] == rows[A]["edges_after"] == []
+ assert all("interaction_type" not in n for n in docs[A]["ecological_interactions"])
+
+
+def test_mucc_predictor_and_genomic_potential_do_not_prove_flux_or_methanol_use():
+ _, _, docs = records()
+ predictor, potential = docs[A]["ecological_interactions"][2:]
+ for phrase in ["within methanogens", "2018", "2015", "not methane-production flux"]:
+ assert phrase in predictor["description"]
+ for phrase in ["107", "methylated sulfides", "methoxylated", "not confirmed substrate use"]:
+ assert phrase in potential["description"]
+ assert {m["term"]["id"] for m in potential["metabolites"]} == {"CHEBI:16183"}
+ assert all("biological_processes" not in n for n in docs[A]["ecological_interactions"])
+
+
+def test_mwf_crossfeeding_has_residual_resource_and_generic_model_limits():
+ _, _, docs = records()
+ node = docs[B]["ecological_interactions"][0]
+ assert node["interaction_type"] == "CROSS_FEEDING"
+ assert node["description"].startswith("PARTIAL -")
+ for phrase in ["not chemically resolved", "applies to simulations", "Generic", "not universal"]:
+ assert phrase in node["description"]
+ assert node["evidence"][0]["supports"] == "PARTIAL"
+ assert node["evidence"][1]["evidence_source"] == "COMPUTATIONAL"
+
+
+def test_mwf_finite_coexistence_keeps_exceptions_and_extension_unfinished():
+ ledger, rows, docs = records()
+ node = docs[B]["ecological_interactions"][1]
+ for phrase in ["eight 72-hour", "5X-malate", "without carbon", "1/10", "four-day"]:
+ assert phrase in node["description"]
+ assert "interaction_type" not in node
+ assert rows[B]["status"] == "needs_research"
+ assert ledger["unresolved_research_issues"] == [1575]
+ assert ledger["edison"]["required_for_pending_extension"] is True
+ assert docs[B]["discussions"][0]["discussion_id"] == "mwf001_exact_byproduct_resolution"
+ assert "#1575" in docs[B]["discussions"][-1]["rationale"]
+
+
+def test_magnetite_response_is_partial_and_does_not_prove_diet():
+ _, _, docs = records()
+ node = docs[C]["ecological_interactions"][0]
+ for phrase in [
+ "19% relative",
+ "not full",
+ "1.2 g/L",
+ "Separate abiotic",
+ "no abiotic hydrogen",
+ ]:
+ assert phrase in node["description"]
+ assert "interaction_type" not in node
+ assert docs[C]["discussions"][0]["discussion_id"] == "kg-magnetite-sulfate-diet-validation"
+
+
+def test_magnetite_retains_model_exchange_with_role_and_replication_limits():
+ _, _, docs = records()
+ acetate, exchange = docs[C]["ecological_interactions"][1:]
+ for node in [acetate, exchange]:
+ assert node["interaction_type"] == "CROSS_FEEDING"
+ assert node["description"].startswith("HYPOTHESIZED -")
+ assert all(e["evidence_source"] == "COMPUTATIONAL" for e in node["evidence"])
+ assert len(node["participating_taxa"]) == 4
+ for phrase in ["DTU8", "DTU25", "DTU38", "DTU36", "gap-filled", "0.7", "One biological"]:
+ assert phrase in acetate["description"]
+ assert "0.1 mmol/gDW/hour" in exchange["description"]
+ assert "Multiple solutions" in exchange["description"]
+
+
+def test_batch66_caches_canonical_participants_and_existing_gaps_preserved():
+ ledger, _, docs = records()
+ for path, digest in ledger["reference_cache_original_hashes"].items():
+ assert hashlib.sha256((ROOT / path).read_bytes()).hexdigest() == digest
+ for doc in docs.values():
+ canonical = {
+ t["taxon_term"]["preferred_term"]: t["taxon_term"]["term"] for t in doc["taxonomy"]
+ }
+ for node in doc["ecological_interactions"]:
+ for taxon in node["participating_taxa"]:
+ assert canonical[taxon["preferred_term"]] == taxon["term"]
+ assert "#1574" in doc["discussions"][-1]["rationale"]
+ assert ledger["unresolved_non_graph_issues"] == [1574]
+ assert ledger["primary_graph_snippet_count"] == 16
+
+
+def test_batch66_whole_node_ledger_history_and_no_false_completion():
+ ledger, rows, docs = records()
+ assert ledger["independent_approval"] is False
+ assert ledger["issues"] == [1571, 1572, 1573]
+ assert ledger["edison"]["provider_submissions"] == ledger["edison"]["credits_spent"] == 0
+ assert sum(len(r["node_decisions"]) for r in rows.values()) == 9
+ for name, row in rows.items():
+ doc = docs[name]
+ assert hashlib.sha256((ROOT / row["path"]).read_bytes()).hexdigest() == row["record_sha256"]
+ assert doc["curation_history"][-1]["llm_assisted"] is True
+ assert len(row["history_files"]) == 1
+ assert row["status"] == ("needs_research" if name == B else "reviewed")
+ assert row["edges_before"] == row["edges_after"] == []
+ names = {n["name"] for n in doc["ecological_interactions"]}
+ assert {d["node"] for d in row["node_decisions"]} == names
+ assert {a.split("#", 1)[1] for a in doc["discussions"][-1]["attaches_to"]} == names
diff --git a/tests/test_participating_taxa.py b/tests/test_participating_taxa.py
index a9b18ccd7..b9fd898f9 100644
--- a/tests/test_participating_taxa.py
+++ b/tests/test_participating_taxa.py
@@ -321,6 +321,8 @@ def test_a_curie_is_ambiguous_where_members_share_an_id(example):
"MSC1_Dominant_Core.yaml",
"MSC2_Model_Soil_Consortium.yaml",
"MUC2_Human_Gut_Commensal_Defined_Consortium.yaml",
+ "MUCC_Freshwater_Wetland_Methane_Network_Community.yaml",
+ "MWF001_FourSpecies_CrossFeeding_Consortium.yaml",
"Magnetite_Sulfate_Stress_Anaerobic_Microbiome.yaml",
"Maize_Root_Simplified_Community.yaml",
"Maize_SC2_RootRot_Biocontrol_SynCom.yaml",