D. vulgaris Hildenborough ferments lactate and provides hydrogen and acetate that support D. mccartyi strain 195 growth and reductive dechlorination in the coculture.
+ DvH fermentation of lactate supplies hydrogen as electron donor and acetate for strain-195 growth in the syntrophic coculture. Hydrogen consumption by the dechlorinator supports fermentative energetics. This does not establish that DvH supplies every required cofactor; later cobalamin-free tests required an additional corrinoid source or cobalamin amendment.
DvH ferments lactate in the defined consortium and supplies hydrogen needed by Dhc195 for reductive dechlorination.
+ DvH ferments lactate and supplies hydrogen for Dhc195 reductive dechlorination in the defined triculture. Dhc195 hydrogen consumption supports DvH fermentative energetics. Sustainable growth in the cobalamin-free experiment additionally depends on the corrinoid-supplying partner and externally supplied DMB.
PfR7 provides corrinoids that allow Dhc195 to sustain dechlorination and cell growth when cobalamin is not supplied exogenously.
+ PfR7 supplies corrinoids to Dhc195 in the DMB-amended, cobalamin-free triculture. These include precursors for recipient remodeling; PfR7 can also form some cobalamin when supplied DMB. DMB is an external amendment, not a demonstrated PfR7 product, and recipient remodeling is not the only possible functional-cofactor route.
"CbiZ-dependent corrinoid-remodeling pathway and BtuFCD corrinoid ABC transporter genes"
@@ -954,13 +953,21 @@ M. barkeri Fusaro produces factor III cobamide, and when DMB is added the coculture can generate a cobalamin that supports Dehalococcoides reductive dechlorination activity and growth.
+ DMB amendment enables compatible cobalamin production and supports BAV1 dechlorination and growth in the Fusaro coculture. Native factor III alone does not supply an adequate cofactor under the tested conditions. The experiment supports conditional partner assistance, not endogenous DMB supply or reciprocal nutrient exchange.
-
BAV1 uses cobalamin-dependent organohalide respiration to detoxify chlorinated ethenes, and insufficient cobalamin causes incomplete dechlorination and vinyl chloride accumulation.
+
BAV1 cobalamin-dependent organohalide respiration converts growth-supporting chlorinated ethenes toward ethene; limited cofactor availability can leave incomplete dechlorination and vinyl chloride. This is the recipient phenotype, not BAV1-to-Fusaro cross-feeding. Pooled BAV1, GT and FL2 responses are not all assigned to this pair.
Source Taxon: Dehalococcoides mccartyi BAV1
-
Target Taxon: Methanosarcina barkeri strain Fusaro
-
Metabolites:
@@ -868,6 +854,25 @@
Evidence
+
+ Knowledge gaps & discussions (1)
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which cofactor-production and remodeling routes support BAV1 in the DMB-amended pair?
+
+
The cached abstract and indexed primary excerpts support DMB-dependent rescue and native-cobamide insufficiency, not an exclusive cell-resolved route or reciprocal transfer. Complete primary body, figure images and supplements were not retrieved; fine-grained strain/substrate comparisons are therefore not generalized. Preserve the positive rescue and negative compatibility observations without equating absence of support with toxicity. Non-graph follow-up: #1386.
+
+
Attaches to: ecological_interactions#DMB-Guided Cobalamin Support, ecological_interactions#Factor III Is Insufficient Without DMB, ecological_interactions#Cobalamin-Dependent Reductive Dechlorination
+
+
+
+
+
@@ -1357,13 +1362,9 @@
Evidence
(function() {
var intId = "interaction:1";
- var intType = "COMMENSALISM";
+ var intType = "UNKNOWN";
var metabolites = [];
-
- metabolites.push("cobalamin");
-
-
var processes = [];
@@ -1399,7 +1400,7 @@
Evidence
(function() {
var intId = "interaction:2";
- var intType = "CROSS_FEEDING";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1436,11 +1437,6 @@
Evidence
- var tgtKey = "Methanosarcina barkeri strain Fusaro";
- if (taxonNodeIds[tgtKey]) {
- links.push({ source: intId, target: taxonNodeIds[tgtKey] });
- }
-
})();
diff --git a/history/records/Dehalococcoides_Desulfovibrio_Lactate_TCE_Syntrophy/2026-10-06T054824Z-codex-33c8ca.yaml b/history/records/Dehalococcoides_Desulfovibrio_Lactate_TCE_Syntrophy/2026-10-06T054824Z-codex-33c8ca.yaml
new file mode 100644
index 000000000..34c283b42
--- /dev/null
+++ b/history/records/Dehalococcoides_Desulfovibrio_Lactate_TCE_Syntrophy/2026-10-06T054824Z-codex-33c8ca.yaml
@@ -0,0 +1,27 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Dehalococcoides_Desulfovibrio_Lactate_TCE_Syntrophy.yaml
+ slug: Dehalococcoides_Desulfovibrio_Lactate_TCE_Syntrophy
+session:
+ id: 2026-10-06T054824Z-codex-33c8ca
+ timestamp: '2026-10-06T05:48:24Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1382
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain positive fermentation support with cofactor and ancillary-mechanism limits.;
+ Represent measured recipient activity without a duplicate transfer claim.; Retain the
+ conditional negative arrow while separating sulfide toxicity from hydrogen competition.
+ details: Primary-source self-adversarial scope correction; all existing nodes/arrows retained.
+ reports/causal_graph_review/decisions/20261006-three-records-batch30.yaml
diff --git a/history/records/Dehalococcoides_Desulfovibrio_Pelosinus_Corrinoid_Triculture/2026-10-06T054824Z-codex-290d65.yaml b/history/records/Dehalococcoides_Desulfovibrio_Pelosinus_Corrinoid_Triculture/2026-10-06T054824Z-codex-290d65.yaml
new file mode 100644
index 000000000..e5ab8ee20
--- /dev/null
+++ b/history/records/Dehalococcoides_Desulfovibrio_Pelosinus_Corrinoid_Triculture/2026-10-06T054824Z-codex-290d65.yaml
@@ -0,0 +1,28 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Dehalococcoides_Desulfovibrio_Pelosinus_Corrinoid_Triculture.yaml
+ slug: Dehalococcoides_Desulfovibrio_Pelosinus_Corrinoid_Triculture
+session:
+ id: 2026-10-06T054824Z-codex-290d65
+ timestamp: '2026-10-06T05:48:24Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1383
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain syntrophic hydrogen support with the required cofactor context.; Retain
+ corrinoid cross-feeding without assigning DMB production or an exclusive cofactor route.;
+ Assign salvaging/remodeling to Dhc195 and classify measured transcript evidence correctly.;
+ Make the complete canonical triculture and DMB-dependent outcome explicit.
+ details: Primary-source self-adversarial scope correction; all existing nodes/arrows retained.
+ reports/causal_graph_review/decisions/20261006-three-records-batch30.yaml
diff --git a/history/records/Dehalococcoides_Methanosarcina_DMB_Cobalamin_Coculture/2026-10-06T054824Z-codex-bed9ca.yaml b/history/records/Dehalococcoides_Methanosarcina_DMB_Cobalamin_Coculture/2026-10-06T054824Z-codex-bed9ca.yaml
new file mode 100644
index 000000000..f2a311f3b
--- /dev/null
+++ b/history/records/Dehalococcoides_Methanosarcina_DMB_Cobalamin_Coculture/2026-10-06T054824Z-codex-bed9ca.yaml
@@ -0,0 +1,27 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Dehalococcoides_Methanosarcina_DMB_Cobalamin_Coculture.yaml
+ slug: Dehalococcoides_Methanosarcina_DMB_Cobalamin_Coculture
+session:
+ id: 2026-10-06T054824Z-codex-bed9ca
+ timestamp: '2026-10-06T05:48:24Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1384
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain conditional DMB-associated cofactor support without assigning an exclusive
+ route.; Retain the negative compatibility result without commensalism or toxicity.; Represent
+ BAV1 dechlorination as a recipient phenotype without reverse cross-feeding.
+ details: Primary-source self-adversarial scope correction; all existing nodes/arrows retained.
+ reports/causal_graph_review/decisions/20261006-three-records-batch30.yaml
diff --git a/kb/communities/Dehalococcoides_Desulfovibrio_Lactate_TCE_Syntrophy.yaml b/kb/communities/Dehalococcoides_Desulfovibrio_Lactate_TCE_Syntrophy.yaml
index 8d2f42243..10b2fc384 100644
--- a/kb/communities/Dehalococcoides_Desulfovibrio_Lactate_TCE_Syntrophy.yaml
+++ b/kb/communities/Dehalococcoides_Desulfovibrio_Lactate_TCE_Syntrophy.yaml
@@ -131,9 +131,10 @@ taxonomy:
explanation: Supports the same DvH strain in later constructed-consortium perturbation experiments.
ecological_interactions:
- name: Lactate Fermentation Supports Dehalococcoides Growth
- description: D. vulgaris Hildenborough ferments lactate and provides hydrogen and
- acetate that support D. mccartyi strain 195 growth and reductive dechlorination
- in the coculture.
+ description: DvH fermentation of lactate supplies hydrogen as electron donor and acetate for strain-195 growth
+ in the syntrophic coculture. Hydrogen consumption by the dechlorinator supports fermentative energetics. This
+ does not establish that DvH supplies every required cofactor; later cobalamin-free tests required an additional
+ corrinoid source or cobalamin amendment.
interaction_type: SYNTROPHY
scope: PAIRWISE
source_taxon:
@@ -170,9 +171,10 @@ ecological_interactions:
label: anaerobic respiration
downstream:
- target: Enhanced TCE Dechlorination By Syntrophic Support
- description: H2 and acetate from DvH lactate fermentation feed the obligately
- H2-consuming D. mccartyi strain 195, enabling and accelerating reductive TCE
- dechlorination (the community's bioremediation function).
+ description: DvH-derived hydrogen and acetate support strain-195 growth and reductive dechlorination in the
+ tested coculture. The faster dechlorination comparison does not isolate every proposed ancillary benefit;
+ proton translocation, amino-acid supply and corrinoid-related effects are not separately demonstrated by this
+ arrow.
evidence:
- reference: PMID:21881617
supports: SUPPORT
@@ -184,18 +186,18 @@ ecological_interactions:
evidence_source: IN_VITRO
snippet: capabilities of DVH to ferment lactate to provide H(2) and acetate for growth
explanation: Supports the hydrogen and acetate cross-feeding mechanism from DvH to strain 195.
+ - reference: PMID:24463969
+ supports: PARTIAL
+ evidence_source: IN_VITRO
+ snippet: Only the triculture exhibited sustainable dechlorination and cell growth
+ explanation: Constrains the cobalamin-free comparison to the tested DMB-amended consortia. It does not mean
+ the cobalamin-supplemented two-member coculture cannot grow.
- name: Enhanced TCE Dechlorination By Syntrophic Support
- description: D. mccartyi strain 195 uses partner-supported reducing equivalents
- to dechlorinate trichloroethene, with coculture dechlorination rates and
- strain 195 cell yield enhanced relative to strain 195 grown alone.
- interaction_type: CROSS_FEEDING
+ description: Strain 195 showed faster reductive dechlorination and greater cell yield in DvH coculture than in
+ isolation. The approximately threefold comparison concerns maximum dechlorination rate, not every growth endpoint.
+ This is the recipient dechlorinator phenotype, not a second DvH-to-Dhc195 metabolite-transfer event.
scope: PAIRWISE
source_taxon:
- preferred_term: Desulfovibrio vulgaris Hildenborough
- term:
- id: NCBITaxon:882
- label: Nitratidesulfovibrio vulgaris str. Hildenborough
- target_taxon:
preferred_term: Dehalococcoides mccartyi strain 195
term:
id: NCBITaxon:243164
@@ -228,17 +230,18 @@ ecological_interactions:
supports: SUPPORT
evidence_source: IN_VITRO
snippet: maximum dechlorination rates of DE195 were enhanced by approximately three times
- explanation: Supports enhanced reductive dechlorination in the coculture.
+ explanation: Supports the measured strain-195 rate comparison; the corresponding cell-yield result is distinct
+ and is not a threefold claim.
- reference: PMID:21881617
supports: SUPPORT
evidence_source: IN_VITRO
snippet: Cell yield of DE195 was enhanced in the co-culture
explanation: Supports improved strain 195 growth in the DvH coculture.
-- name: Sulfate-Reduction Perturbation Of Dechlorination
- description: Later constructed-consortium work tested how sulfate and generated
- sulfide affect dechlorination, showing that sulfide toxicity can inhibit
- growth and dechlorination under electron-acceptor-limiting conditions.
- interaction_type: COMPETITION
+- name: Sulfide-Associated Inhibition Of Dechlorination
+ description: In the electron-acceptor-limited DvH/195 coculture, sulfate reduction at high initial sulfate generated
+ sulfide and inhibited strain-195 dechlorination and growth. This is conditional sulfide-associated inhibition,
+ not a general effect of sulfate itself or demonstrated hydrogen starvation. Donor-limited butyrate-triculture
+ and enrichment outcomes are separate experiments.
scope: PAIRWISE
source_taxon:
preferred_term: Desulfovibrio vulgaris Hildenborough
@@ -274,20 +277,24 @@ ecological_interactions:
label: anaerobic respiration
downstream:
- target: Enhanced TCE Dechlorination By Syntrophic Support
- description: Under high sulfate, DvH sulfate reduction diverts reducing equivalents
- and generates sulfide, whose toxicity suppresses reductive TCE dechlorination —
- opposing the syntrophic support edge.
+ description: Under the tested high-sulfate, electron-donor-excess conditions, accumulated sulfide suppresses
+ strain-195 dechlorination despite available hydrogen. Electron allocation to sulfate reduction is not sufficient
+ evidence that hydrogen competition caused this inhibition. The arrow qualifies the recipient phenotype under
+ this perturbation, not its unperturbed coculture rate.
evidence:
- reference: PMID:28159790
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: high sulfate concentrations (5 mM) inhibited reductive dechlorination due to the toxicity of generated sulfide
- explanation: Supports sulfate/sulfide perturbation as a mechanistic stressor for dechlorination.
+ snippet: high sulfate concentrations (5 mM) inhibited reductive dechlorination due to the toxicity of generated
+ sulfide
+ explanation: Supports generated-sulfide toxicity in electron-acceptor-limited cocultures; does not establish
+ sulfate toxicity or a hydrogen-starvation mechanism.
- reference: PMID:28159790
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: sulfide at 5 mM exhibited inhibitory effects on growth of the sulfate reducer
- explanation: Supports sulfide toxicity to the sulfate-reducing partner and community function.
+ snippet: sulfide at 5 mM exhibited inhibitory effects
+ explanation: Supports sulfide inhibition in the tested cultures. The primary Results distinguish organism-specific
+ thresholds; the abstract and Results differ on the DvH threshold, which is not resolved here.
environmental_factors:
- name: Lactate-fed anaerobic condition
value: lactate as sole energy and carbon source
@@ -511,3 +518,27 @@ rare_earth_elements_present: []
metal_relevance: NOT_APPLICABLE
metal_notes: No metal or rare earth element processing role is curated for this chlorinated-ethene
dechlorinating coculture.
+discussions:
+- discussion_id: dhc_dvh_inhibition_and_support_limits
+ prompt: Which ancillary partner benefits and sulfide-sensitive processes explain strain-195 performance?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Lactate Fermentation Supports Dehalococcoides Growth
+ - ecological_interactions#Enhanced TCE Dechlorination By Syntrophic Support
+ - ecological_interactions#Sulfide-Associated Inhibition Of Dechlorination
+ rationale: 'Keep measured fermentation support and conditional inhibition distinct. The 2012 full body was unavailable;
+ ancillary benefits remain potential. The 2017 primary body distinguishes donor-excess cocultures from donor-limited
+ tricultures and shows inhibition despite hydrogen availability. Its abstract and Results differ on the DvH sulfide
+ threshold. Expression changes do not by themselves identify the inhibited enzyme. Broader field concentrations
+ and mechanisms are not established by these laboratory comparisons. Non-graph follow-up: #1385.'
+ posed_by: codex
+ posed_date: '2026-10-06'
+curation_history:
+- timestamp: '2026-10-06T05:48:23Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: 'Retain positive fermentation support with cofactor and ancillary-mechanism limits.; Represent measured
+ recipient activity without a duplicate transfer claim.; Retain the conditional negative arrow while separating
+ sulfide toxicity from hydrogen competition. Issue #1382; reports/causal_graph_review/decisions/20261006-three-records-batch30.yaml'
+ llm_assisted: true
diff --git a/kb/communities/Dehalococcoides_Desulfovibrio_Pelosinus_Corrinoid_Triculture.yaml b/kb/communities/Dehalococcoides_Desulfovibrio_Pelosinus_Corrinoid_Triculture.yaml
index 1f592d031..4196f5427 100644
--- a/kb/communities/Dehalococcoides_Desulfovibrio_Pelosinus_Corrinoid_Triculture.yaml
+++ b/kb/communities/Dehalococcoides_Desulfovibrio_Pelosinus_Corrinoid_Triculture.yaml
@@ -177,8 +177,9 @@ taxonomy:
explanation: Supports the corrinoid-supplying role assigned to PfR7.
ecological_interactions:
- name: Hydrogen Provision By Desulfovibrio
- description: DvH ferments lactate in the defined consortium and supplies hydrogen
- needed by Dhc195 for reductive dechlorination.
+ description: DvH ferments lactate and supplies hydrogen for Dhc195 reductive dechlorination in the defined triculture.
+ Dhc195 hydrogen consumption supports DvH fermentative energetics. Sustainable growth in the cobalamin-free experiment
+ additionally depends on the corrinoid-supplying partner and externally supplied DMB.
interaction_type: SYNTROPHY
scope: PAIRWISE
source_taxon:
@@ -215,10 +216,9 @@ ecological_interactions:
label: anaerobic respiration
downstream:
- target: Hydrogen- and Corrinoid-Supported TCE Dechlorination
- description: >
- DvH-supplied hydrogen provides the electron donor input that Dhc195 needs,
- together with PfR7-derived corrinoids, for sustainable reductive
- dechlorination in the defined triculture.
+ description: DvH-supplied hydrogen supports the electron-donor requirement of Dhc195 in the lactate-fed triculture,
+ together with partner corrinoids and externally supplied DMB. Hydrogen provision alone does not make the cobalamin-free
+ two-member coculture sustainable.
evidence:
- reference: PMID:24463969
supports: SUPPORT
@@ -231,8 +231,9 @@ ecological_interactions:
snippet: trichloroethene (TCE)- and lactate-amended medium
explanation: Supports lactate and TCE as the donor and acceptor context for the triculture.
- name: Corrinoid Provision By Pelosinus
- description: PfR7 provides corrinoids that allow Dhc195 to sustain dechlorination
- and cell growth when cobalamin is not supplied exogenously.
+ description: PfR7 supplies corrinoids to Dhc195 in the DMB-amended, cobalamin-free triculture. These include precursors
+ for recipient remodeling; PfR7 can also form some cobalamin when supplied DMB. DMB is an external amendment,
+ not a demonstrated PfR7 product, and recipient remodeling is not the only possible functional-cofactor route.
interaction_type: CROSS_FEEDING
scope: PAIRWISE
source_taxon:
@@ -250,10 +251,13 @@ ecological_interactions:
term:
id: CHEBI:30411
label: cobalamin
+ notes: Functional cofactor context; PfR7 also supplies other corrinoids. This entry does not identify every
+ transferred molecule as cobalamin.
- preferred_term: 5,6-dimethylbenzimidazole
term:
id: CHEBI:15890
label: 5,6-dimethylbenzimidazole
+ notes: Externally supplied lower ligand, not a demonstrated PfR7-to-Dhc195 transfer.
biological_processes:
- preferred_term: vitamin metabolic process
term:
@@ -265,9 +269,9 @@ ecological_interactions:
label: cobalamin transport
downstream:
- target: Dhc195 Corrinoid Salvaging And Remodeling
- description: >
- PfR7 corrinoid production supplies the phenolic corrinoids that Dhc195
- imports and remodels into cobalamin when DMB is present.
+ description: PfR7 supplies corrinoid substrates that Dhc195 can salvage and remodel in the presence of externally
+ supplied DMB. This does not exclude donor guided cobalamin biosynthesis or establish that all functional cofactor
+ passes through recipient remodeling.
evidence:
- reference: PMID:24463969
supports: SUPPORT
@@ -280,17 +284,11 @@ ecological_interactions:
snippet: physiological level of 5,6-dimethylbenzimidazole (DMB)
explanation: Supports DMB as the lower-ligand supplement required for sustainable triculture performance.
- name: Dhc195 Corrinoid Salvaging And Remodeling
- description: Dhc195 imports and remodels phenolic corrinoids produced by PfR7
- into cobalamin in the presence of DMB, inducing corrinoid-remodeling and
- corrinoid-transport genes.
- interaction_type: CROSS_FEEDING
+ description: Dhc195 salvages and remodels PfR7-derived corrinoids into cobalamin when DMB is supplied. Corrinoid
+ profiles and laboratory transcript measurements support this recipient-intrinsic process, not another donor-to-recipient
+ exchange or proof that induced transporter/remodeling genes are individually necessary.
scope: PAIRWISE
source_taxon:
- preferred_term: Pelosinus fermentans R7
- term:
- id: NCBITaxon:1122947
- label: Pelosinus fermentans DSM 17108
- target_taxon:
preferred_term: Dehalococcoides mccartyi strain 195
term:
id: NCBITaxon:243164
@@ -315,10 +313,9 @@ ecological_interactions:
label: cobalamin transport
downstream:
- target: Hydrogen- and Corrinoid-Supported TCE Dechlorination
- description: >
- Dhc195 corrinoid salvaging and remodeling turns PfR7-produced corrinoids
- into cobalamin cofactors that support sustainable TCE dechlorination when
- DvH also supplies hydrogen.
+ description: Recipient salvaging and remodeling contributes compatible cofactor for sustainable TCE dechlorination
+ in the DMB-amended triculture when DvH supplies hydrogen. The source supports this route but does not selectively
+ separate its contribution from cobalamin formed by the donor in the presence of DMB.
evidence:
- reference: PMID:24463969
supports: SUPPORT
@@ -327,15 +324,15 @@ ecological_interactions:
explanation: Supports Dhc195 corrinoid remodeling of PfR7-produced corrinoids.
- reference: PMID:24463969
supports: SUPPORT
- evidence_source: COMPUTATIONAL
+ evidence_source: IN_VITRO
snippet: CbiZ-dependent corrinoid-remodeling pathway and BtuFCD corrinoid ABC transporter genes
- explanation: Supports the transcriptomic response associated with corrinoid salvaging and transport.
+ explanation: Supports measured microarray induction in laboratory cultures. Transcript abundance is not a selective
+ gene-necessity experiment or direct transporter activity measurement.
- name: Hydrogen- and Corrinoid-Supported TCE Dechlorination
- description: >
- The three-member consortium combines DvH hydrogen provisioning with
- PfR7-to-Dhc195 corrinoid transfer and Dhc195 cobalamin remodeling to sustain
- TCE dechlorination and Dehalococcoides growth without exogenous cobalamin.
- interaction_type: SYNTROPHY
+ description: The three-member lactate-fed consortium sustains TCE dechlorination and Dhc195 growth without exogenous
+ cobalamin when DMB is supplied. DvH provides hydrogen and PfR7 corrinoids, with Dhc195 remodeling contributing
+ compatible cofactor. This is a DMB-dependent community outcome, not self-sufficiency without any external lower
+ ligand.
scope: COMMUNITY_LEVEL
metabolites:
- preferred_term: dihydrogen
@@ -368,12 +365,26 @@ ecological_interactions:
supports: SUPPORT
evidence_source: IN_VITRO
snippet: Only the triculture exhibited sustainable dechlorination and cell growth
- explanation: Supports the full Dhc195/DvH/PfR7 triculture as the sustainable TCE-dechlorinating state.
+ explanation: The abstract qualifies the sustainable triculture result by DMB provision. It does not deny growth
+ of cobalamin-amended controls or hydrogen-supplemented alternative cocultures.
- reference: PMID:24463969
supports: SUPPORT
evidence_source: IN_VITRO
snippet: DvH provided hydrogen while PfR7 provided corrinoids to Dhc195
explanation: Supports the combined hydrogen and corrinoid inputs needed for the triculture output.
+ participating_taxa:
+ - preferred_term: Dehalococcoides mccartyi strain 195
+ term:
+ id: NCBITaxon:243164
+ label: Dehalococcoides mccartyi 195
+ - preferred_term: Desulfovibrio vulgaris Hildenborough
+ term:
+ id: NCBITaxon:882
+ label: Nitratidesulfovibrio vulgaris str. Hildenborough
+ - preferred_term: Pelosinus fermentans R7
+ term:
+ id: NCBITaxon:1122947
+ label: Pelosinus fermentans DSM 17108
environmental_factors:
- name: Cobalamin-free medium
value: no exogenous cobalamin
@@ -544,3 +555,29 @@ rare_earth_elements_present: []
metal_relevance: NOT_APPLICABLE
metal_notes: No metal or rare earth element processing role is curated for this dechlorinating
corrinoid-transfer triculture.
+discussions:
+- discussion_id: dhc_pelosinus_cofactor_route_partition
+ prompt: How much functional cofactor comes from donor guided synthesis versus recipient remodeling?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Hydrogen Provision By Desulfovibrio
+ - ecological_interactions#Corrinoid Provision By Pelosinus
+ - ecological_interactions#Dhc195 Corrinoid Salvaging And Remodeling
+ - ecological_interactions#Hydrogen- and Corrinoid-Supported TCE Dechlorination
+ rationale: 'The primary corrinoid profiles and transcript measurements support remodeling but do not selectively
+ partition its contribution from PfR7 cobalamin production under DMB supplementation. Gene induction is not genetic
+ necessity. All three arrows retain the external lower-ligand condition. Other observed fermentation relationships
+ are not claimed to be exhaustively represented; no new node or arrow is introduced. Full main body and table
+ text were read, not figure images or supplements. Non-graph follow-up: #1385.'
+ posed_by: codex
+ posed_date: '2026-10-06'
+curation_history:
+- timestamp: '2026-10-06T05:48:23Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: 'Retain syntrophic hydrogen support with the required cofactor context.; Retain corrinoid cross-feeding
+ without assigning DMB production or an exclusive cofactor route.; Assign salvaging/remodeling to Dhc195 and
+ classify measured transcript evidence correctly.; Make the complete canonical triculture and DMB-dependent outcome
+ explicit. Issue #1383; reports/causal_graph_review/decisions/20261006-three-records-batch30.yaml'
+ llm_assisted: true
diff --git a/kb/communities/Dehalococcoides_Methanosarcina_DMB_Cobalamin_Coculture.yaml b/kb/communities/Dehalococcoides_Methanosarcina_DMB_Cobalamin_Coculture.yaml
index 212b851a1..20e76ab8a 100644
--- a/kb/communities/Dehalococcoides_Methanosarcina_DMB_Cobalamin_Coculture.yaml
+++ b/kb/communities/Dehalococcoides_Methanosarcina_DMB_Cobalamin_Coculture.yaml
@@ -108,8 +108,9 @@ taxonomy:
explanation: Supports extracellular cobamide production by M. barkeri Fusaro.
ecological_interactions:
- name: DMB-Guided Cobalamin Support
- description: M. barkeri Fusaro produces factor III cobamide, and when DMB is added the coculture can generate
- a cobalamin that supports Dehalococcoides reductive dechlorination activity and growth.
+ description: DMB amendment enables compatible cobalamin production and supports BAV1 dechlorination and growth
+ in the Fusaro coculture. Native factor III alone does not supply an adequate cofactor under the tested conditions.
+ The experiment supports conditional partner assistance, not endogenous DMB supply or reciprocal nutrient exchange.
interaction_type: CROSS_FEEDING
scope: PAIRWISE
source_taxon:
@@ -142,10 +143,9 @@ ecological_interactions:
label: organohalide respiration
downstream:
- target: Cobalamin-Dependent Reductive Dechlorination
- description: >
- DMB-guided biosynthesis converts the Methanosarcina cobamide supply into
- a cobalamin compatible with the Dehalococcoides reductive
- dechlorination machinery.
+ description: With externally supplied DMB, the partner-associated corrinoid system supplies compatible cofactor
+ and enables BAV1 dechlorination and growth. This does not assign an exclusive donor-versus-recipient remodeling
+ route or imply that DMB is required when compatible cobalamin is supplied directly.
evidence:
- reference: PMID:23479750
supports: SUPPORT
@@ -158,9 +158,9 @@ ecological_interactions:
snippet: supported Dehalococcoides' activity and growth
explanation: Supports the functional outcome of cobalamin generation in the coculture.
- name: Factor III Is Insufficient Without DMB
- description: M. barkeri Fusaro produced factor III extracellular cobamide, but that cobamide alone did not
- satisfy Dehalococcoides corrinoid requirements under the tested chlorinated-ethene conditions.
- interaction_type: COMMENSALISM
+ description: Without DMB or a compatible cobalamin amendment, the tested Fusaro cobamide supply did not adequately
+ support BAV1 reductive dechlorination. This negative compatibility result is not commensalism, active factor-III
+ toxicity or proof that the methanogen inhibits an otherwise adequately supplemented dechlorinator.
scope: PAIRWISE
source_taxon:
preferred_term: Methanosarcina barkeri strain Fusaro
@@ -172,11 +172,6 @@ ecological_interactions:
term:
id: NCBITaxon:216389
label: Dehalococcoides mccartyi BAV1
- metabolites:
- - preferred_term: cobalamin
- term:
- id: CHEBI:30411
- label: cobalamin
biological_processes:
- preferred_term: organohalide respiration
term:
@@ -184,10 +179,9 @@ ecological_interactions:
label: organohalide respiration
downstream:
- target: Cobalamin-Dependent Reductive Dechlorination
- description: >
- Unguided factor III production leaves the Dehalococcoides corrinoid
- requirement unsatisfied, so organohalide respiration remains constrained
- unless DMB enables compatible cobalamin production.
+ description: Failure to supply an adequate compatible cofactor leaves BAV1 dechlorination constrained in the
+ unamended coculture. This denotes a missing nutritional input, not active inhibition by factor III. DMB-associated
+ cofactor production or direct compatible-cobalamin supplementation can overcome that limitation.
evidence:
- reference: PMID:23479750
supports: SUPPORT
@@ -200,20 +194,16 @@ ecological_interactions:
snippet: M. barkeri and the Sporomusa sp. cannot fulfil Dehalococcoides' nutritional requirements
explanation: Supports the caveat that partner-produced cobamides alone were not sufficient.
- name: Cobalamin-Dependent Reductive Dechlorination
- description: BAV1 uses cobalamin-dependent organohalide respiration to detoxify chlorinated ethenes, and
- insufficient cobalamin causes incomplete dechlorination and vinyl chloride accumulation.
- interaction_type: CROSS_FEEDING
+ description: BAV1 cobalamin-dependent organohalide respiration converts growth-supporting chlorinated ethenes
+ toward ethene; limited cofactor availability can leave incomplete dechlorination and vinyl chloride. This is
+ the recipient phenotype, not BAV1-to-Fusaro cross-feeding. Pooled BAV1, GT and FL2 responses are not all assigned
+ to this pair.
scope: PAIRWISE
source_taxon:
preferred_term: Dehalococcoides mccartyi BAV1
term:
id: NCBITaxon:216389
label: Dehalococcoides mccartyi BAV1
- target_taxon:
- preferred_term: Methanosarcina barkeri strain Fusaro
- term:
- id: NCBITaxon:269797
- label: Methanosarcina barkeri str. Fusaro
metabolites:
- preferred_term: chloroethene
term:
@@ -238,12 +228,13 @@ ecological_interactions:
supports: SUPPORT
evidence_source: IN_VITRO
snippet: require vitamin B12 (CN-Cbl) to conserve energy via organohalide respiration
- explanation: Supports cobalamin dependence for Dehalococcoides organohalide respiration.
+ explanation: Supports the recipient cobalamin requirement, not reverse nutrient transfer to the methanogen.
- reference: PMID:23479750
supports: SUPPORT
evidence_source: IN_VITRO
snippet: incomplete leading to vinyl chloride (VC) accumulation
- explanation: Supports vinyl chloride accumulation under insufficient cobalamin.
+ explanation: Supports cofactor-limited incomplete dechlorination across the tested strains. Their substrate
+ and numerical comparisons are not automatically BAV1/Fusaro-specific.
environmental_factors:
- name: DMB amendment
value: 10 microM 5,6-dimethylbenzimidazole
@@ -447,3 +438,27 @@ rare_earth_elements_present: []
metal_relevance: INCIDENTAL
metal_notes: Cobalt-containing cobalamin is central to reductive dechlorination, but no metal or rare
earth extraction/cycling role is curated for this coculture.
+discussions:
+- discussion_id: bav1_fusaro_cofactor_compatibility_limits
+ prompt: Which cofactor-production and remodeling routes support BAV1 in the DMB-amended pair?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#DMB-Guided Cobalamin Support
+ - ecological_interactions#Factor III Is Insufficient Without DMB
+ - ecological_interactions#Cobalamin-Dependent Reductive Dechlorination
+ rationale: 'The cached abstract and indexed primary excerpts support DMB-dependent rescue and native-cobamide
+ insufficiency, not an exclusive cell-resolved route or reciprocal transfer. Complete primary body, figure images
+ and supplements were not retrieved; fine-grained strain/substrate comparisons are therefore not generalized.
+ Preserve the positive rescue and negative compatibility observations without equating absence of support with
+ toxicity. Non-graph follow-up: #1386.'
+ posed_by: codex
+ posed_date: '2026-10-06'
+curation_history:
+- timestamp: '2026-10-06T05:48:23Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: 'Retain conditional DMB-associated cofactor support without assigning an exclusive route.; Retain the
+ negative compatibility result without commensalism or toxicity.; Represent BAV1 dechlorination as a recipient
+ phenotype without reverse cross-feeding. Issue #1384; reports/causal_graph_review/decisions/20261006-three-records-batch30.yaml'
+ llm_assisted: true
diff --git a/reports/causal_graph_review/adversarial-review-20261006-batch30.yaml b/reports/causal_graph_review/adversarial-review-20261006-batch30.yaml
new file mode 100644
index 000000000..b1208f263
--- /dev/null
+++ b/reports/causal_graph_review/adversarial-review-20261006-batch30.yaml
@@ -0,0 +1,141 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: a4ca06d433a89666e12c662b24e7fa488c200355
+scope:
+- kb/communities/Dehalococcoides_Desulfovibrio_Lactate_TCE_Syntrophy.yaml
+- kb/communities/Dehalococcoides_Desulfovibrio_Pelosinus_Corrinoid_Triculture.yaml
+- kb/communities/Dehalococcoides_Methanosarcina_DMB_Cobalamin_Coculture.yaml
+decision_ledger: reports/causal_graph_review/decisions/20261006-three-records-batch30.yaml
+validation_report: reports/causal_graph_review/validation-20261006-batch30.json
+findings:
+- issue: 1382
+ severity: P2
+ status: addressed_in_this_change
+ finding: Recipient dechlorination was duplicated as transfer; sulfate-related inhibition was conflated
+ with hydrogen competition.
+ disposition: Keep three nodes/two arrows; source-only Dhc phenotype and conditional sulfide inhibition,
+ with donor-excess and donor-limited systems distinguished.
+- issue: 1383
+ severity: P2
+ status: addressed_in_this_change
+ finding: Recipient remodeling was assigned as donor transfer and the required external DMB condition
+ was incompletely represented.
+ disposition: Keep four nodes/three arrows; source-only Dhc remodeling, measured transcript evidence,
+ explicit canonical triculture and DMB coinput, with donor cobalamin production retained as an alternative
+ contribution.
+- issue: 1384
+ severity: P2
+ status: addressed_in_this_change
+ finding: BAV1 phenotype was reverse cross-feeding and native cofactor insufficiency was signed as commensalism.
+ disposition: Keep three nodes/two arrows; recipient phenotype and conditional cofactor compatibility,
+ without active toxicity or exclusive cell-resolved route claims.
+- issue: 1385
+ severity: P3
+ status: open_nongraph_followup
+ finding: Non-graph measured transcript evidence classifications and supplementation-arm prose need separate
+ curation.
+ disposition: Metadata blocks preserved, not certified by this graph review.
+- issue: 1386
+ severity: P2
+ status: open_nongraph_followup
+ finding: BAV1/Fusaro medium conflates the cobalamin control, DMB rescue and strain-specific substrates.
+ disposition: Metadata blocks preserved; source-access and exact-system limitations retained.
+adversarial_checks:
+- Actual scientific diffs read against primary sources at the recorded access scope. All ten original
+ nodes and seven arrows retained; the one rename and exact anchors resolve. No invented new causal structure
+ or paid research.
+- Source-only PAIRWISE entries encode recipient capabilities under the existing schema convention, not
+ self-edges or reverse exchange. The DvH fermentation and PfR7 corrinoid transfer observations remain
+ positive.
+- The roughly threefold rate comparison is not extended to cell yield. Sulfide-associated inhibition under
+ donor excess is not inferred from electron allocation alone; the donor-limited butyrate triculture is
+ not the lactate coculture.
+- DMB is an external coinput on all three triculture arrows. PfR7 can form some cobalamin when DMB is
+ supplied; recipient remodeling is not claimed to be the sole route. Measured expression is IN_VITRO
+ and does not establish genetic necessity.
+- Native factor-III insufficiency is not active toxicity. DMB rescue is conditional partner support, and
+ direct compatible cobalamin can bypass the missing input. BAV1, GT, FL2 and different donor populations
+ are not pooled into the curated pair.
+- No figure images or supplements inspected. The 2012 source remains abstract-only; the 2013 source includes
+ partial indexed main-body excerpts, not a complete body. Primary 2014/2017 text access and failed local
+ PDF download are explicit. Textual MATCH is not scientific validation.
+- Exactly three guarded writes, llm-assisted events and append-only histories. All non-graph raw blocks,
+ 457 other records and 920 reference caches preserved. No full article/PDF is committed.
+- Participant registry changes only 173 to 174 users. Measured connectivity survey and all 31 baseline
+ network warnings are unchanged; no numeric bounds or algorithms changed.
+- Deterministic repeated rendering and exact-description parser coverage across 456 pages; no browser
+ screenshot QA claimed. Independent snippet audit and raw reference-validator diagnostics retained separately.
+- 'Deduplication includes 712 all-state issue titles/bodies, broader synonyms and ignored/hidden scoped
+ local files, not every issue comment. Non-graph issues #1385/#1386 remain open.'
+verification:
+ combined_regressions: 348 passed in 189.71s (0:03:09)
+ new_regression_tests: 6
+ schema_strict_terms_history: passed; commands and raw results retained
+ snippet_counts_by_record:
+ kb/communities/Dehalococcoides_Desulfovibrio_Lactate_TCE_Syntrophy.yaml:
+ MATCH: 30
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Dehalococcoides_Desulfovibrio_Pelosinus_Corrinoid_Triculture.yaml:
+ MATCH: 28
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Dehalococcoides_Methanosarcina_DMB_Cobalamin_Coculture.yaml:
+ MATCH: 27
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ network: Zero structural errors; all 31 baseline warnings unchanged, expected warning exit retained.
+ black_ruff_diff: passed
+ tested_file_sha256:
+ reports/causal_graph_review/decisions/20261006-three-records-batch30.yaml: cb60e4a113592fd34842090d5f2db473831a31066febb469d2438a8d8b217c3c
+ tests/test_causal_review_batch30.py: 748df86257f0a17c58fa5633d672aefed827ccf0a685056a711c874b1a650d2c
+ tests/test_participating_taxa.py: 804367466cbbfb68d80865d601ab113d1796dcdfadcb9736fa033e085693d17c
+ kb/communities/Dehalococcoides_Desulfovibrio_Lactate_TCE_Syntrophy.yaml: bc9eebbdf57b937cc87c72ee439f404bb7ab51b99b2f06e2f11fd240a454c629
+ kb/communities/Dehalococcoides_Desulfovibrio_Pelosinus_Corrinoid_Triculture.yaml: 2d771dc7df594f59d55d100bdf4e7ed6bbc571dfea0a4e37a774583e831910dc
+ kb/communities/Dehalococcoides_Methanosarcina_DMB_Cobalamin_Coculture.yaml: fbf9a3612c04d172cd46cc210b069e03e627b5dcec722682651abfe6e0e6afb7
+ post_commit_docs_current: Separate publication gate; not yet claimed by this pre-commit record.
+ protected_ci_and_merge: Require exact-head protected checks and main queue; not asserted here.
+participant_census:
+ connectivity_before:
+ community_level_only: 264
+ credited_solely_by_the_rule: 1220
+ mixed: 124
+ records: 460
+ taxa: 1496
+ with_community_level: 388
+ connectivity_after:
+ community_level_only: 264
+ credited_solely_by_the_rule: 1220
+ mixed: 124
+ records: 460
+ taxa: 1496
+ with_community_level: 388
+ exact_change: 173 -> 174 users; only the Dhc195/DvH/PfR7 triculture added
+ numeric_bounds_changed: false
+corpus:
+ records: 460
+ nodes: 1470
+ edges: 705
+ review_status_counts:
+ needs_research: 4
+ pending: 321
+ reviewed: 135
+limitations:
+- Three graph reviews; all ten nodes and seven arrows retained. No new graph structure or Edison job/spend.
+- Primary-source access differs by study and is recorded per reference. Textual snippet matching is not
+ a scientific endorsement. No figure images or supplements were inspected in this batch.
+- No new article body/PDF is committed. All reference caches and non-graph raw record blocks are preserved.
+ Two separately scoped metadata follow-ups remain open.
+- Source-only PAIRWISE entries represent intrinsic recipient capabilities under the established schema
+ convention, not self-edges or reverse nutrient exchange. This self-review is not independent approval,
+ protected CI success or full-corpus completion.
diff --git a/reports/causal_graph_review/decisions/20261006-three-records-batch30.yaml b/reports/causal_graph_review/decisions/20261006-three-records-batch30.yaml
new file mode 100644
index 000000000..70bd95e5b
--- /dev/null
+++ b/reports/causal_graph_review/decisions/20261006-three-records-batch30.yaml
@@ -0,0 +1,302 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: a4ca06d433a89666e12c662b24e7fa488c200355
+issues:
+- 1382
+- 1383
+- 1384
+open_nongraph_followups:
+- 1385
+- 1386
+issue_deduplication:
+ all_state_issue_titles_bodies: 712
+ ignored_hidden_local_files_included: true
+ comments_exhaustive: false
+ relevant_broader_issues_read:
+ - 765
+ - 650
+ - 543
+ - 529
+ - 384
+ - 383
+ finding: No duplicate exact graph defect in searched titles/bodies or scoped local review records; local hits
+ were whole-corpus rendering/validation inventories.
+reference_cache_original_hashes:
+ references_cache/PMID_12840758.md: 5c4788473d6b8c184ef6ae98f9a46e49182a8a733e2e1465b148cc328399f01c
+ references_cache/PMID_21881617.md: 249f0e7a6b71343881d648f2f539d8f9096fa2dab0e4f2692e370b47ff3fbae7
+ references_cache/PMID_23479750.md: dbae8f2e9156373b1b4a6043c9ecead8a0a4e2368fc55d36fe7c7408fc4e65b7
+ references_cache/PMID_28159790.md: 8a89860f58e10545a3986b093decf43cadec8ac10d8c994b815d497d356e819b
+ references_cache/PMID_24015929.md: 5a8edfdf6d765c4eb0e041310e03ca88fb53a96c64f2d36383ed22f773f4ff49
+ references_cache/PMID_24463969.md: 630100bad057e96e0bca2800ca31a2f1eae6ab54bccfb38c03375a70cc116de1
+limitations:
+- Three graph reviews; all ten nodes and seven arrows retained. No new graph structure or Edison job/spend.
+- Primary-source access differs by study and is recorded per reference. Textual snippet matching is not a scientific
+ endorsement. No figure images or supplements were inspected in this batch.
+- No new article body/PDF is committed. All reference caches and non-graph raw record blocks are preserved. Two
+ separately scoped metadata follow-ups remain open.
+- Source-only PAIRWISE entries represent intrinsic recipient capabilities under the established schema convention,
+ not self-edges or reverse nutrient exchange. This self-review is not independent approval, protected CI success
+ or full-corpus completion.
+records:
+- path: kb/communities/Dehalococcoides_Desulfovibrio_Lactate_TCE_Syntrophy.yaml
+ id: CommunityMech:000199
+ original_sha256: e177715e13530b307c714b59268dc295e35935d12b5d73a0ee7137ba68a927d0
+ record_sha256: bc9eebbdf57b937cc87c72ee439f404bb7ab51b99b2f06e2f11fd240a454c629
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261006-three-records-batch30.yaml
+ scope: Whole record and all original nodes/arrows reviewed at the documented primary-source access scope. Non-graph
+ fields preserved, not certified.
+ summary: Retain positive fermentation support with cofactor and ancillary-mechanism limits.; Represent measured
+ recipient activity without a duplicate transfer claim.; Retain the conditional negative arrow while separating
+ sulfide toxicity from hydrogen competition.
+ renamed_nodes:
+ Sulfate-Reduction Perturbation Of Dechlorination: Sulfide-Associated Inhibition Of Dechlorination
+ node_decisions:
+ - node: Lactate Fermentation Supports Dehalococcoides Growth
+ rationale: Retain positive fermentation support with cofactor and ancillary-mechanism limits.
+ - node: Enhanced TCE Dechlorination By Syntrophic Support
+ rationale: Represent measured recipient activity without a duplicate transfer claim.
+ - node: Sulfide-Associated Inhibition Of Dechlorination
+ rationale: Retain the conditional negative arrow while separating sulfide toxicity from hydrogen competition.
+ removed_node_decisions: []
+ edges_before:
+ - source: Lactate Fermentation Supports Dehalococcoides Growth
+ target: Enhanced TCE Dechlorination By Syntrophic Support
+ description: H2 and acetate from DvH lactate fermentation feed the obligately H2-consuming D. mccartyi strain
+ 195, enabling and accelerating reductive TCE dechlorination (the community's bioremediation function).
+ - source: Sulfate-Reduction Perturbation Of Dechlorination
+ target: Enhanced TCE Dechlorination By Syntrophic Support
+ description: Under high sulfate, DvH sulfate reduction diverts reducing equivalents and generates sulfide, whose
+ toxicity suppresses reductive TCE dechlorination — opposing the syntrophic support edge.
+ edges_after:
+ - source: Lactate Fermentation Supports Dehalococcoides Growth
+ target: Enhanced TCE Dechlorination By Syntrophic Support
+ description: DvH-derived hydrogen and acetate support strain-195 growth and reductive dechlorination in the
+ tested coculture. The faster dechlorination comparison does not isolate every proposed ancillary benefit;
+ proton translocation, amino-acid supply and corrinoid-related effects are not separately demonstrated by this
+ arrow.
+ - source: Sulfide-Associated Inhibition Of Dechlorination
+ target: Enhanced TCE Dechlorination By Syntrophic Support
+ description: Under the tested high-sulfate, electron-donor-excess conditions, accumulated sulfide suppresses
+ strain-195 dechlorination despite available hydrogen. Electron allocation to sulfate reduction is not sufficient
+ evidence that hydrogen competition caused this inhibition. The arrow qualifies the recipient phenotype under
+ this perturbation, not its unperturbed coculture rate.
+ retained_edge_decisions:
+ - source: Lactate Fermentation Supports Dehalococcoides Growth
+ target: Enhanced TCE Dechlorination By Syntrophic Support
+ rationale: DvH-derived hydrogen and acetate support strain-195 growth and reductive dechlorination in the tested
+ coculture. The faster dechlorination comparison does not isolate every proposed ancillary benefit; proton
+ translocation, amino-acid supply and corrinoid-related effects are not separately demonstrated by this arrow.
+ - source: Sulfide-Associated Inhibition Of Dechlorination
+ target: Enhanced TCE Dechlorination By Syntrophic Support
+ rationale: Under the tested high-sulfate, electron-donor-excess conditions, accumulated sulfide suppresses strain-195
+ dechlorination despite available hydrogen. Electron allocation to sulfate reduction is not sufficient evidence
+ that hydrogen competition caused this inhibition. The arrow qualifies the recipient phenotype under this perturbation,
+ not its unperturbed coculture rate.
+ removed_edge_decisions: []
+ references:
+ - PMID:21881617
+ - PMID:28159790
+ - PMID:24463969
+ - PMID:24015929
+ issues:
+ - 1382
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Dehalococcoides_Desulfovibrio_Lactate_TCE_Syntrophy/2026-10-06T054824Z-codex-33c8ca.yaml
+ source_review:
+ PMID:21881617:
+ url: https://pubmed.ncbi.nlm.nih.gov/21881617/
+ scope: 'Complete cached primary abstract and publisher search abstract. Full body not retrieved: PMC challenge,
+ Nature authorization redirect, Oxford CDN failure, CiteSeer 403 and UC repository challenge. No figures
+ or supplements inspected.'
+ PMID:28159790:
+ url: https://journals.asm.org/doi/full/10.1128/aem.03384-16
+ alternate_url: https://escholarship.org/content/qt7b1977v2/qt7b1977v2.pdf
+ scope: Complete primary main body and Methods across publisher and UC Berkeley PDF text; Table 1 text and
+ four main figure captions. No visual figure/table inspection or supplements. Abstract/Results DvH sulfide-threshold
+ discrepancy retained rather than resolved.
+ PMID:24463969: &id001
+ url: https://journals.asm.org/doi/full/10.1128/aem.03477-13
+ alternate_url: https://escholarship.org/content/qt5jp4d275/qt5jp4d275_noSplash_9795bc8ac2dde64b0d71b78169a5c7bd.pdf
+ scope: Complete primary main body, Methods, Tables 1-2 text and six figure captions across publisher and UC
+ PDF. No visual figure/table inspection or supplements. Companion is an editorial-interest notice, not a
+ correction. Local PDF retrieval returned an empty file and was not used. No full text added to git.
+ PMID:24015929:
+ url: https://pubmed.ncbi.nlm.nih.gov/24015929/
+ scope: Complete cached primary abstract only; isotope-fractionation context, not a new causal edge. No fresh
+ full body, figures or supplements.
+- path: kb/communities/Dehalococcoides_Desulfovibrio_Pelosinus_Corrinoid_Triculture.yaml
+ id: CommunityMech:000200
+ original_sha256: 9e9caf7e8dfeeca85868d3bc7509eacd27686582f0090bfbd88af2675248d8bf
+ record_sha256: 2d771dc7df594f59d55d100bdf4e7ed6bbc571dfea0a4e37a774583e831910dc
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261006-three-records-batch30.yaml
+ scope: Whole record and all original nodes/arrows reviewed at the documented primary-source access scope. Non-graph
+ fields preserved, not certified.
+ summary: Retain syntrophic hydrogen support with the required cofactor context.; Retain corrinoid cross-feeding
+ without assigning DMB production or an exclusive cofactor route.; Assign salvaging/remodeling to Dhc195 and
+ classify measured transcript evidence correctly.; Make the complete canonical triculture and DMB-dependent outcome
+ explicit.
+ renamed_nodes: {}
+ node_decisions:
+ - node: Hydrogen Provision By Desulfovibrio
+ rationale: Retain syntrophic hydrogen support with the required cofactor context.
+ - node: Corrinoid Provision By Pelosinus
+ rationale: Retain corrinoid cross-feeding without assigning DMB production or an exclusive cofactor route.
+ - node: Dhc195 Corrinoid Salvaging And Remodeling
+ rationale: Assign salvaging/remodeling to Dhc195 and classify measured transcript evidence correctly.
+ - node: Hydrogen- and Corrinoid-Supported TCE Dechlorination
+ rationale: Make the complete canonical triculture and DMB-dependent outcome explicit.
+ removed_node_decisions: []
+ edges_before:
+ - source: Hydrogen Provision By Desulfovibrio
+ target: Hydrogen- and Corrinoid-Supported TCE Dechlorination
+ description: 'DvH-supplied hydrogen provides the electron donor input that Dhc195 needs, together with PfR7-derived
+ corrinoids, for sustainable reductive dechlorination in the defined triculture.
+
+ '
+ - source: Corrinoid Provision By Pelosinus
+ target: Dhc195 Corrinoid Salvaging And Remodeling
+ description: 'PfR7 corrinoid production supplies the phenolic corrinoids that Dhc195 imports and remodels into
+ cobalamin when DMB is present.
+
+ '
+ - source: Dhc195 Corrinoid Salvaging And Remodeling
+ target: Hydrogen- and Corrinoid-Supported TCE Dechlorination
+ description: 'Dhc195 corrinoid salvaging and remodeling turns PfR7-produced corrinoids into cobalamin cofactors
+ that support sustainable TCE dechlorination when DvH also supplies hydrogen.
+
+ '
+ edges_after:
+ - source: Hydrogen Provision By Desulfovibrio
+ target: Hydrogen- and Corrinoid-Supported TCE Dechlorination
+ description: DvH-supplied hydrogen supports the electron-donor requirement of Dhc195 in the lactate-fed triculture,
+ together with partner corrinoids and externally supplied DMB. Hydrogen provision alone does not make the cobalamin-free
+ two-member coculture sustainable.
+ - source: Corrinoid Provision By Pelosinus
+ target: Dhc195 Corrinoid Salvaging And Remodeling
+ description: PfR7 supplies corrinoid substrates that Dhc195 can salvage and remodel in the presence of externally
+ supplied DMB. This does not exclude donor guided cobalamin biosynthesis or establish that all functional cofactor
+ passes through recipient remodeling.
+ - source: Dhc195 Corrinoid Salvaging And Remodeling
+ target: Hydrogen- and Corrinoid-Supported TCE Dechlorination
+ description: Recipient salvaging and remodeling contributes compatible cofactor for sustainable TCE dechlorination
+ in the DMB-amended triculture when DvH supplies hydrogen. The source supports this route but does not selectively
+ separate its contribution from cobalamin formed by the donor in the presence of DMB.
+ retained_edge_decisions:
+ - source: Hydrogen Provision By Desulfovibrio
+ target: Hydrogen- and Corrinoid-Supported TCE Dechlorination
+ rationale: DvH-supplied hydrogen supports the electron-donor requirement of Dhc195 in the lactate-fed triculture,
+ together with partner corrinoids and externally supplied DMB. Hydrogen provision alone does not make the cobalamin-free
+ two-member coculture sustainable.
+ - source: Corrinoid Provision By Pelosinus
+ target: Dhc195 Corrinoid Salvaging And Remodeling
+ rationale: PfR7 supplies corrinoid substrates that Dhc195 can salvage and remodel in the presence of externally
+ supplied DMB. This does not exclude donor guided cobalamin biosynthesis or establish that all functional cofactor
+ passes through recipient remodeling.
+ - source: Dhc195 Corrinoid Salvaging And Remodeling
+ target: Hydrogen- and Corrinoid-Supported TCE Dechlorination
+ rationale: Recipient salvaging and remodeling contributes compatible cofactor for sustainable TCE dechlorination
+ in the DMB-amended triculture when DvH supplies hydrogen. The source supports this route but does not selectively
+ separate its contribution from cobalamin formed by the donor in the presence of DMB.
+ removed_edge_decisions: []
+ references:
+ - PMID:24463969
+ issues:
+ - 1383
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Dehalococcoides_Desulfovibrio_Pelosinus_Corrinoid_Triculture/2026-10-06T054824Z-codex-290d65.yaml
+ source_review:
+ PMID:24463969: *id001
+- path: kb/communities/Dehalococcoides_Methanosarcina_DMB_Cobalamin_Coculture.yaml
+ id: CommunityMech:000209
+ original_sha256: 07af295ed9a7d53238b5bbcd466fa2d9478b4bb7f896958ea4f1a65d101c4b46
+ record_sha256: fbf9a3612c04d172cd46cc210b069e03e627b5dcec722682651abfe6e0e6afb7
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261006-three-records-batch30.yaml
+ scope: Whole record and all original nodes/arrows reviewed at the documented primary-source access scope. Non-graph
+ fields preserved, not certified.
+ summary: Retain conditional DMB-associated cofactor support without assigning an exclusive route.; Retain the
+ negative compatibility result without commensalism or toxicity.; Represent BAV1 dechlorination as a recipient
+ phenotype without reverse cross-feeding.
+ renamed_nodes: {}
+ node_decisions:
+ - node: DMB-Guided Cobalamin Support
+ rationale: Retain conditional DMB-associated cofactor support without assigning an exclusive route.
+ - node: Factor III Is Insufficient Without DMB
+ rationale: Retain the negative compatibility result without commensalism or toxicity.
+ - node: Cobalamin-Dependent Reductive Dechlorination
+ rationale: Represent BAV1 dechlorination as a recipient phenotype without reverse cross-feeding.
+ removed_node_decisions: []
+ edges_before:
+ - source: DMB-Guided Cobalamin Support
+ target: Cobalamin-Dependent Reductive Dechlorination
+ description: 'DMB-guided biosynthesis converts the Methanosarcina cobamide supply into a cobalamin compatible
+ with the Dehalococcoides reductive dechlorination machinery.
+
+ '
+ - source: Factor III Is Insufficient Without DMB
+ target: Cobalamin-Dependent Reductive Dechlorination
+ description: 'Unguided factor III production leaves the Dehalococcoides corrinoid requirement unsatisfied, so
+ organohalide respiration remains constrained unless DMB enables compatible cobalamin production.
+
+ '
+ edges_after:
+ - source: DMB-Guided Cobalamin Support
+ target: Cobalamin-Dependent Reductive Dechlorination
+ description: With externally supplied DMB, the partner-associated corrinoid system supplies compatible cofactor
+ and enables BAV1 dechlorination and growth. This does not assign an exclusive donor-versus-recipient remodeling
+ route or imply that DMB is required when compatible cobalamin is supplied directly.
+ - source: Factor III Is Insufficient Without DMB
+ target: Cobalamin-Dependent Reductive Dechlorination
+ description: Failure to supply an adequate compatible cofactor leaves BAV1 dechlorination constrained in the
+ unamended coculture. This denotes a missing nutritional input, not active inhibition by factor III. DMB-associated
+ cofactor production or direct compatible-cobalamin supplementation can overcome that limitation.
+ retained_edge_decisions:
+ - source: DMB-Guided Cobalamin Support
+ target: Cobalamin-Dependent Reductive Dechlorination
+ rationale: With externally supplied DMB, the partner-associated corrinoid system supplies compatible cofactor
+ and enables BAV1 dechlorination and growth. This does not assign an exclusive donor-versus-recipient remodeling
+ route or imply that DMB is required when compatible cobalamin is supplied directly.
+ - source: Factor III Is Insufficient Without DMB
+ target: Cobalamin-Dependent Reductive Dechlorination
+ rationale: Failure to supply an adequate compatible cofactor leaves BAV1 dechlorination constrained in the unamended
+ coculture. This denotes a missing nutritional input, not active inhibition by factor III. DMB-associated cofactor
+ production or direct compatible-cobalamin supplementation can overcome that limitation.
+ removed_edge_decisions: []
+ references:
+ - PMID:23479750
+ - PMID:12840758
+ issues:
+ - 1384
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Dehalococcoides_Methanosarcina_DMB_Cobalamin_Coculture/2026-10-06T054824Z-codex-bed9ca.yaml
+ source_review:
+ PMID:23479750:
+ url: https://pmc.ncbi.nlm.nih.gov/articles/PMC3638461/
+ scope: Complete cached abstract and substantial indexed primary Methods, Results, Discussion, Table 1 and
+ figure-caption excerpts. Not complete full text. PMC challenge and publisher 403; no visual figures or supplements.
+ Graph repairs remain abstract-supported; cell-resolved route partition is not claimed.
+ PMID:12840758:
+ url: https://pubmed.ncbi.nlm.nih.gov/12840758/
+ scope: Complete cached primary abstract only, supporting dechlorinator phenotype rather than exact-pair cofactor
+ transfer. No fresh full body, figures or supplements.
diff --git a/reports/causal_graph_review/inventory.tsv b/reports/causal_graph_review/inventory.tsv
index 541bc8594..4c7aef3c2 100644
--- a/reports/causal_graph_review/inventory.tsv
+++ b/reports/causal_graph_review/inventory.tsv
@@ -137,9 +137,9 @@ kb/communities/Dangl_SynComm_35.yaml CommunityMech:000022 9a828b5a59f88ca4169933
kb/communities/Deepwater_Horizon_Deep_Sea_Oil_Plume_Succession.yaml CommunityMech:000166 7cc349b1d2309b6d071aeaea72234305922c0c76458baab1469ce258142083f7 3 2 89.0 reports/causal_graph_review/decisions/20261006-three-records-batch29.yaml reviewed
kb/communities/Defined_Multispecies_Enamel_Caries_Model.yaml CommunityMech:000082 320691301cf3e2d94ca9bf69873471e12309ce32271eecc02c3b222a08e6b9d6 3 0 65.0 reports/causal_graph_review/decisions/20261006-three-records-batch29.yaml reviewed
kb/communities/Defined_ThreeStrain_Organic_Nitrogen_Nitrifying_Community.yaml CommunityMech:000397 b3843b5e2f64d179b4bc11a1558b7f977c025252fa6fe16d8ab82e0dfb292ec1 1 0 65.0 reports/causal_graph_review/decisions/20261006-three-records-batch27.yaml reviewed
-kb/communities/Dehalococcoides_Desulfovibrio_Lactate_TCE_Syntrophy.yaml CommunityMech:000199 e177715e13530b307c714b59268dc295e35935d12b5d73a0ee7137ba68a927d0 3 2 100.0 pending
-kb/communities/Dehalococcoides_Desulfovibrio_Pelosinus_Corrinoid_Triculture.yaml CommunityMech:000200 9e9caf7e8dfeeca85868d3bc7509eacd27686582f0090bfbd88af2675248d8bf 4 3 100.0 pending
-kb/communities/Dehalococcoides_Methanosarcina_DMB_Cobalamin_Coculture.yaml CommunityMech:000209 07af295ed9a7d53238b5bbcd466fa2d9478b4bb7f896958ea4f1a65d101c4b46 3 2 100.0 pending
+kb/communities/Dehalococcoides_Desulfovibrio_Lactate_TCE_Syntrophy.yaml CommunityMech:000199 bc9eebbdf57b937cc87c72ee439f404bb7ab51b99b2f06e2f11fd240a454c629 3 2 93.3 reports/causal_graph_review/decisions/20261006-three-records-batch30.yaml reviewed
+kb/communities/Dehalococcoides_Desulfovibrio_Pelosinus_Corrinoid_Triculture.yaml CommunityMech:000200 2d771dc7df594f59d55d100bdf4e7ed6bbc571dfea0a4e37a774583e831910dc 4 3 95.0 reports/causal_graph_review/decisions/20261006-three-records-batch30.yaml reviewed
+kb/communities/Dehalococcoides_Methanosarcina_DMB_Cobalamin_Coculture.yaml CommunityMech:000209 fbf9a3612c04d172cd46cc210b069e03e627b5dcec722682651abfe6e0e6afb7 3 2 93.3 reports/causal_graph_review/decisions/20261006-three-records-batch30.yaml reviewed
kb/communities/Dehalococcoides_Pelobacter_Acetylene_TCE_Coculture.yaml CommunityMech:000184 cb7e15cd85069763298df062a42ba1f54497fc8db00edd004215590b2a0a8aca 3 2 100.0 pending
kb/communities/Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture.yaml CommunityMech:000183 3c229074814142c66fa8a5a8624c7bf3dbdebc243dfea7eebee3d1840a88f52a 3 2 100.0 pending
kb/communities/Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium.yaml CommunityMech:000301 481d1d0cd521dbf852b91a98589b5f79c6735732afa88bc39c67e73f0e2a93d2 5 3 100.0 pending
diff --git a/reports/causal_graph_review/summary.json b/reports/causal_graph_review/summary.json
index 7a4941320..4c4f57929 100644
--- a/reports/causal_graph_review/summary.json
+++ b/reports/causal_graph_review/summary.json
@@ -8,8 +8,8 @@
"records_without_edges": 143,
"review_status_counts": {
"needs_research": 4,
- "pending": 324,
- "reviewed": 132
+ "pending": 321,
+ "reviewed": 135
},
"structural_defects": [],
"network_audit": [
diff --git a/reports/causal_graph_review/validation-20261006-batch30.json b/reports/causal_graph_review/validation-20261006-batch30.json
new file mode 100644
index 000000000..36a713096
--- /dev/null
+++ b/reports/causal_graph_review/validation-20261006-batch30.json
@@ -0,0 +1,682 @@
+{
+ "base_commit": "a4ca06d433a89666e12c662b24e7fa488c200355",
+ "scope": [
+ "kb/communities/Dehalococcoides_Desulfovibrio_Lactate_TCE_Syntrophy.yaml",
+ "kb/communities/Dehalococcoides_Desulfovibrio_Pelosinus_Corrinoid_Triculture.yaml",
+ "kb/communities/Dehalococcoides_Methanosarcina_DMB_Cobalamin_Coculture.yaml"
+ ],
+ "reference_validator_version": "0.1.7",
+ "results": [
+ {
+ "check": "Dehalococcoides_Desulfovibrio_Lactate_TCE_Syntrophy-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Dehalococcoides_Desulfovibrio_Lactate_TCE_Syntrophy.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch30/Dehalococcoides_Desulfovibrio_Lactate_TCE_Syntrophy-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Dehalococcoides_Desulfovibrio_Lactate_TCE_Syntrophy-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch30/Dehalococcoides_Desulfovibrio_Lactate_TCE_Syntrophy-strict.tsv",
+ "kb/communities/Dehalococcoides_Desulfovibrio_Lactate_TCE_Syntrophy.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch30/Dehalococcoides_Desulfovibrio_Lactate_TCE_Syntrophy-strict.log",
+ "log_sha256": "4d8ed9ece64c2a9f4e7c4cee19cce1bd8626e1faaed66c2452f7ec436dcfb739",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch30/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-batch30/Dehalococcoides_Desulfovibrio_Lactate_TCE_Syntrophy-strict.tsv\n"
+ },
+ {
+ "check": "Dehalococcoides_Desulfovibrio_Lactate_TCE_Syntrophy-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Dehalococcoides_Desulfovibrio_Lactate_TCE_Syntrophy.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch30/Dehalococcoides_Desulfovibrio_Lactate_TCE_Syntrophy-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Dehalococcoides_Desulfovibrio_Lactate_TCE_Syntrophy-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Dehalococcoides_Desulfovibrio_Lactate_TCE_Syntrophy.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch30/Dehalococcoides_Desulfovibrio_Lactate_TCE_Syntrophy-references.log",
+ "log_sha256": "219fde3e59a09883a67a90dc97db7b4bc561f2fa37f0f634130d381c649a2589",
+ "output_tail": "Validating kb/communities/Dehalococcoides_Desulfovibrio_Lactate_TCE_Syntrophy.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n",
+ "explained_output_tail": "Validating kb/communities/Dehalococcoides_Desulfovibrio_Lactate_TCE_Syntrophy.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n"
+ },
+ {
+ "check": "Dehalococcoides_Desulfovibrio_Lactate_TCE_Syntrophy-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Dehalococcoides_Desulfovibrio_Lactate_TCE_Syntrophy.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch30/Dehalococcoides_Desulfovibrio_Lactate_TCE_Syntrophy-snippets.log",
+ "log_sha256": "e8fe5a6250456e2c30f1d505e351e747d7545f77929e05a8d20e9212e652c822",
+ "output_tail": "# 30 evidence snippets scanned across 1 files\n MATCH 30\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": "Dehalococcoides_Desulfovibrio_Lactate_TCE_Syntrophy-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Dehalococcoides_Desulfovibrio_Lactate_TCE_Syntrophy.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch30/Dehalococcoides_Desulfovibrio_Lactate_TCE_Syntrophy-rank.log",
+ "log_sha256": "1df2f74635b82f033ce2706ed0e8f0e330fe93fa6b1711dc25425c2e78cb380e",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000199\",\n \"name\": \"Dehalococcoides-Desulfovibrio Lactate-Fed TCE Dechlorination Coculture\",\n \"score\": 93.3,\n \"taxonomy\": 2,\n \"connected_taxa\": 2,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 3,\n \"downstream_edges\": 2,\n \"interaction_evidence\": 7,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Dehalococcoides_Desulfovibrio_Lactate_TCE_Syntrophy.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Dehalococcoides_Desulfovibrio_Lactate_TCE_Syntrophy-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Dehalococcoides_Desulfovibrio_Lactate_TCE_Syntrophy/2026-10-06T054824Z-codex-33c8ca.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch30/Dehalococcoides_Desulfovibrio_Lactate_TCE_Syntrophy-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Dehalococcoides_Desulfovibrio_Pelosinus_Corrinoid_Triculture-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Dehalococcoides_Desulfovibrio_Pelosinus_Corrinoid_Triculture.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch30/Dehalococcoides_Desulfovibrio_Pelosinus_Corrinoid_Triculture-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Dehalococcoides_Desulfovibrio_Pelosinus_Corrinoid_Triculture-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch30/Dehalococcoides_Desulfovibrio_Pelosinus_Corrinoid_Triculture-strict.tsv",
+ "kb/communities/Dehalococcoides_Desulfovibrio_Pelosinus_Corrinoid_Triculture.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch30/Dehalococcoides_Desulfovibrio_Pelosinus_Corrinoid_Triculture-strict.log",
+ "log_sha256": "72fe6109ec5769a085b4e696f43fd2b95b34221ffab3541fd3424674ed4eab3d",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch30/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-batch30/Dehalococcoides_Desulfovibrio_Pelosinus_Corrinoid_Triculture-strict.tsv\n"
+ },
+ {
+ "check": "Dehalococcoides_Desulfovibrio_Pelosinus_Corrinoid_Triculture-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Dehalococcoides_Desulfovibrio_Pelosinus_Corrinoid_Triculture.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch30/Dehalococcoides_Desulfovibrio_Pelosinus_Corrinoid_Triculture-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Dehalococcoides_Desulfovibrio_Pelosinus_Corrinoid_Triculture-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Dehalococcoides_Desulfovibrio_Pelosinus_Corrinoid_Triculture.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch30/Dehalococcoides_Desulfovibrio_Pelosinus_Corrinoid_Triculture-references.log",
+ "log_sha256": "398218e4eda24028b761d10d2cd38133e111e4a99c049eac28c656b48e5df7b0",
+ "output_tail": "Validating kb/communities/Dehalococcoides_Desulfovibrio_Pelosinus_Corrinoid_Triculture.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n",
+ "explained_output_tail": "Validating kb/communities/Dehalococcoides_Desulfovibrio_Pelosinus_Corrinoid_Triculture.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n"
+ },
+ {
+ "check": "Dehalococcoides_Desulfovibrio_Pelosinus_Corrinoid_Triculture-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Dehalococcoides_Desulfovibrio_Pelosinus_Corrinoid_Triculture.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch30/Dehalococcoides_Desulfovibrio_Pelosinus_Corrinoid_Triculture-snippets.log",
+ "log_sha256": "d353a2e438e49543043d94dbd2d275ccc825dad7bb23be8ad43bf853927d2fe3",
+ "output_tail": "# 28 evidence snippets scanned across 1 files\n MATCH 28\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": "Dehalococcoides_Desulfovibrio_Pelosinus_Corrinoid_Triculture-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Dehalococcoides_Desulfovibrio_Pelosinus_Corrinoid_Triculture.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch30/Dehalococcoides_Desulfovibrio_Pelosinus_Corrinoid_Triculture-rank.log",
+ "log_sha256": "312db8a37357bc5ea4c17f07cdbcc9479fc260b9f765628056ac3e384bc4d967",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000200\",\n \"name\": \"Dehalococcoides-Desulfovibrio-Pelosinus Corrinoid Triculture\",\n \"score\": 95.0,\n \"taxonomy\": 3,\n \"connected_taxa\": 3,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 4,\n \"downstream_edges\": 3,\n \"interaction_evidence\": 8,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Dehalococcoides_Desulfovibrio_Pelosinus_Corrinoid_Triculture.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Dehalococcoides_Desulfovibrio_Pelosinus_Corrinoid_Triculture-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Dehalococcoides_Desulfovibrio_Pelosinus_Corrinoid_Triculture/2026-10-06T054824Z-codex-290d65.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch30/Dehalococcoides_Desulfovibrio_Pelosinus_Corrinoid_Triculture-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Dehalococcoides_Methanosarcina_DMB_Cobalamin_Coculture-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Dehalococcoides_Methanosarcina_DMB_Cobalamin_Coculture.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch30/Dehalococcoides_Methanosarcina_DMB_Cobalamin_Coculture-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Dehalococcoides_Methanosarcina_DMB_Cobalamin_Coculture-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch30/Dehalococcoides_Methanosarcina_DMB_Cobalamin_Coculture-strict.tsv",
+ "kb/communities/Dehalococcoides_Methanosarcina_DMB_Cobalamin_Coculture.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch30/Dehalococcoides_Methanosarcina_DMB_Cobalamin_Coculture-strict.log",
+ "log_sha256": "ccef8fc4cb928434a4f52d39da1d76ec165b24d5acb998dc1a88551013bc9a64",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch30/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-batch30/Dehalococcoides_Methanosarcina_DMB_Cobalamin_Coculture-strict.tsv\n"
+ },
+ {
+ "check": "Dehalococcoides_Methanosarcina_DMB_Cobalamin_Coculture-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Dehalococcoides_Methanosarcina_DMB_Cobalamin_Coculture.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch30/Dehalococcoides_Methanosarcina_DMB_Cobalamin_Coculture-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Dehalococcoides_Methanosarcina_DMB_Cobalamin_Coculture-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Dehalococcoides_Methanosarcina_DMB_Cobalamin_Coculture.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch30/Dehalococcoides_Methanosarcina_DMB_Cobalamin_Coculture-references.log",
+ "log_sha256": "0a357ab41bde87999a4946a5f1d87f40e0bd673a2193206c1ebf0d5ed5a888b3",
+ "output_tail": "Validating kb/communities/Dehalococcoides_Methanosarcina_DMB_Cobalamin_Coculture.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n",
+ "explained_output_tail": "Validating kb/communities/Dehalococcoides_Methanosarcina_DMB_Cobalamin_Coculture.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n"
+ },
+ {
+ "check": "Dehalococcoides_Methanosarcina_DMB_Cobalamin_Coculture-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Dehalococcoides_Methanosarcina_DMB_Cobalamin_Coculture.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch30/Dehalococcoides_Methanosarcina_DMB_Cobalamin_Coculture-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": "Dehalococcoides_Methanosarcina_DMB_Cobalamin_Coculture-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Dehalococcoides_Methanosarcina_DMB_Cobalamin_Coculture.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch30/Dehalococcoides_Methanosarcina_DMB_Cobalamin_Coculture-rank.log",
+ "log_sha256": "333d9e9f4274f665259195a78dc436e9216071d717034be2e9ac1e70773013e1",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000209\",\n \"name\": \"Dehalococcoides-Methanosarcina DMB-Guided Cobalamin Coculture\",\n \"score\": 93.3,\n \"taxonomy\": 2,\n \"connected_taxa\": 2,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 3,\n \"downstream_edges\": 2,\n \"interaction_evidence\": 6,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Dehalococcoides_Methanosarcina_DMB_Cobalamin_Coculture.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Dehalococcoides_Methanosarcina_DMB_Cobalamin_Coculture-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Dehalococcoides_Methanosarcina_DMB_Cobalamin_Coculture/2026-10-06T054824Z-codex-bed9ca.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch30/Dehalococcoides_Methanosarcina_DMB_Cobalamin_Coculture-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-batch30/inventory.log",
+ "log_sha256": "4e1d12250b634644a5997e5687356a5133141a1c95d81f91fcefa15f3f735903",
+ "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\": 1470,\n \"edges\": 705,\n \"records_without_nodes\": 8,\n \"records_without_edges\": 143,\n \"review_status_counts\": {\n \"needs_research\": 4,\n \"pending\": 321,\n \"reviewed\": 135\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-batch30/network.log",
+ "log_sha256": "2cd39b61dfce615081637c0e72d245194c41d4a2a374d65bccad7c69fcff4e63",
+ "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": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch30/rank-all.log",
+ "log_sha256": "08cd6dd5856847871069028f8768c3fc0db9d79fdb754530f2874f23dca8f130",
+ "output_tail": "ities/Soybean_N_Fixation_sfSynCom.yaml\tCommunityMech:000064\tSoybean N-Fixation Simplified SynCom\t4\t4\t0\t3\t2\t3\t\t0\t0\n402\t100.0\tkb/communities/Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture.yaml\tCommunityMech:000267\tSphingobium-Rhodococcus Lignin-Dimer Valorization Coculture\t2\t2\t0\t3\t2\t7\t\t0\t0\n403\t100.0\tkb/communities/Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture.yaml\tCommunityMech:000326\tStaphylococcus-Candida Context-Dependent Biofilm Coculture\t2\t2\t0\t6\t2\t13\t\t0\t0\n404\t100.0\tkb/communities/Stordalen_Mire_Methylotrophic_Methanogenesis_Community.yaml\tCommunityMech:000254\tStordalen Mire Methylotrophic Methanogenesis Community\t3\t3\t0\t4\t4\t9\t\t0\t0\n405\t100.0\tkb/communities/Streptomyces_A2_A5_A11_M7_Pesticide_Consortium.yaml\tCommunityMech:000335\tStreptomyces A2-A5-A11-M7 Pesticide-Bioremediation Consortium\t4\t4\t0\t4\t2\t5\t\t0\t0\n406\t100.0\tkb/communities/Subsurface_Carboxydocella_CO_Aquifer_Community.yaml\tCommunityMech:000251\tSubsurface Carboxydocella CO-Oxidation Aquifer Community\t1\t1\t0\t5\t2\t5\t\t0\t0\n407\t100.0\tkb/communities/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom.yaml\tCommunityMech:000312\tSuillus clintonianus-Bacillus altitudinis Thiamine Cross-Feeding SynCom\t3\t3\t0\t4\t3\t4\t\t0\t0\n408\t100.0\tkb/communities/Sulfide_Spring_Autotrophic_CPR_Biofilm.yaml\tCommunityMech:000222\tSulfide Spring Autotrophic CPR-Hosting Biofilm\t3\t3\t0\t3\t2\t4\t\t0\t0\n409\t100.0\tkb/communities/SynComBac10_Chicken_Intestinal_SynCom.yaml\tCommunityMech:000127\tSynComBac10 Chicken Intestinal SynCom\t3\t3\t0\t3\t2\t3\t\t0\t0\n410\t100.0\tkb/communities/SynCom_ARC_Peanut_Aflatoxin_Nodulation.yaml\tCommunityMech:000314\tSynCom ARC Peanut Aflatoxin-Control and Nodulation-Coupling Community\t5\t5\t0\t3\t2\t3\t\t0\t0\n411\t100.0\tkb/communities/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation.yaml\tCommunityMech:000278\tSynCom BsBv Cigar Tobacco Leaf Fermentation\t2\t2\t0\t3\t2\t3\t\t0\t0\n412\t100.0\tkb/communities/SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System.yaml\tCommunityMech:000285\tSynCom + Chlorella sorokiniana Biogas-slurry Coupling System\t2\t2\t0\t5\t3\t5\t\t0\t0\n413\t100.0\tkb/communities/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience.yaml\tCommunityMech:000302\tSynCom MetG2 Rhizobacteria Sugarcane Stress Resilience\t2\t2\t0\t3\t2\t4\t\t0\t0\n414\t100.0\tkb/communities/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus.yaml\tCommunityMech:000283\tSesame-flavor Baijiu Fuqu SynCom (13-genus)\t13\t13\t0\t3\t2\t3\t\t0\t0\n415\t100.0\tkb/communities/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture.yaml\tCommunityMech:000272\tSynCom Y Agrobacterium-Bacillus Biofilm Biocontrol Co-culture\t2\t2\t0\t4\t2\t6\t\t0\t0\n416\t100.0\tkb/communities/Synechococcus_Azotobacter_Photoproduction_Mutualism.yaml\tCommunityMech:000207\tSynechococcus-Azotobacter Photoproduction Mutualism\t2\t2\t0\t3\t2\t6\t\t0\t0\n417\t100.0\tkb/communities/Synechococcus_Bacillus_SPC.yaml\tCommunityMech:000065\tSynechococcus-Bacillus Synthetic Photosynthetic Consortium\t2\t2\t0\t3\t2\t4\t\t0\t0\n418\t100.0\tkb/communities/Synechococcus_Ecoli_SPC.yaml\tCommunityMech:000066\tSynechococcus-E.coli Synthetic Photosynthetic Consortium\t2\t2\t0\t3\t2\t4\t\t0\t0\n419\t100.0\tkb/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml\tCommunityMech:000198\tSynechococcus-Halomonas Light-Driven PHB Coculture\t2\t2\t0\t3\t2\t6\t\t0\t0\n420\t100.0\tkb/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml\tCommunityMech:000167\tSynechococcus-Pseudomonas Phototrophic PHA and DNT Coculture\t2\t2\t0\t4\t2\t8\t\t0\t0\n421\t100.0\tkb/communities/Synechococcus_Saccharomyces_SPC.yaml\tCommunityMech:000067\tSynechococcus-Saccharomyces Synthetic Photosynthetic Consortium\t2\t2\t0\t3\t2\t4\t\t0\t0\n422\t100.0\tkb/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml\tCommunityMech:000211\tSynechococcus-Shewanella D-Lactate Biophotovoltaic Consortium\t2\t2\t0\t3\t2\t6\t\t0\t0\n423\t100.0\tkb/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml\tCommunityMech:000149\tSynthetic Lichen Synechococcus-Rhodotorula Coculture\t2\t2\t0\t3\t2\t4\t\t0\t0\n424\t100.0\tkb/communities/Syntrophobacter_Methanobacterium_Syntrophy.yaml\tCommunityMech:000068\tSyntrophobacter-Methanobacterium Syntrophic Consortium\t2\t2\t0\t3\t3\t8\t\t0\t0\n425\t100.0\tkb/communities/Syntrophobacter_Methanospirillum_Syntrophy.yaml\tCommunityMech:000069\tSyntrophobacter-Methanospirillum Syntrophic Consortium\t2\t2\t0\t3\t3\t5\t\t0\t0\n426\t100.0\tkb/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml\tCommunityMech:000189\tSyntrophomonas-Methanococcus Butyrate Growth Coordination Coculture\t2\t2\t0\t3\t2\t6\t\t0\t0\n427\t100.0\tkb/communities/Syntrophomonas_Methanospirillum_Syntrophy.yaml\tCommunityMech:000070\tSyntrophomonas-Methanospirillum Syntrophic Consortium\t2\t2\t0\t3\t3\t7\t\t0\t0\n428\t100.0\tkb/communities/Syntrophus_Benzoate_Degrader.yaml\tCommunityMech:000071\tSyntrophus Benzoate Degrader\t2\t2\t0\t3\t2\t6\t\t0\t0\n429\t100.0\tkb/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml\tCommunityMech:000187\tSyntrophus-Methanospirillum Gentianae Benzoate Coculture\t2\t2\t0\t3\t2\t7\t\t0\t0\n430\t100.0\tkb/communities/THOR_Rhizosphere_Model_Community.yaml\tCommunityMech:000079\tTHOR Rhizosphere Model Community\t3\t3\t0\t4\t2\t5\t\t0\t0\n431\t100.0\tkb/communities/TYQ1_Nematode_Biocontrol_SynCom.yaml\tCommunityMech:000072\tTYQ1 Nematode Biocontrol SynCom\t8\t8\t0\t4\t4\t4\t\t0\t0\n432\t100.0\tkb/communities/Teosinte_Maize_Biofertilizer_SynCom7.yaml\tCommunityMech:000100\tTeosinte-Derived Maize Biofertilizer SynCom7\t4\t4\t0\t6\t2\t12\t\t0\t0\n433\t100.0\tkb/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml\tCommunityMech:000259\tThalassiosira-Marinobacter Marine Snow Coculture\t2\t2\t0\t4\t2\t10\t\t0\t0\n434\t100.0\tkb/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml\tCommunityMech:000162\tThalassiosira-Ruegeria Phycosphere Coculture\t2\t2\t0\t3\t2\t4\t\t0\t0\n435\t100.0\tkb/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml\tCommunityMech:000182\tThermacetogenium-Methanothermobacter Acetate Oxidation Coculture\t2\t2\t0\t3\t2\t8\t\t0\t0\n436\t100.0\tkb/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml\tCommunityMech:000282\tThermophilic Lignocellulose-degrading Composting SynCom\t5\t5\t0\t3\t2\t3\t\t0\t0\n437\t100.0\tkb/communities/Thermophilic_Pyrite_QS_Consortium.yaml\tCommunityMech:000073\tThermophilic Pyrite Quorum Sensing Consortium\t3\t3\t0\t6\t2\t14\t\t0\t0\n438\t100.0\tkb/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml\tCommunityMech:000186\tThermotoga-Methanocaldococcus Hyperthermophilic Syntrophy\t2\t2\t0\t3\t2\t8\t\t0\t0\n439\t100.0\tkb/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml\tCommunityMech:000239\tThiocyanate-Degrading Afipia and Thiobacillus Bioreactor Community\t3\t3\t0\t3\t2\t3\t\t0\t0\n440\t100.0\tkb/communities/Tinto_River_Iron_Cycling_Community.yaml\tCommunityMech:000074\tTinto River Iron Cycling Community\t6\t6\t0\t5\t3\t6\t\t0\t0\n441\t100.0\tkb/communities/Tobacco_Chemotactic_Biocontrol_SynCom.yaml\tCommunityMech:000106\tTobacco Chemotactic Biocontrol SynCom\t2\t2\t0\t3\t2\t4\t\t0\t0\n442\t100.0\tkb/communities/Tomato_Oxylipin_SynCom3.yaml\tCommunityMech:000107\tTomato Oxylipin-Protective SynCom3\t3\t3\t0\t3\t2\t4\t\t0\t0\n443\t100.0\tkb/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml\tCommunityMech:000112\tTribromophenol Anaerobic Bioremediation SynCom\t3\t3\t0\t4\t3\t5\t\t0\t0\n444\t100.0\tkb/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml\tCommunityMech:000188\tTrichococcus-Syntrophomonas-Methanospirillum Butyrate Coculture\t3\t3\t0\t3\t2\t6\t\t0\t0\n445\t100.0\tkb/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml\tCommunityMech:000205\tTrichoderma-E. coli Cellulosic Isobutanol Coculture\t2\t2\t0\t3\t2\t5\t\t0\t0\n446\t100.0\tkb/communities/Trichoderma_Lactate_Platform.yaml\tCommunityMech:000075\tTrichoderma Lactate Platform for SCFA Production\t3\t3\t0\t3\t2\t3\t\t0\t0\n447\t100.0\tkb/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml\tCommunityMech:000270\tTrichoderma-Streptomyces Filamentous Cellulose Coculture\t2\t2\t0\t3\t2\t7\t\t0\t0\n448\t100.0\tkb/communities/Trichodesmium_Alteromonas_Marine_Consortium.yaml\tCommunityMech:000147\tTrichodesmium-Alteromonas Marine Consortium\t3\t3\t0\t3\t2\t5\t\t0\t0\n449\t100.0\tkb/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml\tCommunityMech:000337\tTropidoatractus magnetotacticus Magnetotactic Ciliate Tripartite Syntrophy\t3\t3\t0\t4\t2\t9\t\t0\t0\n450\t100.0\tkb/communities/Urine_Nitrification_SynCom.yaml\tCommunityMech:000117\tUrine Nitrification Synthetic Microbial Community\t5\t5\t0\t3\t2\t5\t\t0\t0\n451\t100.0\tkb/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml\tCommunityMech:000213\tVariovorax-Cryptococcus Vitamin Cross-Feeding Microcosm\t2\t2\t0\t3\t2\t4\t\t0\t0\n452\t100.0\tkb/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml\tCommunityMech:000328\tWaste-Sludge Electro-Fermentation Biofilm-Suspension Community\t5\t5\t0\t4\t2\t6\t\t0\t0\n453\t100.0\tkb/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.yaml\tCommunityMech:000098\tWatermelon Rhizosphere Fusarium-Protective SynCom8\t2\t2\t0\t3\t2\t7\t\t0\t0\n454\t100.0\tkb/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml\tCommunityMech:000255\tWetland Oxygen-Sulfate Greenhouse Gas Microcosm Community\t3\t3\t0\t3\t2\t6\t\t0\t0\n455\t100.0\tkb/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.yaml\tCommunityMech:000118\tWheat Straw Biogas Pretreatment SynCom\t4\t4\t0\t3\t2\t4\t\t0\t0\n456\t100.0\tkb/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml\tCommunityMech:000354\tYarrowia lipolytica Division-of-Labor Lipid Consortium\t2\t2\t0\t3\t2\t3\t\t0\t0\n457\t100.0\tkb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml\tCommunityMech:000164\tYogurt Two-Species Starter Culture\t2\t2\t0\t4\t2\t9\t\t0\t0\n458\t100.0\tkb/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml\tCommunityMech:000210\tZymomonas-E. coli Exometabolomics-Designed Obligate Mutualism\t2\t2\t0\t3\t2\t6\t\t0\t0\n459\t100.0\tkb/communities/hCom2_Complex_Gut_Microbiome.yaml\tCommunityMech:000123\thCom2 Complex Gut Microbiome\t1\t1\t0\t3\t2\t3\t\t0\t0\n460\t100.0\tkb/communities/mCAFEs_Brachypodium_RCC.yaml\tCommunityMech:000078\tm-CAFEs Brachypodium Reduced Complexity Consortia\t10\t10\t0\t6\t2\t11\t\t0\t0\nPYTHONPATH=src uv run python scripts/rank_causal_graph_readiness.py \n"
+ },
+ {
+ "check": "render",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "communitymech.render"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch30/render.log",
+ "log_sha256": "138df9a19707ebd693fb6b076f11a110a1b5a9673223a3b4d024fa71bb54457e",
+ "output_tail": "sm.html\n \u2713 Synechococcus_Bacillus_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch30/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch30/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch30/docs/index.html\n"
+ },
+ {
+ "check": "render-repeat",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "communitymech.render"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch30/render-repeat.log",
+ "log_sha256": "138df9a19707ebd693fb6b076f11a110a1b5a9673223a3b4d024fa71bb54457e",
+ "output_tail": "sm.html\n \u2713 Synechococcus_Bacillus_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch30/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch30/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch30/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch30/docs/index.html\n"
+ },
+ {
+ "check": "connectivity-survey",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-c",
+ "import json,runpy; print(json.dumps(runpy.run_path(\"tests/test_community_level_connectivity_credit.py\")[\"_survey\"](),sort_keys=True))"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch30/connectivity-survey.log",
+ "log_sha256": "75f81e775562eccff7b05d37325e53d49d8dd9a033afb56a3af328cded2c0361",
+ "output_tail": "{\"community_level_only\": 264, \"credited_solely_by_the_rule\": 1220, \"mixed\": 124, \"records\": 460, \"taxa\": 1496, \"with_community_level\": 388}\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_batch5.py",
+ "tests/test_causal_review_batch6.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-batch30/regressions.log",
+ "log_sha256": "78c436383b7aea8f868292e9647d807f0c6ad8edb1770abfe895cccda14f6bdc",
+ "output_tail": "........................................................................ [ 20%]\n........................................................................ [ 41%]\n........................................................................ [ 62%]\n........................................................................ [ 82%]\n............................................................ [100%]\n348 passed in 189.71s (0:03:09)\n"
+ },
+ {
+ "check": "black",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/3Q_kifQtLB624D5bBWGIf/bin/black",
+ "--check",
+ "tests/test_causal_review_batch30.py",
+ "tests/test_participating_taxa.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch30/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_batch30.py",
+ "tests/test_participating_taxa.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch30/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-batch30/diff-check.log",
+ "log_sha256": "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855",
+ "output_tail": ""
+ }
+ ],
+ "limitations": [
+ "Three graph reviews; all ten nodes and seven arrows retained. No new graph structure or Edison job/spend.",
+ "Primary-source access differs by study and is recorded per reference. Textual snippet matching is not a scientific endorsement. No figure images or supplements were inspected in this batch.",
+ "No new article body/PDF is committed. All reference caches and non-graph raw record blocks are preserved. Two separately scoped metadata follow-ups remain open.",
+ "Source-only PAIRWISE entries represent intrinsic recipient capabilities under the established schema convention, not self-edges or reverse nutrient exchange. This self-review is not independent approval, protected CI success or full-corpus completion.",
+ "HTML descriptions checked by exact parser and repeat renders, not browser screenshots. Post-commit docs-current is a separate publication gate."
+ ],
+ "snippet_counts_by_record": {
+ "kb/communities/Dehalococcoides_Desulfovibrio_Lactate_TCE_Syntrophy.yaml": {
+ "MATCH": 30,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Dehalococcoides_Desulfovibrio_Pelosinus_Corrinoid_Triculture.yaml": {
+ "MATCH": 28,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Dehalococcoides_Methanosarcina_DMB_Cobalamin_Coculture.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,
+ "network_delta": {
+ "existing_findings_preserved": 31,
+ "new_disconnected": 0,
+ "rationale": "All prior warnings remain exactly unchanged; no structural errors or fabricated connectivity fixes."
+ },
+ "render_determinism": true,
+ "published_description_coverage": {
+ "pages": 456,
+ "nodes": 1456,
+ "arrows": 697
+ },
+ "participant_census": {
+ "connectivity_before": {
+ "community_level_only": 264,
+ "credited_solely_by_the_rule": 1220,
+ "mixed": 124,
+ "records": 460,
+ "taxa": 1496,
+ "with_community_level": 388
+ },
+ "connectivity_after": {
+ "community_level_only": 264,
+ "credited_solely_by_the_rule": 1220,
+ "mixed": 124,
+ "records": 460,
+ "taxa": 1496,
+ "with_community_level": 388
+ },
+ "exact_change": "173 -> 174 users; only the Dhc195/DvH/PfR7 triculture added",
+ "numeric_bounds_changed": false
+ },
+ "corpus": {
+ "scope": "Every YAML under kb/communities and data/isolates; filesystem discovery includes hidden/ignored files.",
+ "records": 460,
+ "nodes": 1470,
+ "edges": 705,
+ "records_without_nodes": 8,
+ "records_without_edges": 143,
+ "review_status_counts": {
+ "needs_research": 4,
+ "pending": 321,
+ "reviewed": 135
+ },
+ "structural_defects": []
+ },
+ "tested_file_sha256": {
+ "reports/causal_graph_review/decisions/20261006-three-records-batch30.yaml": "cb60e4a113592fd34842090d5f2db473831a31066febb469d2438a8d8b217c3c",
+ "tests/test_causal_review_batch30.py": "748df86257f0a17c58fa5633d672aefed827ccf0a685056a711c874b1a650d2c",
+ "tests/test_participating_taxa.py": "804367466cbbfb68d80865d601ab113d1796dcdfadcb9736fa033e085693d17c",
+ "kb/communities/Dehalococcoides_Desulfovibrio_Lactate_TCE_Syntrophy.yaml": "bc9eebbdf57b937cc87c72ee439f404bb7ab51b99b2f06e2f11fd240a454c629",
+ "kb/communities/Dehalococcoides_Desulfovibrio_Pelosinus_Corrinoid_Triculture.yaml": "2d771dc7df594f59d55d100bdf4e7ed6bbc571dfea0a4e37a774583e831910dc",
+ "kb/communities/Dehalococcoides_Methanosarcina_DMB_Cobalamin_Coculture.yaml": "fbf9a3612c04d172cd46cc210b069e03e627b5dcec722682651abfe6e0e6afb7"
+ },
+ "status": "verified_three_completed_reviews_three_changed_records",
+ "previous_attempt": {
+ "report": "/private/tmp/communitymech-batch30/failed-import-order/validation-20261006-batch30.json",
+ "report_sha256": "b3f399672b64e0330bf61b597a757f3bb6d27fcc514ddbe1be5cbde89ede906d",
+ "failure": "Ruff I001 import ordering in the new test file; all 348 regressions had passed.",
+ "resolution": "Reordered standard-library imports; reran every verification gate successfully.",
+ "archived_logs_directory": "/private/tmp/communitymech-batch30/failed-import-order"
+ }
+}
diff --git a/tests/test_causal_review_batch30.py b/tests/test_causal_review_batch30.py
new file mode 100644
index 000000000..94ff4a227
--- /dev/null
+++ b/tests/test_causal_review_batch30.py
@@ -0,0 +1,149 @@
+"""Distinguish recipient processes, conditional support and sulfide inhibition."""
+
+import hashlib
+from collections import Counter
+from pathlib import Path
+
+import yaml
+
+ROOT = Path(__file__).resolve().parents[1]
+LEDGER = ROOT / "reports/causal_graph_review/decisions/20261006-three-records-batch30.yaml"
+
+
+def records():
+ ledger = yaml.safe_load(LEDGER.read_text())
+ return ledger, [yaml.safe_load((ROOT / r["path"]).read_text()) for r in ledger["records"]]
+
+
+def assert_intrinsic(node, taxon):
+ assert node["scope"] == "PAIRWISE"
+ assert node["source_taxon"]["term"]["id"] == taxon
+ assert not {"target_taxon", "participating_taxa", "interaction_type"} & node.keys()
+
+
+def test_lactate_recipient_activity_and_conditional_sulfide_inhibition():
+ _, docs = records()
+ fermentation, output, inhibition = docs[0]["ecological_interactions"]
+ assert_intrinsic(output, "NCBITaxon:243164")
+ assert "maximum dechlorination rate, not every growth endpoint" in output["description"]
+ assert fermentation["interaction_type"] == "SYNTROPHY"
+ assert "not establish that DvH supplies every required cofactor" in fermentation["description"]
+ assert inhibition["name"] == "Sulfide-Associated Inhibition Of Dechlorination"
+ assert "interaction_type" not in inhibition
+ assert inhibition["source_taxon"]["term"]["id"] == "NCBITaxon:882"
+ assert inhibition["target_taxon"]["term"]["id"] == "NCBITaxon:243164"
+ assert (
+ "Donor-limited butyrate-triculture and enrichment outcomes are separate"
+ in inhibition["description"]
+ )
+ assert "despite available hydrogen" in inhibition["downstream"][0]["description"]
+ assert (
+ "not sufficient evidence that hydrogen competition caused"
+ in inhibition["downstream"][0]["description"]
+ )
+ for node in [fermentation, inhibition]:
+ assert node["downstream"][0]["target"] == output["name"]
+
+
+def test_pelosinus_remodeling_belongs_to_recipient_and_expression_is_measured():
+ _, docs = records()
+ hydrogen, provision, remodeling, output = docs[1]["ecological_interactions"]
+ assert_intrinsic(remodeling, "NCBITaxon:243164")
+ assert remodeling["evidence"][1]["evidence_source"] == "IN_VITRO"
+ assert "not a selective gene-necessity experiment" in remodeling["evidence"][1]["explanation"]
+ assert "PfR7 can also form some cobalamin" in provision["description"]
+ assert "Externally supplied lower ligand" in provision["metabolites"][1]["notes"]
+ assert hydrogen["interaction_type"] == "SYNTROPHY"
+ assert provision["interaction_type"] == "CROSS_FEEDING"
+ assert output["scope"] == "COMMUNITY_LEVEL"
+ assert "interaction_type" not in output
+ assert {t["term"]["id"] for t in output["participating_taxa"]} == {
+ "NCBITaxon:243164",
+ "NCBITaxon:882",
+ "NCBITaxon:1122947",
+ }
+
+
+def test_pelosinus_all_retained_arrows_expose_the_dmb_condition():
+ _, docs = records()
+ hydrogen, provision, remodeling, output = docs[1]["ecological_interactions"]
+ for node in [hydrogen, provision, remodeling]:
+ assert len(node["downstream"]) == 1
+ assert "DMB" in node["downstream"][0]["description"]
+ assert hydrogen["downstream"][0]["target"] == output["name"]
+ assert provision["downstream"][0]["target"] == remodeling["name"]
+ assert remodeling["downstream"][0]["target"] == output["name"]
+ assert "when DMB is supplied" in output["description"]
+ assert "does not selectively separate" in remodeling["downstream"][0]["description"]
+
+
+def test_fusaro_compatibility_failure_is_not_toxicity_or_reverse_exchange():
+ _, docs = records()
+ support, insufficient, output = docs[2]["ecological_interactions"]
+ assert_intrinsic(output, "NCBITaxon:216389")
+ assert support["interaction_type"] == "CROSS_FEEDING"
+ assert "not endogenous DMB supply or reciprocal nutrient exchange" in support["description"]
+ assert "interaction_type" not in insufficient and "metabolites" not in insufficient
+ assert "not commensalism, active factor-III toxicity" in insufficient["description"]
+ assert "not active inhibition by factor III" in insufficient["downstream"][0]["description"]
+ assert (
+ "direct compatible-cobalamin supplementation"
+ in insufficient["downstream"][0]["description"]
+ )
+ for node in [support, insufficient]:
+ assert node["downstream"][0]["target"] == output["name"]
+ assert "Pooled BAV1, GT and FL2 responses are not all assigned" in output["description"]
+
+
+def test_batch30_canonical_sources_participants_and_exact_anchors():
+ _, docs = records()
+ for doc in docs:
+ canonical = {t["taxon_term"]["term"]["id"]: t["taxon_term"] for t in doc["taxonomy"]}
+ names = {n["name"] for n in doc["ecological_interactions"]}
+ for node in doc["ecological_interactions"]:
+ terms = node.get("participating_taxa", []) + [
+ node[k] for k in ["source_taxon", "target_taxon"] if k in node
+ ]
+ for term in terms:
+ original = canonical[term["term"]["id"]]
+ assert {k: term[k] for k in ["preferred_term", "term"]} == {
+ k: original[k] for k in ["preferred_term", "term"]
+ }
+ assert all(
+ e["target"] in names and e["target"] != node["name"]
+ for e in node.get("downstream", [])
+ )
+ (gap,) = doc["discussions"]
+ assert gap["kind"] == "KNOWLEDGE_GAP" and gap["status"] == "OPEN"
+ assert set(gap["attaches_to"]) == {"ecological_interactions#" + n for n in names}
+
+
+def test_batch30_preserves_topology_and_records_all_decisions_history_and_limits():
+ ledger, docs = records()
+ assert ledger["independent_approval"] is False
+ assert ledger["issues"] == [1382, 1383, 1384]
+ assert ledger["open_nongraph_followups"] == [1385, 1386]
+ assert sum(len(r["node_decisions"]) for r in ledger["records"]) == 10
+ assert sum(len(r["retained_edge_decisions"]) for r in ledger["records"]) == 7
+ for row, doc in zip(ledger["records"], docs, strict=True):
+ assert row["status"] == "reviewed" and row["outcome"] == "changed"
+ assert not row["removed_node_decisions"] and not row["removed_edge_decisions"]
+ assert row["curation_events_added"] == 1 and len(row["history_files"]) == 1
+ assert doc["curation_history"][-1]["llm_assisted"] is True
+ assert hashlib.sha256((ROOT / row["path"]).read_bytes()).hexdigest() == row["record_sha256"]
+ assert Counter(d["node"] for d in row["node_decisions"]) == Counter(
+ n["name"] for n in doc["ecological_interactions"]
+ )
+ renames = row["renamed_nodes"]
+ assert {(e["source"], e["target"]) for e in row["edges_after"]} == {
+ (renames.get(e["source"], e["source"]), renames.get(e["target"], e["target"]))
+ for e in row["edges_before"]
+ }
+ assert (
+ "Full body not retrieved" in ledger["records"][0]["source_review"]["PMID:21881617"]["scope"]
+ )
+ assert (
+ "Not complete full text" in ledger["records"][2]["source_review"]["PMID:23479750"]["scope"]
+ )
+ for path, digest in ledger["reference_cache_original_hashes"].items():
+ assert hashlib.sha256((ROOT / path).read_bytes()).hexdigest() == digest
diff --git a/tests/test_participating_taxa.py b/tests/test_participating_taxa.py
index 02b155e08..f447e7f41 100644
--- a/tests/test_participating_taxa.py
+++ b/tests/test_participating_taxa.py
@@ -236,6 +236,7 @@ def test_a_curie_is_ambiguous_where_members_share_an_id(example):
"Deepwater_Horizon_Deep_Sea_Oil_Plume_Succession.yaml",
"Defined_Multispecies_Enamel_Caries_Model.yaml",
"Defined_ThreeStrain_Organic_Nitrogen_Nitrifying_Community.yaml",
+ "Dehalococcoides_Desulfovibrio_Pelosinus_Corrinoid_Triculture.yaml",
"Dolichospermum_FBCC_A233_Xenic_Phycosphere_Community.yaml",
"Drought_Rhizosphere_Iron_Actinobacteria_Community.yaml",
"EcoFAB_Ring_Trial_SynCom17.yaml",