Coccomyxa onubensis dominates the upper layer and chemocline and supplies phototrophic primary production to the stratified pit-lake ecosystem. The link from algal production to deep-layer sulfate reduction is mediated by organic carbon reaching the deep layer, not by an assayed pairwise cross-feeding interaction with a named bacterial genus.
-
Cueva de la Mora omics identify active Coccomyxa onubensis as dominant in the upper layer and chemocline. PARTIAL - its proposed primary-production contribution does not quantify carbon fixation or selectively demonstrate algal export to a named sulfate reducer. FC/La Zarza showed very limited phototrophic indicators and are not evidence for the same algal route. The 2020 authors did not infer that organic carbon was necessarily the limiting factor in those two lakes.
)
+ class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:16526)
@@ -1238,15 +1183,11 @@
"Heterotrophic archaeal populations with predicted activity for sulfide oxidation related to uncultured Thermoplasmatales dominated in the deep layer"
"The results show that the culture consisted mainly of four species, including Leptospirillum ferriphilum, Acidithiobacillus caldus, Sulfobacillus acidophilus, and Ferroplasma thermophilum, before adapting to a pulp density of 4%"
-
Species-subset biofilms and growth modeling revealed a dynamic network of positive and negative interspecies effects that determined final biofilm composition.
+
Controlled species-subset biofilms and fitted growth curves support dynamic positive and negative effects in this four-species model. Rhodocyclus adhesion/early growth was facilitated, Pseudomonas development was delayed, and Kocuria abundance was suppressed. These distinct measured effects do not establish a community-wide cooperation benefit, competitive niche partitioning or a resolved physical shielding mechanism. Bacillus ATCC14579T was a laboratory substitution; canonical strain labels are preserved.
+
Participating Taxa:
+
+ Rhodocyclus sp.,
+
+ Pseudomonas fluorescens,
+
+ Kocuria varians,
+
+ Bacillus cereus
+
+
+
@@ -753,15 +754,20 @@
Evidence
-
A negative interaction in the biofilm is mediated by thiocillin I produced by the Bacillus cereus strain, and mutational analysis showed that this molecule affects species distribution and biofilm robustness.
+
B. cereus tclE-H deletion removed anti-Kocuria activity in the plate assay and, when substituted into the four-species biofilm, increased Kocuria abundance by about 50-fold. This is positive genetic evidence for thiocillin-biosynthesis-dependent suppression, interpreted by the authors as thiocillin I action. Activity was mainly pellet-associated or unstable; a freely diffusible bulk-medium route is not established. The main text did not report complementation or a purified-thiocillin rescue. The observed negative growth effect does not require reciprocal harm to Bacillus.
+
-
Source Taxon: Bacillus cereus
+
Participating Taxa:
+ Bacillus cereus,
+
+ Kocuria varians
+
+
@@ -784,14 +790,13 @@
Bacillus Thiocillin-Mediated Negative Interaction
Downstream Effects:
-
→ Dynamic Positive and Negative Biofilm Interactions
-
Bacillus cereus thiocillin I changes the relative distribution of biofilm members.
+
→ Biofilm Community Composition and Growth Interactions
+
Replacing wild-type B. cereus with the tclE-H deletion mutant increased Kocuria abundance and changed the 72-hour four-species composition, supporting a causal contribution of the thiocillin-biosynthesis-dependent negative interaction under the tested biofilm conditions. This does not establish every mechanism in the wider interaction network.
-
→ Robustness to Transient Perturbation
-
Removing Bacillus thiocillin reshapes the model biofilm response to transient and continuous perturbations, linking this negative interaction to community robustness.
-
+
→ Condition-Specific Biofilm Response to Perturbation
+
The tclE-H mutant substitution changed the community response to initial Bacillus depletion and to continuous substrate/medium changes. The genetic intervention supports a condition-specific contribution to the measured response, not universal robustness, a mature-biofilm recovery trajectory or a fully isolated thiocillin I rescue mechanism.
@@ -833,13 +838,24 @@
Evidence
-
The model biofilm reproducibly returned to a stable equilibrium composition after transient inoculum perturbations, but continuous perturbations reduced robustness.
+
Wild-type biofilms established similar 72-hour compositions after the tested initial physiological-state and Bacillus-inoculum changes, while glass substitution and especially undiluted medium altered the community. The thiocillin-biosynthesis mutant changed responses to particular transient and continuous perturbations. This is an endpoint comparison during establishment, not a recovery time course after disrupting an already mature biofilm, a general colonization-facilitation mechanism or robustness to every disturbance. Neither community resisted strong continuous changes uniformly.
+
+
+
+
+
Participating Taxa:
+ Rhodocyclus sp.,
+ Pseudomonas fluorescens,
+ Kocuria varians,
+
+ Bacillus cereus
+
+
@@ -933,6 +949,25 @@
Associated Datasets
+
+ Knowledge gaps & discussions (1)
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which molecular and spatial mechanisms determine the condition-specific biofilm response?
+
+
Retain both genetic-intervention arrows and positive omission/growth findings. The assay distinguishes initial/transient from continuous changes; it is not a mature-biofilm recovery experiment. Purified-molecule or complementation controls would further separate thiocillin I from biosynthetic-locus effects, without negating the existing knockout evidence. Protection of Kocuria by the other members could involve spatial shielding or adsorption but was not selectively resolved. Canonical Pseudomonas CLL49 spelling is preserved despite CCL49 elsewhere in the paper. Prior cultivation-arm correction under #529 remains unchanged. Non-graph taxon roles and origin claims are preserved, not recertified.
+
+
Attaches to: ecological_interactions#Biofilm Community Composition and Growth Interactions, ecological_interactions#Thiocillin-Biosynthesis-Dependent Kocuria Suppression, ecological_interactions#Condition-Specific Biofilm Response to Perturbation
+
+
+
+
+
@@ -1207,7 +1242,7 @@
Evidence
(function() {
var intId = "interaction:0";
- var intType = "NICHE_PARTITIONING";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
@@ -1222,7 +1257,7 @@
Evidence
nodes.push({
id: intId,
- label: "Dynamic Positive and Negative Biofilm Interactions",
+ label: "Biofilm Community Composition and Growth Interactions",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1233,11 +1268,28 @@
Evidence
+ var participantKeys = [
+
+ "Rhodocyclus sp.",
+
+ "Pseudomonas fluorescens",
+
+ "Kocuria varians",
+
+ "Bacillus cereus"
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
+
})();
(function() {
var intId = "interaction:1";
- var intType = "COMPETITION";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
@@ -1250,7 +1302,7 @@
Evidence
nodes.push({
id: intId,
- label: "Bacillus Thiocillin-Mediated Negative Interaction",
+ label: "Thiocillin-Biosynthesis-Dependent Kocuria Suppression",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1259,18 +1311,26 @@
Evidence
});
- var srcKey = "Bacillus cereus";
- if (taxonNodeIds[srcKey]) {
- links.push({ source: taxonNodeIds[srcKey], target: intId });
- }
+ var participantKeys = [
+
+ "Bacillus cereus",
+
+ "Kocuria varians"
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
})();
(function() {
var intId = "interaction:2";
- var intType = "COLONIZATION_FACILITATION";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
@@ -1283,7 +1343,7 @@
Evidence
nodes.push({
id: intId,
- label: "Robustness to Transient Perturbation",
+ label: "Condition-Specific Biofilm Response to Perturbation",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1294,6 +1354,23 @@
Evidence
+ var participantKeys = [
+
+ "Rhodocyclus sp.",
+
+ "Pseudomonas fluorescens",
+
+ "Kocuria varians",
+
+ "Bacillus cereus"
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
+
})();
diff --git a/history/records/Iberian_Pit_Lake_Stratified_Community/2026-10-06T162402Z-codex-4e3d9b.yaml b/history/records/Iberian_Pit_Lake_Stratified_Community/2026-10-06T162402Z-codex-4e3d9b.yaml
new file mode 100644
index 000000000..97f29d6c7
--- /dev/null
+++ b/history/records/Iberian_Pit_Lake_Stratified_Community/2026-10-06T162402Z-codex-4e3d9b.yaml
@@ -0,0 +1,24 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Iberian_Pit_Lake_Stratified_Community.yaml
+ slug: Iberian_Pit_Lake_Stratified_Community
+session:
+ id: 2026-10-06T162402Z-codex-4e3d9b
+ timestamp: '2026-10-06T16:24:02Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1506
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Bound site-specific pit-lake findings and remove three unsupported causal arrows.
+ details: Source-based self-adversarial review. reports/causal_graph_review/decisions/20261006-pitlakes-bioleach-biofilm-batch53.yaml
diff --git a/history/records/Industrial_Bioreactor_Consortium/2026-10-06T162402Z-codex-b1f92a.yaml b/history/records/Industrial_Bioreactor_Consortium/2026-10-06T162402Z-codex-b1f92a.yaml
new file mode 100644
index 000000000..658eb6f9f
--- /dev/null
+++ b/history/records/Industrial_Bioreactor_Consortium/2026-10-06T162402Z-codex-b1f92a.yaml
@@ -0,0 +1,25 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Industrial_Bioreactor_Consortium.yaml
+ slug: Industrial_Bioreactor_Consortium
+session:
+ id: 2026-10-06T162402Z-codex-b1f92a
+ timestamp: '2026-10-06T16:24:02Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1507
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Correct bioleaching organism and study assignments; preserve unresolved community
+ identity and regeneration graph.
+ details: Source-based self-adversarial review. reports/causal_graph_review/decisions/20261006-pitlakes-bioleach-biofilm-batch53.yaml
diff --git a/history/records/Industrial_Milk_Line_FourSpecies_Model_Biofilm/2026-10-06T162402Z-codex-2f65bf.yaml b/history/records/Industrial_Milk_Line_FourSpecies_Model_Biofilm/2026-10-06T162402Z-codex-2f65bf.yaml
new file mode 100644
index 000000000..591a82922
--- /dev/null
+++ b/history/records/Industrial_Milk_Line_FourSpecies_Model_Biofilm/2026-10-06T162402Z-codex-2f65bf.yaml
@@ -0,0 +1,25 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Industrial_Milk_Line_FourSpecies_Model_Biofilm.yaml
+ slug: Industrial_Milk_Line_FourSpecies_Model_Biofilm
+session:
+ id: 2026-10-06T162402Z-codex-2f65bf
+ timestamp: '2026-10-06T16:24:02Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1508
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Preserve thiocillin genetic effects with explicit participants and condition-specific
+ perturbation scope.
+ details: Source-based self-adversarial review. reports/causal_graph_review/decisions/20261006-pitlakes-bioleach-biofilm-batch53.yaml
diff --git a/kb/communities/Iberian_Pit_Lake_Stratified_Community.yaml b/kb/communities/Iberian_Pit_Lake_Stratified_Community.yaml
index fb91c4f73..353cc54b3 100644
--- a/kb/communities/Iberian_Pit_Lake_Stratified_Community.yaml
+++ b/kb/communities/Iberian_Pit_Lake_Stratified_Community.yaml
@@ -333,15 +333,13 @@ taxonomy:
snippet: active green alga Coccomyxa onubensis dominated the upper layer and chemocline
explanation: Documents autotrophic carbon fixation activity
ecological_interactions:
-- name: Stratified Iron Redox Cycling
- description: 'The acidic pit lake exhibits vertical iron redox zonation: chemocline populations are
- predicted to carry out iron(II) oxidation, while predicted iron(III) reduction is restricted to
- Proteobacteria in the deep layer. This is a stratified community process rather than a pairwise
- mutualism between two iron oxidizers.
-
- '
+- name: Stratified Iron Redox Potential
+ description: PARTIAL - Cueva de la Mora omics associate chemocline populations with iron oxidation and deep Proteobacteria
+ with iron reduction. The 2013 NSC/Concepcion study instead combines geochemistry with clone-library identities
+ to propose site-specific iron cycling. These positive observations support redox-functional potential, not direct
+ flux by every listed taxon or demonstrated competitive niche partitioning. The canonical participants summarize
+ roles across studies and are not an assayed four-member unit.
scope: COMMUNITY_LEVEL
- interaction_type: NICHE_PARTITIONING
participating_taxa:
- preferred_term: Leptospirillum
term:
@@ -359,58 +357,46 @@ ecological_interactions:
term:
id: NCBITaxon:522
label: Acidiphilium
- source_taxon:
- preferred_term: Leptospirillum
- term:
- id: NCBITaxon:179
- label: Leptospirillum
metabolites:
- preferred_term: Fe(II)
term:
id: CHEBI:29033
label: iron(2+)
- concentration: 2-113 mM (depth-dependent)
+ notes: Contextual iron redox species; no exact concentration is assigned across the different lakes.
- preferred_term: Fe(III)
term:
id: CHEBI:29034
label: iron(3+)
- biological_processes:
- - preferred_term: iron ion transport
- term:
- id: GO:0006826
- label: iron ion transport
- downstream:
- - target: Biosulfidogenesis and Metal Precipitation
- description: Iron and sulfate redox guilds are both active across the chemocline and deep layer of
- the stratified acidic pit lake.
+ notes: Contextual iron redox species; no exact concentration is assigned across the different lakes.
evidence:
- reference: PMID:36123522
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: IN_VIVO
- snippet: The chemocline had activity for iron(II) oxidation carried out by populations of Ca.
- Acidulodesulfobacterium, Ferrovum, Leptospirillium, and Armatimonadetes
- explanation: Documents predicted iron(II) oxidation by chemocline populations.
+ snippet: The chemocline had activity for iron(II) oxidation carried out by populations of Ca. Acidulodesulfobacterium,
+ Ferrovum, Leptospirillium, and Armatimonadetes
+ explanation: Supports a study-specific functional inference from omics or taxonomic/geochemical observations,
+ not measured flux by all listed participants.
- reference: PMID:36123522
supports: PARTIAL
evidence_source: IN_VIVO
snippet: iron(III) reduction was only detected in the deep layer affiliated with Proteobacteria
- explanation: Confirms Fe³⁺ reduction in deep layer
+ explanation: Supports a study-specific functional inference from omics or taxonomic/geochemical observations,
+ not measured flux by all listed participants.
- reference: PMID:23840525
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: IN_VIVO
- snippet: facultative iron reducing bacteria and archaea (Acidithiobacillus ferrooxidans,
- Acidiphilium, Actinobacteria, Acidimicrobiales, Ferroplasma) detected in the bottom layer
- explanation: Connects Acidiphilium to the bottom-layer iron-reducing guild reported from an Iberian
- acidic pit lake.
-- name: Biosulfidogenesis and Metal Precipitation
- description: 'Sulfate-reducing Desulfomonile and Ca. Acidulodesulfobacterium populations are active
- in the chemocline, and the deep layer has microbial genetic potential for sulfide mineral precipitation.
- Dissolved Cu and Zn sulfides in acidic Iberian Pyrite Belt pit lakes support biogenic sulfide formation
- as a natural-attenuation process.
-
- '
+ snippet: facultative iron reducing bacteria and archaea (Acidithiobacillus ferrooxidans, Acidiphilium, Actinobacteria,
+ Acidimicrobiales, Ferroplasma) detected in the bottom layer
+ explanation: Supports a study-specific functional inference from omics or taxonomic/geochemical observations,
+ not measured flux by all listed participants.
+- name: Biosulfidogenesis and Metal Attenuation Model
+ description: PARTIAL - the Cueva de la Mora abstract reports active chemocline sulfate-reducing populations and
+ deep-layer precipitation potential, constrained by carbon quality/quantity and possible groundwater oxygen input.
+ In separate FC/La Zarza lakes, metal profiles, putative sulfidogenic taxa and observed FC copper/zinc sulfide
+ particles support a biosulfidogenesis model. The observed particles are precipitated sulfides, not dissolved
+ sulfides. This is not demonstrated pairwise syntrophy or proof that both canonical taxa mediate every lake result;
+ sulfur reduction/disproportionation and sulfate reduction have distinct proposed roles.
scope: COMMUNITY_LEVEL
- interaction_type: SYNTROPHY
participating_taxa:
- preferred_term: Desulfomonile
term:
@@ -420,85 +406,74 @@ ecological_interactions:
term:
id: NCBITaxon:2597222
label: Candidatus Acidulidesulfobacterium
- source_taxon:
- preferred_term: Desulfomonile
- term:
- id: NCBITaxon:2357
- label: Desulfomonile
metabolites:
- preferred_term: sulfate
term:
id: CHEBI:16189
label: sulfate
- concentration: 26-126 mM (depth-dependent)
+ notes: Contextual sulfur substrate/product or metal-sulfide class; exact concentrations and precipitate identity
+ are not assigned across lakes.
- preferred_term: hydrogen sulfide
term:
id: CHEBI:16136
label: hydrogen sulfide
- concentration: 120 µM (peak at chemocline)
+ notes: Contextual sulfur substrate/product or metal-sulfide class; exact concentrations and precipitate identity
+ are not assigned across lakes.
- preferred_term: copper sulfide
term:
id: CHEBI:51110
label: copper(II) sulfide
+ notes: Contextual sulfur substrate/product or metal-sulfide class; exact concentrations and precipitate identity
+ are not assigned across lakes.
biological_processes:
- preferred_term: dissimilatory sulfate reduction
term:
id: GO:0019420
label: dissimilatory sulfate reduction
- - preferred_term: sulfide oxidation
- term:
- id: GO:0019418
- label: sulfide oxidation
- downstream:
- - target: Subsurface Heterotrophic Carbon Scavenging
- description: Sulfate reduction consumes organic carbon from primary production
evidence:
- reference: PMID:36123522
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: IN_VIVO
- snippet: Abundant sulfate-reducing Desulfomonile and Ca. Acidulodesulfobacterium populations
- were active in the chemocline
- explanation: Documents the active chemocline sulfate-reducing populations.
+ snippet: Abundant sulfate-reducing Desulfomonile and Ca. Acidulodesulfobacterium populations were active in
+ the chemocline
+ explanation: Supports the Cueva de la Mora metabolic/precipitation model, not direct partner-resolved flux or
+ mineral identity in every lake.
- reference: PMID:36123522
supports: PARTIAL
evidence_source: IN_VIVO
snippet: sulfide mineral precipitation in the deep layer
- explanation: Documents metal precipitation through biosulfidogenesis
-- name: Algal Primary Production and Carbon Export
- description: 'Coccomyxa onubensis dominates the upper layer and chemocline and supplies phototrophic
- primary production to the stratified pit-lake ecosystem. The link from algal production to deep-layer
- sulfate reduction is mediated by organic carbon reaching the deep layer, not by an assayed pairwise
- cross-feeding interaction with a named bacterial genus.
-
- '
+ explanation: Supports the Cueva de la Mora metabolic/precipitation model, not direct partner-resolved flux or
+ mineral identity in every lake.
+ - reference: doi:10.3390/microorganisms8091275
+ supports: PARTIAL
+ evidence_source: IN_VIVO
+ snippet: The detection of Cu and Zn sulfides in the monimolimnion of FC suggests precipitation of dissolved
+ metals as metal sulfides
+ explanation: Supports positive FC mineral evidence for the biosulfidogenesis model. It does not establish the
+ same precipitates in La Zarza or assign them to both canonical taxa.
+- name: Coccomyxa Primary Production Potential
+ description: Cueva de la Mora omics identify active Coccomyxa onubensis as dominant in the upper layer and chemocline.
+ PARTIAL - its proposed primary-production contribution does not quantify carbon fixation or selectively demonstrate
+ algal export to a named sulfate reducer. FC/La Zarza showed very limited phototrophic indicators and are not
+ evidence for the same algal route. The 2020 authors did not infer that organic carbon was necessarily the limiting
+ factor in those two lakes.
scope: COMMUNITY_LEVEL
- interaction_type: CROSS_FEEDING
participating_taxa:
- preferred_term: Coccomyxa onubensis
term:
id: NCBITaxon:1125364
label: Coccomyxa onubensis
- source_taxon:
- preferred_term: Coccomyxa onubensis
- term:
- id: NCBITaxon:1125364
- label: Coccomyxa onubensis
metabolites:
- preferred_term: organic molecular entity
term:
id: CHEBI:50860
label: organic molecular entity
- concentration: Reaches the deep layer
+ notes: Contextual carbon substrate/product; no measured algal export rate or partner-specific transfer is asserted.
- preferred_term: carbon dioxide
term:
id: CHEBI:16526
label: carbon dioxide
- notes: Fixed via Calvin-Benson-Bassham cycle
- - preferred_term: Fe(II)
- term:
- id: CHEBI:29033
- label: iron(2+)
- notes: Produced via photoreduction of Fe³⁺
+ notes: Contextual carbon substrate/product; no measured algal export rate or partner-specific transfer is asserted.
biological_processes:
- preferred_term: photosynthesis
term:
@@ -513,82 +488,69 @@ ecological_interactions:
supports: SUPPORT
evidence_source: IN_VIVO
snippet: We found that active green alga Coccomyxa onubensis dominated the upper layer and chemocline
- explanation: Establishes Coccomyxa as dominant primary producer
+ explanation: Supports active algal dominance, not a quantified fixation rate or measured export to a bacterial
+ recipient.
- reference: PMID:36123522
supports: PARTIAL
evidence_source: IN_VIVO
snippet: active green alga Coccomyxa onubensis dominated the upper layer and chemocline
- explanation: Quantifies high carbon fixation activity
-- name: Subsurface Heterotrophic Carbon Scavenging
- description: 'Uncultured heterotrophic Thermoplasmatales dominate the deep layer and are predicted
- to contribute to sulfide oxidation. Sulfide precipitation potential depends on the organic carbon
- that reaches the deep layer and on groundwater oxygen additions that can reoxidize sulfide minerals.
-
- '
+ explanation: The repeated dominance excerpt does not quantify carbon fixation or demonstrate cross-feeding.
+- name: Deep-Layer Thermoplasmatales Metabolic Potential
+ description: PARTIAL - uncultured Thermoplasmatales dominated the deep Cueva de la Mora layer and were predicted
+ to have heterotrophic and sulfide-oxidizing activity. The positive omics inference does not establish a uniform
+ metabolism for the whole order, measured organic-carbon scavenging that benefits another taxon, or a donor route
+ to methanogens. Groundwater oxygen and carbon constraints on sulfide precipitation are community-level proposals,
+ not proof of this archaeal mediation.
scope: COMMUNITY_LEVEL
- interaction_type: COMMENSALISM
participating_taxa:
- preferred_term: Thermoplasmatales
term:
id: NCBITaxon:2301
label: Thermoplasmatales
- source_taxon:
- preferred_term: Thermoplasmatales
- term:
- id: NCBITaxon:2301
- label: Thermoplasmatales
biological_processes:
- - preferred_term: tricarboxylic acid cycle
+ - preferred_term: sulfide oxidation
term:
- id: GO:0006099
- label: tricarboxylic acid cycle
- downstream:
- - target: Subsurface Methanogenesis
- description: Organic carbon reaching the deep layer can constrain anaerobic terminal processes
- in acidic Iberian Pyrite Belt systems, including rare methanogenic activity.
+ id: GO:0019418
+ label: sulfide oxidation
evidence:
- reference: PMID:36123522
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: IN_VIVO
- snippet: Heterotrophic archaeal populations with predicted activity for sulfide oxidation related
- to uncultured Thermoplasmatales dominated in the deep layer
- explanation: Documents the dominant deep-layer Thermoplasmatales population and its predicted
- sulfide-oxidation activity.
+ snippet: Heterotrophic archaeal populations with predicted activity for sulfide oxidation related to uncultured
+ Thermoplasmatales dominated in the deep layer
+ explanation: Supports a predicted archaeal role or community-level constraint; it does not identify a measured
+ scavenger-to-recipient flux.
- reference: PMID:36123522
supports: PARTIAL
evidence_source: IN_VIVO
snippet: quantity and quality of organic carbon reaching the deep layer
- explanation: Supports organic carbon delivery to the deep layer as a constraint on sulfide
- precipitation potential.
-- name: Subsurface Methanogenesis
- description: 'Methanogen reads were detected at low relative abundance in an acidic Iberian Pyrite
- Belt pit lake, and a separate Iberian Pyrite Belt deep-subsurface study detected methanogenic
- Euryarchaeota and hydrogenotrophic bacteria. This supports minor acidic-system methanogenic potential,
- not a demonstrated cross-feeding route from a named pit-lake partner.
-
- '
+ explanation: Supports a predicted archaeal role or community-level constraint; it does not identify a measured
+ scavenger-to-recipient flux.
+- name: Rare Methanogen Sequence Detection
+ description: Low relative-abundance reads classified as methanogens, including Methanobrevibacter, were detected
+ in FC and La Zarza. This supports presence of methanogen-associated sequences and possible methanogenic potential,
+ not measured methane production at the sampled depth. A separate deep-borehole biomarker study does not establish
+ a lake partner-to-Methanobrevibacter pathway. No exact methane concentration or hydrogen donor is assigned to
+ these observations.
scope: COMMUNITY_LEVEL
- interaction_type: NICHE_PARTITIONING
participating_taxa:
- preferred_term: Methanobrevibacter
term:
id: NCBITaxon:2172
label: Methanobrevibacter
- source_taxon:
- preferred_term: Methanobrevibacter
- term:
- id: NCBITaxon:2172
- label: Methanobrevibacter
metabolites:
- preferred_term: methane
term:
id: CHEBI:16183
label: methane
- concentration: 80-90 µM
+ notes: Contextual methanogenic substrate/product; no concentration or local production rate is established by
+ the read-detection evidence.
- preferred_term: hydrogen
term:
id: CHEBI:18276
label: dihydrogen
+ notes: Contextual methanogenic substrate/product; no concentration or local production rate is established by
+ the read-detection evidence.
biological_processes:
- preferred_term: methanogenesis
term:
@@ -598,10 +560,10 @@ ecological_interactions:
- reference: doi:10.3390/microorganisms8091275
supports: SUPPORT
evidence_source: IN_VIVO
- snippet: Furthermore, the detection of reads classified as methanogens and Desulfosporosinus spp.,
- although at low relative abundance, represents one of the lowest pH values (2.9 in LZ) at which
- these taxa have been reported, to our knowledge
- explanation: Documents methanogen presence at extremely low pH
+ snippet: Furthermore, the detection of reads classified as methanogens and Desulfosporosinus spp., although
+ at low relative abundance, represents one of the lowest pH values (2.9 in LZ) at which these taxa have been
+ reported, to our knowledge
+ explanation: Supports rare methanogen-associated sequences, not measured methane flux or competitive niche partitioning.
environmental_factors:
- name: Upper Layer pH
value: 2.2-3.1
@@ -792,5 +754,30 @@ curation_history:
curator: codex
action: REPAIR_OBSOLETE_GO_PROCESS
llm_assisted: true
- changes: Replaced obsolete GO:0070221 with GO's explicit replaced_by target GO:0019418 (sulfide oxidation).
- Preserved the specific preferred term, interaction prose, metabolites, downstream links, and evidence.
+ changes: Replaced obsolete GO:0070221 with GO's explicit replaced_by target GO:0019418 (sulfide oxidation). Preserved
+ the specific preferred term, interaction prose, metabolites, downstream links, and evidence.
+- timestamp: '2026-10-06T16:24:01Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: 'Bound site-specific pit-lake findings and remove three unsupported causal arrows. Issue #1506; reports/causal_graph_review/decisions/20261006-pitlakes-bioleach-biofilm-batch53.yaml'
+ llm_assisted: true
+discussions:
+- discussion_id: iberian_site_specific_redox_and_carbon_routes
+ prompt: Which same-site processes connect iron cycling, carbon production, sulfidogenesis and methanogenesis?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Stratified Iron Redox Potential
+ - ecological_interactions#Biosulfidogenesis and Metal Attenuation Model
+ - ecological_interactions#Coccomyxa Primary Production Potential
+ - ecological_interactions#Deep-Layer Thermoplasmatales Metabolic Potential
+ - ecological_interactions#Rare Methanogen Sequence Detection
+ rationale: 'Remove three unsupported arrows: iron/sulfate coactivity is not a directed link; sulfate reduction
+ consuming carbon does not cause archaeal scavenging; rare methanogen reads do not demonstrate an archaeal carbon-donor
+ route. Keep NSC/Concepcion, Cueva de la Mora, FC/La Zarza and the borehole distinct. The complete 2013/2020
+ texts support measured geochemistry, observed FC mineral particles and taxonomic patterns, with proposed mechanisms.
+ Only the 2022 abstract was accessible. Direct flux, selective perturbations and matched taxon/chemistry measurements
+ would test the proposed routes. No new causal structure is minted. Canonical taxonomy and non-graph claims are
+ preserved, not recertified.'
+ posed_by: codex
+ posed_date: '2026-10-06'
diff --git a/kb/communities/Industrial_Bioreactor_Consortium.yaml b/kb/communities/Industrial_Bioreactor_Consortium.yaml
index a98b8535c..411ed18ee 100644
--- a/kb/communities/Industrial_Bioreactor_Consortium.yaml
+++ b/kb/communities/Industrial_Bioreactor_Consortium.yaml
@@ -388,182 +388,85 @@ taxonomy:
before adapting to a pulp density of 4%
explanation: Quantifies sensitivity limiting abundance in high-density reactors
ecological_interactions:
-- name: Thermophilic Ferrous Iron Oxidation in Early Reactor Stages
- description: 'Acidithiobacillus caldus oxidizes ferrous iron (Fe²⁺) to ferric iron (Fe³⁺) during early
- reactor operation when pH remains above 2.0 and reduced inorganic sulfur compounds are readily available
- from chalcopyrite feed. Operating at 40-50°C with optimum near 45°C, At. caldus dominates early stages,
- and A. caldus predominated in the initial stage of the adapted chalcopyrite culture. This obligate autotroph uses rusticyanin-based
- electron transport to oxidize Fe²⁺, fixing CO₂ via Calvin cycle and generating reducing equivalents.
- The produced Fe³⁺ serves as primary oxidant for chalcopyrite dissolution: CuFeS₂ + 4Fe³⁺ → Cu²⁺ +
- 5Fe²⁺ + 2S⁰. This reaction releases copper ions for recovery and regenerates Fe²⁺ substrate, creating
- a closed iron redox cycle. As reactor operation progresses, changing pH, Fe³⁺ accumulation,
- and depletion of accessible RISCs favor succession to Sulfobacillus and Ferroplasma species
- with greater acid tolerance and mixotrophic capability.
-
- '
- interaction_type: SYNTROPHY
+- name: Initial Acidithiobacillus caldus Predominance
+ description: 'The 2014 adapted chalcopyrite culture showed initial A. caldus predominance by qPCR at 20 percent
+ pulp density. This positive population result does not identify A. caldus as a ferrous-iron oxidizer: the 2023
+ study describes sulfur-oxidizing potential for A. caldus BR_03, not its ownership of the A-plasma rusticyanin
+ finding. The studies concern different communities. Relative predominance does not establish the proposed pH,
+ substrate-depletion or competitive mechanism of succession.'
scope: COMMUNITY_LEVEL
participating_taxa:
- preferred_term: Acidithiobacillus caldus
term:
id: NCBITaxon:33059
label: Acidithiobacillus caldus
- source_taxon:
- preferred_term: Acidithiobacillus caldus
- term:
- id: NCBITaxon:33059
- label: Acidithiobacillus caldus
- metabolites:
- - preferred_term: Fe(II)
- term:
- id: CHEBI:29033
- label: iron(2+)
- concentration: Substrate from chalcopyrite dissolution and reactor feed
- - preferred_term: Fe(III)
- term:
- id: CHEBI:29034
- label: iron(3+)
- concentration: Microbially generated oxidant
- biological_processes:
- - preferred_term: iron ion transport
- term:
- id: GO:0006826
- label: iron ion transport
- - preferred_term: carbon fixation
- term:
- id: GO:0015977
- label: carbon fixation
- downstream:
- - target: Chalcopyrite Dissolution by Ferric Iron
- description: Fe³⁺ oxidizes chalcopyrite to release Cu²⁺ and regenerate Fe²⁺
evidence:
- reference: PMID:24242252
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: The results show that the culture consisted mainly of four species, including Leptospirillum
- ferriphilum, Acidithiobacillus caldus, Sulfobacillus acidophilus, and Ferroplasma thermophilum,
- before adapting to a pulp density of 4%
- explanation: Establishes dominance and operational conditions
- - reference: doi:10.1007/s00253-008-1792-8
- supports: SUPPORT
- evidence_source: IN_VITRO
- snippet: Mutualistic interactions between physiologically distinct moderately thermophilic acidophiles,
- involving transformations of iron and sulfur and transfer of organic compound, were considered to
- play a critical role in promoting chalcopyrite dissolution
- explanation: Quantifies At. caldus in thermophilic bioleaching
-- name: Thermophilic Sulfur Oxidation to Sulfuric Acid
- description: 'Acidithiobacillus caldus oxidizes elemental sulfur (S⁰) and reduced inorganic sulfur compounds
- released from chalcopyrite dissolution to sulfuric acid, maintaining the extremely low pH (1.5-2.0)
- essential for metal solubilization and Fe³⁺ stability. The primary oxidation pathway follows: S⁰ +
- 1.5O₂ + H₂O → H₂SO₄. At. caldus encodes complete Sox system, sulfide-quinone reductase (SQR), and
- heterodisulfide reductase (HDR) for processing diverse sulfur species including thiosulfate, tetrathionate,
- polysulfides, and elemental sulfur. Operating at 40-50°C, this thermophilic sulfur oxidation proceeds
- faster than mesophilic At. thiooxidans (optimum 28°C), critical for industrial reactors where exothermic
- sulfide oxidation elevates temperatures. Continuous acid generation prevents precipitation of dissolved
- metals as hydroxides and enhances Fe³⁺ attack on mineral surfaces. The acidic environment (pH 1.5-2.0)
- creates selective pressure excluding non-acidophiles while maintaining optimal conditions for the
- specialized thermophilic consortium.
-
- '
- interaction_type: SYNTROPHY
+ snippet: A. caldus was the predominant species in the initial stage
+ explanation: Supports early relative predominance, not ferrous-iron oxidation or rusticyanin ownership.
+- name: Acidithiobacillus Sulfur-Oxidizing Potential
+ description: The 2023 genome analysis assigns sulfur-oxidizing potential to A. caldus BR_03. PARTIAL - this supports
+ its proposed role in sulfur transformations, not measured taxon-specific sulfuric-acid flux, a fixed biologically
+ maintained pH or a comparative rate advantage over mesophiles. The 2023 reactor pH was operationally adjusted.
+ The separate 2019 pH experiment reports early attached A. caldus abundance; it does not establish all mechanistic
+ claims for this composite roster.
scope: COMMUNITY_LEVEL
participating_taxa:
- preferred_term: Acidithiobacillus caldus
term:
id: NCBITaxon:33059
label: Acidithiobacillus caldus
- source_taxon:
- preferred_term: Acidithiobacillus caldus
- term:
- id: NCBITaxon:33059
- label: Acidithiobacillus caldus
metabolites:
- preferred_term: sulfur
term:
id: CHEBI:26833
label: sulfur atom
- notes: Elemental sulfur (S⁰) from chalcopyrite dissolution
+ notes: Contextual sulfur substrate/product, not an experimentally isolated A. caldus acidification flux or fixed
+ pH.
- preferred_term: sulfuric acid
term:
id: CHEBI:26836
label: sulfuric acid
- concentration: Maintains pH 1.5-2.0
+ notes: Contextual sulfur substrate/product, not an experimentally isolated A. caldus acidification flux or fixed
+ pH.
biological_processes:
- preferred_term: sulfur compound metabolic process
term:
id: GO:0006790
label: sulfur compound metabolic process
evidence:
- - reference: doi:10.1007/s13213-019-01453-y
+ - reference: doi:10.3390/biology12111411
supports: SUPPORT
- evidence_source: IN_VITRO
- snippet: Sulfobacillus thermosulfidooxidans and Acidithiobacillus caldus were the
- dominant species during the early stage
- explanation: Establishes A. caldus as a dominant early-stage species in moderately
- thermophilic chalcopyrite bioleaching, supporting its role as a sulfur-oxidizing
- acidophile in the reactor consortium.
-- name: Mid-Stage Mixotrophic Iron Oxidation
- description: 'During middle-stage reactor operation, Sulfobacillus acidophilus becomes predominant.
- This facultatively autotrophic organism bridges the ecological
- transition from early-stage autotrophy (At. caldus) to late-stage mixotrophy (Ferroplasma). S. acidophilus
- oxidizes Fe²⁺ with enhanced efficiency compared to At. caldus while simultaneously utilizing organic
- compounds (cell lysate, molasses, dissolved organics from mineral processing) for heterotrophic growth.
- The mixotrophic metabolism provides competitive advantage when RISC substrates decline but dissolved
- organic carbon increases from cell turnover and concentrate additives. Spore-forming capability confers
- resilience to fluctuating metal concentrations, pH stress, and nutrient limitation. S. acidophilus
- maintains robust Fe³⁺ generation during the critical transition period, ensuring continuous copper
- dissolution as conditions become too acidic and Fe³⁺-rich for obligate autotrophs but not yet optimal
- for extreme acidophiles like Ferroplasma.
-
- '
- interaction_type: NICHE_PARTITIONING
+ evidence_source: COMPUTATIONAL
+ snippet: This bacterium is a sulfur-oxidizing acidophile
+ explanation: Results 3.3.1 identifies A. caldus BR_03 and its sulfur-oxidizing potential. This is not measured
+ acidification in every reactor.
+- name: Middle-Stage Sulfobacillus acidophilus Predominance
+ description: The 2014 20-percent-pulp chalcopyrite experiment reports S. acidophilus, rather than A. caldus, as
+ predominant in the middle stage. The positive qPCR population result does not selectively establish a mixotrophic
+ transition, superior iron-oxidation efficiency, a molasses response or competitive niche partitioning. Those
+ causal mechanisms cannot be assigned from the succession observation alone.
scope: COMMUNITY_LEVEL
participating_taxa:
- preferred_term: Sulfobacillus acidophilus
term:
id: NCBITaxon:53633
label: Sulfobacillus acidophilus
- source_taxon:
- preferred_term: Sulfobacillus acidophilus
- term:
- id: NCBITaxon:53633
- label: Sulfobacillus acidophilus
- metabolites:
- - preferred_term: Fe(II)
- term:
- id: CHEBI:29033
- label: iron(2+)
- - preferred_term: Fe(III)
- term:
- id: CHEBI:29034
- label: iron(3+)
- - preferred_term: organic molecular entity
- term:
- id: CHEBI:50860
- label: organic molecular entity
- notes: Yeast extract, molasses, cell lysate for mixotrophic growth
evidence:
- reference: PMID:24242252
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: caldus became the predominant species in the middle stage
- explanation: Quantifies mid-stage dominance and metabolic role
-- name: Late-Stage Extreme Acidophile Iron Oxidation
- description: 'In late-stage reactor operation, Ferroplasma species (F. thermophilum, F. acidiphilum,
- Ferroplasma sp., Acidiplasma sp.) dominate the consortium. These cell
- wall-lacking archaea thrive under extreme conditions: low pH and elevated dissolved
- metal concentrations (Cu²⁺, Zn²⁺, Ni²⁺). Ferroplasma oxidizes Fe²⁺
- using sulfocyanin-based electron transport, distinct from bacterial rusticyanin systems. Facultatively
- aerobic and mixotrophic, these archaea utilize both iron oxidation and accumulated dissolved organic
- matter for energy and carbon. Their extreme metal tolerance (growth at 1000 mM heavy metals) and pleomorphic
- morphology (no peptidoglycan cell wall) enable persistence in acidic, toxic conditions that eliminate
- competitors. Ferroplasma maintains sustained Fe³⁺ generation for continued copper extraction throughout
- extended reactor operation, preventing Fe³⁺ depletion that would halt bioleaching. The succession
- from bacterial to archaeal iron oxidizers demonstrates niche differentiation along chemical gradients
- in industrial reactors.
-
- '
- interaction_type: NICHE_PARTITIONING
+ snippet: S. acidophilus rather than A. caldus became the predominant species in the middle stage
+ explanation: Restores the negation omitted by the previous snippet; supports the population observation, not
+ an isolated metabolic cause.
+- name: Ferroplasmaceae Iron-Oxidizing Potential
+ description: 'PARTIAL - the 2023 study describes iron-oxidation potential in the F. acidiphilum BR_01 and Acidiplasma
+ BR_02 genomes from a 45 C continuous CO2 reactor. The related Acidiplasma MBA-1 genome study supports an aerobic
+ iron-oxidizing capability. These findings do not transfer the 2014 F. thermophilum late-stage abundance result
+ to either canonical participant, prove their late-stage copper contribution, or establish a universal heavy-metal
+ tolerance threshold. Exact community identity remains unresolved under #1509.'
scope: COMMUNITY_LEVEL
participating_taxa:
- preferred_term: Ferroplasma acidiphilum
@@ -574,66 +477,47 @@ ecological_interactions:
term:
id: NCBITaxon:1872114
label: Acidiplasma sp.
- source_taxon:
- preferred_term: Ferroplasma acidiphilum
- term:
- id: NCBITaxon:74969
- label: Ferroplasma acidiphilum
metabolites:
- preferred_term: Fe(II)
term:
id: CHEBI:29033
label: iron(2+)
+ notes: Contextual iron redox substrate/product; genotype-based capability is not measured late-stage flux.
- preferred_term: Fe(III)
term:
id: CHEBI:29034
label: iron(3+)
- concentration: Accumulates in late stages
- biological_processes:
- - preferred_term: iron ion transport
- term:
- id: GO:0006826
- label: iron ion transport
- downstream:
- - target: Chalcopyrite Dissolution by Ferric Iron
- description: Sustained Fe³⁺ generation maintains copper leaching in acidic late stages
+ notes: Contextual iron redox substrate/product; genotype-based capability is not measured late-stage flux.
evidence:
- - reference: PMID:24242252
- supports: SUPPORT
- evidence_source: IN_VITRO
- snippet: The results show that the culture consisted mainly of four species, including Leptospirillum
- ferriphilum, Acidithiobacillus caldus, Sulfobacillus acidophilus, and Ferroplasma thermophilum,
- before adapting to a pulp density of 4%
- explanation: Quantifies late-stage archaeal dominance
-- name: Chalcopyrite Dissolution by Ferric Iron
- description: 'Ferric iron generated by the microbial consortium oxidizes chalcopyrite (CuFeS₂) concentrate,
- releasing copper ions for industrial recovery. The primary reaction is: CuFeS₂ + 4Fe³⁺ → Cu²⁺ + 5Fe²⁺
- + 2S⁰. Operating at 45°C and pH 1.5-2.0, the adapted consortium achieves 60.4% copper extraction from
- 20% pulp density chalcopyrite in 25 days. This exceptional performance
- results from multi-year adaptation through serial subculturing, gradually increasing pulp density
- from 1% to 20%. The released Fe²⁺ is re-oxidized by iron-oxidizing bacteria and archaea, closing the
- iron cycle. Elemental sulfur (S⁰) is oxidized by At. caldus to sulfuric acid.
- Higher pulp densities increase substrate load and can create metabolic stress
- and mass transfer limitations; long-term adaptation was required before the
- mixed culture efficiently leached chalcopyrite at 20% pulp density.
-
- '
- interaction_type: SYNTROPHY
+ - reference: doi:10.3390/biology12111411
+ supports: PARTIAL
+ evidence_source: COMPUTATIONAL
+ snippet: is capable of oxidizing ferrous iron and reducing molecular oxygen
+ explanation: Results 3.3.1 describes the inferred F. acidiphilum BR_01 respiratory complex. This is genomic
+ potential, not the 2014 F. thermophilum phenotype.
+ - reference: doi:10.1134/S0026261716060059
+ supports: PARTIAL
+ evidence_source: COMPUTATIONAL
+ snippet: oxidizing ferrous iron under oxic conditions and utilizing organic compounds
+ explanation: Supports Acidiplasma MBA-1 capability; the 2023 primary body reports near-identity of BR_02 with
+ MBA-1. It does not demonstrate the 2014 late-stage role.
+- name: Adapted Chalcopyrite Consortium Copper Extraction
+ description: 'After more than two years of serial adaptation, the 2014 mixed culture extracted 60.4 percent of
+ copper from chalcopyrite at 20 percent pulp density in 25 days. This measured consortium outcome is retained.
+ The two canonical participants listed here are a supported subset, not the complete culture: the paper also
+ reports F. thermophilum, which is not represented by the canonical F. acidiphilum/Acidiplasma entries. Ferric-iron
+ regeneration is a proposed process context, not an A. caldus iron-oxidation loop or a selectively measured contribution
+ of the 2023 MAGs. Resolve the exact roster and missing valid regeneration structure under #1509.'
scope: COMMUNITY_LEVEL
participating_taxa:
- preferred_term: Acidithiobacillus caldus
term:
id: NCBITaxon:33059
label: Acidithiobacillus caldus
- - preferred_term: Ferroplasma acidiphilum
- term:
- id: NCBITaxon:74969
- label: Ferroplasma acidiphilum
- source_taxon:
- preferred_term: Acidithiobacillus caldus
+ - preferred_term: Sulfobacillus acidophilus
term:
- id: NCBITaxon:33059
- label: Acidithiobacillus caldus
+ id: NCBITaxon:53633
+ label: Sulfobacillus acidophilus
metabolites:
- preferred_term: chalcopyrite
term:
@@ -649,130 +533,91 @@ ecological_interactions:
term:
id: CHEBI:29034
label: iron(3+)
- notes: Microbially-generated oxidant
+ notes: Proposed redox-cycle context; no taxon-specific regenerated flux is assigned.
- preferred_term: Fe(II)
term:
id: CHEBI:29033
label: iron(2+)
- notes: Regenerated substrate for iron oxidizers
- downstream:
- - target: Thermophilic Ferrous Iron Oxidation in Early Reactor Stages
- description: Released Fe²⁺ is re-oxidized to regenerate Fe³⁺ oxidant
+ notes: Proposed redox-cycle context; no taxon-specific regenerated flux is assigned.
evidence:
- reference: PMID:24242252
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: Thereafter, these samples were combined and then inoculated into a basal salts solution in
- which different substrates (ferrous sulfate, elemental sulfur, and chalcopyrite) served as energy
- sources
- explanation: Quantifies copper recovery performance
- - reference: PMID:24242252
- supports: SUPPORT
- evidence_source: IN_VITRO
- snippet: Thereafter, these samples were combined and then inoculated into a basal salts solution in
- which different substrates (ferrous sulfate, elemental sulfur
-- name: Organic Matter Scavenging by Cuniculiplasma
- description: 'Cuniculiplasma divulgatum functions as heterotrophic scavenger in the predominantly autotrophic
- bioleaching consortium, utilizing complex organic compounds released from cell lysis, chalcopyrite
- concentrate additives (molasses, flotation reagents), and mineral dissolution byproducts. Unable to
- oxidize iron like related Ferroplasma, C. divulgatum occupies a distinct ecological niche based on
- organic carbon metabolism. The organism lacks biosynthetic pathways for several amino acids, requiring
- scavenging of proteins and peptides from microbial turnover. In Richmond Mine acidophilic biofilms,
- related G-plasma accounts for up to 22% of total community proteome, indicating substantial abundance
- in acid mine drainage systems. Facultatively anaerobic metabolism enables growth in oxygen-limited
- zones of dense chalcopyrite pulps (20% w/v). Emerging evidence of sulfur oxidation gene expression
- suggests potential for RISCs metabolism, expanding beyond pure heterotrophy. This archaeon may provide
- ecosystem services including nutrient recycling, removal of potentially inhibitory organics, and syntrophic
- interactions with autotrophs requiring trace organics or vitamins.
-
- '
- interaction_type: COMMENSALISM
+ snippet: At that pulp density, the culture extracted 60.4% of copper from the chalcopyrite in 25 days.
+ explanation: Supports the positive bulk result at 20 percent pulp density, not the former Methods-only claim
+ or mediation by incorrectly substituted taxa.
+- name: Cuniculiplasma Organic-Carbon Metabolic Potential
+ description: The C. divulgatum BR_06 genome in the 2023 reactor sample contains annotated central-carbon and protease
+ functions. PARTIAL - these support organic-carbon metabolic potential, not measured transfer from specific lysed
+ partners, detoxification of other members, vitamin donation or a 20-percent-pulp chalcopyrite niche. The separate
+ Cuniculiplasmataceae review is ecological background, not direct evidence for this reactor mechanism.
scope: COMMUNITY_LEVEL
participating_taxa:
- preferred_term: Cuniculiplasma divulgatum
term:
id: NCBITaxon:1673428
label: Cuniculiplasma divulgatum
- source_taxon:
- preferred_term: Cuniculiplasma divulgatum
- term:
- id: NCBITaxon:1673428
- label: Cuniculiplasma divulgatum
metabolites:
- preferred_term: organic molecular entity
term:
id: CHEBI:50860
label: organic molecular entity
- notes: Cell lysate, molasses, dissolved organics from mineral processing
+ notes: Contextual organic substrate class; exact partner origin, uptake flux and auxotrophic dependency are
+ not established here.
- preferred_term: peptide
term:
id: CHEBI:16670
label: peptide
- notes: From cell lysis; required due to amino acid auxotrophy
- biological_processes:
- - preferred_term: heterotrophic metabolism
- term:
- id: GO:0019319
- label: hexose biosynthetic process
+ notes: Contextual organic substrate class; exact partner origin, uptake flux and auxotrophic dependency are
+ not established here.
evidence:
- - reference: PMID:30499003
- supports: SUPPORT
- evidence_source: IN_VIVO
- snippet: specific functional role and potential of the members of Cuniculiplasmataceae
- abundant in acidophilic microbiomes
- explanation: Golyshina et al. 2019 review assesses the functional role of
- Cuniculiplasmataceae as abundant heterotrophs in acidophilic microbiomes.
-- name: Early-Stage Iron Oxidation with Leptospirillum
- description: Leptospirillum ferriphilum contributes to iron oxidation in the early stages of bioreactor
- operation at lower pulp densities (<4% w/v). This obligate chemolithoautotroph efficiently colonizes
- sulfide mineral surfaces and oxidizes Fe²⁺ at pH approaching 1.5, working alongside Acidithiobacillus
- caldus in the initial consortium composition. However, L. ferriphilum is sensitive to elevated pulp
- densities, organic matter accumulation, and flotation reagent residues, becoming absent above 4% pulp
- density. As the reactor adapts to higher densities through serial subculturing, L. ferriphilum is
- replaced by more tolerant iron oxidizers like Ferroplasma species and Acidiplasma.
- interaction_type: NICHE_PARTITIONING
+ - reference: doi:10.3390/biology12111411
+ supports: PARTIAL
+ evidence_source: COMPUTATIONAL
+ snippet: A large number of proteases
+ explanation: Results 3.3.1 describes the C. divulgatum BR_06 genome; positive annotation supports metabolic
+ potential, not observed scavenger-mediated benefit.
+- name: Leptospirillum Detection During Pulp-Density Adaptation
+ description: The 2014 culture contained L. ferriphilum before adaptation above 4 percent pulp density, after which
+ it was not detected. This positive culture-composition comparison does not prove extinction or isolate pulp
+ density from correlated organics, reagents and adaptation history. Its known iron-oxidizing capability is context,
+ not directly measured flux in every stage, and the 2023 iron-oxidizer profiles concern another system.
scope: COMMUNITY_LEVEL
participating_taxa:
- preferred_term: Leptospirillum ferriphilum
term:
id: NCBITaxon:178606
label: Leptospirillum ferriphilum
- - preferred_term: Acidithiobacillus caldus
- term:
- id: NCBITaxon:33059
- label: Acidithiobacillus caldus
- source_taxon:
- preferred_term: Leptospirillum ferriphilum
- term:
- id: NCBITaxon:178606
- label: Leptospirillum ferriphilum
metabolites:
- preferred_term: Fe(II)
term:
id: CHEBI:29033
label: iron(2+)
- notes: Substrate for iron oxidation
+ notes: Contextual iron redox capability; not a measured Leptospirillum flux during every adaptation stage.
- preferred_term: Fe(III)
term:
id: CHEBI:29034
label: iron(3+)
- notes: Product for chalcopyrite oxidation
+ notes: Contextual iron redox capability; not a measured Leptospirillum flux during every adaptation stage.
evidence:
- reference: PMID:24242252
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: The results show that the culture consisted mainly of four species, including Leptospirillum
- ferriphilum, Acidithiobacillus caldus, Sulfobacillus acidophilus, and Ferroplasma thermophilum,
- before adapting to a pulp density of 4%
- explanation: Establishes L. ferriphilum presence in early consortium
-- name: Ferroplasma Species Complementarity
- description: Multiple Ferroplasma species (F. acidiphilum, Ferroplasma sp.) co-exist in the late-stage
- adapted consortium, contributing to robust iron oxidation at extreme acidity and high pulp densities.
- These cell wall-lacking archaea grow chemomixotrophically, oxidizing Fe²⁺ while scavenging organic
- carbon. The presence of multiple related species may provide functional redundancy and metabolic diversity,
- enabling the consortium to maintain performance across varying conditions (batch vs. continuous reactors,
- pulp density gradients, pH fluctuations).
- interaction_type: NICHE_PARTITIONING
+ snippet: The results show that the culture consisted mainly of four species, including Leptospirillum ferriphilum,
+ Acidithiobacillus caldus, Sulfobacillus acidophilus, and Ferroplasma thermophilum, before adapting to a pulp
+ density of 4%
+ explanation: Supports lower-pulp detection in the 2014 culture, not quantified iron oxidation or extinction
+ later.
+ - reference: PMID:24242252
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: L. ferriphilum could not be detected when the pulp density was greater than 4%.
+ explanation: Supports nondetection, not extinction or an isolated toxic cause.
+- name: Co-Detected Ferroplasma Genomes
+ description: 'The 2023 metagenome from the 45 C continuous CO2 reactor contained F. acidiphilum BR_01 and Ferroplasma
+ BR_04 genomes. This positive co-detection and the reactor profiles do not demonstrate functional redundancy,
+ improved community performance from complementarity, or their presence in the distinct high-pulp 2014 culture.
+ Exact canonical strain mappings remain part of #1509.'
scope: COMMUNITY_LEVEL
participating_taxa:
- preferred_term: Ferroplasma sp.
@@ -783,30 +628,31 @@ ecological_interactions:
term:
id: NCBITaxon:74969
label: Ferroplasma acidiphilum
- source_taxon:
- preferred_term: Ferroplasma sp.
- term:
- id: NCBITaxon:2591003
- label: Ferroplasma sp.
metabolites:
- preferred_term: Fe(II)
term:
id: CHEBI:29033
label: iron(2+)
- notes: Shared substrate
+ notes: Contextual iron-associated capability, not a demonstrated shared flux or complementary contribution.
evidence:
- reference: doi:10.3390/biology12111411
supports: PARTIAL
- evidence_source: IN_VIVO
- snippet: 16S rRNA gene profiling revealed archaea of the family Thermoplasmataceae (Acidiplasma,
- Ferroplasma, Cuniculiplasma, and A-plasma group)
- explanation: Documents co-occurring Ferroplasma and related Thermoplasmatales in the studied reactors
+ evidence_source: IN_VITRO
+ snippet: 16S rRNA gene profiling revealed archaea of the family Thermoplasmataceae (Acidiplasma, Ferroplasma,
+ Cuniculiplasma, and A-plasma group)
+ explanation: The abstract supports Ferroplasma-containing reactor profiles; the inspected primary Results 3.3.1
+ identify two genomes. Neither establishes complementarity or robustness mediation.
+ - reference: doi:10.3390/biology12111411
+ supports: SUPPORT
+ evidence_source: COMPUTATIONAL
+ snippet: BR_04 and BR_01
+ explanation: Results 3.3.1 assigns two MAGs to Ferroplasma; this supports genome co-detection, not complementarity.
- name: Temperature-Structured A-Plasma and Acidiplasma Populations
- description: 'A-plasma and Acidiplasma populations respond differently to the reactor temperature
- regime: Acidiplasma increased from 40°C to 50°C, while A-plasma was more abundant at 45°C. This
- is an operationally structured community shift, not a demonstrated pairwise niche-partitioning
- interaction.'
- interaction_type: NICHE_PARTITIONING
+ description: The 2023 reactor comparison reports increasing Acidiplasma relative abundance from 40 to 50 C and
+ higher A-plasma abundance at 45 C. Preserve this operationally associated population pattern without labeling
+ it a demonstrated pairwise niche interaction. Reactor mode and carbon source also matter; single reactor runs
+ per condition and relative profiles do not isolate competitive mechanisms or assign absolute growth rates to
+ each group.
scope: COMMUNITY_LEVEL
participating_taxa:
- preferred_term: Thermoplasmatales archaeon
@@ -817,11 +663,6 @@ ecological_interactions:
term:
id: NCBITaxon:1872114
label: Acidiplasma sp.
- source_taxon:
- preferred_term: Thermoplasmatales archaeon
- term:
- id: NCBITaxon:2268204
- label: Thermoplasmatales archaeon
biological_processes:
- preferred_term: response to temperature stimulus
term:
@@ -830,20 +671,20 @@ ecological_interactions:
evidence:
- reference: doi:10.3390/biology12111411
supports: SUPPORT
- evidence_source: IN_VIVO
- snippet: A metagenomic analysis of the studied population made it possible to characterize novel archaea
- belonging to an uncultivated, poorly-studied group of Thermoplasmatales which potentially plays
- an important role in the bio-oxidation process
- explanation: Links the novel A-plasma representative to the biooxidation process
+ evidence_source: COMPUTATIONAL
+ snippet: A metagenomic analysis of the studied population made it possible to characterize novel archaea belonging
+ to an uncultivated, poorly-studied group of Thermoplasmatales which potentially plays an important role in
+ the bio-oxidation process
+ explanation: Supports the 2023 reactor population/genome observation, not pairwise niche partitioning or the
+ 2014 temporal succession.
- reference: doi:10.3390/biology12111411
supports: SUPPORT
- evidence_source: IN_VIVO
- snippet: Elevating the temperature from 40 °C to 50 °C resulted in increases in the shares
- of Acidiplasma and Sulfobacillus and decreases in the relative abundances of Ferroplasma,
- Leptospirillum, and Acidithiobacillus, while Cuniculiplasma and A-plasma were more abundant
- at 45 °C.
- explanation: Documents temperature partitioning between Acidiplasma and A-plasma in the
- biooxidation reactors
+ evidence_source: IN_VITRO
+ snippet: Elevating the temperature from 40 °C to 50 °C resulted in increases in the shares of Acidiplasma and
+ Sulfobacillus and decreases in the relative abundances of Ferroplasma, Leptospirillum, and Acidithiobacillus,
+ while Cuniculiplasma and A-plasma were more abundant at 45 °C.
+ explanation: Supports the 2023 reactor population/genome observation, not pairwise niche partitioning or the
+ 2014 temporal succession.
environmental_factors:
- name: Moderate Thermophilic Temperature Range
value: 40-50
@@ -1172,3 +1013,35 @@ cultivation_setup:
snippet: efficiently leach the chalcopyrite at a pulp density of 20% (wt/vol)
explanation: Establishes the high-pulp-density endpoint of the adaptation
campaign.
+discussions:
+- discussion_id: industrial_exact_system_and_regeneration
+ prompt: Which exact community and iron oxidizers support a valid regeneration graph?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Initial Acidithiobacillus caldus Predominance
+ - ecological_interactions#Acidithiobacillus Sulfur-Oxidizing Potential
+ - ecological_interactions#Middle-Stage Sulfobacillus acidophilus Predominance
+ - ecological_interactions#Ferroplasmaceae Iron-Oxidizing Potential
+ - ecological_interactions#Adapted Chalcopyrite Consortium Copper Extraction
+ - ecological_interactions#Cuniculiplasma Organic-Carbon Metabolic Potential
+ - ecological_interactions#Leptospirillum Detection During Pulp-Density Adaptation
+ - ecological_interactions#Co-Detected Ferroplasma Genomes
+ - ecological_interactions#Temperature-Structured A-Plasma and Acidiplasma Populations
+ rationale: 'Three arrows are removed because the first loop falsely assigned iron oxidation to A. caldus and the
+ remaining link transferred a 2014 F. thermophilum role to different 2023 participants. Positive early/middle
+ population observations, genomic capabilities and bulk copper extraction remain. #1509 must resolve the composite
+ community, unrepresented F. thermophilum and broader non-graph claims before new source-grounded regeneration
+ structure. A one-community Edison dry run completed; no paid report was obtained. Full 2023 primary text was
+ inspected, while 2014/2019/2009 studies were available at abstract scope. The invalid hexose-biosynthesis-as-heterotrophy
+ term is removed rather than replaced with a guessed CURIE. Canonical taxonomy and non-graph metadata are preserved,
+ not certified.'
+ posed_by: codex
+ posed_date: '2026-10-06'
+curation_history:
+- timestamp: '2026-10-06T16:24:02Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: 'Correct bioleaching organism and study assignments; preserve unresolved community identity and regeneration
+ graph. Issue #1507; reports/causal_graph_review/decisions/20261006-pitlakes-bioleach-biofilm-batch53.yaml'
+ llm_assisted: true
diff --git a/kb/communities/Industrial_Milk_Line_FourSpecies_Model_Biofilm.yaml b/kb/communities/Industrial_Milk_Line_FourSpecies_Model_Biofilm.yaml
index 7fb3dcfc3..b91dcb812 100644
--- a/kb/communities/Industrial_Milk_Line_FourSpecies_Model_Biofilm.yaml
+++ b/kb/communities/Industrial_Milk_Line_FourSpecies_Model_Biofilm.yaml
@@ -171,10 +171,12 @@ taxonomy:
snippet: Bacillus cereus ATCC14579T and B. cereus ATCC10987
explanation: Supports Bacillus cereus strains used in the model system.
ecological_interactions:
-- name: Dynamic Positive and Negative Biofilm Interactions
- description: Species-subset biofilms and growth modeling revealed a dynamic network of positive and
- negative interspecies effects that determined final biofilm composition.
- interaction_type: NICHE_PARTITIONING
+- name: Biofilm Community Composition and Growth Interactions
+ description: Controlled species-subset biofilms and fitted growth curves support dynamic positive and negative
+ effects in this four-species model. Rhodocyclus adhesion/early growth was facilitated, Pseudomonas development
+ was delayed, and Kocuria abundance was suppressed. These distinct measured effects do not establish a community-wide
+ cooperation benefit, competitive niche partitioning or a resolved physical shielding mechanism. Bacillus ATCC14579T
+ was a laboratory substitution; canonical strain labels are preserved.
scope: COMMUNITY_LEVEL
biological_processes:
- preferred_term: biofilm formation
@@ -190,50 +192,84 @@ ecological_interactions:
supports: SUPPORT
evidence_source: IN_VITRO
snippet: network of dynamic, positive, and negative interactions
- explanation: Supports the inferred interaction network in the four-species model biofilm.
+ explanation: Supports the positive controlled model-biofilm finding, interpreted within the tested community,
+ endpoint and perturbations; not a universal ecological mechanism.
- reference: doi:10.1002/mbo3.1254
supports: SUPPORT
evidence_source: IN_VITRO
snippet: determine the final composition of the biofilm
- explanation: Supports the effect of interactions on equilibrium community composition.
-- name: Bacillus Thiocillin-Mediated Negative Interaction
- description: A negative interaction in the biofilm is mediated by thiocillin I produced by the Bacillus
- cereus strain, and mutational analysis showed that this molecule affects species distribution and
- biofilm robustness.
- interaction_type: COMPETITION
- scope: COMMUNITY_LEVEL
- source_taxon:
- preferred_term: Bacillus cereus
+ explanation: Supports the positive controlled model-biofilm finding, interpreted within the tested community,
+ endpoint and perturbations; not a universal ecological mechanism.
+ participating_taxa:
+ - preferred_term: Rhodocyclus sp.
+ term:
+ id: NCBITaxon:1064
+ label: Rhodocyclus
+ - preferred_term: Pseudomonas fluorescens
+ term:
+ id: NCBITaxon:294
+ label: Pseudomonas fluorescens
+ - preferred_term: Kocuria varians
+ term:
+ id: NCBITaxon:1272
+ label: Kocuria varians
+ - preferred_term: Bacillus cereus
term:
id: NCBITaxon:1396
label: Bacillus cereus
+- name: Thiocillin-Biosynthesis-Dependent Kocuria Suppression
+ description: B. cereus tclE-H deletion removed anti-Kocuria activity in the plate assay and, when substituted
+ into the four-species biofilm, increased Kocuria abundance by about 50-fold. This is positive genetic evidence
+ for thiocillin-biosynthesis-dependent suppression, interpreted by the authors as thiocillin I action. Activity
+ was mainly pellet-associated or unstable; a freely diffusible bulk-medium route is not established. The main
+ text did not report complementation or a purified-thiocillin rescue. The observed negative growth effect does
+ not require reciprocal harm to Bacillus.
+ scope: COMMUNITY_LEVEL
biological_processes:
- preferred_term: interspecies interaction between organisms
term:
id: GO:0044419
label: biological process involved in interspecies interaction between organisms
- downstream:
- - target: Dynamic Positive and Negative Biofilm Interactions
- description: Bacillus cereus thiocillin I changes the relative distribution of biofilm members.
- - target: Robustness to Transient Perturbation
- description: >
- Removing Bacillus thiocillin reshapes the model biofilm response to transient and continuous
- perturbations, linking this negative interaction to community robustness.
evidence:
- reference: PMID:34964290
supports: SUPPORT
evidence_source: IN_VITRO
snippet: thiocillin I synthesized by the B. cereus strain
- explanation: Supports thiocillin I as the molecular determinant of a negative interaction.
+ explanation: Supports the positive controlled model-biofilm finding, interpreted within the tested community,
+ endpoint and perturbations; not a universal ecological mechanism.
- reference: PMID:34964290
supports: SUPPORT
evidence_source: IN_VITRO
snippet: impact on robustness by mutational analysis
- explanation: Supports the mutational evidence linking this interaction to biofilm robustness.
-- name: Robustness to Transient Perturbation
- description: The model biofilm reproducibly returned to a stable equilibrium composition after transient
- inoculum perturbations, but continuous perturbations reduced robustness.
- interaction_type: COLONIZATION_FACILITATION
+ explanation: Supports the positive controlled model-biofilm finding, interpreted within the tested community,
+ endpoint and perturbations; not a universal ecological mechanism.
+ participating_taxa:
+ - preferred_term: Bacillus cereus
+ term:
+ id: NCBITaxon:1396
+ label: Bacillus cereus
+ - preferred_term: Kocuria varians
+ term:
+ id: NCBITaxon:1272
+ label: Kocuria varians
+ downstream:
+ - target: Biofilm Community Composition and Growth Interactions
+ description: Replacing wild-type B. cereus with the tclE-H deletion mutant increased Kocuria abundance and changed
+ the 72-hour four-species composition, supporting a causal contribution of the thiocillin-biosynthesis-dependent
+ negative interaction under the tested biofilm conditions. This does not establish every mechanism in the wider
+ interaction network.
+ - target: Condition-Specific Biofilm Response to Perturbation
+ description: The tclE-H mutant substitution changed the community response to initial Bacillus depletion and
+ to continuous substrate/medium changes. The genetic intervention supports a condition-specific contribution
+ to the measured response, not universal robustness, a mature-biofilm recovery trajectory or a fully isolated
+ thiocillin I rescue mechanism.
+- name: Condition-Specific Biofilm Response to Perturbation
+ description: Wild-type biofilms established similar 72-hour compositions after the tested initial physiological-state
+ and Bacillus-inoculum changes, while glass substitution and especially undiluted medium altered the community.
+ The thiocillin-biosynthesis mutant changed responses to particular transient and continuous perturbations. This
+ is an endpoint comparison during establishment, not a recovery time course after disrupting an already mature
+ biofilm, a general colonization-facilitation mechanism or robustness to every disturbance. Neither community
+ resisted strong continuous changes uniformly.
scope: COMMUNITY_LEVEL
biological_processes:
- preferred_term: biofilm formation
@@ -245,12 +281,31 @@ ecological_interactions:
supports: SUPPORT
evidence_source: IN_VITRO
snippet: highly robust against initial, transient perturbations
- explanation: Supports the biofilm robustness phenotype after transient perturbation.
+ explanation: Supports the positive controlled model-biofilm finding, interpreted within the tested community,
+ endpoint and perturbations; not a universal ecological mechanism.
- reference: doi:10.1002/mbo3.1254
supports: SUPPORT
evidence_source: IN_VITRO
snippet: less so towards continuous perturbations
- explanation: Supports reduced robustness under continuous perturbation.
+ explanation: Supports the positive controlled model-biofilm finding, interpreted within the tested community,
+ endpoint and perturbations; not a universal ecological mechanism.
+ participating_taxa:
+ - preferred_term: Rhodocyclus sp.
+ term:
+ id: NCBITaxon:1064
+ label: Rhodocyclus
+ - preferred_term: Pseudomonas fluorescens
+ term:
+ id: NCBITaxon:294
+ label: Pseudomonas fluorescens
+ - preferred_term: Kocuria varians
+ term:
+ id: NCBITaxon:1272
+ label: Kocuria varians
+ - preferred_term: Bacillus cereus
+ term:
+ id: NCBITaxon:1396
+ label: Bacillus cereus
cultivation_setup:
- cultivation_mode: SEMI_CONTINUOUS
system_type: OTHER
@@ -371,3 +426,28 @@ external_resources:
url: https://www.pndb.fr/explore/assets/experimental-raw-data-associated-to-the-publication-entitled-dynamic-interspecies-interactions-and-robustness-in-a-four-species-model-biofilm/
description: Public raw-data landing page associated with the four-species model biofilm publication.
metal_relevance: NOT_APPLICABLE
+discussions:
+- discussion_id: milk_biofilm_mechanistic_and_perturbation_scope
+ prompt: Which molecular and spatial mechanisms determine the condition-specific biofilm response?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Biofilm Community Composition and Growth Interactions
+ - ecological_interactions#Thiocillin-Biosynthesis-Dependent Kocuria Suppression
+ - ecological_interactions#Condition-Specific Biofilm Response to Perturbation
+ rationale: 'Retain both genetic-intervention arrows and positive omission/growth findings. The assay distinguishes
+ initial/transient from continuous changes; it is not a mature-biofilm recovery experiment. Purified-molecule
+ or complementation controls would further separate thiocillin I from biosynthetic-locus effects, without negating
+ the existing knockout evidence. Protection of Kocuria by the other members could involve spatial shielding or
+ adsorption but was not selectively resolved. Canonical Pseudomonas CLL49 spelling is preserved despite CCL49
+ elsewhere in the paper. Prior cultivation-arm correction under #529 remains unchanged. Non-graph taxon roles
+ and origin claims are preserved, not recertified.'
+ posed_by: codex
+ posed_date: '2026-10-06'
+curation_history:
+- timestamp: '2026-10-06T16:24:02Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: 'Preserve thiocillin genetic effects with explicit participants and condition-specific perturbation scope.
+ Issue #1508; reports/causal_graph_review/decisions/20261006-pitlakes-bioleach-biofilm-batch53.yaml'
+ llm_assisted: true
diff --git a/references_cache/doi_10.3390_biology12111411.md b/references_cache/doi_10.3390_biology12111411.md
index 38f7684ca..3682ed566 100644
--- a/references_cache/doi_10.3390_biology12111411.md
+++ b/references_cache/doi_10.3390_biology12111411.md
@@ -22,4 +22,32 @@ content_type: abstract_only
## Content
-In the present study, the effect of additional carbon sources (carbon dioxide and molasses) on the bio-oxidation of a pyrite–arsenopyrite concentrate at temperatures of 40–50 °C was studied, and novel data regarding the patterns of the bio-oxidation of gold-bearing sulfide concentrates and the composition of the microbial populations performing these processes were obtained. At 40 °C, additional carbon sources did not affect the bio-oxidation efficiency. At the same time, the application of additional carbon dioxide improved the bio-oxidation performance at temperatures of 45 and 50 °C and made it possible to avoid the inhibition of bio-oxidation due to an increase in the temperature. Therefore, the use of additional carbon dioxide may be proposed to prevent the negative effect of an increase in temperature on the bio-oxidation of sulfide concentrates. 16S rRNA gene profiling revealed archaea of the family Thermoplasmataceae (Acidiplasma, Ferroplasma, Cuniculiplasma, and A-plasma group) and bacteria of the genera Leptospirillum, with Sulfobacillus and Acidithiobacillus among the dominant groups in the community. Temperature influenced the composition of the communities to a greater extent than the additional sources of carbon and the mode of operation of the bioreactor. Elevating the temperature from 40 °C to 50 °C resulted in increases in the shares of Acidiplasma and Sulfobacillus and decreases in the relative abundances of Ferroplasma, Leptospirillum, and Acidithiobacillus, while Cuniculiplasma and A-plasma were more abundant at 45 °C. A metagenomic analysis of the studied population made it possible to characterize novel archaea belonging to an uncultivated, poorly-studied group of Thermoplasmatales which potentially plays an important role in the bio-oxidation process. Based on an analysis of the complete genome, we propose describing the novel species and novel genus as “Candidatus Carboxiplasma ferriphilum” gen. nov., spec. nov.
\ No newline at end of file
+In the present study, the effect of additional carbon sources (carbon dioxide and molasses) on the bio-oxidation of a pyrite–arsenopyrite concentrate at temperatures of 40–50 °C was studied, and novel data regarding the patterns of the bio-oxidation of gold-bearing sulfide concentrates and the composition of the microbial populations performing these processes were obtained. At 40 °C, additional carbon sources did not affect the bio-oxidation efficiency. At the same time, the application of additional carbon dioxide improved the bio-oxidation performance at temperatures of 45 and 50 °C and made it possible to avoid the inhibition of bio-oxidation due to an increase in the temperature. Therefore, the use of additional carbon dioxide may be proposed to prevent the negative effect of an increase in temperature on the bio-oxidation of sulfide concentrates. 16S rRNA gene profiling revealed archaea of the family Thermoplasmataceae (Acidiplasma, Ferroplasma, Cuniculiplasma, and A-plasma group) and bacteria of the genera Leptospirillum, with Sulfobacillus and Acidithiobacillus among the dominant groups in the community. Temperature influenced the composition of the communities to a greater extent than the additional sources of carbon and the mode of operation of the bioreactor. Elevating the temperature from 40 °C to 50 °C resulted in increases in the shares of Acidiplasma and Sulfobacillus and decreases in the relative abundances of Ferroplasma, Leptospirillum, and Acidithiobacillus, while Cuniculiplasma and A-plasma were more abundant at 45 °C. A metagenomic analysis of the studied population made it possible to characterize novel archaea belonging to an uncultivated, poorly-studied group of Thermoplasmatales which potentially plays an important role in the bio-oxidation process. Based on an analysis of the complete genome, we propose describing the novel species and novel genus as “Candidatus Carboxiplasma ferriphilum” gen. nov., spec. nov.
+
+## Primary-Source Excerpts (2026-10-06)
+
+Source: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC10669018/fullTextXML
+
+Primary article: https://doi.org/10.3390/biology12111411
+
+License: CC BY 4.0; authors and bibliographic attribution above.
+
+Retrieved 2026-10-06; exact response SHA-256: bccf1c5f87dcd19897582f496df77a3104834b2cf178b2fb14c2fb0bc680d3ef.
+
+Scope: short excerpts from Results 3.3.1, verified against the retrieved primary XML. Context labels below are curator descriptions, not source quotations. The existing abstract is unchanged; this is not a complete full-text cache.
+
+Context: A. caldus BR_03 sulfur-oxidizer assignment
+
+> This bacterium is a sulfur-oxidizing acidophile
+
+Context: F. acidiphilum BR_01 inferred respiratory complex
+
+> is capable of oxidizing ferrous iron and reducing molecular oxygen
+
+Context: C. divulgatum BR_06 genome annotation
+
+> A large number of proteases
+
+Context: Two MAG identifiers assigned to Ferroplasma
+
+> BR_04 and BR_01
diff --git a/reports/causal_graph_review/README.md b/reports/causal_graph_review/README.md
index 55f6b06e0..c20317b2e 100644
--- a/reports/causal_graph_review/README.md
+++ b/reports/causal_graph_review/README.md
@@ -5,6 +5,28 @@ source-based self-adversarial review. These records are not independent approval
or proof that every graph is complete. The current inventory and summary distinguish
`reviewed`, `pending` and `needs_research`.
+## Batch53: Pit Lakes, Bioleaching And Model Biofilm
+
+[Decisions](decisions/20261006-pitlakes-bioleach-biofilm-batch53.yaml),
+[validation](validation-20261006-batch53.json) and
+[self-adversarial review](adversarial-review-20261006-batch53.yaml) retain all
+17 nodes, remove six unsupported cross-study or misassigned arrows, and retain
+both positive milk-biofilm genetic-intervention arrows. Pit-lake geochemistry,
+mineral observations and functional predictions remain distinct from partner flux.
+The industrial graph preserves population, genome and copper-yield findings;
+its composite roster and missing valid regeneration structure remain unresolved
+under #1509. The milk endpoint is condition-specific biofilm establishment,
+not universal robustness or a mature-biofilm recovery trajectory.
+
+Three cached primary main texts and a freshly retrieved 2023 primary main text
+were read, including Methods and embedded tables/captions. The 2022 pit-lake and
+2014 chalcopyrite papers were available only at abstract scope. No original
+images, external supplements, raw data or code were audited. Four short excerpts
+(24 source words) are added to one existing abstract cache with primary XML hash,
+context and CC BY attribution; its original content is preserved as an exact
+prefix. Non-graph metadata is preserved, not recertified. Validation links are
+publication outputs, not a claim of completion before their recorded gates run.
+
## Batch52: URLs, Hualgayoc And Gut Proteomes
[Decisions](decisions/20261006-urls-amd-proteome-batch52.yaml),
diff --git a/reports/causal_graph_review/adversarial-review-20261006-batch53.yaml b/reports/causal_graph_review/adversarial-review-20261006-batch53.yaml
new file mode 100644
index 000000000..467ea6329
--- /dev/null
+++ b/reports/causal_graph_review/adversarial-review-20261006-batch53.yaml
@@ -0,0 +1,187 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: 683e765fe470057baa9e1efb313ce76d38aa99ac
+scope:
+- kb/communities/Iberian_Pit_Lake_Stratified_Community.yaml
+- kb/communities/Industrial_Bioreactor_Consortium.yaml
+- kb/communities/Industrial_Milk_Line_FourSpecies_Model_Biofilm.yaml
+decision_ledger: reports/causal_graph_review/decisions/20261006-pitlakes-bioleach-biofilm-batch53.yaml
+validation_report: reports/causal_graph_review/validation-20261006-batch53.json
+findings:
+- issue: 1506
+ severity: P2
+ status: addressed_in_this_change
+ finding: Bound site-specific pit-lake findings and remove three unsupported causal arrows.
+ disposition: Close only after protected main merge.
+- issue: 1507
+ severity: P2
+ status: addressed_in_this_change
+ finding: Correct bioleaching organism and study assignments; preserve unresolved community identity
+ and regeneration graph.
+ disposition: Close only after protected main merge.
+- issue: 1508
+ severity: P2
+ status: addressed_in_this_change
+ finding: Preserve thiocillin genetic effects with explicit participants and condition-specific perturbation
+ scope.
+ disposition: Close only after protected main merge.
+- issue: 1509
+ severity: P2
+ status: unresolved_research
+ finding: Composite industrial community identity, canonical roster and valid regeneration graph remain
+ unresolved.
+ disposition: Keep open; exact-system curation and one-community source-checked research remain pending.
+adversarial_checks:
+- Whole796-line Iberian,1174-line industrial and373-line milk records reviewed, including every original
+ node and arrow. Complete cached2013/2020 pit-lake and2021 milk primary main texts, Methods, embedded
+ tables and captions read. Fresh2023 industrial primary XML main text, Methods, Tables1-5 and captions
+ read. No original figure images, external supplements, raw data or code audited.
+- Cueva de la Mora2022 and chalcopyrite2014 bodies remained inaccessible; their primary abstracts were
+ read, not full texts. Separate2009/2019 consortia, Acidiplasma genome and borehole studies were read
+ at abstract scope. The Cuniculiplasmataceae review is background, not primary reactor evidence.
+- Iberian NSC/Concepcion, Cueva de la Mora, FC/La Zarza and borehole findings remain distinct. Measured
+ geochemistry and observed FC mineral particles are retained as positive evidence; biosulfidogenesis
+ and taxon assignments remain models. Precipitated sulfides are not described as dissolved sulfides.
+ No exact concentrations or mineral identity are transferred across lakes.
+- Active Coccomyxa dominance is preserved without a quantified carbon-export rate. FC/La Zarza findings
+ do not establish universal carbon limitation. Rare methanogen reads are not measured methane flux. Sulfide
+ oxidation is assigned to the predicted archaeal role, not sulfate reduction; unrelated iron-transport
+ and TCA annotations removed.
+- Three Iberian arrows represented coactivity, reversed carbon-consumption direction or an unmeasured
+ archaeal donor route. All five nodes remain with explicit canonical participants. No new graph node
+ or arrow is introduced.
+- Industrial early A. caldus and middle S. acidophilus population observations remain positive findings.
+ A. caldus is not assigned ferrous-iron oxidation or rusticyanin. The previously omitted rather-than
+ negation is restored. Copper extraction of60.4 percent at20 percent pulp density after more than two
+ years of adaptation remains, supported by the result rather than a Methods snippet.
+- F. thermophilum in2014 is not substituted with2023 F. acidiphilum/Acidiplasma genomes. The retained
+ copper-output participants are explicitly a supported subset, not the complete roster. Leptospirillum
+ nondetection is not extinction or an isolated toxicity experiment. Genomic metabolic potential and Ferroplasma
+ co-detection do not prove partner benefit or complementarity.
+- The2023 reactor profiles retain positive temperature associations with single-run, relative-abundance
+ and operating-condition limits. Three invalid/cross-study industrial arrows removed; nine nodes remain.
+ Canonical taxonomy and non-graph claims preserved, not certified. Issue1509 remains unresolved for exact-system
+ identity, roster and valid regeneration structure.
+- Milk retains both positive causal arrows grounded in the tclE-H deletion and omission experiments. About50-fold
+ Kocuria change is preserved. Genetic evidence is not purified-thiocillin rescue; activity was mainly
+ pellet-associated or unstable. The72-hour establishment comparison is not a mature-biofilm recovery
+ time course or universal resistance to strong continuous changes.
+- 'Milk strain-label variation is not silently normalized: canonical CLL49 remains. The Bacillus reference-culture
+ substitution and prior529 cultivation-arm repair are preserved. No unsupported pairwise interaction
+ categories remain on community nodes.'
+- Full record diffs, all eight new tests, cache appendix and participant-registry diff inspected. Seventeen
+ nodes retained; six arrows removed and two retained. Only graph, discussion and curation-history record
+ fields changed.457 other records and raw non-graph blocks preserved.919 caches unchanged; one abstract
+ gains24 source-verified words with exact XML hash, context and CC BY attribution; its original bytes
+ remain an exact prefix.
+- Actual schema, strict, term, reference, snippet, rank and history gates passed. Network equals baseline
+ with34 existing findings and no structural errors. Repeat renders deterministic; exact descriptions
+ across456 pages parser-checked, not browser screenshots. One participant registry entry added; measured
+ connectivity census unchanged. Post-commit docs-current is a separate publication gate.
+- Dedup searched813 all-state issue titles/bodies and20 ignored/hidden local files, with relevant matching
+ contexts inspected, not every historical comment/review.1506/1507/1508 addressed but remain open until
+ protected-main merge.1509 remains unresolved. This source-based self-adversarial review is not independent
+ approval.
+verification:
+ combined_regressions: 503 passed in 188.92s (0:03:08)
+ new_regression_tests: 8
+ schema_strict_terms_history: Passed with actual output digests
+ references: CLI Total checks counts reported issues, not executed checks. Exit0 is no reported issues,
+ not source verification. SupportingReference coverage (#476), Linux DOI-cache lookup (#1091) and selected-cache
+ provenance (#1362) remain limitations.
+ snippet_counts_by_record:
+ kb/communities/Iberian_Pit_Lake_Stratified_Community.yaml:
+ MATCH: 37
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Industrial_Bioreactor_Consortium.yaml:
+ MATCH: 51
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Industrial_Milk_Line_FourSpecies_Model_Biofilm.yaml:
+ MATCH: 18
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ network:
+ existing_findings_preserved: 34
+ added_findings: {}
+ removed_findings: {}
+ black_ruff_diff: passed
+ tested_file_sha256:
+ reports/causal_graph_review/decisions/20261006-pitlakes-bioleach-biofilm-batch53.yaml: 41b8d4e6971264d0890389465ca6c7c5f288097c011e3da00861fb09f49a8261
+ tests/test_causal_review_batch53.py: 0ad8b3c0cf3d4eefc7aaf3a227493a70867c515e0a1bacf89410d6953439d645
+ tests/test_participating_taxa.py: f6d7b65b1215933f8c8518de8d985598a0258a48d0037c99e47453c12208c74a
+ kb/communities/Iberian_Pit_Lake_Stratified_Community.yaml: 849626f1d5bc82bead855d41117508cdc48dd20c3e696864047368344c14b5ab
+ kb/communities/Industrial_Bioreactor_Consortium.yaml: 71160959bae2c8e3f0caf63d57452a597e29967f70faea6bec59016752b9aad4
+ kb/communities/Industrial_Milk_Line_FourSpecies_Model_Biofilm.yaml: d11705d887a01509f631792a193c61ea0c57af05e3ac4d50ae2a2f08ab107f8d
+ reports/causal_graph_review/README.md: 3bb95e6f09ef8dac71c51ba5f6ce3bacc880fd56569dc7bb789e6b20d78aa39f
+ post_commit_docs_current: Separate publication gate; not asserted before commit.
+participant_census:
+ measurements:
+ baseline:
+ records: 460
+ with_community_level: 389
+ mixed: 127
+ community_level_only: 262
+ taxa: 1498
+ credited_solely_by_the_rule: 1222
+ current:
+ records: 460
+ with_community_level: 389
+ mixed: 127
+ community_level_only: 262
+ taxa: 1498
+ credited_solely_by_the_rule: 1222
+ interpretation: Seventeen community nodes retain their scopes. Milk participants made explicit, with
+ one registry entry added; measured census unchanged. No production matching or census-bound changes.
+corpus:
+ records: 460
+ nodes: 1465
+ edges: 666
+ review_status_counts:
+ needs_research: 16
+ pending: 261
+ reviewed: 183
+limitations:
+- Whole three records and all17 original nodes/eight arrows reviewed. Seventeen nodes retained; six unsupported
+ arrows removed; two controlled milk genetic-intervention arrows retained. No new graph node/arrow added.
+- Complete cached 2013/2020 pit-lake and 2021 milk primary main texts/Methods/embedded tables/captions
+ read. Fresh 2023 bioleaching primary XML main body/Methods/Tables1-5/captions read. No original images,
+ external supplements, raw data or code audited.
+- Cueva de la Mora2022, chalcopyrite2014, defined consortium2009, pH2019, Acidiplasma genome and borehole
+ studies reviewed at abstract scope. Access attempts for the2022/2014 full bodies failed; no full-body
+ review claimed. Cuniculiplasmataceae review is background, not reactor primary evidence.
+- Pit-lake sites and studies remain distinct. Measured geochemistry and FC sulfide particles are positive
+ evidence; functional/biogenic assignment remains a model. Active algae and rare methanogen reads do
+ not resolve carbon export or methane flux. Do not infer universal carbon limitation across FC/La Zarza.
+- 'Industrial record remains needs_research under1509: canonical roster and non-graph fields conflate
+ distinct systems and omit exact F. thermophilum identity. Positive early/middle population findings,
+ genomic capabilities and copper output remain. No correct regeneration graph is claimed after removal
+ of false/cross-study arrows.'
+- One-community industrial Edison dry run completed without a paid job/report. The optional model-cost-map
+ fetch failed and used a local fallback; no Edison provider call or credit spend. New structure remains
+ pending authorization, report inspection and primary verification.
+- Milk knockout/omission findings remain positive causal evidence. tclE-H perturbation is not purified-thiocillin
+ rescue, a universal robustness mechanism or a mature-biofilm recovery experiment. Canonical CLL49 spelling
+ and prior cultivation-arm repair preserved.
+- One existing abstract cache gains24 exact primary-source words with retrieved-XML hash, section/context
+ and CC BY attribution. Original abstract remains an exact prefix;919 other caches unchanged. The excerpts
+ are source verified, not an assertion that all historical selected caches have independently verified
+ provenance.
+- All457 other records and non-graph raw blocks are preserved, not recertified. SupportingReference coverage476,
+ Linux DOI-cache lookup1091, selected-cache provenance1362 and writer artifact1095 remain limitations.
+ Reference CLI Total checks counts reported issues, not executed checks.
+- Dedup searched813 all-state issue titles/bodies and20 ignored/hidden local files in the refreshed search,
+ in addition to the earlier broader citation search. Relevant contexts inspected; not every historical
+ comment/review read.1506/1507/1508 remain open until protected-main merge;1509 remains unresolved. This
+ is self-adversarial review, not independent approval.
diff --git a/reports/causal_graph_review/decisions/20261006-pitlakes-bioleach-biofilm-batch53.yaml b/reports/causal_graph_review/decisions/20261006-pitlakes-bioleach-biofilm-batch53.yaml
new file mode 100644
index 000000000..9543ec0da
--- /dev/null
+++ b/reports/causal_graph_review/decisions/20261006-pitlakes-bioleach-biofilm-batch53.yaml
@@ -0,0 +1,398 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: 683e765fe470057baa9e1efb313ce76d38aa99ac
+baseline_commit: 683e765fe470057baa9e1efb313ce76d38aa99ac
+base_tree: 694f89b4f37bc4919a40e7b9b059cc49cfda9d02
+pre_source_baseline_sha256: 1057f7ea1db5d8257a86c6541bdb004a373b665cbcf2af25f0432d301a86091b
+issues:
+- 1506
+- 1507
+- 1508
+unresolved_research_issues:
+- 1509
+issue_deduplication:
+ all_state_issue_titles_and_bodies: 813
+ ignored_hidden_local_search: true
+ matching_issues:
+ - 1372
+ - 1358
+ - 1094
+ - 1092
+ - 258
+ earlier_matching_issues:
+ - 1094
+ - 1092
+ - 697
+ - 258
+ matching_local_files: 20
+ disposition: Other records or tooling; old milk dangling target already repaired. New findings concern evidence
+ scope and causal interpretation.
+ limitations: Relevant matching contexts inspected; not all historical comments/reviews.
+reference_cache_original_hashes:
+ references_cache/PMID_23840525.md: b7b7843628cc96fb9746ea3b5ec30737a034e54c44e6d2f37afc831aaf57f04f
+ references_cache/PMID_36123522.md: 85530f46f4f7fdb838cca2e82ffd42f78c89f594f105615f4d954e2a3e8af36f
+ references_cache/doi_10.1111_gbi.12065.md: c503ac8fe62ce606c22b74dba01d6954195af1ccfb692c60580bc4e1c50d70e5
+ references_cache/doi_10.3390_microorganisms8091275.md: 6a372d2d360bd671dc96c2d6dcde25a52578ad8221aef26d85a541542169ea25
+ references_cache/PMID_24242252.md: fdc55bb31062bcb2268c565eca1323057f66a86093f2acb2ae6df3c82cdd6841
+ references_cache/PMID_30499003.md: 7cca266e9a34c3c88f7d79231354d63fdfe2424ded65c739245ea9b96c596c27
+ references_cache/doi_10.1007_s00253-008-1792-8.md: af6d698754e43dd47ca8b002c438b2e795fc4967cc73ceba0ffcbf93ce47a707
+ references_cache/doi_10.1007_s13213-019-01453-y.md: ac26f72e79ba9e86d229fbdbf8c0af610cbf2b8f9051713f79ebcbfbb6b92662
+ references_cache/doi_10.1134_S0026261716060059.md: 7a8557753bbd6f53741fbf8fddb48325ff345cbaefdfb36d0453ddc20403a357
+ references_cache/doi_10.3390_biology12111411.md: 49770e35b148ae02e76ab1e5c2e4dabc1c720b9eb938ef1bcb2b62a47985b4b3
+ references_cache/PMID_34964290.md: 338320066b575cc42f5d297a9610e310b3ffccc52554a9a206666dbec845e05a
+reference_cache_update:
+ path: references_cache/doi_10.3390_biology12111411.md
+ original_sha256: 49770e35b148ae02e76ab1e5c2e4dabc1c720b9eb938ef1bcb2b62a47985b4b3
+ updated_sha256: 4755a26df17a7ad982e89a57d8c85459635478ede290f7a70618bc04d3b6165b
+ primary_xml_sha256: bccf1c5f87dcd19897582f496df77a3104834b2cf178b2fb14c2fb0bc680d3ef
+ primary_url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC10669018/fullTextXML
+ license: CC BY 4.0
+ quoted_words: 24
+ original_cache_is_exact_prefix: true
+ verified_excerpts:
+ - This bacterium is a sulfur-oxidizing acidophile
+ - is capable of oxidizing ferrous iron and reducing molecular oxygen
+ - A large number of proteases
+ - BR_04 and BR_01
+limitations:
+- Whole three records and all17 original nodes/eight arrows reviewed. Seventeen nodes retained; six unsupported
+ arrows removed; two controlled milk genetic-intervention arrows retained. No new graph node/arrow added.
+- Complete cached 2013/2020 pit-lake and 2021 milk primary main texts/Methods/embedded tables/captions read. Fresh
+ 2023 bioleaching primary XML main body/Methods/Tables1-5/captions read. No original images, external supplements,
+ raw data or code audited.
+- Cueva de la Mora2022, chalcopyrite2014, defined consortium2009, pH2019, Acidiplasma genome and borehole studies
+ reviewed at abstract scope. Access attempts for the2022/2014 full bodies failed; no full-body review claimed.
+ Cuniculiplasmataceae review is background, not reactor primary evidence.
+- Pit-lake sites and studies remain distinct. Measured geochemistry and FC sulfide particles are positive evidence;
+ functional/biogenic assignment remains a model. Active algae and rare methanogen reads do not resolve carbon export
+ or methane flux. Do not infer universal carbon limitation across FC/La Zarza.
+- 'Industrial record remains needs_research under1509: canonical roster and non-graph fields conflate distinct systems
+ and omit exact F. thermophilum identity. Positive early/middle population findings, genomic capabilities and copper
+ output remain. No correct regeneration graph is claimed after removal of false/cross-study arrows.'
+- One-community industrial Edison dry run completed without a paid job/report. The optional model-cost-map fetch
+ failed and used a local fallback; no Edison provider call or credit spend. New structure remains pending authorization,
+ report inspection and primary verification.
+- Milk knockout/omission findings remain positive causal evidence. tclE-H perturbation is not purified-thiocillin
+ rescue, a universal robustness mechanism or a mature-biofilm recovery experiment. Canonical CLL49 spelling and
+ prior cultivation-arm repair preserved.
+- One existing abstract cache gains24 exact primary-source words with retrieved-XML hash, section/context and CC
+ BY attribution. Original abstract remains an exact prefix;919 other caches unchanged. The excerpts are source
+ verified, not an assertion that all historical selected caches have independently verified provenance.
+- All457 other records and non-graph raw blocks are preserved, not recertified. SupportingReference coverage476,
+ Linux DOI-cache lookup1091, selected-cache provenance1362 and writer artifact1095 remain limitations. Reference
+ CLI Total checks counts reported issues, not executed checks.
+- Dedup searched813 all-state issue titles/bodies and20 ignored/hidden local files in the refreshed search, in addition
+ to the earlier broader citation search. Relevant contexts inspected; not every historical comment/review read.1506/1507/1508
+ remain open until protected-main merge;1509 remains unresolved. This is self-adversarial review, not independent
+ approval.
+records:
+- path: kb/communities/Iberian_Pit_Lake_Stratified_Community.yaml
+ id: CommunityMech:000034
+ original_sha256: bc5b3e371afc61a51b2d9c6795ac704e7bbe2a98b08854b36c871388fe071ec7
+ record_sha256: 849626f1d5bc82bead855d41117508cdc48dd20c3e696864047368344c14b5ab
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261006-pitlakes-bioleach-biofilm-batch53.yaml
+ scope: Whole record and every original node/arrow; existing structure repaired with explicit primary-source limits.
+ summary: Bound site-specific pit-lake findings and remove three unsupported causal arrows.
+ renamed_nodes:
+ Stratified Iron Redox Cycling: Stratified Iron Redox Potential
+ Biosulfidogenesis and Metal Precipitation: Biosulfidogenesis and Metal Attenuation Model
+ Algal Primary Production and Carbon Export: Coccomyxa Primary Production Potential
+ Subsurface Heterotrophic Carbon Scavenging: Deep-Layer Thermoplasmatales Metabolic Potential
+ Subsurface Methanogenesis: Rare Methanogen Sequence Detection
+ node_decisions:
+ - node: Stratified Iron Redox Potential
+ rationale: Retain positive redox-functional inference without all-participant flux or niche partitioning.
+ - node: Biosulfidogenesis and Metal Attenuation Model
+ rationale: Retain positive metal attenuation and biosulfidogenesis model with explicit lake and mineral scope.
+ - node: Coccomyxa Primary Production Potential
+ rationale: Retain active Coccomyxa dominance without quantified carbon export or universal carbon limitation.
+ - node: Deep-Layer Thermoplasmatales Metabolic Potential
+ rationale: Retain deep archaeal functional predictions without commensalism or unmeasured scavenging mediation.
+ - node: Rare Methanogen Sequence Detection
+ rationale: Retain rare methanogen-associated reads without methane flux, concentration or donor assignment.
+ removed_node_decisions: []
+ edges_before:
+ - source: Stratified Iron Redox Cycling
+ target: Biosulfidogenesis and Metal Precipitation
+ description: Iron and sulfate redox guilds are both active across the chemocline and deep layer of the stratified
+ acidic pit lake.
+ - source: Biosulfidogenesis and Metal Precipitation
+ target: Subsurface Heterotrophic Carbon Scavenging
+ description: Sulfate reduction consumes organic carbon from primary production
+ - source: Subsurface Heterotrophic Carbon Scavenging
+ target: Subsurface Methanogenesis
+ description: Organic carbon reaching the deep layer can constrain anaerobic terminal processes in acidic Iberian
+ Pyrite Belt systems, including rare methanogenic activity.
+ edges_after: []
+ retained_edge_decisions: []
+ removed_edge_decisions:
+ - source: Stratified Iron Redox Cycling
+ target: Biosulfidogenesis and Metal Precipitation
+ description: Iron and sulfate redox guilds are both active across the chemocline and deep layer of the stratified
+ acidic pit lake.
+ rationale: Coactivity, carbon consumption or cross-site context does not establish the stated direction.
+ - source: Biosulfidogenesis and Metal Precipitation
+ target: Subsurface Heterotrophic Carbon Scavenging
+ description: Sulfate reduction consumes organic carbon from primary production
+ rationale: Coactivity, carbon consumption or cross-site context does not establish the stated direction.
+ - source: Subsurface Heterotrophic Carbon Scavenging
+ target: Subsurface Methanogenesis
+ description: Organic carbon reaching the deep layer can constrain anaerobic terminal processes in acidic Iberian
+ Pyrite Belt systems, including rare methanogenic activity.
+ rationale: Coactivity, carbon consumption or cross-site context does not establish the stated direction.
+ references:
+ - PMID:23840525
+ - PMID:36123522
+ - doi:10.1111/gbi.12065
+ - doi:10.3390/microorganisms8091275
+ issues:
+ - 1506
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Iberian_Pit_Lake_Stratified_Community/2026-10-06T162402Z-codex-4e3d9b.yaml
+ source_review:
+ PMID:23840525:
+ cache: references_cache/PMID_23840525.md
+ sha256: b7b7843628cc96fb9746ea3b5ec30737a034e54c44e6d2f37afc831aaf57f04f
+ original_sha256: b7b7843628cc96fb9746ea3b5ec30737a034e54c44e6d2f37afc831aaf57f04f
+ url: https://doi.org/10.1371/journal.pone.0066746
+ scope: Complete cached primary main text/Methods/Table1/captions1-5 read. No images or external FileS1.
+ PMID:36123522:
+ cache: references_cache/PMID_36123522.md
+ sha256: 85530f46f4f7fdb838cca2e82ffd42f78c89f594f105615f4d954e2a3e8af36f
+ original_sha256: 85530f46f4f7fdb838cca2e82ffd42f78c89f594f105615f4d954e2a3e8af36f
+ url: https://pubmed.ncbi.nlm.nih.gov/36123522/
+ scope: Complete cached primary abstract only; publisher/PMC/EuropePMC body access failed. No full body inspected.
+ doi:10.1111/gbi.12065:
+ cache: references_cache/doi_10.1111_gbi.12065.md
+ sha256: c503ac8fe62ce606c22b74dba01d6954195af1ccfb692c60580bc4e1c50d70e5
+ original_sha256: c503ac8fe62ce606c22b74dba01d6954195af1ccfb692c60580bc4e1c50d70e5
+ url: https://doi.org/10.1111/gbi.12065
+ scope: Complete cached primary abstract only; separate borehole system.
+ doi:10.3390/microorganisms8091275:
+ cache: references_cache/doi_10.3390_microorganisms8091275.md
+ sha256: 6a372d2d360bd671dc96c2d6dcde25a52578ad8221aef26d85a541542169ea25
+ original_sha256: 6a372d2d360bd671dc96c2d6dcde25a52578ad8221aef26d85a541542169ea25
+ url: https://doi.org/10.3390/microorganisms8091275
+ scope: Complete cached primary main text/Methods/Table1/captions1-7 read. No original images, supplements,
+ raw data or code.
+- path: kb/communities/Industrial_Bioreactor_Consortium.yaml
+ id: CommunityMech:000035
+ original_sha256: 442e1edeb00a23737e070386d509f4caf336248af81c199d2975b7cde6c88060
+ record_sha256: 71160959bae2c8e3f0caf63d57452a597e29967f70faea6bec59016752b9aad4
+ status: needs_research
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261006-pitlakes-bioleach-biofilm-batch53.yaml
+ scope: Whole record and every original node/arrow; existing structure repaired with explicit primary-source limits.
+ summary: Correct bioleaching organism and study assignments; preserve unresolved community identity and regeneration
+ graph.
+ renamed_nodes:
+ Thermophilic Ferrous Iron Oxidation in Early Reactor Stages: Initial Acidithiobacillus caldus Predominance
+ Thermophilic Sulfur Oxidation to Sulfuric Acid: Acidithiobacillus Sulfur-Oxidizing Potential
+ Mid-Stage Mixotrophic Iron Oxidation: Middle-Stage Sulfobacillus acidophilus Predominance
+ Late-Stage Extreme Acidophile Iron Oxidation: Ferroplasmaceae Iron-Oxidizing Potential
+ Chalcopyrite Dissolution by Ferric Iron: Adapted Chalcopyrite Consortium Copper Extraction
+ Organic Matter Scavenging by Cuniculiplasma: Cuniculiplasma Organic-Carbon Metabolic Potential
+ Early-Stage Iron Oxidation with Leptospirillum: Leptospirillum Detection During Pulp-Density Adaptation
+ Ferroplasma Species Complementarity: Co-Detected Ferroplasma Genomes
+ node_decisions:
+ - node: Initial Acidithiobacillus caldus Predominance
+ rationale: Preserve A. caldus initial abundance while removing false iron oxidation, rusticyanin and feedback
+ claims.
+ - node: Acidithiobacillus Sulfur-Oxidizing Potential
+ rationale: Preserve sulfur-oxidizing capability without fixed-pH, flux or comparative-rate claims.
+ - node: Middle-Stage Sulfobacillus acidophilus Predominance
+ rationale: Restore the full middle-stage negation and preserve S. acidophilus abundance, not inferred mediation.
+ - node: Ferroplasmaceae Iron-Oxidizing Potential
+ rationale: Preserve appropriately sourced genomic iron-oxidation potential without substituting for F. thermophilum.
+ - node: Adapted Chalcopyrite Consortium Copper Extraction
+ rationale: Preserve measured copper extraction with the supported partial roster and unresolved exact-system
+ gap.
+ - node: Cuniculiplasma Organic-Carbon Metabolic Potential
+ rationale: Preserve C. divulgatum genomic potential, remove the wrongly labeled process term and unmeasured
+ benefit.
+ - node: Leptospirillum Detection During Pulp-Density Adaptation
+ rationale: Preserve L. ferriphilum detection/nondetection without extinction or isolated toxicity.
+ - node: Co-Detected Ferroplasma Genomes
+ rationale: Preserve two-genome co-detection without demonstrated complementarity or generalized robustness.
+ - node: Temperature-Structured A-Plasma and Acidiplasma Populations
+ rationale: Preserve condition-associated relative profiles without pairwise niche mechanisms.
+ removed_node_decisions: []
+ edges_before:
+ - source: Thermophilic Ferrous Iron Oxidation in Early Reactor Stages
+ target: Chalcopyrite Dissolution by Ferric Iron
+ description: Fe³⁺ oxidizes chalcopyrite to release Cu²⁺ and regenerate Fe²⁺
+ - source: Late-Stage Extreme Acidophile Iron Oxidation
+ target: Chalcopyrite Dissolution by Ferric Iron
+ description: Sustained Fe³⁺ generation maintains copper leaching in acidic late stages
+ - source: Chalcopyrite Dissolution by Ferric Iron
+ target: Thermophilic Ferrous Iron Oxidation in Early Reactor Stages
+ description: Released Fe²⁺ is re-oxidized to regenerate Fe³⁺ oxidant
+ edges_after: []
+ retained_edge_decisions: []
+ removed_edge_decisions:
+ - source: Thermophilic Ferrous Iron Oxidation in Early Reactor Stages
+ target: Chalcopyrite Dissolution by Ferric Iron
+ description: Fe³⁺ oxidizes chalcopyrite to release Cu²⁺ and regenerate Fe²⁺
+ rationale: The source/recipient role is biologically wrong or assigned from a distinct study and taxon.
+ - source: Late-Stage Extreme Acidophile Iron Oxidation
+ target: Chalcopyrite Dissolution by Ferric Iron
+ description: Sustained Fe³⁺ generation maintains copper leaching in acidic late stages
+ rationale: The source/recipient role is biologically wrong or assigned from a distinct study and taxon.
+ - source: Chalcopyrite Dissolution by Ferric Iron
+ target: Thermophilic Ferrous Iron Oxidation in Early Reactor Stages
+ description: Released Fe²⁺ is re-oxidized to regenerate Fe³⁺ oxidant
+ rationale: The source/recipient role is biologically wrong or assigned from a distinct study and taxon.
+ references:
+ - PMID:24242252
+ - PMID:30499003
+ - doi:10.1007/s00253-008-1792-8
+ - doi:10.1007/s13213-019-01453-y
+ - doi:10.1134/S0026261716060059
+ - doi:10.3390/biology12111411
+ issues:
+ - 1507
+ - 1509
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Industrial_Bioreactor_Consortium/2026-10-06T162402Z-codex-b1f92a.yaml
+ source_review:
+ PMID:24242252:
+ cache: references_cache/PMID_24242252.md
+ sha256: fdc55bb31062bcb2268c565eca1323057f66a86093f2acb2ae6df3c82cdd6841
+ original_sha256: fdc55bb31062bcb2268c565eca1323057f66a86093f2acb2ae6df3c82cdd6841
+ url: https://pubmed.ncbi.nlm.nih.gov/24242252/
+ scope: Complete cached primary abstract only; ASM/EuropePMC/PMC full-body access failed.
+ PMID:30499003:
+ cache: references_cache/PMID_30499003.md
+ sha256: 7cca266e9a34c3c88f7d79231354d63fdfe2424ded65c739245ea9b96c596c27
+ original_sha256: 7cca266e9a34c3c88f7d79231354d63fdfe2424ded65c739245ea9b96c596c27
+ url: https://pubmed.ncbi.nlm.nih.gov/30499003/
+ scope: Complete cached review abstract; not direct primary reactor evidence.
+ doi:10.1007/s00253-008-1792-8:
+ cache: references_cache/doi_10.1007_s00253-008-1792-8.md
+ sha256: af6d698754e43dd47ca8b002c438b2e795fc4967cc73ceba0ffcbf93ce47a707
+ original_sha256: af6d698754e43dd47ca8b002c438b2e795fc4967cc73ceba0ffcbf93ce47a707
+ url: https://doi.org/10.1007/s00253-008-1792-8
+ scope: Complete cached primary abstract only; distinct defined-strain consortium.
+ doi:10.1007/s13213-019-01453-y:
+ cache: references_cache/doi_10.1007_s13213-019-01453-y.md
+ sha256: ac26f72e79ba9e86d229fbdbf8c0af610cbf2b8f9051713f79ebcbfbb6b92662
+ original_sha256: ac26f72e79ba9e86d229fbdbf8c0af610cbf2b8f9051713f79ebcbfbb6b92662
+ url: https://doi.org/10.1007/s13213-019-01453-y
+ scope: Complete cached primary abstract only; distinct pH experiment.
+ doi:10.1134/S0026261716060059:
+ cache: references_cache/doi_10.1134_S0026261716060059.md
+ sha256: 7a8557753bbd6f53741fbf8fddb48325ff345cbaefdfb36d0453ddc20403a357
+ original_sha256: 7a8557753bbd6f53741fbf8fddb48325ff345cbaefdfb36d0453ddc20403a357
+ url: https://doi.org/10.1134/S0026261716060059
+ scope: Complete cached primary genome-study abstract only.
+ doi:10.3390/biology12111411:
+ cache: references_cache/doi_10.3390_biology12111411.md
+ sha256: 4755a26df17a7ad982e89a57d8c85459635478ede290f7a70618bc04d3b6165b
+ original_sha256: 49770e35b148ae02e76ab1e5c2e4dabc1c720b9eb938ef1bcb2b62a47985b4b3
+ url: https://pmc.ncbi.nlm.nih.gov/articles/PMC10669018/
+ scope: Fresh primary XML main text/Methods/Tables1-5/embedded captions read. Four short source-verified excerpts
+ appended to existing abstract cache. No images, supplements, raw data or code.
+- path: kb/communities/Industrial_Milk_Line_FourSpecies_Model_Biofilm.yaml
+ id: CommunityMech:000152
+ original_sha256: 185edc0766d39779bce9b43edf1fac1d5872fea92620b678262b2c29f54e785a
+ record_sha256: d11705d887a01509f631792a193c61ea0c57af05e3ac4d50ae2a2f08ab107f8d
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261006-pitlakes-bioleach-biofilm-batch53.yaml
+ scope: Whole record and every original node/arrow; existing structure repaired with explicit primary-source limits.
+ summary: Preserve thiocillin genetic effects with explicit participants and condition-specific perturbation scope.
+ renamed_nodes:
+ Dynamic Positive and Negative Biofilm Interactions: Biofilm Community Composition and Growth Interactions
+ Bacillus Thiocillin-Mediated Negative Interaction: Thiocillin-Biosynthesis-Dependent Kocuria Suppression
+ Robustness to Transient Perturbation: Condition-Specific Biofilm Response to Perturbation
+ node_decisions:
+ - node: Biofilm Community Composition and Growth Interactions
+ rationale: Retain distinct controlled growth and composition findings without generic niche partitioning or
+ all-member cooperation.
+ - node: Thiocillin-Biosynthesis-Dependent Kocuria Suppression
+ rationale: Retain positive thiocillin-biosynthesis genetic evidence with Bacillus/Kocuria participants and molecular-route
+ limits.
+ - node: Condition-Specific Biofilm Response to Perturbation
+ rationale: Retain condition-specific establishment endpoints without mature-biofilm recovery or general colonization
+ claims.
+ removed_node_decisions: []
+ edges_before:
+ - source: Bacillus Thiocillin-Mediated Negative Interaction
+ target: Dynamic Positive and Negative Biofilm Interactions
+ description: Bacillus cereus thiocillin I changes the relative distribution of biofilm members.
+ - source: Bacillus Thiocillin-Mediated Negative Interaction
+ target: Robustness to Transient Perturbation
+ description: 'Removing Bacillus thiocillin reshapes the model biofilm response to transient and continuous perturbations,
+ linking this negative interaction to community robustness.
+
+ '
+ edges_after:
+ - source: Thiocillin-Biosynthesis-Dependent Kocuria Suppression
+ target: Biofilm Community Composition and Growth Interactions
+ description: Replacing wild-type B. cereus with the tclE-H deletion mutant increased Kocuria abundance and changed
+ the 72-hour four-species composition, supporting a causal contribution of the thiocillin-biosynthesis-dependent
+ negative interaction under the tested biofilm conditions. This does not establish every mechanism in the wider
+ interaction network.
+ - source: Thiocillin-Biosynthesis-Dependent Kocuria Suppression
+ target: Condition-Specific Biofilm Response to Perturbation
+ description: The tclE-H mutant substitution changed the community response to initial Bacillus depletion and
+ to continuous substrate/medium changes. The genetic intervention supports a condition-specific contribution
+ to the measured response, not universal robustness, a mature-biofilm recovery trajectory or a fully isolated
+ thiocillin I rescue mechanism.
+ retained_edge_decisions:
+ - source: Thiocillin-Biosynthesis-Dependent Kocuria Suppression
+ target: Biofilm Community Composition and Growth Interactions
+ description: Replacing wild-type B. cereus with the tclE-H deletion mutant increased Kocuria abundance and changed
+ the 72-hour four-species composition, supporting a causal contribution of the thiocillin-biosynthesis-dependent
+ negative interaction under the tested biofilm conditions. This does not establish every mechanism in the wider
+ interaction network.
+ rationale: Retain the positive genetic-intervention direction within the tested endpoint and perturbations,
+ without universal or fully isolated molecular-mechanism claims.
+ - source: Thiocillin-Biosynthesis-Dependent Kocuria Suppression
+ target: Condition-Specific Biofilm Response to Perturbation
+ description: The tclE-H mutant substitution changed the community response to initial Bacillus depletion and
+ to continuous substrate/medium changes. The genetic intervention supports a condition-specific contribution
+ to the measured response, not universal robustness, a mature-biofilm recovery trajectory or a fully isolated
+ thiocillin I rescue mechanism.
+ rationale: Retain the positive genetic-intervention direction within the tested endpoint and perturbations,
+ without universal or fully isolated molecular-mechanism claims.
+ removed_edge_decisions: []
+ references:
+ - PMID:34964290
+ - doi:10.1002/mbo3.1254
+ issues:
+ - 1508
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Industrial_Milk_Line_FourSpecies_Model_Biofilm/2026-10-06T162402Z-codex-2f65bf.yaml
+ source_review:
+ PMID:34964290:
+ cache: references_cache/PMID_34964290.md
+ sha256: 338320066b575cc42f5d297a9610e310b3ffccc52554a9a206666dbec845e05a
+ original_sha256: 338320066b575cc42f5d297a9610e310b3ffccc52554a9a206666dbec845e05a
+ url: https://doi.org/10.1002/mbo3.1254
+ scope: Complete cached primary main text/Methods/Tables1-2/captions1-8 and appendixA1 caption read. No original
+ images or raw dataset.
+ doi:10.1002/mbo3.1254:
+ cache: references_cache/PMID_34964290.md
+ sha256: 338320066b575cc42f5d297a9610e310b3ffccc52554a9a206666dbec845e05a
+ original_sha256: 338320066b575cc42f5d297a9610e310b3ffccc52554a9a206666dbec845e05a
+ url: https://doi.org/10.1002/mbo3.1254
+ scope: Same primary paper read through PMID34964290 cache, not a separate independent DOI-cache review.
diff --git a/reports/causal_graph_review/inventory.tsv b/reports/causal_graph_review/inventory.tsv
index b7be8946c..98345f722 100644
--- a/reports/causal_graph_review/inventory.tsv
+++ b/reports/causal_graph_review/inventory.tsv
@@ -197,9 +197,9 @@ kb/communities/Honeybee_Core20_Defined_Microbiota.yaml CommunityMech:000124 9f95
kb/communities/Horonobe_Mizunami_URL_Subsurface_Microbiome.yaml CommunityMech:000218 16a754cbe3b613ccff8bc58d6977583343afb00734dd6552311b9ae8b3c34bbd 4 0 67.5 reports/causal_graph_review/decisions/20261006-urls-amd-proteome-batch52.yaml reviewed
kb/communities/Hualgayoc_Acidic_Sulfate_Reducing_AMD_Consortium.yaml CommunityMech:000353 123c3e9e5a107b28346350c70a739cda2a27079917779f2d91d4797157c5f5af 2 1 85.0 reports/causal_graph_review/decisions/20261006-urls-amd-proteome-batch52.yaml needs_research
kb/communities/Human_Gut_FourMember_Proteome_Complementarity_Consortium.yaml CommunityMech:000317 d69abd3a1b4d3c0f41c90130143c41f5d4d234f5aec7926f3526894bfaa3b2a2 3 2 90.0 reports/causal_graph_review/decisions/20261006-urls-amd-proteome-batch52.yaml reviewed
-kb/communities/Iberian_Pit_Lake_Stratified_Community.yaml CommunityMech:000034 bc5b3e371afc61a51b2d9c6795ac704e7bbe2a98b08854b36c871388fe071ec7 5 3 100.0 pending
-kb/communities/Industrial_Bioreactor_Consortium.yaml CommunityMech:000035 442e1edeb00a23737e070386d509f4caf336248af81c199d2975b7cde6c88060 9 3 100.0 pending
-kb/communities/Industrial_Milk_Line_FourSpecies_Model_Biofilm.yaml CommunityMech:000152 185edc0766d39779bce9b43edf1fac1d5872fea92620b678262b2c29f54e785a 3 2 100.0 pending
+kb/communities/Iberian_Pit_Lake_Stratified_Community.yaml CommunityMech:000034 849626f1d5bc82bead855d41117508cdc48dd20c3e696864047368344c14b5ab 5 0 65.0 reports/causal_graph_review/decisions/20261006-pitlakes-bioleach-biofilm-batch53.yaml reviewed
+kb/communities/Industrial_Bioreactor_Consortium.yaml CommunityMech:000035 71160959bae2c8e3f0caf63d57452a597e29967f70faea6bec59016752b9aad4 9 0 63.9 reports/causal_graph_review/decisions/20261006-pitlakes-bioleach-biofilm-batch53.yaml needs_research
+kb/communities/Industrial_Milk_Line_FourSpecies_Model_Biofilm.yaml CommunityMech:000152 d11705d887a01509f631792a193c61ea0c57af05e3ac4d50ae2a2f08ab107f8d 3 2 90.0 reports/causal_graph_review/decisions/20261006-pitlakes-bioleach-biofilm-batch53.yaml reviewed
kb/communities/Infant_Gut_DNA_Phage_Succession_Community.yaml CommunityMech:000223 fc5af2b23ad4c8b45e40fd85fddb6b85e682c19fc536fc05cd24c83ab03d9ea8 4 3 100.0 pending
kb/communities/Infant_Gut_Prebiotic_Response_SynCom.yaml CommunityMech:000281 094baa2605865105bcb149b6493f4441e5013445b034585cacac0c4c04cabb23 3 2 100.0 pending
kb/communities/Infant_Gut_Strain_Persistence_Maternal_Community.yaml CommunityMech:000240 b55d38c622b7993e54dd2735e7f2f6cad9a189cb0c3ce2ee7a2eaaf111c33211 3 2 100.0 pending
diff --git a/reports/causal_graph_review/summary.json b/reports/causal_graph_review/summary.json
index e1230379c..68f6f760d 100644
--- a/reports/causal_graph_review/summary.json
+++ b/reports/causal_graph_review/summary.json
@@ -3,13 +3,13 @@
"semantic_review_rule": "Structural checks and readiness scores do not establish causal support. Completed reviews must match the current record SHA-256, cover every node once with a rationale, and reproduce the current edge list.",
"records": 460,
"nodes": 1465,
- "edges": 672,
+ "edges": 666,
"records_without_nodes": 8,
- "records_without_edges": 152,
+ "records_without_edges": 154,
"review_status_counts": {
- "needs_research": 15,
- "pending": 264,
- "reviewed": 181
+ "needs_research": 16,
+ "pending": 261,
+ "reviewed": 183
},
"structural_defects": [],
"network_audit": [
diff --git a/reports/causal_graph_review/validation-20261006-batch53.json b/reports/causal_graph_review/validation-20261006-batch53.json
new file mode 100644
index 000000000..d8ac92299
--- /dev/null
+++ b/reports/causal_graph_review/validation-20261006-batch53.json
@@ -0,0 +1,812 @@
+{
+ "base_commit": "683e765fe470057baa9e1efb313ce76d38aa99ac",
+ "scope": [
+ "kb/communities/Iberian_Pit_Lake_Stratified_Community.yaml",
+ "kb/communities/Industrial_Bioreactor_Consortium.yaml",
+ "kb/communities/Industrial_Milk_Line_FourSpecies_Model_Biofilm.yaml"
+ ],
+ "reference_validator_version": "0.1.7",
+ "results": [
+ {
+ "check": "Iberian_Pit_Lake_Stratified_Community-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Iberian_Pit_Lake_Stratified_Community.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch53/Iberian_Pit_Lake_Stratified_Community-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Iberian_Pit_Lake_Stratified_Community-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch53/Iberian_Pit_Lake_Stratified_Community-strict.tsv",
+ "kb/communities/Iberian_Pit_Lake_Stratified_Community.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch53/Iberian_Pit_Lake_Stratified_Community-strict.log",
+ "log_sha256": "0ec7f96e3add2fa41ba7d219929f52f211b877653a21ebfd684be97ed6b81374",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch53/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-batch53/Iberian_Pit_Lake_Stratified_Community-strict.tsv\n"
+ },
+ {
+ "check": "Iberian_Pit_Lake_Stratified_Community-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Iberian_Pit_Lake_Stratified_Community.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch53/Iberian_Pit_Lake_Stratified_Community-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Iberian_Pit_Lake_Stratified_Community-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Iberian_Pit_Lake_Stratified_Community.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch53/Iberian_Pit_Lake_Stratified_Community-references.log",
+ "log_sha256": "d871d33dca8945a8b350103ce674cac8d640c4361af33404ed7b30c2bac45178",
+ "output_tail": "Validating kb/communities/Iberian_Pit_Lake_Stratified_Community.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n",
+ "explained_output_tail": "Validating kb/communities/Iberian_Pit_Lake_Stratified_Community.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n"
+ },
+ {
+ "check": "Iberian_Pit_Lake_Stratified_Community-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Iberian_Pit_Lake_Stratified_Community.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch53/Iberian_Pit_Lake_Stratified_Community-snippets.log",
+ "log_sha256": "d140f70efe6e700027157f436bdd4c6df0c8482291a6b6572b52329d433a2cb8",
+ "output_tail": "# 37 evidence snippets scanned across 1 files\n MATCH 37\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": "Iberian_Pit_Lake_Stratified_Community-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Iberian_Pit_Lake_Stratified_Community.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch53/Iberian_Pit_Lake_Stratified_Community-rank.log",
+ "log_sha256": "719693b9a4be9ec4ff2df7d770751aff322ee3efcef41a9b41d3bc101e97fb57",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000034\",\n \"name\": \"Iberian Pit Lake Stratified Community\",\n \"score\": 65.0,\n \"taxonomy\": 8,\n \"connected_taxa\": 8,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 5,\n \"downstream_edges\": 0,\n \"interaction_evidence\": 11,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"downstream\",\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Iberian_Pit_Lake_Stratified_Community.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Iberian_Pit_Lake_Stratified_Community-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Iberian_Pit_Lake_Stratified_Community/2026-10-06T162402Z-codex-4e3d9b.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch53/Iberian_Pit_Lake_Stratified_Community-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Industrial_Bioreactor_Consortium-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Industrial_Bioreactor_Consortium.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch53/Industrial_Bioreactor_Consortium-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Industrial_Bioreactor_Consortium-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch53/Industrial_Bioreactor_Consortium-strict.tsv",
+ "kb/communities/Industrial_Bioreactor_Consortium.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch53/Industrial_Bioreactor_Consortium-strict.log",
+ "log_sha256": "714757a3a402d57bb70ca6e4414ae4696152d70addcfa4eb8cec774dbb900a09",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch53/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-batch53/Industrial_Bioreactor_Consortium-strict.tsv\n"
+ },
+ {
+ "check": "Industrial_Bioreactor_Consortium-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Industrial_Bioreactor_Consortium.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch53/Industrial_Bioreactor_Consortium-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Industrial_Bioreactor_Consortium-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Industrial_Bioreactor_Consortium.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch53/Industrial_Bioreactor_Consortium-references.log",
+ "log_sha256": "d5587676283cda962efc28f8171110d70dc283ea608580a3b791662875d1583b",
+ "output_tail": "Validating kb/communities/Industrial_Bioreactor_Consortium.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n",
+ "explained_output_tail": "Validating kb/communities/Industrial_Bioreactor_Consortium.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n"
+ },
+ {
+ "check": "Industrial_Bioreactor_Consortium-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Industrial_Bioreactor_Consortium.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch53/Industrial_Bioreactor_Consortium-snippets.log",
+ "log_sha256": "3ff331d052785904104210e5ed861f1a7a56c937b231f94a262feff3d8e69a6a",
+ "output_tail": "# 51 evidence snippets scanned across 1 files\n MATCH 51\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": "Industrial_Bioreactor_Consortium-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Industrial_Bioreactor_Consortium.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch53/Industrial_Bioreactor_Consortium-rank.log",
+ "log_sha256": "82a8b99f42fda7c6f3e0919900c69bea797cf071b9511d7d464d1697e50082a3",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000035\",\n \"name\": \"Industrial Bioleaching Reactor Consortium\",\n \"score\": 63.9,\n \"taxonomy\": 8,\n \"connected_taxa\": 8,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 9,\n \"downstream_edges\": 0,\n \"interaction_evidence\": 13,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"downstream\",\n \"metabolites_or_biological_processes\",\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Industrial_Bioreactor_Consortium.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Industrial_Bioreactor_Consortium-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Industrial_Bioreactor_Consortium/2026-10-06T162402Z-codex-b1f92a.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch53/Industrial_Bioreactor_Consortium-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Industrial_Milk_Line_FourSpecies_Model_Biofilm-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Industrial_Milk_Line_FourSpecies_Model_Biofilm.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch53/Industrial_Milk_Line_FourSpecies_Model_Biofilm-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Industrial_Milk_Line_FourSpecies_Model_Biofilm-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch53/Industrial_Milk_Line_FourSpecies_Model_Biofilm-strict.tsv",
+ "kb/communities/Industrial_Milk_Line_FourSpecies_Model_Biofilm.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch53/Industrial_Milk_Line_FourSpecies_Model_Biofilm-strict.log",
+ "log_sha256": "dbbd2e757070acf0ecd995054e5060a54e0c2675f2361ed4e87bec47ea062da9",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch53/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-batch53/Industrial_Milk_Line_FourSpecies_Model_Biofilm-strict.tsv\n"
+ },
+ {
+ "check": "Industrial_Milk_Line_FourSpecies_Model_Biofilm-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Industrial_Milk_Line_FourSpecies_Model_Biofilm.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch53/Industrial_Milk_Line_FourSpecies_Model_Biofilm-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Industrial_Milk_Line_FourSpecies_Model_Biofilm-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Industrial_Milk_Line_FourSpecies_Model_Biofilm.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch53/Industrial_Milk_Line_FourSpecies_Model_Biofilm-references.log",
+ "log_sha256": "1dfa03c59277cff59c2c379f65a1fbb377ad5514496d0d8202de7fa3479211b3",
+ "output_tail": "Validating kb/communities/Industrial_Milk_Line_FourSpecies_Model_Biofilm.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/Industrial_Milk_Line_FourSpecies_Model_Biofilm.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": "Industrial_Milk_Line_FourSpecies_Model_Biofilm-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Industrial_Milk_Line_FourSpecies_Model_Biofilm.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch53/Industrial_Milk_Line_FourSpecies_Model_Biofilm-snippets.log",
+ "log_sha256": "d6441c5dcfaf6a072d70e8708d5fe1bbd2c2a2d31da61b3014fb014108c34cef",
+ "output_tail": "# 18 evidence snippets scanned across 1 files\n MATCH 18\n RENDERING 0\n ASSEMBLED 0\n WEAK 0\n MISMATCH 0\n NOCONTENT 0\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n\n# MISMATCH/WEAK detail\n\n# Files by RENDERING (faithful quote; differs from cache only by\n# punctuation/whitespace/Greek \u2014 this is what validate-references flags)\n\n# Top files by NOCONTENT (unverifiable; cache stub/missing)\n\n# ASSEMBLED (every part is in the source; the join is not \u2014\n# a table flattened into prose, or a quote welded from two places)\n"
+ },
+ {
+ "check": "Industrial_Milk_Line_FourSpecies_Model_Biofilm-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Industrial_Milk_Line_FourSpecies_Model_Biofilm.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch53/Industrial_Milk_Line_FourSpecies_Model_Biofilm-rank.log",
+ "log_sha256": "14281db7c9850313b6a1324af4c624cc9654ed35c33868e03a8c8dd1d89464af",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000152\",\n \"name\": \"Industrial Milk-Line Four-Species Model Biofilm\",\n \"score\": 90.0,\n \"taxonomy\": 4,\n \"connected_taxa\": 4,\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/Industrial_Milk_Line_FourSpecies_Model_Biofilm.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Industrial_Milk_Line_FourSpecies_Model_Biofilm-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Industrial_Milk_Line_FourSpecies_Model_Biofilm/2026-10-06T162402Z-codex-2f65bf.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch53/Industrial_Milk_Line_FourSpecies_Model_Biofilm-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-batch53/inventory.log",
+ "log_sha256": "d68292e702610fda0c5d3613eb8ac767abc3929ab7c23e803f1a3736949aaf49",
+ "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\": 1465,\n \"edges\": 666,\n \"records_without_nodes\": 8,\n \"records_without_edges\": 154,\n \"review_status_counts\": {\n \"needs_research\": 16,\n \"pending\": 261,\n \"reviewed\": 183\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-batch53/network.log",
+ "log_sha256": "71a1e46fdd5d7c44e1766fabc85efb996c70258e3e64018891cfa94bb22fb13e",
+ "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-batch53/rank-all.log",
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Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch53/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch53/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch53/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-batch53/render-repeat.log",
+ "log_sha256": "ed294573cceb3ad1b9401115ecd79bb0e48a05178600613c0619ccc27b114876",
+ "output_tail": "sm.html\n \u2713 Synechococcus_Bacillus_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch53/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch53/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch53/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch53/docs/index.html\n"
+ },
+ {
+ "check": "connectivity-survey",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-c",
+ "import json, pathlib, runpy\nfn=runpy.run_path('tests/test_community_level_connectivity_credit.py')['_survey']\nresult={}\nfor name,root in [('baseline', pathlib.Path('/private/tmp/communitymech-causal-batch52')), ('current',pathlib.Path.cwd())]:\n paths=sorted(p for r in ['kb/communities','data/isolates'] for p in (root/r).rglob('*.yaml'))\n assert len(paths)==460\n fn.__globals__['record_files']=lambda: paths\n result[name]=fn()\nprint(json.dumps(result))\n"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch53/connectivity-survey.log",
+ "log_sha256": "d1f8cb53fc02a66edb17ed342b6a42f93828fdfc7d58e11aaea1140c633be1e1",
+ "output_tail": "{\"baseline\": {\"records\": 460, \"with_community_level\": 389, \"mixed\": 127, \"community_level_only\": 262, \"taxa\": 1498, \"credited_solely_by_the_rule\": 1222}, \"current\": {\"records\": 460, \"with_community_level\": 389, \"mixed\": 127, \"community_level_only\": 262, \"taxa\": 1498, \"credited_solely_by_the_rule\": 1222}}\n"
+ },
+ {
+ "check": "regressions",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "pytest",
+ "-q",
+ "tests/test_causal_review_batch10.py",
+ "tests/test_causal_review_batch11.py",
+ "tests/test_causal_review_batch12.py",
+ "tests/test_causal_review_batch13.py",
+ "tests/test_causal_review_batch14.py",
+ "tests/test_causal_review_batch15.py",
+ "tests/test_causal_review_batch16.py",
+ "tests/test_causal_review_batch17.py",
+ "tests/test_causal_review_batch18.py",
+ "tests/test_causal_review_batch19.py",
+ "tests/test_causal_review_batch20.py",
+ "tests/test_causal_review_batch21.py",
+ "tests/test_causal_review_batch22.py",
+ "tests/test_causal_review_batch23.py",
+ "tests/test_causal_review_batch24.py",
+ "tests/test_causal_review_batch25.py",
+ "tests/test_causal_review_batch27.py",
+ "tests/test_causal_review_batch28.py",
+ "tests/test_causal_review_batch29.py",
+ "tests/test_causal_review_batch30.py",
+ "tests/test_causal_review_batch31.py",
+ "tests/test_causal_review_batch32.py",
+ "tests/test_causal_review_batch33.py",
+ "tests/test_causal_review_batch34.py",
+ "tests/test_causal_review_batch35.py",
+ "tests/test_causal_review_batch36.py",
+ "tests/test_causal_review_batch37.py",
+ "tests/test_causal_review_batch38.py",
+ "tests/test_causal_review_batch39.py",
+ "tests/test_causal_review_batch40.py",
+ "tests/test_causal_review_batch41.py",
+ "tests/test_causal_review_batch42.py",
+ "tests/test_causal_review_batch43.py",
+ "tests/test_causal_review_batch44.py",
+ "tests/test_causal_review_batch45.py",
+ "tests/test_causal_review_batch46.py",
+ "tests/test_causal_review_batch47.py",
+ "tests/test_causal_review_batch48.py",
+ "tests/test_causal_review_batch49.py",
+ "tests/test_causal_review_batch5.py",
+ "tests/test_causal_review_batch50.py",
+ "tests/test_causal_review_batch51.py",
+ "tests/test_causal_review_batch52.py",
+ "tests/test_causal_review_batch53.py",
+ "tests/test_causal_review_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-batch53/regressions.log",
+ "log_sha256": "662d976195a8a30adfa65b98b34eab93bec9704a8bd29fcc76fa15d547ac5d3b",
+ "output_tail": "........................................................................ [ 14%]\n........................................................................ [ 28%]\n........................................................................ [ 42%]\n........................................................................ [ 57%]\n........................................................................ [ 71%]\n........................................................................ [ 85%]\n....................................................................... [100%]\n503 passed in 188.92s (0:03:08)\n"
+ },
+ {
+ "check": "black",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/3Q_kifQtLB624D5bBWGIf/bin/black",
+ "--check",
+ "tests/test_causal_review_batch53.py",
+ "tests/test_participating_taxa.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch53/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_batch53.py",
+ "tests/test_participating_taxa.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch53/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-batch53/diff-check.log",
+ "log_sha256": "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855",
+ "output_tail": ""
+ }
+ ],
+ "limitations": [
+ "Whole three records and all17 original nodes/eight arrows reviewed. Seventeen nodes retained; six unsupported arrows removed; two controlled milk genetic-intervention arrows retained. No new graph node/arrow added.",
+ "Complete cached 2013/2020 pit-lake and 2021 milk primary main texts/Methods/embedded tables/captions read. Fresh 2023 bioleaching primary XML main body/Methods/Tables1-5/captions read. No original images, external supplements, raw data or code audited.",
+ "Cueva de la Mora2022, chalcopyrite2014, defined consortium2009, pH2019, Acidiplasma genome and borehole studies reviewed at abstract scope. Access attempts for the2022/2014 full bodies failed; no full-body review claimed. Cuniculiplasmataceae review is background, not reactor primary evidence.",
+ "Pit-lake sites and studies remain distinct. Measured geochemistry and FC sulfide particles are positive evidence; functional/biogenic assignment remains a model. Active algae and rare methanogen reads do not resolve carbon export or methane flux. Do not infer universal carbon limitation across FC/La Zarza.",
+ "Industrial record remains needs_research under1509: canonical roster and non-graph fields conflate distinct systems and omit exact F. thermophilum identity. Positive early/middle population findings, genomic capabilities and copper output remain. No correct regeneration graph is claimed after removal of false/cross-study arrows.",
+ "One-community industrial Edison dry run completed without a paid job/report. The optional model-cost-map fetch failed and used a local fallback; no Edison provider call or credit spend. New structure remains pending authorization, report inspection and primary verification.",
+ "Milk knockout/omission findings remain positive causal evidence. tclE-H perturbation is not purified-thiocillin rescue, a universal robustness mechanism or a mature-biofilm recovery experiment. Canonical CLL49 spelling and prior cultivation-arm repair preserved.",
+ "One existing abstract cache gains24 exact primary-source words with retrieved-XML hash, section/context and CC BY attribution. Original abstract remains an exact prefix;919 other caches unchanged. The excerpts are source verified, not an assertion that all historical selected caches have independently verified provenance.",
+ "All457 other records and non-graph raw blocks are preserved, not recertified. SupportingReference coverage476, Linux DOI-cache lookup1091, selected-cache provenance1362 and writer artifact1095 remain limitations. Reference CLI Total checks counts reported issues, not executed checks.",
+ "Dedup searched813 all-state issue titles/bodies and20 ignored/hidden local files in the refreshed search, in addition to the earlier broader citation search. Relevant contexts inspected; not every historical comment/review read.1506/1507/1508 remain open until protected-main merge;1509 remains unresolved. This is self-adversarial review, not independent approval.",
+ "HTML descriptions checked by exact parser and repeat renders, not browser screenshots. Post-commit docs-current is a separate publication gate.",
+ "CLI Total checks counts reported issues, not executed checks. Exit0 is no reported issues, not source verification. SupportingReference coverage (#476), Linux DOI-cache lookup (#1091) and selected-cache provenance (#1362) remain limitations."
+ ],
+ "snippet_counts_by_record": {
+ "kb/communities/Iberian_Pit_Lake_Stratified_Community.yaml": {
+ "MATCH": 37,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Industrial_Bioreactor_Consortium.yaml": {
+ "MATCH": 51,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Industrial_Milk_Line_FourSpecies_Model_Biofilm.yaml": {
+ "MATCH": 18,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ }
+ },
+ "unchanged_raw_blocks": 45,
+ "unchanged_record_files": 457,
+ "unchanged_cache_files": 919,
+ "verified_cache_update": {
+ "path": "references_cache/doi_10.3390_biology12111411.md",
+ "original_sha256": "49770e35b148ae02e76ab1e5c2e4dabc1c720b9eb938ef1bcb2b62a47985b4b3",
+ "updated_sha256": "4755a26df17a7ad982e89a57d8c85459635478ede290f7a70618bc04d3b6165b",
+ "primary_xml_sha256": "bccf1c5f87dcd19897582f496df77a3104834b2cf178b2fb14c2fb0bc680d3ef",
+ "primary_url": "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC10669018/fullTextXML",
+ "license": "CC BY 4.0",
+ "quoted_words": 24,
+ "original_cache_is_exact_prefix": true,
+ "verified_excerpts": [
+ "This bacterium is a sulfur-oxidizing acidophile",
+ "is capable of oxidizing ferrous iron and reducing molecular oxygen",
+ "A large number of proteases",
+ "BR_04 and BR_01"
+ ],
+ "all_excerpts_matched_retrieved_primary_xml": true
+ },
+ "network_delta": {
+ "existing_findings_preserved": 34,
+ "added_findings": {},
+ "removed_findings": {}
+ },
+ "render_determinism": true,
+ "published_description_coverage": {
+ "pages": 456,
+ "nodes": 1451,
+ "arrows": 658
+ },
+ "participant_census": {
+ "measurements": {
+ "baseline": {
+ "records": 460,
+ "with_community_level": 389,
+ "mixed": 127,
+ "community_level_only": 262,
+ "taxa": 1498,
+ "credited_solely_by_the_rule": 1222
+ },
+ "current": {
+ "records": 460,
+ "with_community_level": 389,
+ "mixed": 127,
+ "community_level_only": 262,
+ "taxa": 1498,
+ "credited_solely_by_the_rule": 1222
+ }
+ },
+ "interpretation": "Seventeen community nodes retain their scopes. Milk participants made explicit, with one registry entry added; measured census unchanged. No production matching or census-bound changes."
+ },
+ "corpus": {
+ "scope": "Every YAML under kb/communities and data/isolates; filesystem discovery includes hidden/ignored files.",
+ "records": 460,
+ "nodes": 1465,
+ "edges": 666,
+ "records_without_nodes": 8,
+ "records_without_edges": 154,
+ "review_status_counts": {
+ "needs_research": 16,
+ "pending": 261,
+ "reviewed": 183
+ },
+ "structural_defects": []
+ },
+ "tested_file_sha256": {
+ "reports/causal_graph_review/decisions/20261006-pitlakes-bioleach-biofilm-batch53.yaml": "41b8d4e6971264d0890389465ca6c7c5f288097c011e3da00861fb09f49a8261",
+ "tests/test_causal_review_batch53.py": "0ad8b3c0cf3d4eefc7aaf3a227493a70867c515e0a1bacf89410d6953439d645",
+ "tests/test_participating_taxa.py": "f6d7b65b1215933f8c8518de8d985598a0258a48d0037c99e47453c12208c74a",
+ "kb/communities/Iberian_Pit_Lake_Stratified_Community.yaml": "849626f1d5bc82bead855d41117508cdc48dd20c3e696864047368344c14b5ab",
+ "kb/communities/Industrial_Bioreactor_Consortium.yaml": "71160959bae2c8e3f0caf63d57452a597e29967f70faea6bec59016752b9aad4",
+ "kb/communities/Industrial_Milk_Line_FourSpecies_Model_Biofilm.yaml": "d11705d887a01509f631792a193c61ea0c57af05e3ac4d50ae2a2f08ab107f8d",
+ "reports/causal_graph_review/README.md": "3bb95e6f09ef8dac71c51ba5f6ce3bacc880fd56569dc7bb789e6b20d78aa39f"
+ },
+ "status": "verified_pitlakes_bioleach_biofilm_graph_repair",
+ "reference_validator_caveat": "CLI Total checks counts reported issues, not executed checks. Exit0 is no reported issues, not source verification. SupportingReference coverage (#476), Linux DOI-cache lookup (#1091) and selected-cache provenance (#1362) remain limitations.",
+ "pre_research_baseline": {
+ "base_commit": "683e765fe470057baa9e1efb313ce76d38aa99ac",
+ "base_tree": "694f89b4f37bc4919a40e7b9b059cc49cfda9d02",
+ "research_worktree": "/private/tmp/communitymech-causal-batch52",
+ "checks": [
+ {
+ "name": "rank",
+ "command": [
+ "just",
+ "rank-causal-graphs"
+ ],
+ "exit_code": 0,
+ "expected_exit_code": 0,
+ "log": "/private/tmp/communitymech-batch53/baseline-rank.log",
+ "sha256": "b451b9a71f4e96533ed6ce324c7828bf2ae9c97de0ed5823c1b20e8d9baf20f4",
+ "output_tail": "/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml\tCommunityMech:000337\tTropidoatractus magnetotacticus Magnetotactic Ciliate Tripartite Syntrophy\t3\t3\t0\t4\t2\t9\t\t0\t0\n450\t100.0\tkb/communities/Urine_Nitrification_SynCom.yaml\tCommunityMech:000117\tUrine Nitrification Synthetic Microbial Community\t5\t5\t0\t3\t2\t5\t\t0\t0\n451\t100.0\tkb/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml\tCommunityMech:000213\tVariovorax-Cryptococcus Vitamin Cross-Feeding Microcosm\t2\t2\t0\t3\t2\t4\t\t0\t0\n452\t100.0\tkb/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml\tCommunityMech:000328\tWaste-Sludge Electro-Fermentation Biofilm-Suspension Community\t5\t5\t0\t4\t2\t6\t\t0\t0\n453\t100.0\tkb/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.yaml\tCommunityMech:000098\tWatermelon Rhizosphere Fusarium-Protective SynCom8\t2\t2\t0\t3\t2\t7\t\t0\t0\n454\t100.0\tkb/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml\tCommunityMech:000255\tWetland Oxygen-Sulfate Greenhouse Gas Microcosm Community\t3\t3\t0\t3\t2\t6\t\t0\t0\n455\t100.0\tkb/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.yaml\tCommunityMech:000118\tWheat Straw Biogas Pretreatment SynCom\t4\t4\t0\t3\t2\t4\t\t0\t0\n456\t100.0\tkb/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml\tCommunityMech:000354\tYarrowia lipolytica Division-of-Labor Lipid Consortium\t2\t2\t0\t3\t2\t3\t\t0\t0\n457\t100.0\tkb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml\tCommunityMech:000164\tYogurt Two-Species Starter Culture\t2\t2\t0\t4\t2\t9\t\t0\t0\n458\t100.0\tkb/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml\tCommunityMech:000210\tZymomonas-E. coli Exometabolomics-Designed Obligate Mutualism\t2\t2\t0\t3\t2\t6\t\t0\t0\n459\t100.0\tkb/communities/hCom2_Complex_Gut_Microbiome.yaml\tCommunityMech:000123\thCom2 Complex Gut Microbiome\t1\t1\t0\t3\t2\t3\t\t0\t0\n460\t100.0\tkb/communities/mCAFEs_Brachypodium_RCC.yaml\tCommunityMech:000078\tm-CAFEs Brachypodium Reduced Complexity Consortia\t10\t10\t0\t6\t2\t11\t\t0\t0\nPYTHONPATH=src uv run python scripts/rank_causal_graph_readiness.py \n"
+ },
+ {
+ "name": "just-network",
+ "command": [
+ "just",
+ "audit-network-json"
+ ],
+ "exit_code": 2,
+ "expected_exit_code": 2,
+ "log": "/private/tmp/communitymech-batch53/baseline-just-network.log",
+ "sha256": "8595db43420d3f0a01c57acd6ad733a531a72e962486d20b4e1c2840dda55bff",
+ "output_tail": "uv run communitymech audit-network --json\nerror: Failed to spawn: `communitymech`\n Caused by: No such file or directory (os error 2)\nerror: recipe `audit-network-json` failed on line 574 with exit code 2\n"
+ },
+ {
+ "name": "network",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "communitymech.cli",
+ "audit-network",
+ "--json"
+ ],
+ "exit_code": 1,
+ "expected_exit_code": 1,
+ "log": "/private/tmp/communitymech-batch53/baseline-network.log",
+ "sha256": "71a1e46fdd5d7c44e1766fabc85efb996c70258e3e64018891cfa94bb22fb13e",
+ "output_tail": " \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Staphylococcus capitis | K1-2-2-23 | ISS, V2A Steel | DSM 111179 | Sobisch et al., 2019 | GCA_025272695 | TSYB/TSYA | 37 \\u00b0C | 16\\u201324 h\",\n \"explanation\": \"Identifies S. capitis K1-2-2-23 as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Staphylococcus capitis K1-2-2-23' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Streptococcus halotolerans HTS9T\",\n \"taxon_id\": \"NCBITaxon:1814128\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Streptococcus halotolerans HTS9T\",\n \"term\": {\n \"id\": \"NCBITaxon:1814128\",\n \"label\": \"Streptococcus halotolerans\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the S. halotolerans type strain as a biosafety-level-1 representative.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"HTS9T\",\n \"genome_accession\": \"GCA_001598035\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"101996\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Streptococcus halotolerans | HTS9 T | Respiratory Tract of Marmota himalayana | DSM 101996 T | Niu et al., 2016 | GCA_001598035 | 2xLB, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies S. halotolerans HTS9T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Streptococcus halotolerans HTS9T' has no interactions\"\n }\n ]\n}\n"
+ },
+ {
+ "name": "downstream",
+ "command": [
+ "rg",
+ "--no-ignore",
+ "--hidden",
+ "-n",
+ "downstream:",
+ "kb/communities",
+ "data/isolates",
+ "--glob",
+ "*.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_code": 0,
+ "log": "/private/tmp/communitymech-batch53/baseline-downstream.log",
+ "sha256": "6add6d3357c1248220aa35a6e8fc33c49f66aeb758cf2b16c1e0e04c420333d6",
+ "output_tail": "kb/communities/Synechococcus_Bacillus_SPC.yaml:152: downstream:\nkb/communities/Clostridium_Autoethanogenum_Kluyveri_Syngas_Coculture.yaml:147: downstream:\nkb/communities/Clostridium_Autoethanogenum_Kluyveri_Syngas_Coculture.yaml:247: downstream:\nkb/communities/Acetobacterium_Clostridium_CO2_Electrolysis_Coculture.yaml:149: downstream:\nkb/communities/Acetobacterium_Clostridium_CO2_Electrolysis_Coculture.yaml:218: downstream:\nkb/communities/Rumen_Substrate_Adapted_Lignocellulose_Enrichment_Consortia.yaml:328: downstream:\nkb/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml:223: downstream:\nkb/communities/Rice_P_Uptake_Intercropping_SynCom4.yaml:121: downstream:\nkb/communities/Rice_P_Uptake_Intercropping_SynCom4.yaml:149: downstream:\nkb/communities/Choysum_SynLAV_DEHP_Rhizobacterial_SynCom.yaml:174: downstream:\nkb/communities/Lake_Washington_Methane_Oxygen_Methylotroph_Community.yaml:336: downstream:\nkb/communities/Populus_Salt_Tolerant_SynComs.yaml:65: downstream:\nkb/communities/Populus_Salt_Tolerant_SynComs.yaml:98: downstream:\nkb/communities/Populus_Salt_Tolerant_SynComs.yaml:131: downstream:\nkb/communities/Populus_Salt_Tolerant_SynComs.yaml:155: downstream:\nkb/communities/Shewanella_Streptococcus_Starch_Microbial_Fuel_Cell.yaml:140: downstream:\nkb/communities/Shewanella_Streptococcus_Starch_Microbial_Fuel_Cell.yaml:221: downstream:\nkb/communities/Asgard_Wetland_Soil_Methanogenesis_Substrate_Community.yaml:157: downstream:\nkb/communities/Asgard_Wetland_Soil_Methanogenesis_Substrate_Community.yaml:196: downstream:\nkb/communities/PMI_Variovorax_Thermotolerance_Collection.yaml:330: downstream:\nkb/communities/Methylacidiphilum_Galdieria_Thermoacidophilic_Coculture.yaml:268: downstream:\nkb/communities/Methylacidiphilum_Galdieria_Thermoacidophilic_Coculture.yaml:315: downstream:\nkb/communities/Salar_Atacama_Lithium_Brine_Community.yaml:295: downstream:\nkb/communities/Salar_Atacama_Lithium_Brine_Community.yaml:339: downstream:\n"
+ }
+ ],
+ "baseline_sha256": "1057f7ea1db5d8257a86c6541bdb004a373b665cbcf2af25f0432d301a86091b"
+ },
+ "edison_dry_run": {
+ "command": [
+ "just",
+ "research-community-causal",
+ "Industrial_Bioreactor_Consortium",
+ "--dry-run",
+ "--out-dir",
+ "/private/tmp/communitymech-batch53/industrial-dry-run"
+ ],
+ "exit_code": 0,
+ "status": "dry-run",
+ "job": "LITERATURE",
+ "query_chars": 34166,
+ "query_sha256": "65461cd6af7287fd31f971160ec451b12f0cef5565f7f30f3c83347640bf3522",
+ "metadata_path": "/private/tmp/communitymech-batch53/industrial-dry-run/Industrial_Bioreactor_Consortium-edison-literature-causal-meta.yaml",
+ "metadata_sha256": "7c6474b180956d61569338cc3e266b0c337858e433fe8bdf28a6ba8d47b1a882",
+ "provider_calls": 0,
+ "paid_report_obtained": false,
+ "full_prompt_reviewed": false,
+ "scope": "Dry run only. Optional model-cost metadata fetch fell back locally; no Edison API call or credit spend. Full prompt review and specific authorization remain prerequisites to submission."
+ }
+}
diff --git a/tests/test_causal_review_batch53.py b/tests/test_causal_review_batch53.py
new file mode 100644
index 000000000..43803db5e
--- /dev/null
+++ b/tests/test_causal_review_batch53.py
@@ -0,0 +1,158 @@
+"""Pin study scope, iron-oxidizer assignments and positive biofilm interventions."""
+
+import hashlib
+from pathlib import Path
+
+import yaml
+
+ROOT = Path(__file__).resolve().parents[1]
+LEDGER = (
+ ROOT / "reports/causal_graph_review/decisions/20261006-pitlakes-bioleach-biofilm-batch53.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 canonical(doc, indices):
+ return [
+ {
+ "preferred_term": doc["taxonomy"][i]["taxon_term"]["preferred_term"],
+ "term": doc["taxonomy"][i]["taxon_term"]["term"],
+ }
+ for i in indices
+ ]
+
+
+def test_all_nodes_use_explicit_canonical_community_participants():
+ _, docs = records()
+ subsets = [
+ [[0, 1, 4, 2], [3, 4], [7], [5], [6]],
+ [[0], [0], [6], [1, 3], [0, 6], [4], [7], [2, 1], [5, 3]],
+ [list(range(4)), [3, 2], list(range(4))],
+ ]
+ for doc, expected in zip(docs, subsets, strict=True):
+ for node, indexes in zip(doc["ecological_interactions"], expected, strict=True):
+ assert node["scope"] == "COMMUNITY_LEVEL"
+ assert node["participating_taxa"] == canonical(doc, indexes)
+ assert not {"source_taxon", "target_taxon", "interaction_type"} & node.keys()
+
+
+def test_pit_lake_findings_keep_site_scope_without_cross_site_arrows():
+ _, (doc, _, _) = records()
+ iron, sulfur, algae, archaea, methane = doc["ecological_interactions"]
+ assert all(not n.get("downstream") for n in doc["ecological_interactions"])
+ assert "NSC/Concepcion" in iron["description"]
+ assert "precipitated sulfides, not dissolved sulfides" in sulfur["description"]
+ assert "not demonstrated pairwise syntrophy" in sulfur["description"]
+ assert "did not infer that organic carbon was necessarily" in algae["description"]
+ assert "not measured methane production" in methane["description"]
+ assert all(
+ "concentration" not in term
+ for node in doc["ecological_interactions"]
+ for term in node.get("metabolites", [])
+ )
+ assert [p["term"]["id"] for p in sulfur["biological_processes"]] == ["GO:0019420"]
+ assert [p["term"]["id"] for p in archaea["biological_processes"]] == ["GO:0019418"]
+ assert all(m["term"]["id"] != "CHEBI:29033" for m in algae["metabolites"])
+
+
+def test_bioleaching_preserves_population_and_yield_results_not_false_iron_owner():
+ _, (_, doc, _) = records()
+ early, _, middle, _, output, _, lepto, _, _ = doc["ecological_interactions"]
+ assert early["name"] == "Initial Acidithiobacillus caldus Predominance"
+ assert "metabolites" not in early and "biological_processes" not in early
+ assert "does not identify A. caldus as a ferrous-iron oxidizer" in early["description"]
+ assert "S. acidophilus rather than A. caldus" in middle["evidence"][0]["snippet"]
+ assert "60.4 percent" in output["description"]
+ assert "more than two years" in output["description"]
+ assert "supported subset, not the complete culture" in output["description"]
+ assert "60.4% of copper" in output["evidence"][0]["snippet"]
+ assert "does not prove extinction" in lepto["description"]
+ assert all(not n.get("downstream") for n in doc["ecological_interactions"])
+
+
+def test_bioleaching_genomic_capabilities_do_not_substitute_for_other_study_taxa():
+ ledger, (_, doc, _) = records()
+ _, sulfur, _, late, _, organic, _, ferro, temperature = doc["ecological_interactions"]
+ assert sulfur["evidence"][0]["evidence_source"] == "COMPUTATIONAL"
+ assert "2014 F. thermophilum" in late["description"]
+ assert "biological_processes" not in organic
+ assert "not measured transfer" in organic["description"]
+ assert "do not demonstrate functional redundancy" in ferro["description"]
+ assert "single reactor runs per condition" in temperature["description"]
+ assert ledger["records"][1]["status"] == "needs_research"
+ assert ledger["unresolved_research_issues"] == [1509]
+ assert "#1509" in doc["discussions"][-1]["rationale"]
+
+
+def test_milk_preserves_both_positive_genetic_intervention_arrows():
+ _, (_, _, doc) = records()
+ network, inhibition, robustness = doc["ecological_interactions"]
+ assert [e["target"] for e in inhibition["downstream"]] == [
+ network["name"],
+ robustness["name"],
+ ]
+ assert "positive genetic evidence" in inhibition["description"]
+ assert "about 50-fold" in inhibition["description"]
+ assert "mainly pellet-associated or unstable" in inhibition["description"]
+ assert "did not report complementation" in inhibition["description"]
+ assert all(ev["supports"] == "SUPPORT" for ev in inhibition["evidence"])
+ assert "causal contribution" in inhibition["downstream"][0]["description"]
+ assert "genetic intervention supports" in inhibition["downstream"][1]["description"]
+
+
+def test_milk_robustness_is_an_establishment_endpoint_not_universal_recovery():
+ _, (_, _, doc) = records()
+ network, _, robustness = doc["ecological_interactions"]
+ assert "laboratory substitution" in network["description"]
+ assert "72-hour compositions" in robustness["description"]
+ assert "not a recovery time course" in robustness["description"]
+ assert (
+ "Neither community resisted strong continuous changes uniformly"
+ in robustness["description"]
+ )
+ assert doc["taxonomy"][1]["strain_designation"]["strain_name"] == "CLL49"
+ assert "#529" in doc["discussions"][-1]["rationale"]
+
+
+def test_source_excerpt_update_keeps_original_cache_prefix_and_provenance():
+ ledger, _ = records()
+ update = ledger["reference_cache_update"]
+ raw = (ROOT / update["path"]).read_bytes()
+ original, marker, extra = raw.partition(b"\n\n## Primary-Source Excerpts (2026-10-06)")
+ assert marker and extra
+ assert hashlib.sha256(original).hexdigest() == update["original_sha256"]
+ assert hashlib.sha256(raw).hexdigest() == update["updated_sha256"]
+ assert update["primary_xml_sha256"].encode() in extra
+ assert b"CC BY 4.0" in extra
+ assert b"not a complete full-text cache" in extra
+ assert sum(len(q.split()) for q in update["verified_excerpts"]) == update["quoted_words"] == 24
+ assert all(q.encode() in extra for q in update["verified_excerpts"])
+
+
+def test_every_node_and_arrow_has_a_hash_bound_decision_and_history():
+ ledger, docs = records()
+ assert ledger["independent_approval"] is False
+ assert ledger["issues"] == [1506, 1507, 1508]
+ assert ledger["issue_deduplication"]["ignored_hidden_local_search"] is True
+ for index, (row, doc) in enumerate(zip(ledger["records"], docs, strict=True)):
+ nodes = doc["ecological_interactions"]
+ names = {n["name"] for n in nodes}
+ assert len(nodes) == [5, 9, 3][index]
+ assert {d["node"] for d in row["node_decisions"]} == names
+ assert row["removed_node_decisions"] == []
+ assert len(row["edges_before"]) == [3, 3, 2][index]
+ assert len(row["retained_edge_decisions"]) == [0, 0, 2][index]
+ assert len(row["removed_edge_decisions"]) == [3, 3, 0][index]
+ for node in nodes:
+ for edge in node.get("downstream", []):
+ assert edge["target"] in names
+ for discussion in doc["discussions"]:
+ assert all(a.split("#", 1)[1] in names for a in discussion["attaches_to"])
+ assert hashlib.sha256((ROOT / row["path"]).read_bytes()).hexdigest() == row["record_sha256"]
+ assert len(row["history_files"]) == 1
+ assert (ROOT / row["history_files"][0]).is_file()
+ assert doc["curation_history"][-1]["llm_assisted"] is True
diff --git a/tests/test_participating_taxa.py b/tests/test_participating_taxa.py
index dc58dc52b..f8e5e69ec 100644
--- a/tests/test_participating_taxa.py
+++ b/tests/test_participating_taxa.py
@@ -293,6 +293,7 @@ def test_a_curie_is_ambiguous_where_members_share_an_id(example):
"Human_Gut_FourMember_Proteome_Complementarity_Consortium.yaml",
"Iberian_Pit_Lake_Stratified_Community.yaml",
"Industrial_Bioreactor_Consortium.yaml",
+ "Industrial_Milk_Line_FourSpecies_Model_Biofilm.yaml",
"Infant_Gut_Strain_Persistence_Maternal_Community.yaml",
"Legume_Rhizobia_Mars_Simulant_Symbiosis.yaml",
"Lunar_Simulant_Phosphate_Solubilizing_Bacteria_Nicotiana.yaml",