Enrich causal graphs for the 6 single-edge DIET/syntrophy records

NEXT_TASKS.md

@@ -360,19 +360,56 @@ errors, e.g. sulfite → CHEBI:16731 *(E)-cinnamaldehyde* instead of CHEBI:17359
 the primary full text isn't retrievable, keep edges to abstract-supported/directly-implied
 claims and file the rest as a KNOWLEDGE_GAP (000176 is the worked example).
 
-**PENDING — enrich the single-edge records via a full causal-graph run.** Six 2-node
-records already carry one hand-authored `downstream` edge (donor→acceptor) from original
-curation but have not had an Edison causal-graph pass: the DIET trio
-`Geobacter_Clostridium_DIET` (000031, PMID:28287150),
-`Geobacter_Methanosaeta_DIET` (000032, doi:10.1039/C3EE42189A),
-`Geobacter_Methanosarcina_DIET` (000033, PMID:24837373); and the syntrophies
-`Syntrophobacter_Methanobacterium_Syntrophy` (000068), `Syntrophobacter_Methanospirillum_Syntrophy`
-(000069), `Syntrophomonas_Methanospirillum_Syntrophy` (000070). A full run could add
-mechanistic nodes/edges (e.g. conductive pili / OmcS-OmcZ cytochromes, conductive-material
-mediation, formate-vs-H2 routes, reverse/feedback edges) beyond the single existing edge.
-Run `just research-community-causal CommunityMech:0000NN` per record, then curate
-conservatively as usual. NB: stray untracked `*.yaml.bak` backups exist alongside these in
-`kb/communities/` (gitignored, not in the repo) — target the `.yaml` files.
+**DONE — single-edge record enrichment (#254).** All six 2-node records got an Edison
+causal-graph pass and conservative curation. What actually landed, per record:
+
+- **000070 `Syntrophomonas_Methanospirillum`** — reverse feedback edge (methanogen H2
+  scavenging → enables butyrate β-oxidation). Best evidence was already in the cached
+  abstract, not in the Edison report: PMID:16345745 reports both the dependency
+  ("Growth and degradation of fatty acids occur only in syntrophic association with
+  H(2)-using bacteria") and the perturbation ("The addition of H(2) … stopped growth and
+  butyrate degradation"). No new reference needed.
+- **000069 `Syntrophobacter_Methanospirillum`** — reverse feedback edge, on the
+  axenic-vs-syntrophic contrast in PMID:9828440 (exact pair: M. hungateii).
+- **000068 `Syntrophobacter_Methanobacterium`** — reverse feedback edge + **fixed a real
+  misattribution**: two evidence items quoted the Harmsen M. *hungateii* passage but were
+  explained as establishing M. *formicicum* (this record's partner). Downgraded to PARTIAL,
+  added exact-pair support from PMID:29611893, and filed discussion
+  `kg-syntrophobacter-methanobacterium-partner-attribution`.
+- **000033 `Geobacter_Methanosarcina`** — new `T6SS-Associated Delay of DIET Establishment`
+  interaction + NEGATIVE edge to the DIET node (>30 d lag wild-type vs very little lag for
+  the Hcp-deficient mutant, PMID:37650614, OA full text cached). Curated as *T6SS-associated*,
+  not T6SS-caused: the mutant is pleiotropic (also reduces Fe(III) oxide faster).
+- **000031 `Geobacter_Clostridium`** — no new edge; filed CONTROVERSY discussion
+  `kg-geobacter-clostridium-contact-dependence-contested`. **This record's core framing is
+  contested**: the follow-up study (PMID:34939136) concludes the interaction is *mediated*
+  (putative cobamide), and its full text reports that 0.22-µm-filtered cell-free spent
+  medium reproduces the metabolic shift — which would make pili contact unnecessary.
+  Curator decision still open on whether to re-scope the record away from `community_category:
+  DIET`; not applied unilaterally.
+- **000032 `Geobacter_Methanosaeta`** — no new edge (000176 precedent). Edison proposed an
+  acetate cross-feeding node, but its quotations came from secondary reviews; the primary
+  (doi:10.1039/C3EE42189A) is cached abstract-only and is silent on acetate. Filed as
+  `kg-geobacter-methanosaeta-acetate-route-unresolved`.
+
+Verification: all 6 `just validate` clean; snippet audit MATCH 4086→4101 (all 12 new
+snippets match, zero new mismatches) and caching PMID:29611893 OA full text also cleared the
+3 pre-existing 000068 Methods-snippet mismatches (169→166 repo-wide); network-integrity audit
+clean for all 6. New reference caches: PMID:34939136, PMID:37650614.
+
+**Follow-ups this batch surfaced:**
+1. **000031 re-scoping decision** (above) — the highest-value open item.
+2. **Li et al. 2024** (`doi:10.3390/w16243551`, *Water*) has exact-pair graded-formate
+   perturbation data for 000068 (5–10 mM promotes, ≥30 mM inhibits; FDH/hydrogenase
+   transcript downregulation). **Not ingested**: the journal is not in PubMed and has no PMC
+   record, so `scripts/cache_fulltext.py` can't verify its snippets. Would need a
+   DOI-based full-text cache path.
+3. `just validate-references` is a **no-op** — it reports `Total checks: 0` even on untouched
+   files. `scripts/evidence_snippet_audit.py` is what actually validates snippets. Worth
+   fixing or documenting, since the justfile recipe implies coverage it isn't providing.
+
+NB: stray untracked `*.yaml.bak` backups still exist alongside these in `kb/communities/`
+(gitignored, not in the repo).
 
 **Edison auth (resolved 2026-07-21):** the key was refreshed in `.env`
 (`EDISON_API_KEY`) and authenticates (HTTP 200). The stale-key shadowing footgun is

kb/communities/Geobacter_Clostridium_DIET.yaml

@@ -498,3 +498,55 @@ related_ingredients:
 metals_present: []
 metal_relevance: SIGNIFICANT
 metal_notes: Metal/REE detected via environmental factor measurements
+discussions:
+- discussion_id: kg-geobacter-clostridium-contact-dependence-contested
+  prompt: >
+    Is the G. sulfurreducens-induced metabolic shift in C. pasteurianum actually caused by
+    contact-dependent direct interspecies electron transfer along conductive pili, or by a
+    diffusible mediator (candidate: a cobamide) released by G. sulfurreducens?
+  kind: CONTROVERSY
+  status: OPEN
+  attaches_to:
+  - ecological_interactions#Acetate Oxidation and Direct Electron Transfer
+  - ecological_interactions#Glycerol Fermentation with DIET-Induced Metabolic Shift
+  rationale: >
+    This record asserts contact-dependent DIET through electrically conductive pili
+    (nanowires) as the established mechanism, following the original coculture study
+    (PMID:28287150), which inferred interspecies electron transfer rather than
+    demonstrating contact dependence. A follow-up study by the same group
+    (PMID:34939136) set out to identify the mechanism and concluded that the interaction
+    is MEDIATED: it proposes that G. sulfurreducens releases cobamide molecules that act
+    on the C. pasteurianum glycerol dehydratase, with electron entry via a transmembrane
+    flavin-bound polyferredoxin / cytochrome b5-rubredoxin route offered only as a
+    putative reinforcement. The published full text (not open access, so only the
+    abstract is snippet-verifiable here) additionally reports that 0.22-um-filtered,
+    cell-free G. sulfurreducens spent medium reproduces the metabolic shift, which would
+    make Geobacter cells - and therefore pili contact - unnecessary for the shift.
+    Until that contrast is verified against the full text, the nanowire/contact-dependent
+    framing in this record's description, its `Acetate Oxidation and Direct Electron
+    Transfer` interaction, and its DIET `community_category` should be treated as
+    CONTESTED rather than established. Resolving this may require re-scoping the record
+    away from DIET; that is a curator decision, not applied here.
+  evidence:
+  - reference: PMID:34939136
+    supports: PARTIAL
+    evidence_source: IN_VITRO
+    snippet: It was assumed that this metabolic shift of the fermentative species resulted
+      from an interspecies electron transfer
+    explanation: The follow-up study characterizes the interspecies-electron-transfer reading
+      of the original experiment as an assumption, not a demonstrated mechanism.
+  - reference: PMID:34939136
+    supports: REFUTE
+    evidence_source: IN_VITRO
+    snippet: 'C. pasteurianum-G. sulfurreducens interaction inducing a metabolic shift is
+      mediated'
+    explanation: Key-point conclusion that the interaction is mediated (via a diffusible
+      molecule), contradicting the contact-dependent nanowire mechanism asserted by this record.
+  - reference: PMID:34939136
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: 'a putative interaction model was proposed: G. sulfurreducens produces cobamide
+      molecules that possibly modify C. pasteurianum metabolic pathway at the key enzyme
+      glycerol dehydratase'
+    explanation: States the competing diffusible-cobamide mechanism, and marks it as putative -
+      so it must not be asserted as an interaction in place of the current one.

kb/communities/Geobacter_Methanosaeta_DIET.yaml

@@ -372,3 +372,37 @@ metals_present: []
 metal_relevance: SIGNIFICANT
 metal_notes: Metal/REE detected via environmental factor measurements; Metal/REE detected
   via keyword matching in description (context-validated)
+discussions:
+- discussion_id: kg-geobacter-methanosaeta-acetate-route-unresolved
+  prompt: >
+    Alongside DIET-driven CO2 reduction, does M. harundinacea also cross-feed on the
+    acetate generated by G. metallireducens ethanol oxidation, and what fraction of
+    methane comes from each route in this defined coculture?
+  kind: KNOWLEDGE_GAP
+  status: OPEN
+  attaches_to:
+  - ecological_interactions#Ethanol Oxidation and Direct Electron Transfer
+  - ecological_interactions#Direct Electron Acceptance and Methanogenesis
+  rationale: >
+    A causal-graph pass on this record proposed an additional acetate cross-feeding node
+    and an acetate -> methanogenesis edge, on the reasoning that Methanosaeta is
+    classically an acetoclastic genus and that ethanol oxidation by G. metallireducens
+    yields acetate, giving an overall stoichiometry near 1.5 mol CH4 per mol ethanol.
+    That claim is NOT curated here as an interaction: the primary source
+    (doi:10.1039/C3EE42189A) is cached abstract-only and its full text was not
+    retrievable, and the abstract states only that M. harundinacea "accepted electrons
+    via DIET for the reduction of carbon dioxide to methane" - it does not report acetate
+    cross-feeding, the acetate/DIET split, or the per-route methane stoichiometry. The
+    supporting quotations offered for the acetate route came from secondary reviews
+    attributing findings to this study, which per this repo's conservative-curation rule
+    (see CommunityMech:000176) is not a sufficient basis for an exact-system causal edge.
+    Resolving this needs the primary full text or a radiotracer/isotope partition
+    experiment in this exact coculture.
+  evidence:
+  - reference: doi:10.1039/C3EE42189A
+    supports: PARTIAL
+    evidence_source: IN_VITRO
+    snippet: Transcriptomic, radiotracer, and genetic analysis demonstrated that M. harundinacea
+      accepted electrons via DIET for the reduction of carbon dioxide to methane
+    explanation: The abstract demonstrates only the DIET/CO2-reduction route; it is silent on an
+      acetate cross-feeding route, which is why that edge is filed as a gap rather than curated.

kb/communities/Geobacter_Methanosarcina_DIET.yaml

@@ -201,6 +201,66 @@ ecological_interactions:
     evidence_source: IN_VITRO
     snippet: Direct interspecies electron transfer (DIET) is potentially an effective
       form of syntrophy in methanogenic communities, but little is known about the
+- name: T6SS-Associated Delay of DIET Establishment
+  description: 'Geobacter metallireducens expresses a type VI secretion system (T6SS) during
+    the initiation of DIET cocultures, and this is associated with a long delay before the
+    partnership becomes productive. Cocultures started with wild-type G. metallireducens showed
+    a lag of more than 30 days before methane production, whereas cocultures started with an
+    Hcp-deficient (T6SS structural protein) mutant had very little lag and established DIET
+    with M. barkeri faster. The sign of this edge is NEGATIVE: the wild-type T6SS-expressing
+    state suppresses the rate at which the DIET partnership is established. The molecular
+    attribution is confounded and must not be curated as demonstrated antagonism toward the
+    archaeon - the same mutant also reduced Fe(III) oxide faster than wild type, a phenotype
+    not expected from loss of the T6SS, and the authors state that the effect of T6SSs on
+    archaeal cells still requires study. Encoded as a delay of establishment, not as
+    predation, killing, or toxin delivery to M. barkeri.
+
+    '
+  interaction_type: COMPETITION
+  source_taxon:
+    preferred_term: Geobacter metallireducens
+    term:
+      id: NCBITaxon:28232
+      label: Geobacter metallireducens
+  biological_processes:
+  - preferred_term: protein secretion by the type VI secretion system
+    term:
+      id: GO:0033103
+      label: protein secretion by the type VI secretion system
+  downstream:
+  - target: Ethanol Oxidation and Direct Electron Transfer
+    description: NEGATIVE edge - the wild-type T6SS-expressing state of G. metallireducens
+      delays establishment of the DIET partnership (>30 d lag vs very little lag for the
+      Hcp-deficient mutant). Demonstrated by knockout phenotype in this exact coculture, but
+      the mutant is pleiotropic, so the causal attribution to the T6SS specifically is
+      HYPOTHESIZED rather than proven.
+  evidence:
+  - reference: PMID:37650614
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: there was a lag period of more than 30 d in co-cultures initiated with wild-type
+      G. metallireducens
+    explanation: Wild-type baseline for the delay, measured in the G. metallireducens-M. barkeri
+      ethanol coculture that this record describes.
+  - reference: PMID:37650614
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: In contrast, there was very little lag in co-cultures initiated with the Hcp-deficient
+      G. metallireducens strain
+    explanation: Knockout arm of the perturbation - removing the T6SS structural protein Hcp
+      largely removes the lag, which is the basis for the negative causal edge.
+  - reference: PMID:37650614
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: The hcp-deficient mutant also established DIET quicker with Methanosarcina barkeri
+    explanation: Confirms the phenotype specifically for the M. barkeri partner of this community.
+  - reference: PMID:37650614
+    supports: PARTIAL
+    evidence_source: IN_VITRO
+    snippet: the mutant also reduced Fe(III) oxide faster than the wild-type strain, a phenotype
+      not expected from the loss of the T6SS
+    explanation: Records the pleiotropy confounder - the reason this edge is curated as
+      T6SS-associated rather than T6SS-caused.
 environmental_factors:
 - name: Anaerobic Conditions
   value: Strict anaerobic