From 439740b4f07d8c6e63d6a335327fd17a87a6b6f2 Mon Sep 17 00:00:00 2001 From: "marcin p. joachimiak" <4625870+realmarcin@users.noreply.github.com> Date: Sun, 14 Jun 2026 00:34:43 -0700 Subject: [PATCH] Backfill related_ingredients for Cable Bacteria via re-fetched abstract (#30) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Part (b) of the backfill effort: re-fetch fuller abstracts for high-value un-backfillable files, then curate. Re-fetched PMID:27058505 (was a stub cache) and folded the full abstract into references_cache/PMID_27058505.md (the validator's primary cache), unlocking the cable-bacteria sulfur/oxygen chemistry. Added 4 CHEBI-grounded ingredients to Cable_Bacteria_Photosynthetic_Biofilm_Sediment: sulfide (CHEBI:15138), dioxygen (CHEBI:15379), sulfate (CHEBI:16189), iron sulfide (CHEBI:75896) — all snippets verbatim from cited+cached references, all labels OAK-canonical. Also re-fetched PMID:38228683 (CeMbio), PMID:34135464 (PMI Variovorax), and PMID:19395564 (Yogurt) but their full abstracts name no metabolite chemistry (behaviour / phenotypic-variation / in-silico HGT papers) — confirmed genuinely un-backfillable, no changes made. Verified: 4/4 labels canonical, 4/4 snippets exact, linkml-validate passes. Co-Authored-By: Claude Fable 5 --- ...teria_Photosynthetic_Biofilm_Sediment.yaml | 53 +++++++++++++++++++ references_cache/PMID_27058505.md | 22 ++++++++ 2 files changed, 75 insertions(+) diff --git a/kb/communities/Cable_Bacteria_Photosynthetic_Biofilm_Sediment.yaml b/kb/communities/Cable_Bacteria_Photosynthetic_Biofilm_Sediment.yaml index 95502281..774d799d 100644 --- a/kb/communities/Cable_Bacteria_Photosynthetic_Biofilm_Sediment.yaml +++ b/kb/communities/Cable_Bacteria_Photosynthetic_Biofilm_Sediment.yaml @@ -196,6 +196,59 @@ environmental_factors: evidence_source: IN_VITRO snippet: oxic-anoxic interfaces in aquifer sediments explanation: Supports the redox-interface setting for cable-bacteria activity. +related_ingredients: +- preferred_term: sulfide + chebi_term: + id: CHEBI:15138 + label: sulfide(2-) + relevance: > + Free sulfide in the reduced sediment is the electron donor that cable bacteria oxidize, + harvesting electrons that are conducted to oxygen near the surface. + evidence: + - reference: PMID:25416774 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: harvesting electrons from free sulfide + explanation: Names sulfide as the electron-donor substrate for cable-bacteria oxidation. +- preferred_term: dioxygen + chebi_term: + id: CHEBI:15379 + label: dioxygen + relevance: > + Oxygen near the sediment-water interface is the terminal electron acceptor for long-distance + electron transfer, spatially separated from sulfide at depth. + evidence: + - reference: PMID:27058505 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: spatial separation of oxygen and sulfide + explanation: Names oxygen as the acceptor separated from sulfide across the redox interface. +- preferred_term: sulfate + chebi_term: + id: CHEBI:16189 + label: sulfate + relevance: > + Cable-bacteria long-distance electron transfer drives direct recycling of sulfate over + centimeter distances at oxic-anoxic interfaces. + evidence: + - reference: PMID:27058505 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: direct recycling of sulfate by electron transfer + explanation: Names sulfate as the product recycled by cable-bacteria electron transfer. +- preferred_term: iron sulfide + chebi_term: + id: CHEBI:75896 + label: iron sulfides + relevance: > + Aquifer sediment was amended with iron sulfide as a reduced sulfur source supporting + sulfur-oxidizing cable-bacteria activity in the incubations. + evidence: + - reference: PMID:27058505 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: amended with iron sulfide + explanation: Names iron sulfide as the amended reduced-sulfur source in the sediment incubation. associated_datasets: - name: Cable bacteria photosynthetic biofilm sediment article dataset_type: PHENOTYPE diff --git a/references_cache/PMID_27058505.md b/references_cache/PMID_27058505.md index 360b0aa2..3418fb3f 100644 --- a/references_cache/PMID_27058505.md +++ b/references_cache/PMID_27058505.md @@ -20,3 +20,25 @@ Key snippets used in curated records: - "hydrocarbon-contaminated aquifer" - "identified by sequencing of 16S rRNA genes" - "belonging to the Desulfobulbaceae" + +Full abstract (re-fetched 2026-06-14 via communitymech.literature): + +The biodegradation of organic pollutants in aquifers is often restricted to the +fringes of contaminant plumes where steep countergradients of electron donors +and acceptors are separated by limited dispersive mixing. However, long-distance +electron transfer (LDET) by filamentous 'cable bacteria' has recently been +discovered in marine sediments to couple spatially separated redox half +reactions over centimeter scales. Here we provide primary evidence that such +sulfur-oxidizing cable bacteria can also be found at oxic-anoxic interfaces in +aquifer sediments, where they provide a means for the direct recycling of +sulfate by electron transfer over 1-2-cm distance. Sediments were taken from a +hydrocarbon-contaminated aquifer, amended with iron sulfide and saturated with +water, leaving the sediment surface exposed to air. Steep geochemical gradients +developed in the upper 3 cm, showing a spatial separation of oxygen and sulfide +by 9 mm together with a pH profile characteristic for sulfur oxidation by LDET. +Bacterial filaments, which were highly abundant in the suboxic zone, were +identified by sequencing of 16S rRNA genes and fluorescence in situ +hybridization (FISH) as cable bacteria belonging to the Desulfobulbaceae. The +detection of similar Desulfobulbaceae at the oxic-anoxic interface of fresh +sediment cores taken at a contaminated aquifer suggests that LDET may indeed be +active at the capillary fringe in situ.