From cac5093349142c517061d856a2d255ed1056b713 Mon Sep 17 00:00:00 2001 From: "marcin p. joachimiak" <4625870+realmarcin@users.noreply.github.com> Date: Mon, 1 Jun 2026 23:54:48 -0700 Subject: [PATCH] #30 backfill: electroactive/MFC peripheral set (4 communities) Closes the electroactive/MFC tail of the syntrophy/methanogenesis work. CHEBI ids verified live via OAK; snippets verbatim from cached abstracts. related_ingredients adoption: 65/265 -> 69/265. | Community | Ingredients (CHEBI-verified) | |---|---| | Rhodopseudomonas_Geobacter_Magnetite_Redox | magnetite, iron(2+), iron(3+) | | Clostridium_Cellulolyticum_Geobacter_Cellulose_MFC | cellulose [(1->4)-beta-D-glucan], acetate, ethanol, dihydrogen | | Methylocaldum_Cupriavidus_Methane_Acetate_Crossfeeding | methane, acetate, methanol | | High_Solids_Switchgrass_Methanogenic_Microbiome | lignocellulose, dihydrogen, methane | Shewanella_Geobacter_Exoelectrogenic_Biofilm left unchanged: its one cached reference names only generic "organic substrates", nothing verbatim-supportable. Pre-existing CHEBI label issues flagged (out of scope): CHEBI:18246 is labeled "cellulose" in several files but its canonical label is "(1->4)-beta-D-glucan"; CHEBI:37686 "xylan" is alpha-D-allose; CHEBI:50821 "iron(II,III) oxide" canonical label is "ferrosoferric oxide". Added to the cleanup list. Test plan: just test (136 passed, 9 skipped), all 4 files validate clean. Co-Authored-By: Claude Opus 4.8 (1M context) --- ...cum_Geobacter_Cellulose_MFC_Coculture.yaml | 49 +++++++++++++++++++ ...s_Switchgrass_Methanogenic_Microbiome.yaml | 39 +++++++++++++++ ...ethane_Acetate_Crossfeeding_Coculture.yaml | 40 +++++++++++++++ ...s_Geobacter_Magnetite_Redox_Coculture.yaml | 46 +++++++++++++++++ 4 files changed, 174 insertions(+) diff --git a/kb/communities/Clostridium_Cellulolyticum_Geobacter_Cellulose_MFC_Coculture.yaml b/kb/communities/Clostridium_Cellulolyticum_Geobacter_Cellulose_MFC_Coculture.yaml index 077eb74b..efdd5009 100644 --- a/kb/communities/Clostridium_Cellulolyticum_Geobacter_Cellulose_MFC_Coculture.yaml +++ b/kb/communities/Clostridium_Cellulolyticum_Geobacter_Cellulose_MFC_Coculture.yaml @@ -285,6 +285,55 @@ growth_media: evidence_source: IN_VITRO snippet: from 1 g/L carboxymethyl cellulose explanation: Supports the CMC concentration included in the medium summary. +related_ingredients: +- preferred_term: cellulose + chebi_term: + id: CHEBI:18246 + label: (1->4)-beta-D-glucan + relevance: Central insoluble substrate of the coculture; C. cellulolyticum hydrolyzes and + ferments cellulose, providing the electron donor that ultimately drives anode respiration. + evidence: + - reference: PMID:17695929 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: the conversion of cellulosic biomass to electricity requires a + explanation: Anchors cellulose as the central cellulosic substrate converted by the coculture. +- preferred_term: acetate + chebi_term: + id: CHEBI:30089 + label: acetate + relevance: Major fermentation product of C. cellulolyticum cellulose metabolism and a + cross-fed electron-donor substrate for G. sulfurreducens anode respiration. + evidence: + - reference: PMID:17695929 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Hydrogen, acetate, and ethanol were the main residual metabolites + explanation: Lists acetate among the main residual fermentation metabolites of the binary culture. +- preferred_term: ethanol + chebi_term: + id: CHEBI:16236 + label: ethanol + relevance: Fermentation product of cellulose metabolism by C. cellulolyticum, present as a + residual intermediate in the cellulose-fed coculture. + evidence: + - reference: PMID:17695929 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Hydrogen, acetate, and ethanol were the main residual metabolites + explanation: Lists ethanol among the main residual fermentation metabolites of the binary culture. +- preferred_term: dihydrogen + chebi_term: + id: CHEBI:18276 + label: dihydrogen + relevance: Hydrogen is a primary fermentation product of cellulose catabolism by C. + cellulolyticum and a cross-fed reductant in the coculture's metabolic exchange. + evidence: + - reference: PMID:17695929 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Hydrogen, acetate, and ethanol were the main residual metabolites + explanation: The abstract names hydrogen (dihydrogen) as a main residual fermentation metabolite. external_resources: - name: Exact-system primary publication - cellulose-to-electricity binary MFC coculture repository: OTHER diff --git a/kb/communities/High_Solids_Switchgrass_Methanogenic_Microbiome.yaml b/kb/communities/High_Solids_Switchgrass_Methanogenic_Microbiome.yaml index 1c63e5b6..36fe07f0 100644 --- a/kb/communities/High_Solids_Switchgrass_Methanogenic_Microbiome.yaml +++ b/kb/communities/High_Solids_Switchgrass_Methanogenic_Microbiome.yaml @@ -365,6 +365,45 @@ external_resources: resource_id: doi:10.25345/C5H85T url: https://doi.org/10.25345/C5H85T description: Dataset DOI for raw metaproteomics mass spectra. +related_ingredients: +- preferred_term: lignocellulose + chebi_term: + id: CHEBI:180683 + label: lignocellulose + relevance: Switchgrass lignocellulose is the central substrate the microbiome + deconstructs and utilizes at increasing high-solids loadings. + evidence: + - reference: PMID:35790765 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: lignocellulose at high solids + explanation: Names lignocellulose as the substrate the microbiome deconstructs and + utilizes at high solids, anchoring it as the central feedstock. +- preferred_term: dihydrogen + chebi_term: + id: CHEBI:18276 + label: dihydrogen + relevance: Hydrogen is the key fermentation-derived intermediate consumed by the + hydrogenotrophic methanogenesis pathway that dominates at high solids. + evidence: + - reference: PMID:35790765 + supports: SUPPORT + evidence_source: COMPUTATIONAL + snippet: all hydrogenotrophic methanogenesis pathway enzymes + explanation: Detection of all hydrogenotrophic methanogenesis pathway enzymes anchors + H2 as the central electron-donor intermediate for archaeal methane formation. +- preferred_term: methane + chebi_term: + id: CHEBI:16183 + label: methane + relevance: Methane is the main steady-state product of this methanogenic microbiome. + evidence: + - reference: PMID:35790765 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: The main products observed were methane + explanation: Identifies methane as a main observed reactor product, anchoring it as the + central end-product of the community. metals_present: [] rare_earth_elements_present: [] metal_relevance: NOT_APPLICABLE diff --git a/kb/communities/Methylocaldum_Cupriavidus_Methane_Acetate_Crossfeeding_Coculture.yaml b/kb/communities/Methylocaldum_Cupriavidus_Methane_Acetate_Crossfeeding_Coculture.yaml index 0d5405ae..d0622616 100644 --- a/kb/communities/Methylocaldum_Cupriavidus_Methane_Acetate_Crossfeeding_Coculture.yaml +++ b/kb/communities/Methylocaldum_Cupriavidus_Methane_Acetate_Crossfeeding_Coculture.yaml @@ -267,6 +267,46 @@ external_resources: evidence_source: IN_VITRO snippet: M. marinum S8 excreted acetate explanation: Supports the primary article as the source for this curated community. +related_ingredients: +- preferred_term: methane + chebi_term: + id: CHEBI:16183 + label: methane + relevance: Methane is the sole carbon and energy input oxidized by the methanotroph M. + marinum S8, driving the entire cross-feeding system. + evidence: + - reference: doi:10.1093/bbb/zbab150 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Methane-oxidizing bacteria (methanotrophs) often coexist with methylotrophs that + utilize methanol excreted by methanotrophs + explanation: Anchors methane as the substrate oxidized by methanotrophs such as M. marinum + S8. +- preferred_term: acetate + chebi_term: + id: CHEBI:30089 + label: acetate + relevance: Acetate is the methane-derived intermediate excreted by M. marinum S8 and the + likely cross-fed carbon source supporting the non-methylotrophic partner. + evidence: + - reference: doi:10.1093/bbb/zbab150 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: M. marinum S8 excreted acetate during the exponential growth phase + explanation: Anchors acetate as the compound excreted by M. marinum S8 during growth. +- preferred_term: methanol + chebi_term: + id: CHEBI:17790 + label: methanol + relevance: Methanol is the classical methanotroph-excreted intermediate against which this + system contrasts a methanol-independent, acetate-based cross-feeding route. + evidence: + - reference: doi:10.1093/bbb/zbab150 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: possibly utilizes acetate rather than methanol + explanation: Anchors methanol as the alternative intermediate distinguished from acetate + in this cross-feeding system. metals_present: [] rare_earth_elements_present: [] metal_relevance: NOT_APPLICABLE diff --git a/kb/communities/Rhodopseudomonas_Geobacter_Magnetite_Redox_Coculture.yaml b/kb/communities/Rhodopseudomonas_Geobacter_Magnetite_Redox_Coculture.yaml index 3b22c2ba..f3ca7737 100644 --- a/kb/communities/Rhodopseudomonas_Geobacter_Magnetite_Redox_Coculture.yaml +++ b/kb/communities/Rhodopseudomonas_Geobacter_Magnetite_Redox_Coculture.yaml @@ -328,6 +328,52 @@ external_resources: evidence_source: OTHER snippet: Iron acts as both a source and sink of electrons for microorganisms in the environment explanation: Supports the primary publication context linked by this DOE highlight. +related_ingredients: +- preferred_term: magnetite + chebi_term: + id: CHEBI:46726 + label: magnetite + relevance: > + Magnetite (Fe3O4) nanoparticles are the central shared mineral substrate that + acts as a recyclable electron donor and acceptor, allowing electron exchange + between the phototrophic Fe(II)-oxidizer and the anaerobic Fe(III)-reducer. + evidence: + - reference: PMID:25814583 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: oxidizes magnetite (Fe3O4) nanoparticles using light energy + explanation: Names magnetite (Fe3O4) nanoparticles as the mineral substrate being redox-cycled. + - reference: PMID:25814583 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: effectively rendering magnetite a naturally occurring battery + explanation: Anchors magnetite as the central electron-storage compound of the coculture. +- preferred_term: iron(2+) + chebi_term: + id: CHEBI:29033 + label: iron(2+) + relevance: > + Fe(II) is the reduced iron pool in magnetite that R. palustris TIE-1 oxidizes + phototrophically, serving as the electron-donor side of the shared mineral redox cycle. + evidence: + - reference: doi:10.1126/science.aaa4834 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: phototrophic bacteria can use reduced Fe(II) as an electron donor + explanation: Anchors Fe(II) as the reduced iron pool used as an electron donor by the phototroph. +- preferred_term: iron(3+) + chebi_term: + id: CHEBI:29034 + label: iron(3+) + relevance: > + Fe(III) is the oxidized iron pool in magnetite that G. sulfurreducens reduces + anaerobically, serving as the electron-acceptor side of the shared mineral redox cycle. + evidence: + - reference: doi:10.1126/science.aaa4834 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Some anaerobic bacteria use oxidized Fe(III) as an electron acceptor + explanation: Anchors Fe(III) as the oxidized iron pool used as an electron acceptor by the iron-reducer. metals_present: - IRON rare_earth_elements_present: []