diff --git a/kb/communities/Acetylene_Fueled_TCE_Dechlorination_Groundwater_Enrichment.yaml b/kb/communities/Acetylene_Fueled_TCE_Dechlorination_Groundwater_Enrichment.yaml index 7883d02a..c24ead14 100644 --- a/kb/communities/Acetylene_Fueled_TCE_Dechlorination_Groundwater_Enrichment.yaml +++ b/kb/communities/Acetylene_Fueled_TCE_Dechlorination_Groundwater_Enrichment.yaml @@ -160,6 +160,49 @@ environmental_factors: evidence_source: IN_VITRO snippet: TCE and perchloroethene (PCE) reductive dechlorination explanation: Supports the chlorinated electron acceptors. +related_ingredients: +- preferred_term: acetylene + chebi_term: + id: CHEBI:27518 + label: acetylene + relevance: > + Acetylene (C2H2) is supplied as the sole electron donor and organic carbon + source for the enrichment and arises in situ as an abiotic degradation + product of TCE. + evidence: + - reference: PMID:33531396 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: acetylene (C2H2) is a product of abiotic degradation of + explanation: Names acetylene (C2H2) as the substrate central to the + enrichment. +- preferred_term: trichloroethene + chebi_term: + id: CHEBI:16602 + label: trichloroethene + relevance: > + Trichloroethene (TCE) is the chlorinated electron acceptor reductively + dechlorinated by the enrichment community. + evidence: + - reference: PMID:33531396 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: multiple microbial processes including TCE dechlorination + explanation: Names TCE as the substrate undergoing reductive dechlorination. +- preferred_term: tetrachloroethene + chebi_term: + id: CHEBI:17300 + label: tetrachloroethene + relevance: > + Perchloroethene (PCE), i.e. tetrachloroethene, is reductively dechlorinated + by the groundwater enrichment alongside TCE. + evidence: + - reference: PMID:33531396 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: perchloroethene (PCE) reductive dechlorination by a microbial community enriched + explanation: Names perchloroethene (PCE) as a substrate reductively + dechlorinated by the enrichment. growth_media: [] external_resources: - name: Primary publication for the acetylene TCE-dechlorination community diff --git a/kb/communities/Clostridium_Carboxidivorans_Kluyveri_CO_Chain_Elongation_Coculture.yaml b/kb/communities/Clostridium_Carboxidivorans_Kluyveri_CO_Chain_Elongation_Coculture.yaml index 009ff30c..8da675bb 100644 --- a/kb/communities/Clostridium_Carboxidivorans_Kluyveri_CO_Chain_Elongation_Coculture.yaml +++ b/kb/communities/Clostridium_Carboxidivorans_Kluyveri_CO_Chain_Elongation_Coculture.yaml @@ -91,6 +91,99 @@ taxonomy: evidence_source: IN_VITRO snippet: Clostridium kluyveri monocultures in batch operated stirred-tank bioreactors explanation: Supports C. kluyveri as the chain-elongating organism whose CO sensitivity and process role were studied. +related_ingredients: +- preferred_term: carbon monoxide + chebi_term: + id: CHEBI:17245 + label: carbon monoxide + relevance: > + CO is the primary gaseous carbon/energy feedstock fed to the coculture; its + fermentation drives autotrophic growth and the downstream conversion to + longer-chain alcohols. + evidence: + - reference: PMID:37110426 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: 1-Butanol and 1-Hexanol from CO + explanation: Names CO as the gaseous feedstock converted by the synthetic clostridial coculture. +- preferred_term: carbon dioxide + chebi_term: + id: CHEBI:16526 + label: carbon dioxide + relevance: > + CO2 is co-fed with CO in the continuous gassing regime that sustains the + autotrophic acetogenic partner. + evidence: + - reference: PMID:34669248 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: continuous CO/CO2 -gassing + explanation: Names CO2 as part of the continuous gas supply to the coculture. +- preferred_term: acetate + chebi_term: + id: CHEBI:30089 + label: acetate + relevance: > + Acetate is one of the main C2 products of acetogenic syngas fermentation + that feeds the chain-elongation partner. + evidence: + - reference: PMID:34669248 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: produce mainly acetate and + explanation: Names acetate as a primary product of syngas fermentation in this system. +- preferred_term: ethanol + chebi_term: + id: CHEBI:16236 + label: ethanol + relevance: > + Ethanol is a main C2 product of the acetogenic partner and a substrate for + chain elongation by C. kluyveri. + evidence: + - reference: PMID:34669248 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: ethanol efficiently + explanation: Names ethanol as a primary product of syngas fermentation. +- preferred_term: 1-butanol + chebi_term: + id: CHEBI:28885 + label: butan-1-ol + relevance: > + Butanol is a longer-chain alcohol product whose final concentration + increased threefold in coculture relative to C. carboxidivorans monoculture. + evidence: + - reference: PMID:34669248 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: the corresponding alcohols butanol and hexanol + explanation: Names butanol as an alcohol produced by acid reduction in the coculture. +- preferred_term: 1-hexanol + chebi_term: + id: CHEBI:87393 + label: hexan-1-ol + relevance: > + Hexanol is a target medium-chain alcohol whose production was enabled by the + coculture but not the acetogen monoculture. + evidence: + - reference: PMID:34669248 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: the corresponding alcohols butanol and hexanol + explanation: Names hexanol as an alcohol produced by acid reduction in the coculture. +- preferred_term: sulfide + chebi_term: + id: CHEBI:26822 + label: sulfide + relevance: > + Continuous sulfide supply increased autotrophic growth and ethanol formation + by C. carboxidivorans under low-CO conditions in the continuous cascade. + evidence: + - reference: PMID:37110426 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: continuous supply of sulfide led to + explanation: Names sulfide as a supplement improving autotrophic growth and ethanol formation. ecological_interactions: - name: Acetogen-Chain Elongator Product Coupling description: > diff --git a/kb/communities/Lake_Washington_Methane_Oxygen_Methylotroph_Community.yaml b/kb/communities/Lake_Washington_Methane_Oxygen_Methylotroph_Community.yaml index c48389f0..80ab8953 100644 --- a/kb/communities/Lake_Washington_Methane_Oxygen_Methylotroph_Community.yaml +++ b/kb/communities/Lake_Washington_Methane_Oxygen_Methylotroph_Community.yaml @@ -423,6 +423,118 @@ associated_datasets: evidence_source: COMPUTATIONAL snippet: Genome-based metabolic reconstruction highlights metabolic versatility of Methylophilaceae explanation: Links Methylophilaceae genomic evidence to the curated methylotroph guild. +related_ingredients: +- preferred_term: methane + chebi_term: + id: CHEBI:16183 + label: methane + relevance: > + Methane is the selective carbon and energy substrate supplied to the Lake + Washington sediment microcosms and the primary carbon source oxidized by the + methanotrophic members of the methane-cycling community. + evidence: + - reference: PMID:25755930 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: methane supplied to lake sediment microbial + explanation: Methane is the substrate fed to the lake sediment community. + - reference: PMID:32655999 + supports: SUPPORT + evidence_source: COMPUTATIONAL + snippet: oxidize methane as their primary carbon + explanation: Methanotrophs in the modeled community oxidize methane as their primary carbon source. +- preferred_term: dioxygen + chebi_term: + id: CHEBI:15379 + label: dioxygen + relevance: > + Oxygen tension is the controlled environmental variable that structures which + methanotroph and methylotroph genera dominate the methane-fed microcosms. + evidence: + - reference: PMID:25755930 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: different oxygen tensions + explanation: Oxygen was varied across microcosms as a key factor in community composition. +- preferred_term: methanol + chebi_term: + id: CHEBI:17790 + label: methanol + relevance: > + Methanol is a one-carbon intermediate of methylotrophy; Lake Washington + Methylophilaceae ecotypes carry methanol dehydrogenase substrate-oxidation + systems. + evidence: + - reference: PMID:25058595 + supports: SUPPORT + evidence_source: COMPUTATIONAL + snippet: MxaFI-type methanol dehydrogenase + explanation: Methylophilaceae ecotypes possess methanol dehydrogenase oxidation systems. +- preferred_term: formaldehyde + chebi_term: + id: CHEBI:16842 + label: formaldehyde + relevance: > + Formaldehyde is a central one-carbon intermediate whose excretion and transfer + between community members is predicted by the genome-scale community model. + evidence: + - reference: PMID:32655999 + supports: SUPPORT + evidence_source: COMPUTATIONAL + snippet: excretion of formaldehyde + explanation: The community model predicts formaldehyde excretion among community members. +- preferred_term: carbon dioxide + chebi_term: + id: CHEBI:16526 + label: carbon dioxide + relevance: > + Carbon dioxide is a predicted excreted product of the methane-cycling community + in the genome-scale metabolic model. + evidence: + - reference: PMID:32655999 + supports: SUPPORT + evidence_source: COMPUTATIONAL + snippet: and carbon di-oxide in the community + explanation: The community model predicts carbon dioxide excretion (text spells it "carbon di-oxide"). +- preferred_term: methylamine + chebi_term: + id: CHEBI:16830 + label: methylamine + relevance: > + Methylamine is a methylotrophy substrate oxidized by Lake Washington + Methylophilaceae ecotypes, which encode methylamine dehydrogenase. + evidence: + - reference: PMID:25058595 + supports: SUPPORT + evidence_source: COMPUTATIONAL + snippet: methylamine dehydrogenase versus N-methylglutamate pathway + explanation: Methylophilaceae ecotypes possess methylamine dehydrogenase oxidation systems. +- preferred_term: pyruvate + chebi_term: + id: CHEBI:15361 + label: pyruvate + relevance: > + Pyruvate metabolism is one of the internal metabolic pathways that varied + across conditions in the genome-scale community model of the methanotrophs. + evidence: + - reference: PMID:32655999 + supports: SUPPORT + evidence_source: COMPUTATIONAL + snippet: pyruvate metabolism, and the TCA cycle + explanation: Pyruvate metabolism is a modeled pathway shifting across conditions. +- preferred_term: nitrate + chebi_term: + id: CHEBI:17632 + label: nitrate + relevance: > + Nitrate reduction is part of the nitrogen-metabolism versatility of Lake + Washington Methylophilaceae ecotypes, which vary in denitrification potential. + evidence: + - reference: PMID:25058595 + supports: SUPPORT + evidence_source: COMPUTATIONAL + snippet: nitrate reduction + explanation: Methylophilaceae ecotypes differ in assimilatory versus respiratory nitrate reduction. metal_relevance: NOT_APPLICABLE metal_notes: > No metal or rare earth element processing role is curated for this diff --git a/kb/communities/Methylocystis_Rhodococcus_Methane_VFA_PHBV_Coculture.yaml b/kb/communities/Methylocystis_Rhodococcus_Methane_VFA_PHBV_Coculture.yaml index 1b3b8f66..3e91b43a 100644 --- a/kb/communities/Methylocystis_Rhodococcus_Methane_VFA_PHBV_Coculture.yaml +++ b/kb/communities/Methylocystis_Rhodococcus_Methane_VFA_PHBV_Coculture.yaml @@ -210,6 +210,95 @@ growth_media: evidence_source: IN_VITRO snippet: under a CH4:O2 or air atmosphere explanation: Supports the headspace conditions for the PHBV accumulation stage. +related_ingredients: +- preferred_term: poly(3-hydroxybutyrate-co-3-hydroxyvalerate) + relevance: > + PHBV is the target biopolymer produced by the coculture from methane and + volatile fatty acid cosubstrates. + evidence: + - reference: PMID:38516398 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: synthesize poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) + explanation: Names PHBV as the polymer synthesized by the coculture. +- preferred_term: methane + chebi_term: + id: CHEBI:16183 + label: methane + relevance: > + Methane is the primary gaseous feedstock supplied to the methanotroph for + growth and PHBV accumulation. + evidence: + - reference: PMID:38516398 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: previously grown on methane + explanation: Names methane as the growth substrate for the cultures. +- preferred_term: oxygen + chebi_term: + id: CHEBI:15379 + label: dioxygen + relevance: > + Oxygen is supplied as part of the CH4:O2 headspace used for methanotrophic + growth and the PHBV accumulation tests. + evidence: + - reference: PMID:38516398 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: under a CH4:O2 + explanation: Names oxygen (O2) as a component of the CH4:O2 atmosphere. +- preferred_term: valeric acid + chebi_term: + id: CHEBI:17418 + label: valeric acid + relevance: > + Valeric acid was supplied alone as a cosubstrate and promoted PHBV + accumulation in the coculture. + evidence: + - reference: PMID:38516398 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: enriched with valeric acid + explanation: Names valeric acid as a medium cosubstrate. +- preferred_term: acetic acid + chebi_term: + id: CHEBI:15366 + label: acetic acid + relevance: > + Acetic acid was a component of the mixed VFA cosubstrate fed to the + coculture for PHBV accumulation. + evidence: + - reference: PMID:38516398 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: acetic, propionic, butyric, and valeric acids + explanation: Names acetic acid in the mixed VFA cosubstrate. +- preferred_term: propionic acid + chebi_term: + id: CHEBI:30768 + label: propionic acid + relevance: > + Propionic acid was a component of the mixed VFA cosubstrate fed to the + coculture for PHBV accumulation. + evidence: + - reference: PMID:38516398 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: acetic, propionic, butyric, and valeric acids + explanation: Names propionic acid in the mixed VFA cosubstrate. +- preferred_term: butyric acid + chebi_term: + id: CHEBI:30772 + label: butyric acid + relevance: > + Butyric acid was a component of the mixed VFA cosubstrate fed to the + coculture for PHBV accumulation. + evidence: + - reference: PMID:38516398 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: acetic, propionic, butyric, and valeric acids + explanation: Names butyric acid in the mixed VFA cosubstrate. external_resources: - name: Exact-system PHBV primary publication repository: OTHER diff --git a/kb/communities/Naica_Deep_Subsurface_Thermophilic.yaml b/kb/communities/Naica_Deep_Subsurface_Thermophilic.yaml index 70a541a4..f55ae68e 100644 --- a/kb/communities/Naica_Deep_Subsurface_Thermophilic.yaml +++ b/kb/communities/Naica_Deep_Subsurface_Thermophilic.yaml @@ -563,6 +563,36 @@ environmental_factors: snippet: The "Cave of Crystals" (aka 'Naica') in Chihuahua Mexico is a natural unique subterranean ecosystem which mainly consists of crystals made of calcium sulfate explanation: Highlights astrobiology significance +related_ingredients: +- preferred_term: calcium sulfate + chebi_term: + id: CHEBI:31346 + label: calcium sulfate + relevance: > + The Naica crystal cave system is composed of giant selenite crystals made of + calcium sulfate, which defines the mineralogical matrix of this deep-subsurface + thermophilic habitat. + evidence: + - reference: PMID:23640690 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: subterranean ecosystem which mainly consists of crystals made of calcium + sulfate + explanation: Reference names calcium sulfate as the crystal-forming mineral of the Naica cave. +- preferred_term: gypsum + chebi_term: + id: CHEBI:48838 + label: gypsum + relevance: > + The giant Naica crystals are gypsum (calcium sulfate dihydrate), formed in + cavities filled by low-salinity hydrothermal water and potentially trapping + microorganisms in fluid inclusions. + evidence: + - reference: doi:10.3389/fmicb.2013.00037 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: The Naica Mine in northern Mexico is famous for its giant gypsum crystals + explanation: Reference names gypsum as the crystal-forming mineral of the Naica system. metals_present: - IRON metal_relevance: SIGNIFICANT diff --git a/kb/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml b/kb/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml index 75e732e8..4d708373 100644 --- a/kb/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml +++ b/kb/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml @@ -212,3 +212,55 @@ rare_earth_elements_present: [] metal_relevance: NOT_APPLICABLE metal_notes: No metal or rare earth element processing role is curated for this thiocyanate bioremediation community. +related_ingredients: +- preferred_term: thiocyanate + chebi_term: + id: CHEBI:18022 + label: thiocyanate + relevance: > + Thiocyanate (SCN-) is the primary contaminant substrate driving selection in + this bioreactor community and is degraded by the dominant strains. + evidence: + - reference: PMID:33897653 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Thiocyanate (SCN-) contamination threatens aquatic ecosystems + explanation: Names thiocyanate as the contaminant substrate of the community. +- preferred_term: cyanate + chebi_term: + id: CHEBI:29195 + label: cyanate + relevance: > + Cyanate is the intermediate product released during SCN- breakdown and is + further degraded by cyanate hydratase. + evidence: + - reference: PMID:33897653 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: degrade product cyanate to ammonia and CO2 via cyanate + explanation: Names cyanate as the intermediate degraded via cyanate hydratase. +- preferred_term: ammonia + chebi_term: + id: CHEBI:16134 + label: ammonia + relevance: > + Ammonia is a product of cyanate degradation by the Afipia variant. + evidence: + - reference: PMID:33897653 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: degrade product cyanate to ammonia and CO2 via cyanate + explanation: Names ammonia as a product of cyanate degradation. +- preferred_term: carbon dioxide + chebi_term: + id: CHEBI:16526 + label: carbon dioxide + relevance: > + Carbon dioxide is produced from cyanate degradation and subsequently fixed + by the autotrophic Afipia variant via the Calvin-Benson-Bassham cycle. + evidence: + - reference: PMID:33897653 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: degrade product cyanate to ammonia and CO2 via cyanate + explanation: Names CO2 as a product of cyanate degradation. diff --git a/kb/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml b/kb/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml index 5648f44d..7f091617 100644 --- a/kb/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml +++ b/kb/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml @@ -272,6 +272,21 @@ associated_datasets: evidence_source: IN_VITRO snippet: Tunable population dynamics in a synthetic filamentous coculture explanation: Lists the primary publication for this exact synthetic filamentous coculture. +related_ingredients: +- preferred_term: cellulose + chebi_term: + id: CHEBI:18246 + label: (1->4)-beta-D-glucan + relevance: > + alpha-Cellulose was supplied as the sole carbon source, forcing the + noncellulolytic S. coelicolor to depend on hydrolysate sugars released by + T. reesei cellulases acting on the cellulose substrate. + evidence: + - reference: PMID:36314761 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: α-cellulose as a carbon source + explanation: Names cellulose as the designed carbon source for the coculture. metal_relevance: NOT_APPLICABLE metal_notes: > No metal or rare earth element processing role is curated for this diff --git a/kb/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml b/kb/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml index b10abbd3..a80dad8d 100644 --- a/kb/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml +++ b/kb/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml @@ -9,6 +9,35 @@ description: > increase for both organisms, supporting the bidirectional vitamin-dependent mutualism predicted from metagenome-informed abundance correlation networks of mine-tailings-derived consortia grown under dozens of conditions. +related_ingredients: +- preferred_term: thiamine + chebi_term: + id: CHEBI:18385 + label: thiamine(1+) + relevance: > + Thiamine (vitamin B1) is the vitamin produced at high levels by the + Variovorax hub and cross-fed to correlated thiamine auxotrophs, anchoring + one direction of the validated vitamin mutualism. + evidence: + - reference: PMID:37553333 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: high levels of thiamine production, up to 100 mg/L + explanation: Quantifies thiamine production by Variovorax in minimal media. +- preferred_term: pantothenate + chebi_term: + id: CHEBI:7916 + label: pantothenic acid + relevance: > + Pantothenate (vitamin B5) is the B-vitamin produced by the Cryptococcus + yeast and required for growth of Variovorax, supplying the reciprocal + direction of the bidirectional vitamin cross-feeding mutualism. + evidence: + - reference: PMID:37553333 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: the B-vitamin pantothenate + explanation: Names pantothenate as the B-vitamin produced by the Cryptococcus yeast. ecological_state: ENGINEERED community_origin: SYNTHETIC community_category: BIOTECHNOLOGY