trophic type

Edge evidence

• carbon source utilization causes trophic type biolink:causes

  Carbon-source utilization defines the auto/heterotrophy axis of the trophic classification.

  • DOI:10.1146/annurev.micro.61.080706.093130 carbon source Supports carbon-source utilization as a primary trophic-type axis.
• energy source utilization causes trophic type biolink:causes

  Energy-source utilization defines the photo/chemotrophy axis of the trophic classification.

  • DOI:10.1146/annurev.micro.61.080706.093130 energy source Supports energy-source utilization as a primary trophic-type axis.
• electron donor utilization causes trophic type biolink:causes

  Electron-donor utilization defines the litho/organotrophy axis of the trophic classification.

  • DOI:10.1146/annurev.micro.61.080706.093130 electron donor Supports electron-donor utilization as a primary trophic-type axis.
• encoded metabolic pathways realizes trophic type

  The genome-encoded set of carbon-fixation, energy-conserving, and electron-transfer pathways realizes the organism's trophic type.

  • DOI:10.1073/pnas.0903507106 molecular mechanisms of adaptation Supports genome-encoded pathway repertoires as the proximate determinant of trophic phenotypes.
• autotrophic is a trophic type rdfs:subClassOf

  Autotrophy is a child phenotype of trophic type.

  • DOI:10.1146/annurev.micro.61.080706.093130 carbon source Supports autotrophy as one carbon-source-defined trophic phenotype.
• heterotrophic is a trophic type rdfs:subClassOf

  Heterotrophy is a child phenotype of trophic type.

  • DOI:10.1146/annurev.micro.61.080706.093130 carbon source Supports heterotrophy as one carbon-source-defined trophic phenotype.
• phototrophic is a trophic type rdfs:subClassOf

  Phototrophy is a child phenotype of trophic type.

  • DOI:10.1146/annurev.micro.61.080706.093130 energy source Supports phototrophy as one energy-source-defined trophic phenotype.
• chemotrophic is a trophic type rdfs:subClassOf

  Chemotrophy is a child phenotype of trophic type.

  • DOI:10.1146/annurev.micro.61.080706.093130 energy source Supports chemotrophy as one energy-source-defined trophic phenotype.
• Calvin-Benson-Bassham cycle (RuBisCO) enables CO2 fixation RO:0002327

  Form II RuBisCO and a full Calvin-Benson-Bassham cycle enable CO2 fixation, marking autotrophic carbon-assimilation potential.

  • DOI:10.1128/AEM.00599-24 All MAGs encode Form II RuBisCO (rbcL/cbbM) and a full CBB cycle, indicating CO2 fixation potential.
• CO2 fixation causes carbon source utilization biolink:causes

  CO2 fixation establishes inorganic-carbon (autotrophic) use on the carbon-source axis of trophic type.

  • DOI:10.1128/AEM.00599-24 CBB-driven CO2 fixation defines autotrophic carbon assimilation on the carbon-source classification axis.
• SOX sulfur/thiosulfate oxidation causes electron donor utilization biolink:causes

  SOX-mediated thiosulfate/sulfur oxidation supplies inorganic electron donors, defining lithotrophy on the electron-donor axis.

  • DOI:10.1128/AEM.00599-24 Presence of soxABXYZ (and soxCD) is tied to thiosulfate oxidation, enabling use of sulfur species as electron donors.
• sugar/polysaccharide uptake and CAZyme catabolism causes carbon source utilization biolink:causes

  Sugar transporters and CAZyme catabolism enable heterotrophic/organotrophic use of organic carbon on the carbon-source axis.

  • DOI:10.1128/AEM.00599-24 Sugar transporters (gtsABC, frcABC), maltodextrin import/degradation and CAZy enzymes indicate capacity for heterotrophic use of sugars and polysaccharides.
• [NiFe]-hydrogenase H2 oxidation causes electron donor utilization biolink:causes

  [NiFe]-hydrogenase H2 oxidation supplies an inorganic electron donor, contributing hydrogen lithotrophy to the electron-donor axis.

  • DOI:10.1128/mSystems.00148-24 Hydrogenase genes link hydrogen-based lithotrophy to chemoautotrophic metabolism.