TraitMech

TraitMech › PHYSIOLOGY

autotrophic

METPO:1000632 · CLASS · REVIEWED

A trophic type in which an organism produces organic compounds from inorganic carbon sources (primarily carbon dioxide or bicarbonate) using energy from light (photoautotrophy) or from the oxidation of inorganic compounds (chemoautotrophy).

Trait evidence (3)

  • DOI:10.1038/nrmicro.2016.130
    require only CO2 as a carbon source

    Review defines autotrophic organisms by CO2 use as carbon source for growth.

  • DOI:10.1128/AEM.02473-10
    autotrophic CO2 fixation

    Minireview supports Calvin-Benson and other microbial CO2-fixation pathways.

  • PMID:8590279
    Synechocystis sp. strain PCC6803

    Organism example: Synechocystis sp. PCC 6803 is a model autotrophic cyanobacterium that fixes CO2 via the Calvin-Benson cycle (Kaneko et al. 1996, DNA Res, full genome).

Autotrophic inorganic carbon fixation

DOI-backed graph linking inorganic carbon, energy and reductant supply, CO2-fixation pathways, carboxylating enzymes, precursor metabolites, and biomass.

MECHANISTIC · This cross-pathway graph represents alternative autotrophic carbon-fixation mechanisms rather than a claim that one organism carries the Calvin-Benson and Wood-Ljungdahl pathways together. The C. necator H16 example anchors the RuBisCO branch.

Autotrophic inorganic carbon fixation Interactive directed graph showing evidence-backed causal relationships for autotrophic.

Edge evidence

  • autotrophic has carbon source carbon dioxide METPO:2007806

    Autotrophs use CO2 as an inorganic carbon source.

  • bicarbonate alternative inorganic carbon source for autotrophic

    Bicarbonate is another inorganic carbon species available for autotrophic fixation.

    • DOI:10.1128/AEM.02473-10 autotrophic carbon dioxide assimilation pathway Supports inorganic carbon assimilation by autotrophic pathways.
  • energy and reductant regulates CO2-fixation pathway RO:0002211

    Autotrophic carbon fixation requires energy and reducing power.

    • DOI:10.1038/nrmicro2365 energy demand of the autotrophic pathways Supports energy requirements of autotrophic carbon fixation pathways.
  • carbon dioxide fixed by CO2-fixation pathway METPO:2007404

    CO2 is converted into organic carbon by autotrophic fixation pathways.

  • Calvin-Benson cycle example of CO2-fixation pathway rdfs:subClassOf

    The Calvin-Benson cycle is a major autotrophic CO2-fixation pathway.

    • DOI:10.1128/AEM.02473-10 Calvin-Benson reductive pentose phosphate cycle Supports the Calvin-Benson cycle as a microbial autotrophic pathway.
  • RuBisCO catalyzes Calvin-Benson cycle biolink:catalyzes

    RuBisCO is the key carboxylating enzyme of the Calvin-Benson cycle.

    • DOI:10.1128/AEM.02473-10 ribulose-1,5-bisphosphate carboxylase Supports RuBisCO as the marker enzyme for Calvin-Benson autotrophy.
  • CO2-fixation pathway has output precursor metabolites RO:0002234

    Fixed carbon is converted into central biosynthetic precursors.

    • DOI:10.1128/AEM.02473-10 converted to other central intermediates Supports conversion of fixed carbon into central metabolites.
  • precursor metabolites incorporated into biomass biolink:part_of

    Fixed-carbon precursors are incorporated into cellular biomass.

  • environmental pH determines speciation of dissolved inorganic carbon

    pH sets the relative abundance of CO2, bicarbonate, and carbonate available for fixation.

    • DOI:10.1128/aem.01557-23 CO2 predominates below ~pH 6.4, HCO3- at circumneutral pH, and CO32- above ~pH 10.3; DIC form availability constrains the fixation route.
  • carbon-concentrating mechanism supplies substrate to CO2-fixation pathway

    CCMs elevate intracellular CO2 to enhance autotrophic carbon fixation.

    • DOI:10.1128/aem.01557-23 Transporters and CO2-active systems generate elevated intracellular HCO3- delivered for carboxysomal CO2 fixation.
  • carboxysome contains RuBisCO

    Carboxysomes encapsulate RuBisCO to concentrate CO2 around the carboxylating enzyme.

    • DOI:10.1111/ppl.14140 Carboxysomes are protein shell encapsulated ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO).
  • carboxysome contains carbonic anhydrase

    Carboxysomes house carbonic anhydrase alongside RuBisCO.

  • carbonic anhydrase converts carbon dioxide

    Carbonic anhydrase converts bicarbonate to CO2 for RuBisCO fixation.

    • DOI:10.1128/aem.01075-24 When cytoplasmic HCO3- enters carboxysomes, CA converts it to CO2, which is fixed by RuBisCO.
  • Wood-Ljungdahl pathway example of CO2-fixation pathway rdfs:subClassOf

    The Wood-Ljungdahl pathway is an autotrophic CO2-fixation pathway producing acetyl-CoA.

    • DOI:10.1039/D4CB00099D Two CO2 molecules are fixed to acetyl-CoA via the WLP, requiring one ATP and eight electrons.
  • Wood-Ljungdahl pathway has output acetyl-CoA RO:0002234

    The Wood-Ljungdahl pathway yields acetyl-CoA from fixed CO2.

  • CO dehydrogenase/acetyl-CoA synthase (CODH/ACS) catalyzes Wood-Ljungdahl pathway biolink:catalyzes

    CODH/ACS catalyzes the terminal acetyl-CoA-forming step of the Wood-Ljungdahl pathway.

  • molecular hydrogen provides reductant for Wood-Ljungdahl pathway

    H2 supplies reducing equivalents driving CO2 reduction in the Wood-Ljungdahl pathway.

    • DOI:10.1039/D4CB00099D H2 or CO must be utilized as an energy source to provide reducing equivalents for full CO2 reduction.
  • dissolved inorganic carbon participates in CO2-fixation pathway biolink:participates_in

    The environmental dissolved-inorganic-carbon pool supplies substrate to autotrophic carbon-fixation pathways.

    • DOI:10.1128/aem.01557-23 DIC transporters and carbonic anhydrase enzymes (CA) to facilitate DIC fixation Verified against the open Applied and Environmental Microbiology article.

Protein and taxon examples

Graph nodeProteinTaxonUniProt statusRole and evidence
RuBisCO UniProtKB:P42721
Ribulose bisphosphate carboxylase large chain, plasmid (cbbL2) 		Cupriavidus necator H16
NCBITaxon:381666 		REVIEWED
retrieved 2026-08-24 · entry v153 · sequence v3

Large-chain component of the plasmid-encoded RuBisCO in one of the two active CBB operons of C. necator H16.

  • DOI:10.1186/s12934-020-01494-y both CBB operons were active and contributed almost equally to the carbon fixation process The strain-level perturbation study supports activity of both H16 CBB operons; UniProtKB P42721 identifies the reviewed plasmid cbbL2 large chain in that strain.

Provenance

Identifier source
METPO (2026-06-12)
Author
Jed Dongjin Kim-Ozaeta
Definition source
DOI:10.1038/nrmicro.2016.130

Parent traits (1)

Synonyms (3)

  • TT_autotroph RELATED_SYNONYM · metpo.owl
  • autotroph RELATED_SYNONYM · metpo.owl
  • autotrophy RELATED_SYNONYM · metpo.owl

kg-microbe context

Matched 1 kg-microbe node via direct_metpo.

  • METPO:1000632 [-2.568, +0.105, -3.476, -0.957, …]

512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

Nearest neighbors in embedding space

Top-8 cosine-similar METPO traits from the 2026-04-25 deepwalk (512-D).

Deep research

Generated by just research-trait; source: research/traits/physiology/autotrophic-deep-research-falcon.md

Unreviewed literature output — not curated TraitMech content Ontology identifiers suggested below have not been resolved against their ontologies, and some are known to be wrong. Check any CURIE against the source before using it. 
# Curation report: microbial trait **autotrophic**

## 1. Trait record and scope

- **Trait label:** autotrophic
- **Trait identifier:** **METPO:1000632**
- **Category / kind / status:** PHYSIOLOGY / CLASS / REVIEWED
- **Parent:** METPO:1000631
- **Synonyms:** TT_autotroph; autotroph; autotrophy

### Operational definition

For TraitMech, **autotrophic** should denote an organism-level physiological capacity to grow while obtaining biomass carbon from inorganic carbon—principally CO₂ or HCO₃⁻—with energy and reducing power supplied by either light (**photoautotrophy**) or oxidation/uptake of inorganic electron donors (**chemolithoautotrophy**). Claassens et al. explicitly define autotrophs as organisms requiring “only CO₂ as a carbon source for growth” and state that microbial autotrophs derive energy from light or inorganic electron donors. Thus, the terminal phenotype should be **growth/biomass production from inorganic carbon**, not merely expression of a carboxylase or detectable CO₂ incorporation. (claassens2016harnessingthepower pages 1-2)

The supplied definition is therefore current and suitable, with one practical refinement: assays may provide HCO₃⁻ rather than gaseous CO₂, and a valid demonstration should show that inorganic carbon supplies essentially all net biomass carbon under the tested condition.

### Boundary cases

1. **Carbon fixation is not equivalent to autotrophy.** Heterotrophs routinely incorporate inorganic carbon through anaplerotic and biosynthetic carboxylation. Estimated inorganic-carbon contributions are commonly 1–8% of heterotrophic microbial biomass; the broader review estimates at least 1–5%, and as much as 50% in methanotrophs. Such incorporation must not be curated as autotrophy without inorganic-carbon-supported growth. (braun2021reviewsandsyntheses pages 1-2)
2. **Mixotrophy is distinct.** Concurrent use of organic and inorganic carbon is mixotrophy, even when an autotrophic fixation pathway operates. A strain capable of both modes may receive the autotrophic trait only when growth is demonstrated under an inorganic-carbon-only condition. (claassens2016harnessingthepower pages 1-2)
3. **Photoautotrophy and chemolithoautotrophy are child mechanisms, not synonyms for the entire trait.** Phototrophy describes energy acquisition and does not by itself establish the carbon source; similarly, oxidation of H₂, sulfur, Fe²⁺, NH₃, or extracellular minerals does not establish autotrophy unless coupled to net inorganic-carbon assimilation.
4. **Genomic potential is weaker than phenotype.** A MAG containing Rubisco, CODH/ACS, or another pathway should support a candidate mechanism or “autotrophic potential,” not a definitive organismal trait, unless expression, isotope incorporation, or growth data are available. The 2024 deep-aquifer study, for example, reports genes for autotrophic pathways in 60% of MAGs but properly interprets these as chemosynthetic capacity. (atencio2024metabolicadaptationsunderpin pages 1-2)
5. **Methanotrophy and methylotrophy are generally not autotrophy.** CH₄ and methanol are organic C₁ carbon sources. Auxiliary CO₂ assimilation does not change that classification.
6. **Carbon-concentrating mechanisms are enabling modules, not universal requirements.** Carboxysomes are central to cyanobacterial and some bacterial CBB systems, but autotrophs using Wood–Ljungdahl, rTCA, 3HP, or archaeal cycles need not possess them. (pulsford2024cyanobacterialαcarboxysomecarbonic pages 1-2)

## 2. Candidate graph nodes

Only identifiers that can be stated confidently are proposed. Label-only nodes should remain ungrounded until checked against the project’s preferred ontology release.

### A. Trait and biological-process nodes

| Candidate node | Suggested grounding | Curation role |
|---|---|---|
| autotrophic | **METPO:1000632** | Terminal phenotype |
| carbon fixation | GO:0015977 | General inorganic-carbon assimilation process |
| Calvin–Benson–Bassham cycle | label-only; verify MetaCyc/KEGG pathway identifier | Dominant cyclic fixation module |
| Wood–Ljungdahl pathway / reductive acetyl-CoA pathway | label-only; verify MetaCyc identifier | Linear anaerobic fixation module |
| reductive TCA cycle | label-only | Fixation module |
| 3-hydroxypropionate bicycle | label-only | Fixation module |
| 3-hydroxypropionate/4-hydroxybutyrate cycle | label-only | Archaeal fixation module |
| dicarboxylate/4-hydroxybutyrate cycle | label-only | Archaeal fixation module |
| reductive glycine pathway | label-only | Natural/synthetic C₁ assimilation candidate |
| cyanobacterial carbon-concentrating mechanism (CCM) | label-only | Carbon acquisition and concentration module |
| oxygenic photosynthesis | GO term should be release-verified | Light-energy module |
| extracellular electron uptake | label-only | Alternative electron-acquisition module |

A recent review lists CBB, Wood–Ljungdahl, rTCA, 3HP, 3HP/4HB, DC/4HB, reductive glycine, and reverse oxidative TCA mechanisms, but pathway counts and whether the last two qualify as established natural *autotrophic growth* cycles vary among reviews. The safest core graph should begin with the six canonical pathways and add newer routes only with organism-level growth evidence. (li2024processstudyon pages 1-2, li2024productionofsuccinate pages 1-2)

### B. Chemicals, energy sources, and environmental nodes

| Candidate node | Suggested grounding | Role |
|---|---|---|
| carbon dioxide | CHEBI:16526 | Inorganic carbon substrate |
| hydrogencarbonate/bicarbonate | CHEBI:17544 | Inorganic carbon substrate and CCM pool |
| dioxygen | CHEBI:15379 | Photosynthetic product, Rubisco competitor, electron acceptor, and pathway constraint |
| water | CHEBI:15377 | Oxygenic photosynthesis/CA substrate |
| ATP | CHEBI:15422 | Energy currency for fixation and transport |
| NADPH | CHEBI:16474 | Reducing power for CBB and biosynthesis |
| molecular hydrogen | CHEBI identifier should be release-verified | Common chemolithotrophic electron donor |
| reduced sulfur compounds; Fe²⁺; ammonia; nitrite; phosphite | label-only pending exact species | Taxon-specific inorganic electron donors |

Showing the first 60 of 246 lines of findings; the linked file also carries the run's front matter and the prompt it was given — read the full report.

Canonical examples (3)

Organisms cited as exemplars of this trait. Taxon ids are NCBITaxon and link out to the NCBI record.

Curation history

  1. · SEEDED_FROM_METPO · seed_from_metpo

    imported from data/raw/metpo.owl (CLASS)

  2. · ADDED_CAUSAL_GRAPH · codex

    Added DOI-backed causal graph for inorganic carbon fixation, Calvin-Benson cycle, RuBisCO, precursor metabolites, and biomass formation.

  3. · ADDED_ORGANISM_EXAMPLE · claude

    Added Synechocystis sp. PCC 6803 organism example with PMID-backed evidence.

  4. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000006×1, METPO:2000202×1).

  5. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:catalyzes×1).

  6. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (rdfs:subClassOf×1).

  7. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007404×1).

  8. · RENAME_PREDICATE_LABELS · claude

    Renamed 1 causal-edge predicate label(s) to align with existing groundings: drives → regulates ×1.

  9. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211×1).

  10. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0019253×1).

  11. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007501×1).

  12. · RETYPE_CAUSAL_NODES · claude

    Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum semantics: biomass: BIOLOGICAL_PROCESS → CHEMICAL ×1.

  13. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0015977×1).

  14. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A075WF79×1).

  15. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:part_of×1).

  16. · ENRICH_CAUSAL_GRAPH · claude

    Added 9 evidence-backed generic edges (9 new nodes) from the deep-research report.

  17. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (rdfs:subClassOf×1, METPO:2000202×1, biolink:catalyzes×1).

  18. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0030634×1).

  19. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0031470×1).

  20. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A009PMS8×1).

  21. · RETRACT_DEAD_UNIPROT_GROUNDINGS · claude

    Retracted 2 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)

  22. · GROUND_CAUSAL_NODES · claude

    Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (InterPro:IPR033966×1, InterPro:IPR001765×1).

  23. · MIGRATE_MICROBE_DOMAIN_EDGES · claude

    Re-grounded 3 causal edge(s) off microbe-domain METPO predicates (1 to has carbon source, 2 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.

  24. · REVIEWED_CAUSAL_GRAPH_PROTEIN_TAXON · codex

    Marked the graph mechanistic, documented the alternative-pathway scope, reviewed the composite CODH/ACS node as label-only, upgraded canonical citations to DOI references, and added a reviewed C. necator H16 cbbL2 protein example.

  25. · CONNECT_CAUSAL_GRAPH_COMPONENTS · codex

    Resolved issue #183 graph fragmentation (2 components to 1) with 1 public-source, verbatim-snippet-backed connector(s). No paid research service was called.