chemoautolithotrophic

Deep research

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

# Curation report: chemoautolithotrophic

**Trait:** chemoautolithotrophic  
**Identifier:** `METPO:1000634`  
**Category/kind/status:** PHYSIOLOGY / CLASS / REVIEWED

## 1. Scope and current interpretation

`METPO:1000634` denotes a trophic phenotype in which chemical oxidation of an inorganic electron donor supplies energy and reductant, while CO2 or HCO3− supplies the principal carbon incorporated into biomass. “Chemolithoautotrophic” is the more common literature spelling; “chemoautolithotrophic” and “chemoautolithotroph” are defensible ontology labels/synonyms. Recent authors operationalize the phenotype through growth with an inorganic donor plus inorganic carbon, donor consumption/product formation, and preferably ^13CO2/^13C-bicarbonate incorporation—not merely by finding marker genes. For example, a 2023 hydrothermal study measured active fixation using ^13C-NaHCO3 across 30–65°C incubations, while a 2024 Sulfurospirillum study combined culture phenotype with hydrogenase, Sox, and rTCA genes. (wang2024novelisolatesof pages 12-15, deng2023strategiesofchemolithoautotrophs pages 1-2)

A minimal causal abstraction is:

**inorganic electron donor oxidation → electron transfer/energy conservation → ATP and reducing equivalents → inorganic-carbon fixation → biomass synthesis.**

This abstraction should be the graph’s conserved core. Donor-specific oxidation systems, terminal acceptors, electron-transfer chains, and carbon-fixation pathways should be represented as alternative, taxon-qualified modules rather than asserted as universal.

### Boundary cases

- **Photolithoautotrophy:** also uses inorganic donors and inorganic carbon, but light—not chemical oxidation—is the primary energy source. Exclude from this trait.
- **Chemoorganoheterotrophy:** both electrons/energy and carbon are obtained mainly from organic compounds. Exclude.
- **Chemolithoheterotrophy:** inorganic oxidation supplies energy, but organic carbon is required or predominant. Do not infer `METPO:1000634` from lithotrophy alone.
- **Chemoorganoautotrophy:** inorganic carbon is fixed, but an organic compound supplies the relevant electrons/energy. It satisfies autotrophy but not lithotrophy.
- **Mixotrophy:** simultaneous or conditional use of inorganic and organic carbon. It may coexist with a chemolithoautotrophic capacity, but environmental activity should not automatically be annotated as strict chemolithoautotrophy. In sulfur-stimulated groundwater, active mixotrophs—not strict autotrophs—were most abundant and replaced 43% and 80% of microbial carbon with ^13C after 21 and 70 days, respectively. (taubert2022bolsteringfitnessvia pages 6-7)
- **Electroautotrophy:** electrode electrons plus CO2 fixation are mechanistically adjacent but the electrode is not conventionally an inorganic chemical compound. A 2024 comparison found distinct extracellular-electron-uptake phenotypes and 493 differentially expressed genes relative to Fe2+-based chemoautotrophy. Treat electroautotrophy as a sibling or experimental variant, not an unqualified instance of `METPO:1000634`. (wang2024characterizethegrowth pages 22-23, wang2024characterizethegrowth pages 1-2)
- **Methanotrophy:** CH4 is commonly classified as an organic one-carbon compound; therefore methane oxidation plus CO2 assimilation should not be used as a clean lithotrophy example despite occasional broad “reduced compound” terminology.
- **Genomic potential:** genes such as `rbcL`, `aclAB`, `sox`, or hydrogenases establish potential, not the complete phenotype. Curate the trait most strongly when growth, donor oxidation, and inorganic-carbon assimilation are jointly demonstrated.

## 2. Candidate causal-graph nodes

### Trait and phenotype nodes

- `METPO:1000634` — chemoautolithotrophic.
- Chemoautolithotrophic growth; autotrophic biomass production; dark CO2 fixation.
- Growth with inorganic donor and CO2/HCO3− as principal or sole carbon source.
- Experimental readouts: growth yield/doubling, donor depletion, oxidized product accumulation, O2 or nitrate consumption, Rubisco activity, and ^13CO2/^13C-HCO3− incorporation.

### Environmental and experimental factors

- Availability and concentration of H2, NH3/NH4+, NO2−, H2S/HS−, elemental sulfur, thiosulfate, Fe2+, CO, or phosphite.
- CO2/HCO3− concentration; organic-carbon exclusion or limitation.
- O2, nitrate/nitrite, sulfate, CO2, or other taxon-specific terminal electron acceptors.
- Redox potential, pH, temperature, salinity, donor/acceptor gradients, and trace metals.
- Microoxic conditions and oxic–anoxic interfaces, hydrothermal vents, serpentinizing systems, groundwater, mine drainage, sediments, biofilms, and engineered reactors.
- Acid stress and temperature are modifiers, not defining conditions. Campylobacterales fixed carbon at pH 5.6 and 2.2 at 30–45°C, whereas Nautiliales fixation increased from 45 to 65°C under moderately acidic conditions. (deng2023strategiesofchemolithoautotrophs pages 1-2)

### Chemicals and metabolites

Confidently groundable examples include carbon dioxide (`CHEBI:16526`) and molecular hydrogen (`CHEBI:18276`). Other candidate chemicals should be mapped by an ontology lookup during YAML preparation rather than assigning identifiers from memory: bicarbonate, ammonia/ammonium, nitrite, nitrate, sulfide/hydrogen sulfide, elemental sulfur, thiosulfate, sulfate, Fe2+/Fe3+, phosphite/phosphate, O2, NADH/NADPH, quinones, reduced/oxidized ferredoxin, ATP/ADP, acetyl-CoA, pyruvate, and 2-oxoglutarate.

### Donor-oxidation proteins and modules

- Uptake [NiFe]-hydrogenases and associated electron-transfer proteins.
- Ammonia monooxygenase (AMO), hydroxylamine oxidation machinery, and nitrite oxidoreductase (NXR)—important nitrifier modules, but not evidenced sufficiently in the retrieved excerpts for edge-level curation here.
- Sox multienzyme system (`soxABCDYZ`), sulfide:quinone oxidoreductase (SQR), flavocytochrome c sulfide dehydrogenase, and reverse dissimilatory sulfite oxidation modules.
- Cyc2, rusticyanin (Rus), Cyc1, quinones, and terminal oxidases in *Acidithiobacillus ferrooxidans* iron oxidation.
- Carbon monoxide dehydrogenase for CO oxidation; phosphite dehydrogenase for phosphite oxidation.
- Rnf complex, NADH:quinone oxidoreductase, cytochromes, quinones, ferredoxins, proton-translocating complexes, and F-type or A/V-type ATP synthases.

### Carbon acquisition and fixation modules

Showing the first 60 of 185 lines of findings; the linked file also carries the run's front matter and the prompt it was given — read the full report.