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phagotrophy

traitmech:000628 · CLASS · PROPOSED

A physiological phenotype in which a microbial organism ingests particulate food and assimilates nutrients derived from that food.

Trait evidence (2)

  • DOI:10.1038/ismej.2017.68
    NanoSIMS and bulk IRMS isotope analyses revealed that Ochromonas obtained 84-99% of its carbon and 88-95% of its nitrogen from consumed bacteria.

    PMID:28524870, PMC5563956. This contiguous scientific-abstract quote uses the directly retrieved Europe PMC abstract's ASCII range hyphens; the full-text XML uses en dashes. The maintained resolver verifies the API form but flags the en-dash form as LIKELY_PARAPHRASE solely for that typography difference. Full Introduction, Methods, Results and Discussion were read, and actual Figures 1 and 4 were inspected. Axenic Ochromonas sp. BG-1 cultures received washed heat-killed bacterial prey or labeled inorganic substrates in triplicate light/dark treatments with unlabeled controls. Isotope incorporation and prey-dependent growth support nutritional use, not merely particle uptake. The percentages describe the nutrient source under these conditions, not a universal rate or an exclusively direct organic-carbon assimilation route: bacterial carbon can be respired and refixed, and uncontrolled pH/atmospheric exchange may underestimate inorganic carbon fixation. NanoSIMS and bulk carbon estimates differ. Actual Figures 2, 3 and 5 and supplements were not visually audited; no unique claims from those panels are imported. Heat-killed prey do not demonstrate that the consumer kills living prey.

  • DOI:10.1007/s00248-001-1024-6
    nutrient acquisition for this species in the presence of bacteria was accomplished primarily via ingestion of bacteria.

    Sanders et al. (2001), PMID:12024234. Scientific Abstract and full Introduction, Methods, Results, Discussion and Conclusions were directly read from the author-institution PDF. Actual PDF pages 2 and 7, including Figure 4, were inspected. The study compares axenic and bacterized BG-1 cultures with light, dissolved-organic and nutrient treatments. Live Pasteurella sp. prey in this experiment are distinct from the 2017 heat-killed prey treatment. Population abundance and biovolume are separate readouts; cell division alone need not mean biomass increase. Authors cannot exclude contributions from bacterial trace compounds or nutrient recycling. Fluorescent prey added above ambient prey abundance can inflate grazing estimates, while prey-disappearance estimates omit bacterial growth. No unqualified grazing rate, specific MES assimilation or BG-1 cannibalism claim is imported. This is a separate study of the same strain, not independent taxon replication.

Provenance

Identifier source
TraitMech local identifier
Definition source
DOI:10.1038/ismej.2017.68

Parent traits (1)

kg-microbe context

No kg-microbe node embedding matched this record in the 2026-04-25 deepwalk.

Canonical examples (1)

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

  • Ochromonas sp. BG-1 NCBITaxon:1616673 DOI:10.1038/ismej.2017.68 Strain-qualified BG-1 example: washed heat-killed bacterial prey supported growth and supplied cellular carbon and nitrogen in the 2017 isotope experiments; actual Figures 1 and 4 were inspected. This is not a claim that every Ochromonas isolate has the same trophic dependence. NCBI ESearch and EFetch independently resolve the exact name and identifier on 2026-10-05; NCBI assigns species rank despite the BG-1 name. Natural isolation from a Malaysian freshwater pond after dark organic enrichment, followed by single-cell transfers and antibiotic axenization, is documented in the 2001 primary Methods (DOI:10.1007/s00248-001-1024-6), directly read at https://dornsife.usc.edu/caron/wp-content/uploads/sites/263/2023/11/2001_Sanders_etal_ME.pdf. Antibiotic axenization is not evidence of genetic engineering. Nutrient-source fractions do not identify the complete intracellular assimilation pathway.

Discussions and Knowledge Gaps (2)

Open questions attached to this trait. Seeded by just knowledge-gap-scan and curated; see the corpus-wide index.

Keep particulate nutrition distinct from uptake and carbon-source axes.

CURATION TODO OPEN phagotrophy-nutrition-and-hierarchy-scope · raised by codex · 2026-10-05

Not yet attached to a section of this record — a curator sets attaches_to (e.g. causal_graphs#some_edge) so the gap shows beside the mechanism it concerns.

The class requires nutritional assimilation after ingestion; particle contact, retention or engulfment alone is insufficient. Phagocytosis traitmech:000627 describes membrane-mediated uptake and explicitly leaves nutrition separate. Its existing discussion is not an unresolved exact phagotrophy node. The 2001 Introduction describes carbon, macronutrient and growth-factor benefits of phagotrophy as variable, partly speculative roles across mixotrophs; the 2017 Introduction attributes growth-factor cases to earlier papers not independently audited here. Those statements frame terminology, not new canonical examples. Trophic type METPO:1000631 is locally defined by carbon, energy and electron-donor sources, heterotrophic METPO:1000644 by organic carbon, and mixotrophic METPO:1000652 by dual carbon use. This broader nutrient-acquisition mode does not prescribe a carbon source or require photosynthesis, so retain phenotype METPO:1000059 pending review of a closer nutritional-mode hierarchy. Nutrient adaptation METPO:1000731 concerns nutrient regimes, not specifically particle feeding. Do not equate phagotrophy with phagocytosis, mixotrophy, bacterivory or the bacteria-only predatory-bacterium class. Extracellular digestion without particle ingestion is outside this definition. No unverified synonym or process-level ontology xref is asserted.

Resolve nutrient processing with native functional evidence.

KNOWLEDGE GAP OPEN phagotrophy-assimilation-mechanism-evidence · raised by codex · 2026-10-05

Not yet attached to a section of this record — a curator sets attaches_to (e.g. causal_graphs#some_edge) so the gap shows beside the mechanism it concerns.

Growth and isotope incorporation establish nutritional use without identifying a universal phagosomal digestion or assimilation mechanism. Distinguish prey origin, release of dissolved metabolites, direct organic assimilation and respiration followed by carbon refixation. Isotope mass balance does not by itself separate all these routes. Sequence annotation or differential expression alone would not establish native protein function. Obtain taxon-paired functional evidence and inspect relevant supplements before adding protein accessions or a causal graph.

Curation history

  1. · MINTED_TRAITMECH_ID · codex

    Added phagotrophy as an organism-level particulate-nutrition phenotype with two DOI-backed snippets, primary growth/isotope evidence and a natural BG-1 exemplar. Ignored-and-hidden novelty searches and pinned METPO review found no exact record. Reserved METPO:1058100 in v504. Kept uptake, nutrient sources, carbon-source classification and molecular mechanisms separate; no graph inferred.