TraitMech

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phagocytosis

traitmech:000627 · CLASS · PROPOSED

A physiological phenotype in which a microbial cell engulfs extracellular particles by enclosing them within its membrane and internalizes them into membrane-bound compartments.

Trait evidence (2)

  • DOI:10.1371/journal.pone.0095577
    remodeling of the collar membrane to engulf the prey, and transport of engulfed bacteria into the cell.

    Dayel and King (2014), PMID:24806026, PMC4012994, scientific Abstract directly checked in Europe PMC XML and the PLOS article. Results, Discussion and Methods were read; actual Figures 1 and 4 were inspected. Live-cell images and SEM/TEM support collar-associated engulfment and internalization in Salpingoeca rosetta. Mere contact or retention on the collar is not ingestion. Nutrient assimilation and the molecular identity of collar links are not established by these images. Actual supplements and movies were not inspected. The culture-provenance papers cited by the Methods were not followed, so this study is retained as trait evidence without a canonical strain assignment.

  • DOI:10.1111/nph.20388
    We found cells ingested proxy (up to 2 μm diameter) and natural (bacteria and cyanobacteria) prey particles

    Scientific Summary directly checked in Europe PMC full-text XML and PMC11982794; PMID:40035416. Results, Discussion and Methods were read, and actual Figures 5, 6, 9 and 10 were inspected. Scyphosphaera apsteinii RCC1456 cultures internalized particles and labeled bacteria into a prominent vacuole. Distinguish pHrodo Escherichia coli BioParticles from Acridine Orange-labeled marine bacteria and from inert beads. Acidic-organelle staining alone is not prey uptake; some imaging used EGTA decalcification. The paper uses phagotrophy for the nutritional interpretation; this record asserts particle engulfment, not a measured carbon assimilation rate. Figure 10 is a conceptual sequence-based model, not native protein validation: its S. apsteinii transcripts come from RCC1455, not the assayed RCC1456, and some candidates are from Gephyrocapsa huxleyi. Actual supplements and movies were not inspected. No negative comparator-species claim, bead-degrading enzyme assignment or inferred nutrient quota is imported.

Provenance

Identifier source
TraitMech local identifier
Definition source
DOI:10.1371/journal.pone.0095577

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.

  • Scyphosphaera apsteinii NCBITaxon:418940 DOI:10.1111/nph.20388 Strain-qualified example: diploid RCC1456, also AC504, TW15 and NIES-3344. Mid- to late-exponential nonaxenic cultures ingested labeled marine bacteria and particles under the reported incubation conditions; Figures 5 and 6 were inspected. The species taxon ID and scientific name were independently verified at NCBI on 2026-10-05; this is not a strain-level taxon ID or a claim about every isolate. Natural isolation from the Spanish coast of the Balearic Sea by single-cell micropipetting on 2001-02-01 was checked directly in the collection record https://www.roscoff-culture-collection.org/rcc-strain-details/1456. The transcript-source strain RCC1455 (AC505/TW16) is distinct and is not substituted for this exemplar.

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 particle uptake distinct from nutrition and process-level mappings.

CURATION TODO OPEN phagocytosis-trait-and-process-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.

This class denotes the microbial organism's particle-engulfment phenotype, not a host immune cell's response to the microbe. Existing capsule and pathogenic-to-host descriptions concern host immune evasion and are not same-scope unresolved trait nodes. Phagotrophy denotes a nutritional strategy; the coccolithophore paper uses that interpretation, but ingestion of inert particles does not by itself establish carbon assimilation. Trophic type METPO:1000631 and heterotrophic METPO:1000644 require nutritional source use, while predatory bacterium traitmech:000054 is bacteria-specific. Endocytosis traitmech:000636 is the direct broader trait because the existing particle-enclosure definition entails membrane-bound internalization; phenotype METPO:1000059 remains an ancestor. Do not equate phagocytosis with all endocytosis, pinocytosis, bacterial predation or phagotrophy. Review external process terms separately before asserting any trait-level xref; no synonym or ontology equivalence is proposed here.

Require native functional evidence before assigning molecular mechanisms.

KNOWLEDGE GAP OPEN phagocytosis-native-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.

The observed cellular uptake phenotypes do not identify a universal microbial protein mechanism. Collar-link composition in S. rosetta remains unresolved. The coccolithophore study's KEGG and Swiss-Prot sequence annotations concern RCC1455 transcripts and G. huxleyi gene models, not direct validation of the RCC1456 uptake mechanism. Keep strain provenance, homology, localization, experimental dependence and nutrient assimilation as separate evidence requirements. Inspect supplements and obtain taxon-paired native protein evidence before adding a causal graph or protein accessions.

Curation history

  1. · MINTED_TRAITMECH_ID · codex

    Added phagocytosis as an organism-level particle-engulfment phenotype with two DOI-backed snippets, inspected primary figures and a strain-qualified natural RCC1456 example. Ignored-and-hidden novelty searches and pinned METPO review found no exact record. Reserved METPO:1058000 in v503. Kept nutritional, mapping and sequence-based mechanism interpretations separate; no protein graph was inferred.

  2. · REFINE_ENDOCYTOSIS_PARENT · codex

    Refined the direct parent to endocytosis traitmech:000636 by definition-based inference. Updated only the parent statement in the scope discussion, which remains OPEN for process-mapping review. Preserved definition, evidence, example and prior history.