identifier: traitmech:000664
label: fungal arbuscule formation
definition: A morphological phenotype in which a fungus forms highly branched hyphal
  structures, called arbuscules, within living plant cells during arbuscular mycorrhizal
  symbiosis.
definition_source: DOI:10.3390/plants8060142
trait_category: MORPHOLOGY
term_kind: CLASS
mapping_status: PROPOSED
parent_traits:
- METPO:1000059
evidence:
- reference: DOI:10.1104/pp.109.141879
  snippet: In the arbuscular mycorrhizal symbiosis, the fungal symbiont colonizes
    root cortical cells, where it establishes differentiated hyphae called arbuscules.
  notes: Pumplin and Harrison (2009), PMID:19692536, PMC2754618; scientific-abstract
    sentence checked against Europe PMC and https://academic.oup.com/plphys/article/151/2/809/6108581.
    Main text, Figures 1-7 and supplementary Figures S1-S9 were inspected; Figure
    7 is a model. The supplementary movie was not viewed. Glomus versiforme colonized
    transgenic Medicago truncatula A17 roots. Host fluorescent markers distinguish
    periarbuscular membrane domains; they are not fungal protein anchors or nutrient-flux
    measurements. The host-derived membrane separates fungal branches from host cytoplasm.
    Fungal isolate provenance was not established, so this experiment is not a natural
    canonical example.
- reference: DOI:10.3390/plants8060142
  snippet: All AMF strains formed arbuscules in the parenchyma cells of the mycothalli
  notes: Kobae et al. (2019), PMID:31151150, PMC6631804; Results 2.2 clause. Primary
    text and Figures 1-4 on pages 1-11 of https://rakuno.repo.nii.ac.jp/record/6472/files/R-2020-321_kobae.pdf
    and all four supplementary pages were inspected. Liverwort Marchantia paleacea
    thallus observations support plant-cell, not root-only, scope. Methods 3.2 and
    Figure S1 identify cultures separately from unidentified field-root trapping.
    For DAOM197198, Results 2.2 reports arbuscules at 18 dps and none until 14 dps;
    S2A instead describes rhizoid-only hyphae at 18 dps and S2B arbuscules at 28 dps.
    Onset remains unresolved. Pigmentation alone is insufficient. Figure 4C shows
    root arbuscules, although Results points to 4B and uses dps instead of the caption's
    dpi. Figure 3 and Methods 3.6 disagree on phylogenetic method; no independent
    fungal species assignment from mixed rDNA is asserted.
canonical_examples:
- taxon_id: NCBITaxon:937382
  taxon_label: Entrophospora etunicata
  reference: DOI:10.3390/plants8060142
  note: MAFF520053 (H1-1), reported as Claroideoglomus etunicatum in Methods 3.2 and
    actual Figure S1, forms arbuscules in Marchantia paleacea thallus cells. NARO's
    collection record https://www.gene.affrc.go.jp/databases-micro_search_detail_en.php?maff=520053
    lists soybean-field soil, Tokyo, October 1987, H. Hirata; it was deposited as
    Glomus etunicatum. These separate fields support this culture's field-isolate
    origin, not a trait evidence snippet. NCBI Taxonomy resolves species 937382 to
    Entrophospora etunicata, with Claroideoglomus etunicatum as a homotypic synonym;
    name correspondence is not independent reidentification of the culture.
discussions:
- discussion_id: fungal-arbuscule-scope-and-hierarchy
  prompt: Resolve the phenotype parent and attributed haustorium umbrella.
  kind: CURATION_TODO
  status: OPEN
  rationale: 'Use active phenotype METPO:1000059; METPO:1000198 mycorrhization is
    obsolete. Mutualism traitmech:000041 requires reciprocal benefit, which formation
    alone does not establish. Direct QuickGO checks identify GO:0085041 arbuscule
    as a cellular component below GO:0085035 haustorium. This attributed umbrella
    classification is not silently rejected: microbial haustorium formation traitmech:000663
    and this formation phenotype are not asserted equivalent, disjoint or in a subclass
    relation. GO''s root-cortex wording is narrower than the liverwort observations,
    and a structure is not an organism-level phenotype. No exact xrefs, synonyms or
    SSSOM mappings are asserted. Plant cells includes thallus cells; within-cell location
    does not mean free in host cytoplasm.'
  posed_by: codex
  posed_date: '2026-10-07'
- discussion_id: fungal-arbuscule-formation-and-function
  prompt: Separate formation, timing and nutrient-exchange mechanisms.
  kind: KNOWLEDGE_GAP
  status: OPEN
  rationale: Do not infer nutrient flux, obligatory benefit, universal onset or lifespan
    from these morphology observations. Keep the 2019 main-text/supplement timing
    discrepancy open. The 2009 host membrane markers do not identify a fungal formation
    pathway. A protein-resolved causal graph needs direct perturbation evidence and
    authority-verified protein examples; it is deferred, not claimed absent. Extraradical
    branching alone does not satisfy this intracellular morphology definition.
  posed_by: codex
  posed_date: '2026-10-07'
curation_history:
- timestamp: '2026-10-07T13:21:20Z'
  curator: codex
  action: MINTED_TRAITMECH_ID
  changes: Added fungal arbuscule formation with two primary DOI citations, verbatim
    snippets and a culture-qualified fungal example. Ignored-and-hidden novelty and
    main/worktree/open-PR reservation checks support local ID 000664 and v540 block
    1061700-1061799. Kept host markers, timing disagreements and ontology scope explicit;
    protein-level mechanism deferred.
  llm_assisted: true