HabitatMech

tree-associated environment

habitatmech:BACDIVE.3192a0f47e ·HOST_ASSOCIATED ·UNGROUNDED REVIEWED

An environmental system determined by a tree. — HabitatMech

Source attestations

Each upstream vocabulary's own account of this habitat. Assertion counts are per-source units and are not comparable across sources — GOLD counts organisms, BacDive strains, PREGO taxa.

What each upstream vocabulary says about this habitat
SourceLabel / pathAssertionsUnit
BACDIVE Tree
kg-microbe's isolation-source mapping table has a row for this source with no ontology target; treated as ungrounded rather than re-grounded by lexical match.		 872 STRAIN

Broader habitats

Associated taxa

Taxa reported from this habitat, which is weaker than being characteristic of it. rank is out of pool: a high rank in a pool of thousands of near-tied scores is a weak claim. Entries corroborated by a second, independent source are listed first.

Taxa reported from this habitat
TaxonSourceRankPoolCorroborated
Sorangium cellulosum NCBITaxon:56 BACDIVE 1 481
Corallococcus coralloides NCBITaxon:184914 BACDIVE 2 481
Myxococcus fulvus NCBITaxon:33 BACDIVE 3 481
Nannocystis exedens NCBITaxon:54 BACDIVE 4 481
Pseudomonas syringae NCBITaxon:317 BACDIVE 5 481
Archangium sp. NCBITaxon:1872627 BACDIVE 6 481
Herpetosiphon sp. NCBITaxon:71864 BACDIVE 7 481
Xanthomonas campestris NCBITaxon:339 BACDIVE 8 481
Sporocytophaga myxococcoides NCBITaxon:153721 BACDIVE 9 481
Pseudomonas sp. NCBITaxon:306 BACDIVE 10 481
Agrobacterium radiobacter NCBITaxon:362 BACDIVE 11 481
Melittangium lichenicola NCBITaxon:45 BACDIVE 12 481
Corallococcus exiguus NCBITaxon:83462 BACDIVE 13 481
Myxococcales NCBITaxon:29 BACDIVE 14 481
Myxococcus xanthus NCBITaxon:34 BACDIVE 15 481
NCBITaxon:57 BACDIVE 16 481
Myxococcus virescens NCBITaxon:83456 BACDIVE 17 481
Bacteria NCBITaxon:2 BACDIVE 18 481
Erwinia pyrifoliae NCBITaxon:79967 BACDIVE 19 481
Myxococcus stipitatus NCBITaxon:83455 BACDIVE 20 481
Allostigmatella erecta NCBITaxon:83460 BACDIVE 21 481
Lonsdalea populi NCBITaxon:1172565 BACDIVE 22 481
Streptomyces sp. NCBITaxon:1931 BACDIVE 23 481
Cystobacter sp. NCBITaxon:1965334 BACDIVE 24 481
Cystobacter armeniaca NCBITaxon:394090 BACDIVE 25 481

Also called

Curation

What a curator decided about this record, and why. A record built from several source concepts can carry one decision per concept.

  1. CONFIRM_UNGROUNDED 2026-08-12 · claude-opus-5

    Confirmed UNGROUNDED: no ontology term fits this concept. Nearest broader term ENVO:01001001 'plant-associated environment' attached as a parent. A tree as host. No tree-associated environment term exists; BTO:0005516 wood is the material, not the living host. Parented to plant-associated environment as the nearest broader term. ENVO term request. Category set to HOST_ASSOCIATED (#205): the row already parents this to ENVO:01001001 'plant-associated environment', which is the claim that a living plant host defines the habitat, and 17 of the 18 records under that parent are HOST_ASSOCIATED. Same cause as the five domestic-mammal hosts of #200 - the category column was left blank, so the seeder's default stood. The reasoning above is unchanged. (source concept habitatmech:BACDIVE.3192a0f47e)

  2. DEFINED 2026-08-16 · claude-opus-5

    Defined as 'tree-associated environment' under ENVO:01001001 'plant-associated environment'. The habitat is the host clade, and it is the entire content of the concept: GOLD and BacDive both organise host-associated isolates by host, and every downstream anatomical path hangs off it. HabitatMech deliberately does not ground these to plant-associated environment, because every clade would then merge onto one record and the distinction the sources are making would be lost. ENVO already has this shape at plant-, animal- and fungi-associated environment; this asks for the same pattern one level down. Parented to plant-associated environment rather than the organism root, since a tree is a plant.

Provenance

Generated by scripts/seed_from_sources.py from the committed inventories in data/raw/. View the record.