root-or-stem rot environment

habitatmech:BACDIVE.04ddbbeabe ·OTHER ·UNGROUNDED REVIEWED

An environment associated with a plant part or small plant which is determined by macerated or necrotic tissue of a root or stem undergoing in situ decomposition by an invading plant-pathogenic microorganism. — 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
Source	Label / path	Assertions	Unit
BACDIVE	Rot-Root,Stem	2	STRAIN

Broader habitats

environment associated with a plant part or small plant ENVO:01001057

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
Taxon	Source	Rank	Pool	Corroborated
Pectobacterium polaris `NCBITaxon:2042057`	BACDIVE	1	2
Pectobacterium carotovorum `NCBITaxon:554`	BACDIVE	2	2

Also called

Rot (Root,Stem) — HabitatMech curation
Rot-Root,Stem — HabitatMech curation

Curation

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

CONFIRM_UNGROUNDED 2026-08-14 · claude-opus-5
Confirmed UNGROUNDED: no ontology term fits this concept. Cohort review: root-or-stem rot. Same PO:0009047 'stem' merge as the leaf-spot source, and the same objection — the dropped alternative is half the concept. (source concept habitatmech:BACDIVE.04ddbbeabe)
DEFINED 2026-09-10 · codex-gpt-5
Defined as 'root-or-stem rot environment' under ENVO:01001057 'environment associated with a plant part or small plant'. Definition authored from the record's committed deep-research report under research/habitats/, read in full; no new paid research was commissioned. The report confirms BacDive's #Rot (Root,Stem) source can denote the rotted root or stem tissue and distinguishes it from BacDive's separate body-site facet, PO:0009005 'root', PO:0009047 'stem', rhizosphere and rhizoplane compartments, detached plant litter, necromass, and disease classes. ENVO:01001057 'environment associated with a plant part or small plant' is the tightest vendored environment genus and matches the sibling leaf-or-stem spot lesion definition. The definition deliberately avoids pH or fungal and oomycete specificity because the record's two BacDive strain attestations are bacterial soft rot and the report found no source for a general pH range.

Provenance

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