plant-associated environment

ENVO:01001001 ·resolve ·HOST_ASSOCIATED ·EXACT SEEDED

An environmental system determined by a green plant. — ENVO

SEEDED workflow status. The source-seeding rules supplied this record; consult its curation history for later attributed changes. This status does not establish human review.

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	Herbaceous-plants-Grass,Crops 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.	2451	STRAIN
ENVIRONMENTS_TABLE	host_plant Physicochemical parameter bands from kg-microbe's environment table.	—
GOLD	Host-associated > Plants 4 GOLD ecosystem node ids share this path; first shown. See data/raw/gold_ecosystem_paths.tsv.	12638	ORGANISM
MADIN	plant-associated environment	1206	TAXON

Broader habitats

environmental system determined by an organism ENVO:01001000

Environmental parameters

Physicochemical parameters
Parameter	Value	Source
GRADIENTS	high	kg-microbe environments.csv (host_plant)
PRESSURE	low	kg-microbe environments.csv (host_plant)
SALINITY_VARIABILITY	small	kg-microbe environments.csv (host_plant)

Causal graphs

Plant root exudate microbiome assembly

Root exudates, microbial substrate preferences, and plant immune signaling filter soil microbes into plant-associated root microbiomes that support plant-beneficial functions.

Directed graph · arrows run from subject to object. Focus or hover over a node or arrow for details; the evidence table follows.

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plant_root_exudate_microbiome_assembly edges
Edge	Subject	Predicate	Object	Evidence
`plant_roots_release_exudates`	plant-associated environment	provides Green plant roots release diverse exuded chemicals into plant-associated root environments.	root exudates	`DOI:10.1139/cjb-2013-0225` Huang and colleagues summarize root exudates as plant-released chemical mixtures at the plant-root and rhizosphere interface.
`exudates_select_rhizosphere_microbes`	root exudates	recruits Root-exudate chemistry attracts and selects microorganisms in the rhizosphere.	rhizosphere microbiome assembly	`DOI:10.1139/cjb-2013-0225` Huang and colleagues review plant exudate compounds that mediate both plant-microbe and plant-microbiome interactions.
`substrate_traits_match_exudates`	microbial substrate preferences	responds to Rhizosphere bacteria are filtered by the exuded substrates they can consume.	root exudates	`PMID:29556109` Zhalnina and colleagues compared rhizosphere bacterial growth responses with genome-predicted and measured substrate preferences.
`substrate_traits_drive_assembly`	microbial substrate preferences	drives Microbial substrate-use traits help translate dynamic exudate chemistry into rhizosphere community-assembly patterns.	rhizosphere microbiome assembly	`PMID:29556109` Zhalnina and colleagues linked exudate chemistry and bacterial substrate preferences to observed rhizosphere community assembly.
`salicylic_acid_modulates_root_colonization`	salicylic acid signaling	modulates Plant immune signaling through salicylic acid modulates which bacterial taxa colonize roots.	root bacterial colonization	`PMID:26184915` Lebeis and colleagues measured Arabidopsis root communities and found specific bacterial-taxon responses to salicylic acid signaling.
`colonization_contributes_to_microbiome_assembly`	root bacterial colonization	contributes to Host-filtered root colonization contributes to the assembled plant-associated root microbiome.	rhizosphere microbiome assembly	`PMID:32788714` Trivedi and colleagues review genetic, biochemical, physical, and metabolic interactions as drivers of plant microbiome assembly.
`assembly_modulates_plant_beneficial_functions`	rhizosphere microbiome assembly	modulates Assembled plant microbiomes modulate beneficial functions, including nutrient acquisition and plant health.	plant-beneficial functions	`PMID:32788714` Trivedi and colleagues summarize how plant microbiome interactions influence beneficial traits.

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
Sphingomonas sp. `NCBITaxon:28214`	BACDIVE	1	1394
Methylobacterium sp. `NCBITaxon:409`	BACDIVE	2	1394
Xanthomonas campestris `NCBITaxon:339`	BACDIVE	3	1394
Sorangium cellulosum `NCBITaxon:56`	BACDIVE	4	1394
Nannocystis exedens `NCBITaxon:54`	BACDIVE	5	1394
Corallococcus coralloides `NCBITaxon:184914`	BACDIVE	6	1394
Pseudomonas syringae `NCBITaxon:317`	BACDIVE	7	1394
Rhizobium sp. `NCBITaxon:391`	BACDIVE	8	1394
Pectobacterium carotovorum `NCBITaxon:554`	BACDIVE	9	1394
Pseudomonas sp. `NCBITaxon:306`	BACDIVE	10	1394
Ralstonia solanacearum `NCBITaxon:305`	BACDIVE	11	1394
Streptomyces scabiei `NCBITaxon:1930`	BACDIVE	12	1394
Streptomyces sp. `NCBITaxon:1931`	BACDIVE	13	1394
uncultured Bacillus sp. `NCBITaxon:83428`	BACDIVE	14	1394
Microbacterium sp. `NCBITaxon:51671`	BACDIVE	15	1394
Bacillus mycoides `NCBITaxon:1405`	BACDIVE	16	1394
Methanobacterium bryantii `NCBITaxon:2161`	BACDIVE	17	1394
Nocardioides sp. `NCBITaxon:35761`	BACDIVE	18	1394
Paenibacillus sp. `NCBITaxon:58172`	BACDIVE	19	1394
Ensifer sp. `NCBITaxon:1872086`	BACDIVE	20	1394
Bacillus thuringiensis `NCBITaxon:1428`	BACDIVE	21	1394
Acidovorax sp. `NCBITaxon:1872122`	BACDIVE	22	1394
Curtobacterium flaccumfaciens `NCBITaxon:2035`	BACDIVE	23	1394
Pedobacter sp. `NCBITaxon:1411316`	BACDIVE	24	1394
Aeromicrobium sp. `NCBITaxon:1871063`	BACDIVE	25	1394

Showing 25 of 50 kept associations.

Also called

Herbaceous-plants-Grass,Crops — BacDive
Plants — GOLD
Viridiplantae-associated environment — ENVO
plant environment — ENVO

Curation

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

GROUND 2026-08-12 · claude-opus-5
Grounded to ENVO:01001001 'plant-associated environment' (BROAD). Herbaceous plants, grasses and crops as hosts. ENVO:01001001 covers all plant-associated environments and so is broader than this specific host group. (source concept habitatmech:BACDIVE.d3209b6b2d)
GROUND 2026-08-12 · claude-opus-5
Grounded to ENVO:01001001 'plant-associated environment' (EXACT). GOLD's Host-associated > Plants is exactly what ENVO:01001001 denotes. Unlike the animal clades there is a single matching term, so no conflation risk. (source concept habitatmech:GOLD.1b21002a97)
ADD_CAUSAL_GRAPH 2026-09-04 · codex
Added a root-exudate microbiome-assembly graph backed by DOI:10.1139/cjb-2013-0225, PMID:29556109, PMID:26184915, and PMID:32788714.

Provenance

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