HabitatMech

fungi-associated environment

ENVO:01001041 ·resolve ·HOST_ASSOCIATED ·EXACT REVIEWED

An environmental system determined by a fungal structure. — ENVO

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
ENVIRONMENTS_TABLE host_fungus
Physicochemical parameter bands from kg-microbe's environment table.		 —
GOLD Host-associated > Fungi
4 GOLD ecosystem node ids share this path; first shown. See data/raw/gold_ecosystem_paths.tsv.		 635 ORGANISM
MADIN fungi-associated environment 38 TAXON

Broader habitats

Environmental parameters

Physicochemical parameters
ParameterValueSource
GRADIENTShighkg-microbe environments.csv (host_fungus)
NUTRIENTShighkg-microbe environments.csv (host_fungus)
ORGANIC_MATTERhighkg-microbe environments.csv (host_fungus)
PRESSURElowkg-microbe environments.csv (host_fungus)
SALINITYlowkg-microbe environments.csv (host_fungus)
SALINITY_VARIABILITYsmallkg-microbe environments.csv (host_fungus)
STRUCTURAL_COMPLEXITYhighkg-microbe environments.csv (host_fungus)
TEMPERATURE_VARIABILITYmediumkg-microbe environments.csv (host_fungus)
WATER_AVAILABILITYhighkg-microbe environments.csv (host_fungus)
WATER_VARIABILITYpermanently wetkg-microbe environments.csv (host_fungus)

Causal graphs

Fungi-associated hyphae mycosphere dispersal

Fungal structures create host-associated microsites by extending hyphae through soil and organic matter, releasing fungal exudates, exposing chitin-rich cell walls, and forming hydrated surfaces that bacteria can colonize. These hyphal traits recruit mycosphere bacteria, provide fungal highways for motile dispersers, support fungus-feeding chitinolytic bacteria, and contain intracellular niches for endofungal symbionts.

Directed graph · arrows run from subject to object. Focus or hover over a node or arrow for details; the evidence table follows.
Fungi-associated hyphae mycosphere dispersal 15 nodes and 14 directed relationships. Labels and evidence are also available in the adjacent table. fungi-associated environment — determined by → fungal structure; Evidence: PMID:16102603 determined by fungal structure — extends → fungal hyphae; Evidence: PMID:16102603 extends fungal hyphae — releases → hyphal exudates; Evidence: PMID:16102603 releases hyphal exudates — selects for → mycosphere bacteria; Evidence: PMID:16102603; PMID:19286795 selects for fungal hyphae — supports → hyphal water films; Evidence: PMID:16047804 supports hyphal water films — selects for → motile bacteria; Evidence: PMID:23995942 selects for motile bacteria — expresses → flagellar motility; Evidence: PMID:23995942 expresses flagellar motility — drives → bacterial dispersal; Evidence: PMID:16047804 drives fungal hyphae — exposes → chitin-rich cell wall; Evidence: PMID:15143036 exposes chitin-rich cell wall — selects for → chitinolytic bacteria; Evidence: PMID:15143036 selects for chitinolytic bacteria — performs → bacterial mycophagy; Evidence: PMID:15143036; DOI:10.1186/s12864-015-2289-3 performs bacterial mycophagy — induces → antifungal metabolites; Evidence: PMID:21614084 induces fungal structure — contains → fungal cytoplasm; Evidence: PMID:17978222 contains fungal cytoplasm — harbors → endofungal bacteria; Evidence: PMID:17978222 harbors fungi-associated environment (HABITAT); fungi_associated_environment; ENVO:01001041 HABITAT fungi-associated environment fungal structure (HABITAT); fungal_structure HABITAT fungal structure fungal hyphae (ENVIRONMENTAL_FACTOR); fungal_hyphae ENVIRONMENTAL_FACTOR fungal hyphae hyphal exudates (CHEMICAL); hyphal_exudates CHEMICAL hyphal exudates hyphal water films (ENVIRONMENTAL_FACTOR); hyphal_water_films ENVIRONMENTAL_FACTOR hyphal water films chitin-rich cell wall (CHEMICAL); chitin_cell_wall CHEMICAL chitin-rich cell wall fungal cytoplasm (HABITAT); fungal_cytoplasm HABITAT fungal cytoplasm mycosphere bacteria (TAXON); mycosphere_bacteria TAXON mycosphere bacteria motile bacteria (TAXON); motile_bacteria TAXON motile bacteria flagellar motility (TRAIT); flagellar_motility TRAIT flagellar motility bacterial dispersal (COMMUNITY_PROCESS); bacterial_dispersal COMMUNITY_PROCESS bacterial dispersal chitinolytic bacteria (TAXON); chitinolytic_bacteria TAXON chitinolytic bacteria bacterial mycophagy (PATHWAY); mycophagy PATHWAY bacterial mycophagy antifungal metabolites (CHEMICAL); antifungal_metabolites CHEMICAL antifungal metabolites endofungal bacteria (TAXON); endofungal_bacteria TAXON endofungal bacteria
fungi_associated_hyphae_mycosphere_dispersal edges
EdgeSubjectPredicateObjectEvidence
fungi_environment_determined_by_structure fungi-associated environment determined by
Fungi-associated environments are host-associated systems whose bacterial niches are determined by fungal tissues and mycelia.		 fungal structure PMID:16102603
De Boer and colleagues reviewed how fungal activity creates physical and chemical niches for bacteria.
fungal_structure_extends_hyphae fungal structure extends
Filamentous fungi extend hyphae into surrounding substrates, increasing the fungal surface available for colonization.		 fungal hyphae PMID:16102603
The fungal-bacterial interaction review emphasizes fungal hyphae as habitat-forming structures for bacteria.
fungal_hyphae_release_exudates fungal hyphae releases
Growing hyphae release carbon-rich exudates into adjacent soil or organic matter, enriching the mycosphere.		 hyphal exudates PMID:16102603
De Boer and colleagues reviewed fungal exudation and nutrient translocation as drivers of nearby bacterial niches.
exudates_recruit_mycosphere_bacteria hyphal exudates selects for
Exudates near fungal hyphae select bacterial populations able to use fungal-derived carbon compounds.		 mycosphere bacteria PMID:16102603
The review describes the mycosphere as a nutrient-enriched zone where fungi shape bacterial abundance and composition. PMID:19286795
Warmink and van Elsas found bacterial migration and enrichment in soil microcosms containing Lyophyllum hyphae.
hyphae_generate_water_films fungal hyphae supports
Hydrated films along fungal hyphae create a continuous surface that bacteria can swim across in otherwise unsaturated substrates.		 hyphal water films PMID:16047804
Kohlmeier and colleagues demonstrated mycelium-mediated bacterial movement in a water-unsaturated model system.
water_films_select_motile_bacteria hyphal water films selects for
Liquid films on hyphae favor bacteria with motility traits that let them spread along fungal highways.		 motile bacteria PMID:23995942
Pion and colleagues used selection experiments to show that fungal highways can favor gains of bacterial flagellar motility.
motile_bacteria_express_flagella motile bacteria expresses
Motile mycosphere bacteria use flagella to migrate along the hydrated surface of fungal hyphae.		 flagellar motility PMID:23995942
The fungal-highway evolution experiment linked flagella to movement on fungal mycelia.
flagellar_motility_drives_dispersal flagellar motility drives
Flagellar motility lets bacteria disperse along hyphae and reach nutrient patches inaccessible through air-filled pores.		 bacterial dispersal PMID:16047804
Kohlmeier and colleagues showed that fungal hyphae mobilized pollutant-degrading bacteria across an unsaturated matrix.
hyphae_expose_chitin_cell_wall fungal hyphae exposes
Fungal hyphae expose chitinous cell-wall polymers that can be attacked by chitinolytic bacteria.		 chitin-rich cell wall PMID:15143036
De Boer and colleagues described Collimonas fungivorans as a chitinolytic bacterium able to grow on living fungal hyphae.
chitin_cell_wall_selects_chitinolytic_bacteria chitin-rich cell wall selects for
Chitin-rich fungal walls favor bacteria capable of producing chitinolytic enzymes during fungal feeding.		 chitinolytic bacteria PMID:15143036
The species description established Collimonas fungivorans as a chitinolytic soil bacterium with fungus-feeding ability.
chitinolytic_bacteria_perform_mycophagy chitinolytic bacteria performs
Fungus-feeding bacteria can attack living hyphae and use fungal biomass as a carbon and nutrient source.		 bacterial mycophagy PMID:15143036
The Collimonas fungivorans type strain was characterized by growth on living fungal hyphae. DOI:10.1186/s12864-015-2289-3
Song and colleagues compared Collimonas genomes to identify traits associated with fungal feeding.
mycophagy_induces_antifungal_metabolites bacterial mycophagy induces
Direct bacterial-fungal confrontation can induce Collimonas gene expression for antifungal metabolites and use of fungal-derived compounds.		 antifungal metabolites PMID:21614084
Mela and colleagues profiled Collimonas fungivorans and Aspergillus niger during confrontation and found activation of genes for fungal-derived compound use and antifungal production.
fungal_structure_contains_cytoplasm fungal structure contains
Fungal hyphae provide intracellular cytoplasmic compartments that some specialized bacteria can inhabit.		 fungal cytoplasm PMID:17978222
Partida-Martinez and colleagues described Burkholderia endofungorum and Burkholderia rhizoxinica as endosymbionts of Rhizopus microsporus.
fungal_cytoplasm_harbors_endofungal_bacteria fungal cytoplasm harbors
Some fungi harbor bacterial endosymbionts inside the fungal cytoplasm rather than only on hyphal surfaces.		 endofungal bacteria PMID:17978222
The Burkholderia endofungorum species description documented bacteria living as Rhizopus microsporus endosymbionts.

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
Pseudomonas tolaasii PMS117 NCBITaxon:1030145 MADIN — 38
Pseudomonas tolaasii 6264 NCBITaxon:1161101 MADIN — 38
Bacillus marmarensis DSM 21297 NCBITaxon:1188261 MADIN — 38
Pseudomonas sp. NS1 NCBITaxon:1189289 MADIN — 38
Corynebacterium maris DSM 45190 NCBITaxon:1224163 MADIN — 38
Mucilaginibacter sp. PAMC 26640 NCBITaxon:1300914 MADIN — 38
Bacillus subtilis subtilis MP11 NCBITaxon:1310431 MADIN — 38
Janthinobacterium agaricidamnosum NBRC 102515 = DSM 9628 NCBITaxon:1349767 MADIN — 38
Hymenobacter sp. PAMC 26554 NCBITaxon:1484116 MADIN — 38
Hymenobacter sp. PAMC 26628 NCBITaxon:1484118 MADIN — 38
collimonas_fungivorans NCBITaxon:158899 MADIN — 38
Bosea sp. PAMC 26642 NCBITaxon:1792307 MADIN — 38
Microbacterium sp. PAMC 28756 NCBITaxon:1795053 MADIN — 38
Frondihabitans sp. PAMC 28766 NCBITaxon:1795630 MADIN — 38
Variovorax sp. PAMC 28711 NCBITaxon:1795631 MADIN — 38
actinomyces_griseus NCBITaxon:1911 MADIN — 38
Kutzneria sp. 744 NCBITaxon:345341 MADIN — 38
burkholderia_endofungorum NCBITaxon:417203 MADIN — 38
Pseudomonas fluorescens BBc6R8 NCBITaxon:463794 MADIN — 38
streptomyces_canescens NCBITaxon:53445 MADIN — 38
Pseudomonas fluorescens NZ052 NCBITaxon:564421 MADIN — 38
Pseudomonas fluorescens NZ17 NCBITaxon:564422 MADIN — 38
Pseudomonas tolaasii NCPPB 2192 NCBITaxon:564423 MADIN — 38
pseudonocardia_parietis NCBITaxon:570936 MADIN — 38
prauserella_muralis NCBITaxon:588067 MADIN — 38

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. REVIEW 2026-08-16 · claude-opus-5

    Reviewed and endorsed the seeder's own resolution. Risky-grounding review (#12), co-attestor pass: this source concept feeds a record whose grounding was flagged and reviewed, and the record could not reach REVIEWED until every source feeding it was decided. This one is a self-grounding: the source vocabulary names the concept with the ontology term's own label, so there is nothing to adjudicate between the two — checked that the term is the one the label denotes, and that the record it merges into is the same concept rather than a homonym. (source concept habitatmech:MADIN.38094577e7)

  2. GROUND 2026-08-17 · claude-opus-5

    Grounded to ENVO:01001041 'fungi-associated environment' (EXACT). Definitions-from-research pass (#110): the research run recommended GROUND rather than a term request, and it is right — the same over-correction #123 found for Cnidaria. #114 rightly undid NOT_APPLICABLE, because a fungal host is a habitat, but moved this to CONFIRM_UNGROUNDED when a third option existed all along: ENVO:01001041 'fungi-associated environment' is in the vendored slice with that exact label. Grounding merges GOLD's 635 organism assertions onto the record the environments table and Madin already attest, which is the correct outcome rather than a side effect. (source concept habitatmech:GOLD.a8fc5001d1)

  3. ADD_CAUSAL_GRAPH 2026-09-04 · codex

    Added a fungi-associated hyphae mycosphere dispersal graph backed by PMID:16102603, PMID:19286795, PMID:16047804, PMID:23995942, PMID:15143036, DOI:10.1186/s12864-015-2289-3, PMID:21614084, and PMID:17978222.

Provenance

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