HabitatMech

soil

ENVO:00001998 ·resolve ·TERRESTRIAL ·EXACT SEEDED

An environmental material which is primarily composed of minerals, varying proportions of sand, silt, and clay, organic material such as humus, interstitial gases, liquids, and a broad range of resident micro- and macroorganisms. — 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
SourceLabel / pathAssertionsUnit
ENVIRONMENTS_TABLE soil
Physicochemical parameter bands from kg-microbe's environment table.		 —
GOLD Environmental > Terrestrial > Soil
3 GOLD ecosystem node ids share this path; first shown. See data/raw/gold_ecosystem_paths.tsv.		 26399 ORGANISM
MADIN soil 2934 TAXON
PREGO soil 8715 TAXON

Broader habitats

Environmental parameters

Physicochemical parameters
ParameterValueSource
GRADIENTShighkg-microbe environments.csv (soil)
PRESSURElowkg-microbe environments.csv (soil)
STRUCTURAL_COMPLEXITYhighkg-microbe environments.csv (soil)
TEMPERATURE_VARIABILITYmediumkg-microbe environments.csv (soil)

Causal graphs

Soil pore organic-matter microhabitats

Soil pore geometry, dynamic water films, patchy organic resources, and mineral occlusion create microscale habitats that constrain microbial dispersal and organic-matter turnover.

Directed graph · arrows run from subject to object. Focus or hover over a node or arrow for details; the evidence table follows.
Soil pore organic-matter microhabitats 10 nodes and 8 directed relationships. Labels and evidence are also available in the adjacent table. soil — has structure → soil pore network; Evidence: PMID:28961933 has structure soil pore network — organizes → dynamic soil aqueous phase; Evidence: PMID:28961933 organizes dynamic soil aqueous phase — constrains → microbial dispersal constraints; Evidence: PMID:28961933 constrains soil — has condition → patchy organic resources; Evidence: PMID:28961933 has condition patchy organic resources — creates → microscale environmental conditions; Evidence: PMID:28961933 creates mineral occlusion — reduces → organic-matter access; Evidence: PMID:23055998 reduces extracellular enzyme activity — controls → soil carbon turnover; Evidence: PMID:23055998 controls organic-matter access — modulates → soil carbon turnover; Evidence: PMID:23055998 modulates soil (HABITAT); soil; ENVO:00001998 HABITAT soil soil pore network (ENVIRONMENTAL_FACTOR); soil_pore_network ENVIRONMENTAL_FACTOR soil pore network dynamic soil aqueous phase (ENVIRONMENTAL_PARAMETER); dynamic_aqueous_phase ENVIRONMENTAL_PARAMETER dynamic soil aqueous phase microbial dispersal constraints (STATE); microbial_dispersal_constraints STATE microbial dispersal constraints patchy organic resources (ENVIRONMENTAL_PARAMETER); patchy_organic_resources ENVIRONMENTAL_PARAMETER patchy organic resources microscale environmental conditions (ENVIRONMENTAL_PARAMETER); microscale_environmental_conditions ENVIRONMENTAL_PARAMETER microscale environmental conditions mineral occlusion (ENVIRONMENTAL_FACTOR); mineral_occlusion ENVIRONMENTAL_FACTOR mineral occlusion organic-matter access (STATE); organic_matter_access STATE organic-matter access extracellular enzyme activity (MOLECULAR_FUNCTION); extracellular_enzyme_activity MOLECULAR_FUNCTION extracellular enzyme activity soil carbon turnover (BIOLOGICAL_PROCESS); soil_carbon_turnover BIOLOGICAL_PROCESS soil carbon turnover
soil_pore_organic_matter_microhabitats edges
EdgeSubjectPredicateObjectEvidence
soil_contains_pore_network soil has structure
Soil pore geometry creates microscale physical structure across the soil habitat.		 soil pore network PMID:28961933
Tecon and Or treat soil pores as the fine spatial scale at which soil physical processes shape microbial life.
soil_pores_structure_aqueous_phase soil pore network organizes
Soil pore geometry organizes the dynamic water phase that connects or isolates microbial cells.		 dynamic soil aqueous phase PMID:28961933
Tecon and Or review how water organization in pores links soil physics to microbial life.
aqueous_phase_limits_dispersal dynamic soil aqueous phase constrains
The spatial organization of pore water constrains how soil microbes move and disperse.		 microbial dispersal constraints PMID:28961933
Tecon and Or identify the spatially organized, dynamic aqueous phase as a determinant of microbial dispersal ranges in soil.
soil_contains_patchy_organic_resources soil has condition
Soil contains heterogeneously distributed organic substrates.		 patchy organic resources PMID:28961933
Tecon and Or describe patchy organic-resource distribution as one of the biophysical features that makes soil a microbial habitat.
patchy_resources_create_microscale_conditions patchy organic resources creates
Patchy organic substrates and pore-water variation create local environmental conditions for soil microbes.		 microscale environmental conditions PMID:28961933
Tecon and Or connect resource patchiness and water-organization variation to microscale environmental conditions in soil.
mineral_occlusion_limits_organic_access mineral occlusion reduces
Occlusion and sorption on mineral particles can limit microbial physical access to organic substrates.		 organic-matter access PMID:23055998
Schimel and Schaeffer describe physical access to protected substrates as a rate-limiting control on mineral-soil carbon turnover.
enzyme_activity_controls_carbon_turnover extracellular enzyme activity controls
Extracellular enzymes are microbial controls on decomposition and carbon turnover in soil.		 soil carbon turnover PMID:23055998
Schimel and Schaeffer identify extracellular enzymes as key microbial controls over soil structure, function, and carbon fate.
organic_access_modulates_carbon_turnover organic-matter access modulates
Physical access to protected organic matter modulates microbial organic-matter breakdown in mineral soil.		 soil carbon turnover PMID:23055998
Schimel and Schaeffer argue that physical access, rather than only decomposer identity, can limit mineral-soil organic-matter turnover.

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
Enterobacter cloacae NCBITaxon:550 PREGO 4 8715 MADIN
Acidovorax sp. JS42 NCBITaxon:232721 PREGO 18 8715 MADIN
Aminivibrio pyruvatiphilus NCBITaxon:1005740 PREGO 24 8715 MADIN
Rhodococcus jostii RHA1 NCBITaxon:101510 MADIN — 2934 PREGO
nonomuraea_soli NCBITaxon:1032476 MADIN — 2934 PREGO
Massilia lurida NCBITaxon:1036180 MADIN — 2934 PREGO
kutzneria_kofuensis NCBITaxon:103725 MADIN — 2934 PREGO
actinomadura_flava NCBITaxon:103732 MADIN — 2934 PREGO
actinomadura_flexuosa NCBITaxon:103836 MADIN — 2934 PREGO
actinomadura_turkmeniaca NCBITaxon:103838 MADIN — 2934 PREGO
acetobacter_lovaniensis NCBITaxon:104100 MADIN — 2934 PREGO
kutzneria_buriramensis NCBITaxon:1045776 MADIN — 2934 PREGO
chitinophaga_japonensis NCBITaxon:104662 MADIN — 2934 PREGO
chitinophaga_filiformis NCBITaxon:104663 MADIN — 2934 PREGO
Sporichthya polymorpha DSM 43042 NCBITaxon:1048339 MADIN — 2934 PREGO
Actinopolyspora mortivallis HS-1, DSM 44261 NCBITaxon:1050202 MADIN — 2934 PREGO
geodermatophilus_soli NCBITaxon:1052260 MADIN — 2934 PREGO
Streptomyces purpureus KA281, ATCC 21405 NCBITaxon:1054860 MADIN — 2934 PREGO
alcaligenes_eutrophus NCBITaxon:106590 MADIN — 2934 PREGO
ensifer_adhaerens NCBITaxon:106592 MADIN — 2934 PREGO
Amycolatopsis methanolica 239 NCBITaxon:1068978 MADIN — 2934 PREGO
Amycolatopsis thermoflava N1165, DSM 44574 NCBITaxon:1068979 MADIN — 2934 PREGO
rhodopseudomonas_palustris NCBITaxon:1076 MADIN — 2934 PREGO
Pontibacter lucknowensis NCBITaxon:1077936 MADIN — 2934 PREGO
Amycolatopsis balhimycina FH 1894 NCBITaxon:1089545 MADIN — 2934 PREGO

Showing 25 of 49 kept associations.

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 2026-08-13 · claude-opus-5

    Reviewed and endorsed the seeder's own resolution. Multi-source review pass: this record is attested by more than one independent vocabulary, and this source's label or path was read against the record's ontology term to check the merge is right. It agrees. Source concepts in the same pass whose labels did not agree were re-decided rather than endorsed; see the pass's other decisions of the same date. (source concept habitatmech:GOLD.3fcb71c158)

  2. REVIEW 2026-08-13 · claude-opus-5

    Reviewed and endorsed the seeder's own resolution. Multi-source review pass: this record is attested by more than one independent vocabulary, and this source's label or path was read against the record's ontology term to check the merge is right. It agrees. Source concepts in the same pass whose labels did not agree were re-decided rather than endorsed; see the pass's other decisions of the same date. (source concept habitatmech:PREGO.492544997f)

  3. ADD_CAUSAL_GRAPH 2026-09-04 · codex

    Added a soil pore and organic-matter microhabitat graph backed by PMID:28961933 and PMID:23055998.

Provenance

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