HabitatMech

agricultural soil

ENVO:00002259 ·resolve ·TERRESTRIAL ·EXACT SEEDED

Soil which is part of an ecosystem used for agricultural activities. — 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_agricultural
Physicochemical parameter bands from kg-microbe's environment table.		 —
GOLD Environmental > Terrestrial > Soil > Loam > Agricultural soil 77 ORGANISM
MADIN agricultural soil 117 TAXON
PREGO agricultural soil 1767 TAXON

Broader habitats

Environmental parameters

Physicochemical parameters
ParameterValueSource
GRADIENTShighkg-microbe environments.csv (soil_agricultural)
NUTRIENTSmediumkg-microbe environments.csv (soil_agricultural)
ORGANIC_MATTERmediumkg-microbe environments.csv (soil_agricultural)
PRESSURElowkg-microbe environments.csv (soil_agricultural)
SALINITYlowkg-microbe environments.csv (soil_agricultural)
SALINITY_VARIABILITYsmallkg-microbe environments.csv (soil_agricultural)
STRUCTURAL_COMPLEXITYhighkg-microbe environments.csv (soil_agricultural)
TEMPERATURE_VARIABILITYhighkg-microbe environments.csv (soil_agricultural)
WATER_AVAILABILITYmediumkg-microbe environments.csv (soil_agricultural)
WATER_VARIABILITYoccasionally drykg-microbe environments.csv (soil_agricultural)

Causal graphs

Agricultural nitrogen nitrification loss

Agricultural nitrogen inputs regulate ammonium substrate supply, nitrifier populations, nitrate production, and nitrification-linked nitrogen losses from managed soil.

Directed graph · arrows run from subject to object. Focus or hover over a node or arrow for details; the evidence table follows.
Agricultural nitrogen nitrification loss 9 nodes and 9 directed relationships. Labels and evidence are also available in the adjacent table. agricultural soil — has management input → nitrogen fertilizer management; Evidence: PMID:31543867 has management input nitrogen fertilizer management — controls → ammonium availability; Evidence: PMID:31543867 controls ammonium availability — selects for → nitrifier populations; Evidence: PMID:31543867 selects for nitrifier populations — carries out → microbial nitrification; Evidence: PMID:29398704 carries out ammonium availability — fuels → microbial nitrification; Evidence: PMID:22936929 fuels microbial nitrification — produces → nitrate pool; Evidence: PMID:31543867 produces microbial nitrification — contributes to → nitrogen loss; Evidence: PMID:22936929 contributes to microbial nitrification — generates → nitrous oxide; Evidence: PMID:22936929 generates nitrification inhibitors — inhibits → microbial nitrification; Evidence: PMID:22936929 inhibits agricultural soil (HABITAT); agricultural_soil; ENVO:00002259 HABITAT agricultural soil nitrogen fertilizer management (EXPERIMENTAL_FACTOR); nitrogen_fertilizer_management EXPERIMENTAL_FACTOR nitrogen fertilizer management ammonium availability (STATE); ammonium_availability STATE ammonium availability nitrifier populations (TAXON); nitrifier_populations TAXON nitrifier populations microbial nitrification (BIOLOGICAL_PROCESS); microbial_nitrification BIOLOGICAL_PROCESS microbial nitrification nitrate pool (CHEMICAL); nitrate_pool CHEMICAL nitrate pool nitrogen loss (BIOLOGICAL_PROCESS); nitrogen_loss BIOLOGICAL_PROCESS nitrogen loss nitrous oxide (CHEMICAL); nitrous_oxide CHEMICAL nitrous oxide nitrification inhibitors (CHEMICAL); nitrification_inhibitors CHEMICAL nitrification inhibitors
agricultural_nitrogen_nitrification_loss edges
EdgeSubjectPredicateObjectEvidence
agriculture_controls_fertilizer_inputs agricultural soil has management input
Agricultural soil is managed through decisions about the amount, chemical form, and timing of nitrogen fertilizer inputs.		 nitrogen fertilizer management PMID:31543867
Norton and Ouyang identify fertilizer amount, form, and timing as land-manager controls on agricultural soil nitrification.
fertilizer_controls_ammonium_availability nitrogen fertilizer management controls
Nitrogen fertilizer management changes how much ammonium substrate is available to nitrifiers.		 ammonium availability PMID:31543867
Norton and Ouyang present ammonium substrate management as one of the two main agricultural nitrification-control strategies.
ammonium_supply_drives_nitrifier_growth ammonium availability selects for
Ammonium availability helps determine which active nitrifying microbes grow in agricultural soil.		 nitrifier populations PMID:31543867
Norton and Ouyang connect active nitrifier populations to the substrates that drive nitrifier metabolism and growth.
nitrifiers_carry_out_nitrogen_transformations nitrifier populations carries out
Nitrifier populations are part of the microbial network that transforms bioavailable nitrogen species.		 microbial nitrification PMID:29398704
Kuypers, Marchant, and Kartal review nitrogen transformations as reactions carried out by networks of microorganisms.
ammonium_is_nitrification_substrate ammonium availability fuels
Ammonium is the reduced nitrogen substrate oxidized during nitrification.		 microbial nitrification PMID:22936929
Shen and colleagues describe ammonia oxidation as the first, rate-limiting step of nitrification.
nitrification_produces_nitrate microbial nitrification produces
Nitrification converts ammonium into nitrate that can accumulate in agricultural soil solution.		 nitrate pool PMID:31543867
Norton and Ouyang highlight rapid nitrate formation as a dominant process in most agricultural soils.
nitrification_contributes_to_n_loss microbial nitrification contributes to
Nitrification can make fertilizer nitrogen unavailable to crop plants through nitrate leaching.		 nitrogen loss PMID:22936929
Shen and colleagues describe nitrification as a potential loss path that moves fertilizer nitrogen out of the plant-available pool.
nitrification_generates_nitrous_oxide microbial nitrification generates
Nitrification contributes to agricultural soil greenhouse-gas loss through nitrous oxide formation.		 nitrous oxide PMID:22936929
Shen and colleagues connect agricultural nitrification to N2O production.
inhibitors_slow_nitrification nitrification inhibitors inhibits
Nitrification inhibitors slow microbial ammonium-to-nitrate conversion.		 microbial nitrification PMID:22936929
Shen and colleagues describe nitrification inhibitors as tools for decreasing ammonia oxidation rates.

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
actinomyces_griseus NCBITaxon:1911 MADIN — 117 PREGO
Pseudomonas fluorescens Pf0-1 NCBITaxon:205922 MADIN — 117 PREGO
Candidatus Solibacter usitatus Ellin6076 NCBITaxon:234267 MADIN — 117 PREGO
Burkholderia thailandensis E264 NCBITaxon:271848 MADIN — 117 PREGO
Methanocella paludicola SANAE NCBITaxon:304371 MADIN — 117 PREGO
Burkholderia cenocepacia HI2424 NCBITaxon:331272 MADIN — 117 PREGO
Burkholderia cenocepacia MC0-3 NCBITaxon:406425 MADIN — 117 PREGO
Acinetobacter oleivorans DR1 NCBITaxon:436717 MADIN — 117 PREGO
Streptosporangium roseum DSM 43021 NCBITaxon:479432 MADIN — 117 PREGO
Cellvibrio japonicus Ueda107 NCBITaxon:498211 MADIN — 117 PREGO
Bacillus thuringiensis sv. pulsiensis BGSC 4CC1 NCBITaxon:527028 MADIN — 117 PREGO
Candidatus Liberibacter solanacearum CLso-ZC1 NCBITaxon:658172 MADIN — 117 PREGO
Paludibacter propionicigenes WB4 NCBITaxon:694427 MADIN — 117 PREGO
Sinorhizobium meliloti BL225C NCBITaxon:698936 MADIN — 117 PREGO
Allobosea thiooxidans NCBITaxon:53254 PREGO 1 1767
Geodermatophilus obscurus DSM 43160 NCBITaxon:526225 PREGO 2 1767
Gemmatimonas aurantiaca T-27 NCBITaxon:379066 PREGO 3 1767
Gemmata sp. Wa1-1 NCBITaxon:235140 PREGO 4 1767
Intrasporangium calvum DSM 43043 NCBITaxon:710696 PREGO 5 1767
Conexibacter woesei DSM 14684 NCBITaxon:469383 PREGO 6 1767
Bradyrhizobium diazoefficiens USDA 110 NCBITaxon:224911 PREGO 7 1767
Sorangium cellulosum So ce56 NCBITaxon:448385 PREGO 8 1767
Polaromonas sp. JS666 NCBITaxon:296591 PREGO 9 1767
Sorangium cellulosum NCBITaxon:56 PREGO 10 1767
Nakamurella multipartita DSM 44233 NCBITaxon:479431 PREGO 11 1767

Showing 25 of 50 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.842c30e44d)

  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.d61ebbc0a8)

  3. ADD_CAUSAL_GRAPH 2026-09-04 · codex

    Added an agricultural nitrogen nitrification-loss graph backed by PMID:31543867, PMID:29398704, and PMID:22936929.

Provenance

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