sediment

ENVO:00002007 ·resolve ·TERRESTRIAL ·EXACT SEEDED

Particulate environmental material which is formed as a result of the transport and deposition of particles by flowing liquid. — 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
ENVIRONMENTS_TABLE	sediment Physicochemical parameter bands from kg-microbe's environment table.	—
MADIN	sediment	523	TAXON
PREGO	sediment	3153	TAXON

Broader habitats

particulate environmental material ENVO:01000060

Environmental parameters

Physicochemical parameters
Parameter	Value	Source
SALINITY_VARIABILITY	small	kg-microbe environments.csv (sediment)
STRUCTURAL_COMPLEXITY	medium	kg-microbe environments.csv (sediment)
WATER_AVAILABILITY	high	kg-microbe environments.csv (sediment)
WATER_VARIABILITY	permanently wet	kg-microbe environments.csv (sediment)

Causal graphs

Sediment porewater redox ladder

Water-saturated sediment buries organic matter in diffusion- limited porewater, creating a depth-ordered redox ladder in which microbes consume progressively lower-energy terminal electron acceptors.

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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sediment_porewater_redox_ladder edges
Edge	Subject	Predicate	Object	Evidence
`sediment_accumulates_particles`	sediment	accumulates Flowing water deposits particles that accumulate as sediment beds.	deposited particles	`PMID:31388058` D'Hondt and colleagues review buried sediment particles as a habitat for subseafloor microbial life.
`particles_bury_organic_matter`	deposited particles	buries Deposited sediment particles bury organic matter that later supplies electrons for microbial respiration.	buried organic matter	`PMID:15618510` D'Hondt and colleagues mapped how buried organic matter supports microbial activity in deep subseafloor sediments.
`particles_create_porewater`	deposited particles	creates Sediment particle beds trap porewater where solute transport is constrained by diffusion and reaction.	diffusion-limited porewater	`PMID:31388058` D'Hondt and colleagues describe how sediment depth and porewater chemistry structure electron-accepting processes.
`buried_organic_matter_depletes_oxygen`	buried organic matter	contributes to Organic-matter remineralization consumes oxygen and pushes deeper porewater into anoxic metabolism.	oxygen depletion	`PMID:35308366` Nagakura and colleagues studied organic-matter mineralization by sulfate reduction in anoxic subseafloor sediment.
`oxygen_depletion_creates_redox_zonation`	oxygen depletion	creates As oxygen is depleted, sediment communities shift to a depth-ordered sequence of anaerobic respiration pathways.	redox zonation	`PMID:31388058` D'Hondt and colleagues review the depth ordering of terminal electron-accepting processes in marine sediment.
`redox_zonation_orders_electron_acceptors`	redox zonation	orders Redox zonation sorts oxygen, nitrate, manganese, iron, sulfate, and carbon dioxide reduction with increasing sediment depth.	terminal electron acceptor ladder	`PMID:31388058` D'Hondt and colleagues describe the canonical sequence of electron-acceptor reduction with depth in marine sediment.
`electron_acceptors_select_sulfate_reducers`	terminal electron acceptor ladder	selects for The sulfate-reduction zone selects microorganisms that use sulfate as a terminal electron acceptor.	sulfate-reducing microorganisms	`PMID:35308366` Nagakura and colleagues summarize sulfate reduction as the major organic-matter-degradation process in anoxic marine sediment.
`sulfate_reducers_perform_sulfate_reduction`	sulfate-reducing microorganisms	performs Sulfate-reducing microorganisms oxidize organic matter with sulfate when higher-energy acceptors are depleted.	sulfate reduction	`PMID:35308366` Nagakura and colleagues measured biological sulfate reduction in organic-rich subseafloor sediment.
`sulfate_depletion_selects_methanogens`	terminal electron acceptor ladder	selects for Once sulfate becomes depleted with depth, methanogenic archaea are selected as carbon dioxide becomes the terminal electron acceptor.	methanogenic archaea	`PMID:31388058` D'Hondt and colleagues place carbon dioxide reduction at the deep end of the standard sediment redox ladder.
`methanogens_perform_methanogenesis`	methanogenic archaea	performs Methanogenic archaea produce methane in the deepest, sulfate-depleted sediment redox zone.	methanogenesis	`PMID:15618510` D'Hondt and colleagues measured methanogenic activity in deep subseafloor sediments.
`methanogenesis_produces_methane`	methanogenesis	produces Methanogenesis produces methane below shallower nitrate, metal, and sulfate reduction zones.	methane	`PMID:31388058` D'Hondt and colleagues review carbon dioxide reduction as the terminal step of the marine sediment redox ladder.

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
Nitriliruptor alkaliphilus DSM 45188 `NCBITaxon:1069448`	MADIN	—	523	PREGO
rhodopseudomonas_palustris `NCBITaxon:1076`	MADIN	—	523	PREGO
Methylomonas sp. LW13 `NCBITaxon:107637`	MADIN	—	523	PREGO
Methanolobus tindarius DSM 2278 `NCBITaxon:1090322`	MADIN	—	523	PREGO
Natronorubrum tibetense DSM 13204 `NCBITaxon:1114856`	MADIN	—	523	PREGO
Aestuariibacter salexigens DSM 15300 `NCBITaxon:1120953`	MADIN	—	523	PREGO
Anaerovorax odorimutans DSM 5092 `NCBITaxon:1120998`	MADIN	—	523	PREGO
Arenibacter latericius DSM 15913 `NCBITaxon:1121012`	MADIN	—	523	PREGO
Arsenicicoccus bolidensis DSM 15745 `NCBITaxon:1121017`	MADIN	—	523	PREGO
Bacillus aidingensis DSM 18341 `NCBITaxon:1121085`	MADIN	—	523	PREGO
Bacillus aurantiacus DSM 18675 `NCBITaxon:1121086`	MADIN	—	523	PREGO
Clostridium halophilum DSM 5387 `NCBITaxon:1121317`	MADIN	—	523	PREGO
Clostridium magnum DSM 2767 `NCBITaxon:1121326`	MADIN	—	523	PREGO
Desulfomicrobium escambiense DSM 10707 `NCBITaxon:1121411`	MADIN	—	523	PREGO
Desulfosporosinus lacus DSM 15449 `NCBITaxon:1121420`	MADIN	—	523	PREGO
Desulfovibrio cuneatus DSM 11391 `NCBITaxon:1121443`	MADIN	—	523	PREGO
Desulfovibrio frigidus DSM 17176 `NCBITaxon:1121447`	MADIN	—	523	PREGO
Desulfovibrio idahonensis DSM 15450 `NCBITaxon:1121452`	MADIN	—	523	PREGO
Desulfovibrio litoralis DSM 11393 `NCBITaxon:1121455`	MADIN	—	523	PREGO
Ferrimonas futtsuensis DSM 18154 `NCBITaxon:1121878`	MADIN	—	523	PREGO
Flexithrix dorotheae DSM 6795 `NCBITaxon:1121904`	MADIN	—	523	PREGO
Gaetbulibacter saemankumensis DSM 17032 `NCBITaxon:1121909`	MADIN	—	523	PREGO
Geothrix fermentans DSM 14018 `NCBITaxon:1121920`	MADIN	—	523	PREGO
Gracilibacillus lacisalsi DSM 19029 `NCBITaxon:1121929`	MADIN	—	523	PREGO
Hahella ganghwensis DSM 17046 `NCBITaxon:1121935`	MADIN	—	523	PREGO

Showing 25 of 50 kept associations.

Also called

sediments — PREGO

Curation

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

ADD_CAUSAL_GRAPH 2026-09-04 · codex
Added a sediment porewater redox-ladder graph backed by PMID:31388058, PMID:15618510, and PMID:35308366.

Provenance

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