HabitatMech

sludge

ENVO:00002044 ·resolve ·OTHER ·EXACT SEEDED

The residual semi-solid material left from domestic or industrial processes, or wastewater treatment processes. — 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
BACDIVE Mud-Sludge 540 STRAIN
BACDIVE Sewage-sludge 152 STRAIN
ENVIRONMENTS_TABLE sludge
Physicochemical parameter bands from kg-microbe's environment table.		 —
MADIN sludge 153 TAXON
PREGO sludge 803 TAXON

Broader habitats

Environmental parameters

Physicochemical parameters
ParameterValueSource
GRADIENTSlowkg-microbe environments.csv (sludge)
NUTRIENTShighkg-microbe environments.csv (sludge)
ORGANIC_MATTERhighkg-microbe environments.csv (sludge)
STRUCTURAL_COMPLEXITYmediumkg-microbe environments.csv (sludge)
TEMPERATUREmediumkg-microbe environments.csv (sludge)
TEMPERATURE_VARIABILITYmediumkg-microbe environments.csv (sludge)
WATER_AVAILABILITYhighkg-microbe environments.csv (sludge)
WATER_VARIABILITYpermanently wetkg-microbe environments.csv (sludge)

Causal graphs

Sludge floc oxygen partitioning

Sludge aggregates extracellular-polymeric substances, cells, and adsorbed particles into flocs whose oxygen gradients partition nitrification and denitrification into adjacent oxic and anoxic microsites.

Directed graph · arrows run from subject to object. Focus or hover over a node or arrow for details; the evidence table follows.
Sludge floc oxygen partitioning 11 nodes and 11 directed relationships. Labels and evidence are also available in the adjacent table. sludge — contains → activated sludge flocs; Evidence: PMID:12926675 contains extracellular polymeric substances — structures → activated sludge flocs; Evidence: PMID:12926675 structures activated sludge flocs — creates → heterogeneous floc matrix; Evidence: PMID:12926675 creates heterogeneous floc matrix — creates → oxygen gradients; Evidence: PMID:12827702 creates bulk dissolved oxygen — controls → oxygen gradients; Evidence: PMID:12827702 controls oxygen gradients — creates → oxic floc zones; Evidence: PMID:12827702 creates oxygen gradients — creates → anoxic floc zones; Evidence: PMID:12827702 creates oxic floc zones — enables → nitrification; Evidence: PMID:12827702 enables anoxic floc zones — enables → denitrification; Evidence: PMID:12827702 enables nitrification — contributes to → simultaneous nitrification and denitrification; Evidence: PMID:12827702 contributes to denitrification — contributes to → simultaneous nitrification and denitrification; Evidence: PMID:12827702 contributes to sludge (HABITAT); sludge; ENVO:00002044 HABITAT sludge activated sludge flocs (STATE); activated_sludge_flocs STATE activated sludge flocs extracellular polymeric substances (CHEMICAL); extracellular_polymeric_substances CHEMICAL extracellular polymeric substances heterogeneous floc matrix (STATE); heterogeneous_floc_matrix STATE heterogeneous floc matrix bulk dissolved oxygen (ENVIRONMENTAL_PARAMETER); bulk_dissolved_oxygen ENVIRONMENTAL_PARAMETER bulk dissolved oxygen oxygen gradients (ENVIRONMENTAL_PARAMETER); oxygen_gradients ENVIRONMENTAL_PARAMETER oxygen gradients oxic floc zones (ENVIRONMENTAL_PARAMETER); oxic_floc_zones ENVIRONMENTAL_PARAMETER oxic floc zones anoxic floc zones (ENVIRONMENTAL_PARAMETER); anoxic_floc_zones ENVIRONMENTAL_PARAMETER anoxic floc zones nitrification (BIOLOGICAL_PROCESS); nitrification BIOLOGICAL_PROCESS nitrification denitrification (BIOLOGICAL_PROCESS); denitrification BIOLOGICAL_PROCESS denitrification simultaneous nitrification and denitrification (COMMUNITY_PROCESS); simultaneous_nitrification_denitrification COMMUNITY_PROCESS simultaneous nitrification and denitrification
sludge_floc_oxygen_partitioning edges
EdgeSubjectPredicateObjectEvidence
sludge_contains_flocs sludge contains
Wastewater sludge contains flocs made of microbial cells, EPS, and adsorbed organic and inorganic material.		 activated sludge flocs PMID:12926675
Wilen and colleagues describe activated sludge flocs as aggregates of microorganisms, EPS, and adsorbed material.
eps_structures_flocs extracellular polymeric substances structures
Extracellular polymeric substances help define the composition, charge, hydrophobicity, and flocculation behavior of sludge flocs.		 activated sludge flocs PMID:12926675
Wilen and colleagues found that EPS quantity and quality were important for activated-sludge floc properties.
flocs_create_heterogeneous_matrix activated sludge flocs creates
Sludge flocs create heterogeneous suspended aggregate matrices.		 heterogeneous floc matrix PMID:12926675
Wilen and colleagues report heterogeneity in floc structure, morphology, and properties across activated sludges.
floc_matrix_generates_oxygen_gradients heterogeneous floc matrix creates
Oxygen consumption and diffusion limitation inside individual sludge flocs generate steep oxygen gradients.		 oxygen gradients PMID:12827702
Satoh and colleagues used microelectrodes to measure oxygen gradients inside individual activated-sludge flocs.
bulk_oxygen_controls_anoxic_interiors bulk dissolved oxygen controls
The bulk dissolved-oxygen concentration controls how deeply oxygen penetrates into sludge flocs.		 oxygen gradients PMID:12827702
Satoh and colleagues showed that oxygen penetration depth depended on the bulk oxygen concentration.
oxygen_gradients_form_oxic_zones oxygen gradients creates
Oxygen gradients partition aerated sludge flocs into oxic zones where oxygen is available.		 oxic floc zones PMID:12827702
Satoh and colleagues localized nitrification activity to oxic zones within activated-sludge flocs.
oxygen_gradients_form_anoxic_zones oxygen gradients creates
Limited oxygen penetration leaves anoxic zones inside larger activated-sludge flocs.		 anoxic floc zones PMID:12827702
Satoh and colleagues detected anoxic zones inside larger flocs at low bulk oxygen concentrations.
oxic_zones_enable_nitrification oxic floc zones enables
Oxic regions in sludge flocs support nitrification.		 nitrification PMID:12827702
Satoh and colleagues observed nitrification in the oxic parts of single activated-sludge flocs.
anoxic_zones_enable_denitrification anoxic floc zones enables
Anoxic regions in sludge flocs support denitrification.		 denitrification PMID:12827702
Satoh and colleagues observed denitrification mainly in anoxic parts of single activated-sludge flocs.
nitrification_contributes_to_snd nitrification contributes to
Oxic-zone nitrification contributes to simultaneous nitrification and denitrification in aerated sludge.		 simultaneous nitrification and denitrification PMID:12827702
Satoh and colleagues investigated simultaneous nitrification and denitrification in floccular municipal activated sludge.
denitrification_contributes_to_snd denitrification contributes to
Anoxic-zone denitrification contributes to simultaneous nitrification and denitrification in aerated sludge.		 simultaneous nitrification and denitrification PMID:12827702
Satoh and colleagues observed simultaneous nitrification and denitrification at intermediate dissolved-oxygen concentrations.

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
Tepidanaerobacter syntrophicus NCBITaxon:224999 BACDIVE 3 128 MADIN
Nannocystis exedens NCBITaxon:54 BACDIVE 4 441 PREGO
Sorangium cellulosum NCBITaxon:56 BACDIVE 5 441 PREGO
Micrococcus luteus NCBITaxon:1270 PREGO 13 803 MADIN
Methanobrevibacter arboriphilus NCBITaxon:39441 BACDIVE 14 128 PREGO
Anaerocolumna aminovalerica DSM 1283 NCBITaxon:1121297 BACDIVE 19 128 PREGO
Clostridium homopropionicum DSM 5847 NCBITaxon:1121318 BACDIVE 21 128 PREGO
[Clostridium] viride DSM 6836 NCBITaxon:1121344 BACDIVE 23 128 PREGO
Humibacter albus DSM 18994 NCBITaxon:1121952 BACDIVE 25 128 PREGO
gordonia_caeni NCBITaxon:1007097 MADIN — 153 BACDIVE
Methylophilus methylotrophus DSM 46235 NCBITaxon:1122236 MADIN — 153 PREGO
Moorella stamsii NCBITaxon:1266720 MADIN — 153 BACDIVE
bacteroides_coprosuis NCBITaxon:151276 MADIN — 153 PREGO
thauera_aminoaromatica NCBITaxon:164330 MADIN — 153 BACDIVE
thauera_phenylacetica NCBITaxon:164400 MADIN — 153 BACDIVE
herminiimonas_arsenicoxydans NCBITaxon:204773 MADIN — 153 PREGO
caenibacterium_thermophilum NCBITaxon:215580 MADIN — 153 BACDIVE
Anaerolinea thermolimosa NCBITaxon:229919 MADIN — 153 BACDIVE
Leptolinea tardivitalis NCBITaxon:229920 MADIN — 153 BACDIVE
Levilinea saccharolytica NCBITaxon:229921 MADIN — 153 BACDIVE
ethanoligenens_harbinense NCBITaxon:253239 MADIN — 153 BACDIVE
Methylobacillus flagellatus KT NCBITaxon:265072 MADIN — 153 PREGO
castellaniella_caeni NCBITaxon:266123 MADIN — 153 BACDIVE
Azonexus caeni NCBITaxon:266126 MADIN — 153 BACDIVE
Pseudomonas stutzeri NCBITaxon:316 MADIN — 153 PREGO

Showing 25 of 95 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:BACDIVE.75167cfd4a)

  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:BACDIVE.fa04cf38bb)

  3. 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.14620241d0)

  4. ADD_CAUSAL_GRAPH 2026-09-04 · codex

    Added a sludge floc oxygen-partitioning graph backed by PMID:12926675 and PMID:12827702.

Provenance

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