bioreactor

ENVO:00002123 ·resolve ·ENGINEERED ·EXACT SEEDED

A biomaterial containment unit which is capable of 1) containing a mass of environmental material which hosts an active collection of organisms and 2) maintaining conditions which are conducive to one or more metabolic activities of the organisms it contains. — 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	bioreactor/digester Physicochemical parameter bands from kg-microbe's environment table.	—
GOLD	Engineered > Bioreactor 4 GOLD ecosystem node ids share this path; first shown. See data/raw/gold_ecosystem_paths.tsv.	604	ORGANISM
MADIN	bioreactor	232	TAXON
PREGO	bioreactor	101	TAXON

Broader habitats

biomaterial containment unit ENVO:01001816
Engineered habitatmech:GOLD.2acb39dd08

Environmental parameters

Physicochemical parameters
Parameter	Value	Source
GRADIENTS	low	kg-microbe environments.csv (bioreactor/digester)
NUTRIENTS	high	kg-microbe environments.csv (bioreactor/digester)
ORGANIC_MATTER	high	kg-microbe environments.csv (bioreactor/digester)
WATER_AVAILABILITY	high	kg-microbe environments.csv (bioreactor/digester)
WATER_VARIABILITY	permanently wet	kg-microbe environments.csv (bioreactor/digester)

Causal graphs

Bioreactor feed dilution biomass selection

Engineered bioreactor operation turns a containment vessel, liquid feed, hydraulic exchange, biomass retention, and physicochemical setpoints into a wet, nutrient-rich microbial habitat. The feed stream sets organic loading, outflow creates dilution pressure on suspended cells, retention surfaces keep attached biomass inside the vessel, and choices such as aeration, temperature, ammonia, organic loading rate, and hydraulic retention time select the community processes that transform influent into engineered products.

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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bioreactor_feed_dilution_biomass_selection edges
Edge	Subject	Predicate	Object	Evidence
`bioreactor_determined_by_containment`	bioreactor	determined by The parent bioreactor habitat is defined by a contained, actively managed reactor vessel that keeps microbial biomass and process medium inside engineered boundaries.	engineered containment vessel	`PMID:16207900` Hoskisson and Hobbs reviewed controlled continuous-culture bioreactors as vessels with managed inflow, outflow, and cultivation parameters.
`containment_maintains_liquid_medium`	engineered containment vessel	maintains The vessel holds the water-rich process medium in which feed, suspended biomass, products, and wastes are mixed.	liquid reactor medium	`PMID:16207900` The continuous-culture review describes liquid reactor cultures kept at controlled volume by matched medium addition and removal.
`containment_allows_operating_setpoints`	engineered containment vessel	enables Bioreactor construction gives operators levers such as flow, mixing, gas transfer, pH, and temperature control.	managed operating setpoints	`PMID:19041387` Garcia-Ochoa and Gomez reviewed how stirred-tank geometry, agitation, and gas flow control microbial oxygen transfer and mixing.
`setpoints_control_influent_feed`	managed operating setpoints	controls The selected feed composition and feed rate determine which carbon and nutrient substrates enter the reactor.	influent feed	`PMID:16207900` Continuous culture is operated by defined medium input and culture removal, making the feed stream an engineered selective pressure.
`influent_feed_sets_organic_loading`	influent feed	determines Influent substrate concentration and flow rate together set the organic loading rate experienced by the reactor microbiome.	organic loading rate	`PMID:36610483` Zhang and colleagues experimentally varied organic loading rate and hydraulic retention time in thermophilic anaerobic co-digestion reactors.
`setpoints_control_hydraulic_retention`	managed operating setpoints	controls Operators set the liquid flow relative to reactor volume, which fixes how long soluble substrates remain in the vessel.	hydraulic retention time	`PMID:36610483` The anaerobic co-digestion experiment treated HRT as an operational variable coupled to organic loading.
`hydraulic_retention_creates_dilution`	hydraulic retention time	determines Shorter hydraulic retention increases the rate at which medium and suspended cells leave the bioreactor.	dilution pressure	`PMID:16207900` Hoskisson and Hobbs reviewed chemostat operation, where dilution rate links flow through the vessel to steady-state microbial growth.
`dilution_selects_retained_microbiome`	dilution pressure	selects for Reactor outflow selects organisms and attachment modes able to persist despite washout of non-retained suspended cells.	retained bioreactor microbiome	`PMID:16207900` In continuous culture, dilution rate constrains the growth rate needed for planktonic organisms to remain in the reactor.
`setpoints_control_mixing_aeration`	managed operating setpoints	controls Agitation and gas flow set mixing intensity and oxygen transfer into the liquid reactor medium.	mixing and aeration regime	`PMID:19041387` The bioreactor scale-up review identifies stirring and gas-flow variables as controls over microbial mass transfer and mixing.
`mixing_aeration_shapes_microbiome`	mixing and aeration regime	selects for Aeration and mixing alter oxygen availability and substrate exposure, making them physicochemical filters on reactor communities.	retained bioreactor microbiome	`PMID:19041387` Garcia-Ochoa and Gomez linked reactor agitation and oxygen transfer to the microbial process environment.
`containment_supports_retention_surfaces`	engineered containment vessel	supports Biofilm-based reactor designs add fixed or carrier surfaces inside the vessel to keep attached microbial biomass in contact with the flowing liquid.	biomass retention surface	`DOI:10.1186/s13068-024-02592-4` Abera and colleagues reviewed fixed-film and carrier-based anaerobic digesters in which biofilms retain microbial biomass.
`surfaces_harbor_attached_biofilm`	biomass retention surface	harbors Carrier surfaces and fixed-bed matrices give reactor microorganisms places to attach as biofilms rather than leave with the bulk liquid.	attached biofilm	`DOI:10.1186/s13068-024-02592-4` Abera and colleagues systematically reviewed anaerobic-digestion biofilm systems and their use to retain reactor biomass.
`attached_biofilm_retains_microbiome`	attached biofilm	retains Biofilms increase biomass retention, protecting reactor communities from hydraulic washout.	retained bioreactor microbiome	`DOI:10.1186/s13068-024-02592-4` The biofilm review summarized fixed-film strategies that extend biomass retention time in anaerobic digesters.
`organic_loading_hydraulic_retention_select_microbiome`	organic loading rate	selects for Organic loading rate and hydraulic residence jointly shape reactor performance, community interactions, and functional traits.	retained bioreactor microbiome	`PMID:36610483` Zhang and colleagues found that HRT and OLR changed organics degradation, syntrophic interactions, and functional profiles in anaerobic co-digestion.
`operating_setpoints_select_microbiome`	managed operating setpoints	selects for Shared operating conditions impose deterministic selection on replicate engineered digester communities.	retained bioreactor microbiome	`DOI:10.1038/ismej.2014.50` Vanwonterghem and colleagues observed synchronized population dynamics across replicate anaerobic digesters run under the same conditions. `PMID:25819618` De Vrieze and colleagues found ammonia and temperature separated clusters of anaerobic-digestion microbiomes.
`retained_microbiome_performs_syntrophy`	retained bioreactor microbiome	performs In anaerobic digester variants, retained bacterial and archaeal populations cooperate through syntrophic conversion of fermentation intermediates.	anaerobic syntrophy	`PMID:24246480` Town and colleagues profiled anaerobic digester communities and linked microbial populations with reactor performance. `PMID:21558697` Hattori reviewed syntrophic acetate-oxidizing microbes that cooperate with methanogens in anaerobic systems.
`syntrophy_produces_acetate_hydrogen_formate`	anaerobic syntrophy	produces Syntrophic food webs interconvert fermentation products into acetate, hydrogen, and formate used by methanogens.	acetate, hydrogen, and formate	`PMID:21558697` Hattori reviewed acetate oxidation as a syntrophic process coupled to hydrogen- or formate-consuming methanogenesis.
`methanogens_convert_intermediates_to_methane`	acetate, hydrogen, and formate	fuels Methanogenic archaea consume acetate or reduced one-carbon intermediates to produce methane in anaerobic reactor communities.	methanogenic archaea	`PMID:21558697` Syntrophic acetate oxidation depends on methanogens that keep hydrogen or formate low enough to make acetate oxidation favorable.
`methanogenic_archaea_produce_methane`	methanogenic archaea	produces Methanogenic archaea are the terminal methane-producing guild in anaerobic bioreactor food webs.	methane	`PMID:24246480` The anaerobic digester community study used methanogenic archaea as a key guild when relating community composition to methane-producing reactor function.

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
Tepidanaerobacter acetatoxydans Re1 `NCBITaxon:1209989`	PREGO	2	101	MADIN
clostridium_amylolyticum `NCBITaxon:1121298`	MADIN	—	232	PREGO
clostridium_caenicola `NCBITaxon:659425`	MADIN	—	232	PREGO
Hydrogenispora ethanolica `NCBITaxon:1082276`	PREGO	1	101
Bacteroides luti `NCBITaxon:1297750`	PREGO	3	101
Clostridiaceae bacterium JGI 000176CP_B01 `NCBITaxon:1938638`	PREGO	4	101
Clostridiaceae bacterium JGI 000176CP_E08 `NCBITaxon:1938639`	PREGO	5	101
Clostridiales bacterium JGI 000170CP_A02 `NCBITaxon:1938641`	PREGO	6	101
Clostridiales bacterium JGI 000170CP_C01 `NCBITaxon:1938642`	PREGO	7	101
Clostridiales bacterium JGI 000170CP_C03 `NCBITaxon:1938643`	PREGO	8	101
Clostridiales bacterium JGI 000176CP_B07 `NCBITaxon:1938647`	PREGO	9	101
Clostridiales bacterium JGI 000176CP_E06 `NCBITaxon:1938649`	PREGO	10	101
Lachnospiraceae bacterium JGI 000170CP_F01 `NCBITaxon:1938652`	PREGO	11	101
Ruminococcaceae bacterium JGI 000176CP_B03 `NCBITaxon:1938653`	PREGO	12	101
Alkaliphilus sp. JGI 000170CP_B06 `NCBITaxon:1938739`	PREGO	13	101
Clostridium sp. JGI 000170CP_A06 `NCBITaxon:1938748`	PREGO	14	101
Clostridium sp. JGI 000170CP_E05 `NCBITaxon:1938750`	PREGO	15	101
Comamonas sp. JGI 000176CP_D06 `NCBITaxon:1938752`	PREGO	16	101
Spirosoma sp. JGI 000178CP_D11 `NCBITaxon:1938825`	PREGO	17	101
Streptococcus sp. JGI 000170CP_B04 `NCBITaxon:1938826`	PREGO	18	101
Streptococcus sp. JGI 000170CP_G01 `NCBITaxon:1938829`	PREGO	19	101
Syntrophomonas sp. JGI 000170CP_G06 `NCBITaxon:1938864`	PREGO	20	101
Syntrophomonas sp. JGI 000170CP_C07 `NCBITaxon:1938865`	PREGO	21	101
Alkaliphilus sp. JGI 000170CP_H07 `NCBITaxon:1938867`	PREGO	22	101
Clostridium sp. JGI 000170CP_A08 `NCBITaxon:1938868`	PREGO	23	101

Showing 25 of 49 kept associations.

Also called

bioreactors — PREGO

Curation

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

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.a6d15fca9f)
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.653b468218)
ADD_CAUSAL_GRAPH 2026-09-04 · codex
Added a bioreactor feed dilution biomass selection graph backed by PMID:16207900, PMID:19041387, PMID:36610483, DOI:10.1186/s13068-024-02592-4, DOI:10.1038/ismej.2014.50, PMID:25819618, PMID:24246480, and PMID:21558697.

Provenance

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