root nodule

ENVO:01000164 ·resolve ·HOST_ASSOCIATED ·EXACT REVIEWED

Root nodules occur on the roots of plants that associate with symbiotic nitrogen-fixing bacteria. — ENVO

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	host_plant_rootnodule Physicochemical parameter bands from kg-microbe's environment table.	—
GOLD	Host-associated > Plants > Nodule 3 GOLD ecosystem node ids share this path; first shown. See data/raw/gold_ecosystem_paths.tsv.	369	ORGANISM
MADIN	root nodule	40	TAXON

Broader habitats

organ ENVO:01000162
plant-associated environment ENVO:01001001

Environmental parameters

Physicochemical parameters
Parameter	Value	Source
GRADIENTS	high	kg-microbe environments.csv (host_plant_rootnodule)
NUTRIENTS	high	kg-microbe environments.csv (host_plant_rootnodule)
ORGANIC_MATTER	high	kg-microbe environments.csv (host_plant_rootnodule)
PH	medium	kg-microbe environments.csv (host_plant_rootnodule)
PRESSURE	low	kg-microbe environments.csv (host_plant_rootnodule)
SALINITY_VARIABILITY	small	kg-microbe environments.csv (host_plant_rootnodule)
STRUCTURAL_COMPLEXITY	high	kg-microbe environments.csv (host_plant_rootnodule)
TEMPERATURE_VARIABILITY	medium	kg-microbe environments.csv (host_plant_rootnodule)
WATER_AVAILABILITY	high	kg-microbe environments.csv (host_plant_rootnodule)
WATER_VARIABILITY	permanently wet	kg-microbe environments.csv (host_plant_rootnodule)

Causal graphs

Root nodule symbiotic nitrogen fixation

Plant root nodules are organ-level microbial habitats formed when roots recruit compatible nitrogen-fixing bacteria. Rhizobial Nod-factor signaling induces root-hair infection and nodule organogenesis, infection threads carry bacteria into developing nodule cells, symbiosomes house differentiated bacteroids, and the plant-controlled low-oxygen nodule cytoplasm allows nitrogenase to reduce atmospheric N2 to ammonia. Actinorhizal nodules use Frankia rather than rhizobia but converge on the same protected intracellular nitrogen-fixation habitat.

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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root_nodule_symbiotic_nitrogen_fixation edges
Edge	Subject	Predicate	Object	Evidence
`root_nodule_determined_by_root`	root nodule	determined by Root nodules are specialized root outgrowths on plants that maintain symbiotic nitrogen-fixing bacteria.	host plant root	`PMID:33526611` Ledermann, Schulte, and Poole reviewed nodules as root organs that house diazotrophic bacterial symbionts.
`root_releases_flavonoids`	host plant root	releases Host roots exude flavonoid signals that initiate compatible rhizobial nodulation responses.	flavonoid signals	`PMID:15187185` Gage reviewed flavonoid induction of rhizobial nod genes during legume nodule initiation.
`flavonoids_select_rhizobia`	flavonoid signals	selects for Flavonoid signaling favors rhizobia carrying compatible nod gene regulation and host-specific signal production.	rhizobia	`PMID:15187185` The nodulation review describes flavonoid-regulated rhizobial Nod factor synthesis as an early specificity step.
`rhizobia_produce_nod_factors`	rhizobia	produces Compatible rhizobia respond to host signals by producing lipochitooligosaccharide Nod factors.	Nod factors	`DOI:10.1128/MMBR.68.2.280-300.2004` Gage reviewed how rhizobial Nod factors trigger host root-hair and cortical responses in temperate legumes.
`nod_factors_induce_infection`	Nod factors	induces Nod-factor perception redirects root-hair growth around rhizobia and starts the infection process.	root hair infection	`PMID:15187185` The MMBR review details root-hair curling and infection-thread initiation during rhizobial invasion.
`nod_factors_initiate_primordium`	Nod factors	induces Nod-factor signaling coordinates infection with cortical cell divisions that initiate the nodule primordium.	nodule primordium	`PMID:15187185` Gage reviewed the coupling of bacterial invasion to host developmental events that form the root nodule.
`root_hair_infection_forms_thread`	root hair infection	produces Root-hair infection produces infection threads that conduct rhizobia through the host root tissue.	infection thread	`DOI:10.1128/MMBR.68.2.280-300.2004` The rhizobial infection review describes infection-thread growth from curled root hairs into developing nodules.
`infection_thread_delivers_rhizobia`	infection thread	transports Infection threads carry rhizobial cells toward developing nodule primordia.	rhizobia	`PMID:15187185` Gage reviewed infection threads as plant-derived channels that advance the invading rhizobial population through host tissue.
`nodule_primordium_forms_infected_cells`	nodule primordium	produces Primordium development creates nodule cells that are invaded by bacterial symbionts.	infected nodule cell	`PMID:33526611` The nodule-environment review summarizes rhizobial release into plant cells and subsequent adaptation to intracellular life.
`infected_cell_contains_symbiosome`	infected nodule cell	contains In legume nodules, plant-derived symbiosomes form intracellular compartments around rhizobia.	symbiosome	`PMID:33526611` Ledermann and colleagues reviewed the intracellular symbiosome as the compartment in which rhizobia differentiate.
`symbiosome_harbors_bacteroids`	symbiosome	harbors Symbiosomes contain differentiated bacteroids that specialize in symbiotic nitrogen fixation.	bacteroids	`PMID:34330708` Schulte and colleagues modeled and experimentally studied nitrogen fixation by bacteroids inside legume symbiosomes.
`infected_cell_supplies_dicarboxylates`	infected nodule cell	feeds Host nodule cells provide C4-dicarboxylate carbon sources that fuel bacteroid energy metabolism.	plant dicarboxylates	`DOI:10.1126/sciadv.abh2433` Schulte and colleagues showed that plant control of dicarboxylate supply is central to rhizobial nitrogen-fixation metabolism.
`dicarboxylates_fuel_bacteroids`	plant dicarboxylates	fuels Bacteroids oxidize host-supplied dicarboxylates to generate energy and reductant for nitrogen fixation.	bacteroids	`PMID:34330708` The Sci Adv study identified dicarboxylate use as the dominant energy and electron source for nitrogen-fixing bacteroids.
`infected_cells_express_leghemoglobin`	infected nodule cell	produces Infected legume nodule cells express leghemoglobin as part of the plant oxygen-control system.	leghemoglobin	`PMID:31655741` Rutten and Poole reviewed the oxygen paradox of root nodules and mechanisms that maintain respiration while protecting nitrogenase.
`leghemoglobin_maintains_low_oxygen`	leghemoglobin	maintains Leghemoglobin buffers free oxygen in infected cells, preserving a low-oxygen state around bacteroids.	low-oxygen nodule cytoplasm	`DOI:10.1016/bs.ampbs.2019.08.001` The rhizobial oxygen-regulation review describes the low-oxygen nodule environment that permits microaerobic respiration and nitrogenase activity.
`low_oxygen_enables_nitrogenase`	low-oxygen nodule cytoplasm	enables The microoxic nodule state protects oxygen-sensitive nitrogenase while permitting enough respiration for ATP production.	nitrogenase	`PMID:31655741` Rutten and Poole reviewed why nodules tightly regulate oxygen around bacteroids performing nitrogen fixation.
`bacteroids_express_nitrogenase`	bacteroids	expresses Mature bacteroids express nitrogenase to reduce atmospheric dinitrogen inside nodules.	nitrogenase	`PMID:33526611` The rhizobial adaptation review links bacteroid differentiation to the nitrogen-fixing physiology required in nodules.
`nitrogenase_drives_fixation`	nitrogenase	drives Nitrogenase catalyzes biological reduction of atmospheric N2 within infected nodule cells.	biological nitrogen fixation	`DOI:10.1126/sciadv.abh2433` Schulte and colleagues studied rhizobial nitrogenase activity as the terminal sink for carbon and reductant supplied by the host.
`fixation_produces_ammonia`	biological nitrogen fixation	produces Symbiotic nitrogen fixation reduces N2 into ammonia that can be assimilated into plant nitrogen metabolism.	ammonia	`PMID:34330708` The metabolic-control study found that legume hosts promote ammonia secretion by bacteroids by coupling oxygen and dicarboxylate supply.
`root_nodules_harbor_frankia`	root nodule	harbors Actinorhizal root nodules are intracellular habitats for nitrogen-fixing Frankia actinobacteria.	Frankia	`PMID:33863007` Huss-Danell reviewed root nodule symbioses between actinorhizal plants and the actinomycete genus Frankia.
`frankia_expresses_nitrogenase`	Frankia	expresses Frankia in actinorhizal nodules protects nitrogenase inside specialized infected cells or vesicles.	nitrogenase	`DOI:10.1046/j.1469-8137.1997.00755.x` The actinorhizal review describes Frankia vesicles and host adaptations that balance oxygen tension near nitrogenase.

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
Neorhizobium galegae bv. orientalis str. HAMBI 540 `NCBITaxon:1028800`	MADIN	—	40
Bradyrhizobium sp. CCGE-LA001 `NCBITaxon:1223566`	MADIN	—	40
Bradyrhizobium icense `NCBITaxon:1274631`	MADIN	—	40
Rhizobium sp. N113 `NCBITaxon:1703960`	MADIN	—	40
Rhizobium sp. N1314 `NCBITaxon:1703961`	MADIN	—	40
Rhizobium sp. N1341 `NCBITaxon:1703962`	MADIN	—	40
Rhizobium sp. N561 `NCBITaxon:1703963`	MADIN	—	40
Rhizobium sp. N621 `NCBITaxon:1703964`	MADIN	—	40
Rhizobium sp. N6212 `NCBITaxon:1703965`	MADIN	—	40
Rhizobium sp. N731 `NCBITaxon:1703966`	MADIN	—	40
Rhizobium sp. N741 `NCBITaxon:1703967`	MADIN	—	40
Rhizobium sp. N871 `NCBITaxon:1703968`	MADIN	—	40
Rhizobium sp. N324 `NCBITaxon:1703969`	MADIN	—	40
Rhizobium sp. N541 `NCBITaxon:1703970`	MADIN	—	40
Rhizobium sp. N941 `NCBITaxon:1703971`	MADIN	—	40
Rhizobium sp. WYCCWR10014 `NCBITaxon:1825933`	MADIN	—	40
sinorhizobium_americanum `NCBITaxon:194963`	MADIN	—	40
burkholderia_sabiae `NCBITaxon:273251`	MADIN	—	40
kribbella_lupini `NCBITaxon:291602`	MADIN	—	40
Frankia sp. EAN1pec `NCBITaxon:298653`	MADIN	—	40
Phyllobacterium leguminum `NCBITaxon:314237`	MADIN	—	40
Phyllobacterium ifriqiyense `NCBITaxon:314238`	MADIN	—	40
ochrobactrum_ciceri `NCBITaxon:391287`	MADIN	—	40
rhizobium_phaseoli `NCBITaxon:396`	MADIN	—	40
ochrobactrum_cytisi `NCBITaxon:407152`	MADIN	—	40

Also called

Nodule — GOLD

Curation

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

GROUND 2026-08-14 · claude-opus-5
Grounded to ENVO:01000164 'root nodule' (EXACT). Grounding-cohort review (#62): was UBERON:0004083 'cerebellum vermis lobule X', matched because that term carries 'nodule' as a synonym. GOLD's path is Host-associated > Plants > Nodule, so this is a plant root nodule. Merges with the environment table's and Madin's root-nodule records, which is three sources agreeing on one habitat. (source concept habitatmech:GOLD.c6e9ea67fd)
REVIEW 2026-08-16 · claude-opus-5
Reviewed and endorsed the seeder's own resolution. Risky-grounding review (#12), co-attestor pass: this source concept feeds a record whose grounding was flagged and reviewed, and the record could not reach REVIEWED until every source feeding it was decided. This one is a self-grounding: the source vocabulary names the concept with the ontology term's own label, so there is nothing to adjudicate between the two — checked that the term is the one the label denotes, and that the record it merges into is the same concept rather than a homonym. (source concept habitatmech:MADIN.08ac66c193)
ADD_CAUSAL_GRAPH 2026-09-04 · codex
Added a root nodule symbiotic nitrogen fixation graph backed by PMID:33526611, PMID:15187185, DOI:10.1128/MMBR.68.2.280-300.2004, PMID:34330708, DOI:10.1126/sciadv.abh2433, PMID:31655741, DOI:10.1016/bs.ampbs.2019.08.001, PMID:33863007, and DOI:10.1046/j.1469-8137.1997.00755.x.

Provenance

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