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Oak Ridge FRC Uranium-Nitrate Groundwater Community

Community ID CommunityMech:000136
Ecological State PERTURBED
Environment contaminated groundwater — ontology label: groundwater
ENVO:01001004 · HabitatMech ↗

A natural contaminated-groundwater microbial community from the U.S. DOE Oak Ridge Field Research Center, where groundwater wells span strong gradients in acidity, nitrate, uranium, and other metal contaminants. Clone-library and isolate studies link geochemistry to community structure, with lower diversity in highly contaminated wells and enrichment of organisms capable of uranium, nitrate, and iron reduction. This record represents the field community, distinct from existing defined ENIGMA denitrifying SynCom records derived from Oak Ridge isolates.

Taxonomy

Taxon Ontology ID Functional Roles Abundance
Rhodanobacter denitrificans and related Rhodanobacter spp. — ontology label: Rhodanobacter denitrificans NCBITaxon:666685 · TaxonMech · TraitMech
PRIMARY_DEGRADER SYNTROPHIC_PARTNER
DOMINANT
  • PMID:30523276 - SUPPORT (IN_VIVO)
    "In the most contaminated wells, the microbial community is enriched in the Rhodanobacter genus."
  • PMID:22140175 - SUPPORT (IN_VITRO)
    "these strains represent the first member of the genus Rhodanobacter shown to be capable of complete denitrification."
Pseudomonas spp. — ontology label: Pseudomonas NCBITaxon:286 · TaxonMech · TraitMech
PRIMARY_DEGRADER
N/A
  • PMID:22988623 - SUPPORT (IN_VIVO)
    "The high concentrations of contaminants present in well FW113-47 stimulated the growth of organisms capable of reducing uranium (Shewanella and Pseudomonas), nitrate (Pseudomonas, Rhodanobacter and Xanthomonas) and iron (Stenotrophomonas), and which were unique to this well."
Shewanella spp. — ontology label: Shewanella NCBITaxon:22 · TaxonMech · TraitMech
PRIMARY_DEGRADER
N/A
  • PMID:22988623 - SUPPORT (IN_VIVO)
    "The high concentrations of contaminants present in well FW113-47 stimulated the growth of organisms capable of reducing uranium (Shewanella and Pseudomonas), nitrate (Pseudomonas, Rhodanobacter and Xanthomonas) and iron (Stenotrophomonas), and which were unique to this well."
Stenotrophomonas spp. — ontology label: Stenotrophomonas NCBITaxon:40323 · TaxonMech · TraitMech
PRIMARY_DEGRADER
N/A
  • PMID:22988623 - SUPPORT (IN_VIVO)
    "The high concentrations of contaminants present in well FW113-47 stimulated the growth of organisms capable of reducing uranium (Shewanella and Pseudomonas), nitrate (Pseudomonas, Rhodanobacter and Xanthomonas) and iron (Stenotrophomonas), and which were unique to this well."

Ecological Interactions

The graph shows only explicitly linked interaction participants. Community members without an asserted participant link are omitted; membership alone does not imply an interaction.

Ecological interaction network for Oak Ridge FRC Uranium-Nitrate Groundwater Community Bipartite graph where circles represent taxa and non-circular symbols represent interactions. Rare or untyped interactions share the Other symbol; exact curated types remain in the interaction details.
Taxon
Other

Low-pH Mixed-Ion Rhodanobacter Tolerance

R2A dose-response and mixture assays support differential tolerance to low pH and seven metal ions: uranyl, manganese, aluminium, cadmium, zinc, cobalt and nickel. Eight Rhodanobacter isolates from contaminated wells grew under the pH-4 mixture, whereas 186 tested isolates from uncontaminated wells did not. This is an isolate-panel result, not a whole-groundwater-community perturbation or universal genus trait; strain provenance is confounded with genus, and some Pseudomonas isolates tolerate neutral-pH mixtures.

Metabolites: uranyl ion (CHEBI:43515 · MediaIngredientMech · CMMMech), manganese(2+) (CHEBI:29035 · MediaIngredientMech · CMMMech), aluminium(3+) (CHEBI:49470 · MediaIngredientMech · CMMMech), cadmium(2+) (CHEBI:48775 · MediaIngredientMech · CMMMech), zinc(2+) (CHEBI:29105 · MediaIngredientMech · CMMMech), cobalt(2+) (CHEBI:48828 · MediaIngredientMech · CMMMech), nickel(2+) (CHEBI:49786 · MediaIngredientMech · CMMMech)

Biological Processes:

Downstream Effects:
→ Contaminant-Selected Rhodanobacter Dominance

PARTIAL - Differential survival under low-pH mixed-metal stress supplies an experimentally supported selection mechanism for field Rhodanobacter enrichment when relevant ions reach inhibitory concentrations. This combines isolate perturbations with field abundance/geochemistry, not an in situ manipulation or proof that nitrate toxicity selects Rhodanobacter. Organic matter, speciation and strain provenance limit transfer of thresholds to groundwater.

Evidence

  • PMID:30523276 - SUPPORT (IN_VITRO)
    "few isolates aside from Rhodanobacter can tolerate these eight ions."
  • PMID:30523276 - SUPPORT (IN_VITRO)
    "selectively inhibitory of non-Rhodanobacter isolates from uncontaminated wells"

Contaminant-Selected Rhodanobacter Dominance

PARTIAL - Rhodanobacter genus enrichment in the most contaminated groundwater wells is consistent with the experimentally supported acid/mixed-metal tolerance mechanism. The field association and isolate perturbations support selective filtering, not demonstrated niche partitioning, species-resolved denitrification flux or universal Rhodanobacter resistance. Nitrate is a correlated co-contaminant and possible electron acceptor, not a selectively toxic driver in the tested strain comparison.

Metabolites: uranyl ion (CHEBI:43515 · MediaIngredientMech · CMMMech), nitrate (CHEBI:17632 · MediaIngredientMech · CMMMech)

Evidence

  • PMID:30523276 - SUPPORT (IN_VIVO)
    "In the most contaminated wells, the microbial community is enriched in the Rhodanobacter genus."
  • PMID:30523276 - SUPPORT (IN_VITRO)
    "few isolates aside from Rhodanobacter can tolerate these eight ions."

Mixed Metal and Nitrate Reduction Potential

PARTIAL - The four-well 16S clone-library study associates taxa in FW113-47 with previously recognized uranium-, nitrate- and iron-reducing capabilities and identifies bioremediation potential across the wells. The accessible abstract does not quantify community reduction rates or metabolite exchange. This redox-capacity inference is distinct from the later mixed-ion isolate-tolerance experiment; it does not demonstrate cross-feeding or prove that tolerant Rhodanobacter drive uranium immobilization.

Metabolites: nitrate (CHEBI:17632 · MediaIngredientMech · CMMMech)

Biological Processes:

Evidence

  • PMID:22988623 - PARTIAL (IN_VIVO)
    "Metal-reducing bacteria were present in all four wells, which may suggest that there is potential for successful bioremediation of the groundwater at the Oak Ridge FRC."
  • PMID:22988623 - PARTIAL (IN_VIVO)
    "The high concentrations of contaminants present in well FW113-47 stimulated the growth of organisms capable of reducing uranium (Shewanella and Pseudomonas), nitrate (Pseudomonas, Rhodanobacter and Xanthomonas) and iron (Stenotrophomonas), and which were unique to this well."

Knowledge gaps & discussions (1)

KNOWLEDGE_GAP OPEN How do isolate-specific metal tolerance and groundwater chemistry alter actual redox fluxes in the same wells?

The full tolerance paper supports a likely selective mechanism, but not the removed tolerance-to-redox-guild arrow. Field clone-library evidence remains abstract bounded after normal publisher access returned403. Quantify exact-well activity and distinguish nitrate respiration from selective nitrate toxicity. Canonical membership is preserved, not recertified at species level.

Attaches to: ecological_interactions#Low-pH Mixed-Ion Rhodanobacter Tolerance, ecological_interactions#Contaminant-Selected Rhodanobacter Dominance, ecological_interactions#Mixed Metal and Nitrate Reduction Potential

1 evidence item(s)
IN_VIVO PARTIAL PMID:22988623

Metal-reducing bacteria were present in all four wells, which may suggest that there is potential for successful bioremediation of the groundwater at the Oak Ridge FRC.

Supports taxon-associated redox potential in the field survey, not measured reduction flux, chemical speciation or interspecies transfer.

Environmental Factors

Factor Value Unit
Groundwater pH, nitrate, uranium, and metals pH 3 to 7; nitrate 44 to 23,400 mg/L; uranium 0.73 to 60.36 mg/L N/A
  • PMID:22988623 - SUPPORT (IN_VIVO)
    "Four groundwater wells (GW835, GW836, FW113-47 and FW215-49) with a wide range of pH (3 to 7), nitrate (44 to 23,400 mg L(-1)), uranium (0.73 to 60.36 mg L(-1)) and other metal contamination, were investigated."
Diversity loss under high contamination lower gene diversity in highly contaminated well FW113-47 N/A
  • PMID:22988623 - SUPPORT (IN_VIVO)
    "Microbial diversity decreased in relation to the contamination levels of the wells."
Selective metal ion stress low pH with UO2(2+), Zn(2+), Co(2+), Ni(2+), and other selective ions N/A
  • PMID:30523276 - SUPPORT (IN_VITRO)
    "low pH and high UO_{2}^{2+}, Mn^{2+}, Al^{3+}, Cd^{2+}, Zn^{2+}, Co^{2+}, and Ni^{2+} are both (a) selectively inhibitory of a Pseudomonas isolate from an uncontaminated well vs. a Rhodanobacter isolate from a contaminated well"

Cross-Mech Suite Links

Explore related entities across the CultureBotAI X-Mech knowledge bases:

HabitatMech: contaminated groundwater ↗ TaxonMech: Rhodanobacter denitrificans and related Rhodanobacter spp. ↗ TraitMech: Rhodanobacter denitrificans and related Rhodanobacter spp. ↗ TaxonMech: Pseudomonas spp. ↗ TraitMech: Pseudomonas spp. ↗ TaxonMech: Shewanella spp. ↗ TraitMech: Shewanella spp. ↗ TaxonMech: Stenotrophomonas spp. ↗ TraitMech: Stenotrophomonas spp. ↗ CMMMech (Critical Minerals & REE) ↗ CultureMech Growth Media ↗ PathwayMech Pathways ↗