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ENIGMA Denitrifying SynCom

Community ID CommunityMech:000024
Ecological State ENGINEERED
Environment contaminated soil
ENVO:00002116 · HabitatMech ↗

A two-member denitrifying synthetic community from the ENIGMA program, composed of Rhodanobacter thiooxydans FW510-R12 and Acidovorax sp. GW101-3H11 isolated from a heavily nitrate-contaminated superfund site. The consortium exhibits pathway-partitioned denitrification via nitrite and nitric oxide exchange, with cooperativity that can be disrupted under high nitrate conditions leading to nitrite accumulation and nitrous oxide off-gassing.

Taxonomy

Taxon Ontology ID Functional Roles Abundance
Rhodanobacter thiooxydans FW510-R12 — ontology label: Rhodanobacter thiooxydans NCBITaxon:416169 · TaxonMech · TraitMech
SYNTROPHIC_PARTNER CROSS_FEEDER
N/A
  • PMID:40349173 - SUPPORT (IN_VITRO)
    "We have investigated mechanisms and consequences of process partitioning of denitrification through detailed physiological characterization and kinetic modeling of a synthetic community of Rhodanobacter thiooxydans FW510-R12 and Acidovorax sp. GW101-3H11"
  • PMID:40349173 - SUPPORT (IN_VITRO)
    "We have discovered that these two bacterial isolates, from a heavily nitrate (NO3-) contaminated superfund site, complete denitrification through the exchange of nitrite (NO2-) and nitric oxide (NO)"
Acidovorax sp. GW101-3H11 — ontology label: Acidovorax sp. NCBITaxon:1872122 · TaxonMech · TraitMech
SYNTROPHIC_PARTNER CROSS_FEEDER
N/A
  • PMID:40349173 - SUPPORT (IN_VITRO)
    "We have investigated mechanisms and consequences of process partitioning of denitrification through detailed physiological characterization and kinetic modeling of a synthetic community of Rhodanobacter thiooxydans FW510-R12 and Acidovorax sp. GW101-3H11"
  • PMID:40349173 - SUPPORT (IN_VITRO)
    "We have discovered that these two bacterial isolates, from a heavily nitrate (NO3-) contaminated superfund site, complete denitrification through the exchange of nitrite (NO2-) and nitric oxide (NO)"

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 ENIGMA Denitrifying SynCom 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

Pathway-Partitioned Denitrification Cooperation

The anaerobic two-member SynCom grows faster than either monoculture and clears transient nitrite without accumulating N2O under the tested cooperative conditions. 3H11 supplies nitrite to R12; reverse nitric-oxide transfer from R12 to 3H11 is a kinetic-model inference supported by transcription, not directly measured NO flux. Both isolates grow separately on nitrate, so this is not obligate partner dependence. Complete reduction to N2 was inferred from product accounting, not a direct N2 measurement.

Participating Taxa: Rhodanobacter thiooxydans FW510-R12, Acidovorax sp. GW101-3H11

Metabolites: nitrite (CHEBI:16301 · MediaIngredientMech · CMMMech), nitric oxide (CHEBI:16480 · MediaIngredientMech · CMMMech)

Biological Processes:

Evidence

  • PMID:40349173 - PARTIAL (COMPUTATIONAL)
    "We have discovered that these two bacterial isolates, from a heavily nitrate (NO3-) contaminated superfund site, complete denitrification through the exchange of nitrite (NO2-) and nitric oxide (NO)"
  • PMID:40349173 - SUPPORT (IN_VITRO)
    "The SynCom growth rate was significantly greater than the growth rate of both isolates in monoculture"

High-Nitrate Destabilization of Cooperation

Experiments varied initial nitrate (1-40 mM at equal inoculation) or starting composition (5-98% 3H11 at 10 mM nitrate). Higher nitrate and larger initial 3H11 fractions were associated with greater endpoint N2O. Differences in substrate kinetics can unbalance nitrite production and removal; proteomic trends suggest competition but also admit nutritional complementarity. This is a context-dependent community response, not established pairwise competitive harm.

Participating Taxa: Rhodanobacter thiooxydans FW510-R12, Acidovorax sp. GW101-3H11

Biological Processes:

Downstream Effects:
→ Toxic Nitrite Accumulation and N2O Off-Gassing

PARTIAL - faster 3H11 nitrate reduction relative to R12 nitrite removal can increase toxic nitrite exposure. Across varied nitrate and inoculum ratios, kinetic-model predictions of nitrite exposure correlate with measured endpoint N2O; selective SynCom nitrite mediation was not isolated.

Evidence

  • PMID:40349173 - SUPPORT (IN_VITRO)
    "We demonstrate that certain contexts, such as high NO3-, cause unbalanced growth of community members, due to differences in their substrate utilization kinetics"
  • PMID:40349173 - PARTIAL (COMPUTATIONAL)
    "The altered growth characteristics of community members drives accumulation of toxic NO2-, which disrupts denitrification causing N2O off gassing"

Toxic Nitrite Accumulation and N2O Off-Gassing

Nitrite inhibited both isolates in monoculture. In nitrate- and composition-varied SynCom experiments, predicted nitrite exposure correlated with measured endpoint N2O accumulation, supporting toxicity as a mechanism that limits complete denitrification. High-condition SynCom nitrite exposure and the approximate toxicity threshold were model-derived; N2O accumulation was measured. This does not establish pairwise competition or prove that N2O itself inhibits cooperation.

Participating Taxa: Rhodanobacter thiooxydans FW510-R12, Acidovorax sp. GW101-3H11

Metabolites: nitrite (CHEBI:16301 · MediaIngredientMech · CMMMech), dinitrogen oxide (CHEBI:17045 · MediaIngredientMech · CMMMech)

Biological Processes:

Downstream Effects:
→ Pathway-Partitioned Denitrification Cooperation

PARTIAL - accumulated nitrite can inhibit partner growth and thereby impair completion of the shared denitrification pathway. Monoculture inhibition and model-to-N2O correspondence support this negative effect, not selective proof that NO exchange fails in the SynCom or that N2O is the inhibitory agent.

Evidence

  • PMID:40349173 - PARTIAL (COMPUTATIONAL)
    "The altered growth characteristics of community members drives accumulation of toxic NO2-, which disrupts denitrification causing N2O off gassing"

Associated Datasets

Dataset Type Repository Accession
SynCom transcriptome sequencing
Raw sequencing data for transcriptomics analysis of monoculture and SynCom contexts. 		METATRANSCRIPTOMICS OTHER GSE272493
SynCom proteomics dataset
Mass spectrometry proteomics data deposited through PRIDE/ProteomeXchange. 		METAPROTEOMICS OTHER PXD051979
Rhodanobacter thiooxydans FW510-R12 genome
Genome resource used for R12-specific transcript quantification and modeling. 		GENOMICS NCBI_BIOPROJECT PRJNA255897
Acidovorax sp. GW101-3H11 genome
Genome resource used for 3H11-specific transcript quantification and modeling. 		GENOMICS NCBI_BIOPROJECT PRJNA314893
SynCom model and analysis code
Code, summary tables, and model outputs for growth, metabolite, transcriptomics, and proteomics analyses. 		OTHER OTHER github:baliga-lab/3H11_R12_SynCom

Knowledge gaps & discussions (1)

KNOWLEDGE_GAP OPEN Which exchange fluxes and inhibitory steps directly mediate SynCom behavior?

NO reduction rates and transfer were not measured; the model combined NO2-to-N2O steps and adjusted energetic contributions to represent the proposed NO handoff. Preserve measured nitrate/nitrite/N2O physiology separately from modeled exchange and high-condition exposure. Selective nitrite/NO perturbations and direct flux measurements would distinguish mechanisms; proteomic competition and amino-acid exchange remain alternative hypotheses. Non-graph certainty language is tracked by #1415.

Attaches to: ecological_interactions#Pathway-Partitioned Denitrification Cooperation, ecological_interactions#High-Nitrate Destabilization of Cooperation, ecological_interactions#Toxic Nitrite Accumulation and N2O Off-Gassing

Environmental Factors

Factor Value Unit
Nitrate loading context high NO3- N/A
  • PMID:40349173 - SUPPORT (IN_VITRO)
    "We demonstrate that certain contexts, such as high NO3-, cause unbalanced growth of community members, due to differences in their substrate utilization kinetics"
Nitrite toxicity and N2O off-gassing toxic NO2- accumulation with N2O release N/A
  • PMID:40349173 - SUPPORT (IN_VITRO)
    "The altered growth characteristics of community members drives accumulation of toxic NO2-, which disrupts denitrification causing N2O off gassing"

Growth Media

defined anaerobic minimal medium (20 mM sodium acetate, 10 mM sodium nitrate, 0.1 g/L yeast extract)

pH 7.2
Temperature 30 °C
Atmosphere ANAEROBIC

Preparation notes: NO3- reduction growth studies were run in a defined minimal medium with 20 mM sodium acetate and 10 mM sodium NO3- plus 0.1 g/L yeast extract to support growth of 3H11 and R12; media were prepared in serum bottles and aliquoted into N2-CO2-flushed, pressurized Balch tubes. Starter cultures were grown in R2A liquid medium at 30 °C with shaking at 100 rpm.

Evidence

PMID:40349173

"NO3− reduction growth studies were performed in Balch tubes (10-ml culture volume) at 30°C in a defined minimal medium as described previously containing 20 mM sodium acetate and 10 mM sodium NO3− at pH 7.2 with a 80:20 N2-CO2 headspace"

PMID:40349173

"Liquid R2A cultures were incubated at 30°C with shaking at 100 rpm."

Cross-Mech Suite Links

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

HabitatMech: contaminated soil ↗ TaxonMech: Rhodanobacter thiooxydans FW510-R12 ↗ TraitMech: Rhodanobacter thiooxydans FW510-R12 ↗ TaxonMech: Acidovorax sp. GW101-3H11 ↗ TraitMech: Acidovorax sp. GW101-3H11 ↗ CultureMech Growth Media ↗ PathwayMech Pathways ↗