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KBase ORT Workflow Community Model

Community ID CommunityMech:000038
Ecological State ENGINEERED
Environment river sediment
ENVO:00002127

Public KBase ORT workflow narrative that includes genome annotation, metabolic model reconstruction and gapfilling, merged community model generation, and flux balance analysis.

Taxonomy

Taxon Ontology ID Functional Roles Abundance
Nitrososphaeraceae archaeon NCBITaxon:1033997
PRIMARY_PRODUCER
N/A
  • PMID:34726691 - PARTIAL (COMPUTATIONAL)
    "environmental metagenomic data from a river system"
Nitrospiraceae bacterium NCBITaxon:189779
PRIMARY_PRODUCER
N/A
  • PMID:34726691 - PARTIAL (COMPUTATIONAL)
    "environmental metagenomic data from a river system"
Steroidobacteraceae denitrifier 1 NCBITaxon:2689614
SECONDARY_FERMENTER
N/A
  • PMID:34726691 - PARTIAL (COMPUTATIONAL)
    "environmental metagenomic data from a river system"
Steroidobacteraceae denitrifier 2 NCBITaxon:2689614
SECONDARY_FERMENTER
N/A
  • PMID:34726691 - PARTIAL (COMPUTATIONAL)
    "environmental metagenomic data from a river system"

Ecological Interactions

Ecological interaction network for KBase ORT Workflow Community Model Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction (syntrophy).
Taxon
Syntrophy

Coupled Nitrification in Columbia River Sediments

SYNTROPHY

Metabolites: ammonium (CHEBI:28938), nitrite (CHEBI:16301), nitrate (CHEBI:17632)

Biological Processes:

Evidence

  • PMID:34726691 - SUPPORT (COMPUTATIONAL)
    "predict nitrogen cycling patterns with site-specific insight into the chemical and biological drivers of nitrification and denitrification processes"

Nitrate-to-Nitrogen Gas Denitrification

SYNTROPHY

Metabolites: nitrate (CHEBI:17632), nitrogen (CHEBI:17997), betaine (CHEBI:17750), leucine (CHEBI:15603), choline (CHEBI:15354)

Biological Processes:

Evidence

  • PMID:34726691 - SUPPORT (COMPUTATIONAL)
    "GSMs identified additional carbon sources utilized, enabling more precise identification of the biogeochemical limiting factors in the system"
  • PMID:34726691 - SUPPORT (COMPUTATIONAL)
    "predict nitrogen cycling patterns with site-specific insight into the chemical and biological drivers of nitrification and denitrification processes"

Associated Datasets

Dataset Type Repository Accession
Primary publication
Bioinformatics publication describing the ORT workflow coupling genome-scale metabolic models with reactive transport modeling for nitrogen cycling. 		OTHER OTHER PMID:34726691

External Resources

Name Repository Resource ID
KBase narrative
ORT: KBase Workflow narrative page with merged community modeling steps. 		KBASE ws.71260.obj.262
  • PMID:34726691 - SUPPORT (COMPUTATIONAL)
    "The approach is applied to environmental metagenomic data from a river system predicted nitrogen cycling patterns"
  • PMID:29979655 - SUPPORT (COMPUTATIONAL)
    "KBase: The United States Department of Energy Systems Biology Knowledgebase."