KBase ORT Workflow Community Model

Community ID CommunityMech:000038

Ecological State ENGINEERED

Environment river sediment
ENVO:00002359

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:2157	PRIMARY_PRODUCER	N/A
PMID:34726691 - PARTIAL (COMPUTATIONAL) "environmental metagenomic data from a river system"
Nitrospiraceae bacterium	NCBITaxon:1236	PRIMARY_PRODUCER	N/A
PMID:34726691 - PARTIAL (COMPUTATIONAL) "environmental metagenomic data from a river system"
Steroidobacteraceae denitrifier 1	NCBITaxon:1236	SECONDARY_FERMENTER	N/A
PMID:34726691 - PARTIAL (COMPUTATIONAL) "environmental metagenomic data from a river system"
Steroidobacteraceae denitrifier 2	NCBITaxon:1236	SECONDARY_FERMENTER	N/A
PMID:34726691 - PARTIAL (COMPUTATIONAL) "environmental metagenomic data from a river system"

Ecological Interactions

Taxon

Cross-feeding

Mutualism

Syntrophy

Competition

Commensalism

Niche partitioning

Colonization facilitation

Strain competition

Predation

Coupled Nitrification in Columbia River Sediments

SYNTROPHY

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

Biological Processes:

nitrification (GO:0019329)

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:

denitrification (GO:0019333)

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."