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 — ontology label: Nitrososphaeraceae | NCBITaxon:1033997 · TaxonMech · TraitMech |
PRIMARY_PRODUCER
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N/A |
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| Nitrospiraceae bacterium — ontology label: Nitrospiraceae | NCBITaxon:189779 · TaxonMech · TraitMech |
PRIMARY_PRODUCER
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N/A |
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| Steroidobacteraceae denitrifier 1 — ontology label: Steroidobacteraceae | NCBITaxon:2689614 · TaxonMech · TraitMech |
SECONDARY_FERMENTER
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N/A |
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| Steroidobacteraceae denitrifier 2 — ontology label: Steroidobacteraceae | NCBITaxon:2689614 · TaxonMech · TraitMech |
SECONDARY_FERMENTER
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N/A |
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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.
Modeled Coupled Nitrification
The ORT proof-of-concept uses Nitrososphaeraceae and Nitrospiraceae MAG-derived models for ammonium-to-nitrite and nitrite-to-nitrate transformations. Sequential substrate coupling is represented computationally, not experimentally measured partner transfer, obligatory syntrophy or an assembled two-strain culture.
Participating Taxa: Nitrososphaeraceae archaeon, Nitrospiraceae bacterium
Metabolites: ammonium (CHEBI:28938 · MediaIngredientMech · CMMMech), nitrite (CHEBI:16301 · MediaIngredientMech · CMMMech), nitrate (CHEBI:17632 · MediaIngredientMech · CMMMech)
Biological Processes:
- ammonia oxidation (GO:0019329 · PathwayMech)
PARTIAL - sequential modeled nitrification supplies nitrate for modeled denitrification. This is a substrate route in the proof-of-concept simulation, not proof of an exclusive environmental nitrate source, obligatory partner dependence or genome-supported completion to nitrogen gas.
Evidence
-
PMID:34726691 - SUPPORT (COMPUTATIONAL)"nitrification and denitrification"
Modeled Nitrate Reduction with Gapfilled Nitrogen Production
Two Steroidobacteraceae MAG-derived models represent nitrate reduction to dissolved nitrogen. Neither MAG encoded nitrogen-gas production; the N2O-to-N2 reaction was added by gapfilling. The positive simulation output is therefore conditional on model assumptions, not demonstrated complete metabolism of either organism or measured field nitrogen loss. The two canonical denitrifier names remain distinct despite sharing a family identifier.
Participating Taxa: Steroidobacteraceae denitrifier 1, Steroidobacteraceae denitrifier 2
Metabolites: nitrate (CHEBI:17632 · MediaIngredientMech · CMMMech), nitrogen (CHEBI:17997 · MediaIngredientMech · CMMMech)
Biological Processes:
- denitrification (GO:0019333 · PathwayMech)
Evidence
-
PMID:34726691 - SUPPORT (COMPUTATIONAL)"nitrification and denitrification"
Modeled Metabolome-Informed Carbon Utilization
Site models used 15-23 additional carbon substrates, with betaine, leucine and choline among the examples. Bulk metabolomics informed model media, with some unmeasured necessities assumed nonlimiting. These modeled exchanges add chemical detail; they are not traced member flux or experimentally identified field limitations, and the reported substrate count is not assigned to every denitrifier.
Participating Taxa: Nitrososphaeraceae archaeon, Nitrospiraceae bacterium, Steroidobacteraceae denitrifier 1, Steroidobacteraceae denitrifier 2
Metabolites: glycine betaine (CHEBI:17750 · MediaIngredientMech · CMMMech), leucine (CHEBI:15603 · MediaIngredientMech · CMMMech), choline (CHEBI:15354 · MediaIngredientMech · CMMMech)
Biological Processes:
- organic substance catabolic process (GO:0009056 · PathwayMech)
PARTIAL - modeled carbon uptake contributes substrate and stoichiometric context to the denitrification representation. The exchange calculations support this model-level coupling, not selective demonstration that these example compounds control field denitrification or are consumed by both denitrifiers.
Evidence
-
PMID:34726691 - SUPPORT (COMPUTATIONAL)"site models used 15–23 unique additional carbon sources, such as betaine, leucine and choline"
Associated Datasets
| Dataset | Type | Repository | Accession |
|---|---|---|---|
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Primary publication
Bioinformatics publication describing the ORT workflow coupling genome-scale metabolic models with reactive transport modeling for nitrogen cycling. |
OTHER | OTHER | PMID:34726691 |
Knowledge gaps & discussions (1)
KNOWLEDGE_GAP OPEN Which modeled nitrogen and carbon routes are supported by measured organism activity?
Retain both existing model-level substrate arrows, explicitly PARTIAL for biological validation. Nitrogen-gas completion is gapfilled, and neither denitrifier MAG encoded it. The single-chemistry-input demonstration compares model stoichiometries using common rate assumptions; no high-resolution empirical time series validates its predicted trajectories. Iterative KBase/PFLOTRAN coupling is a proposed capability, not a demonstrated feedback experiment. Full publisher main text/Methods/Table1/captions read; no figure pixels, supplements, code, raw data or narrative execution inspected. #1527 tracks non-graph metadata and #1528 cache provenance; all canonical IDs/labels remain unchanged. No new graph structure.
Attaches to: ecological_interactions#Modeled Coupled Nitrification, ecological_interactions#Modeled Nitrate Reduction with Gapfilled Nitrogen Production, ecological_interactions#Modeled Metabolome-Informed Carbon Utilization
External Resources
| Name | Repository | Resource ID |
|---|---|---|
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KBase narrative
ORT: KBase Workflow narrative page with merged community modeling steps. |
KBASE | ws.71260.obj.262 |
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Cross-Mech Suite Links
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