A natural floodplain-soil microbial community from the DOE-supported East River watershed in Colorado. Metagenomic and metatranscriptomic sampling across upper, middle, and lower East River meander-bound floodplains reconstructed 248 representative subspecies-level genomes and identified a core floodplain microbiome. The core community is enriched in aerobic respiration, aerobic carbon monoxide oxidation, thiosulfate oxidation, nitrification, methanol and formate oxidation, and carbon fixation capacities that vary with soil organic carbon and floodplain position.
Taxonomy
| Taxon | Ontology ID | Functional Roles | Abundance |
|---|---|---|---|
| Betaproteobacteria-dominated core floodplain microbiome — ontology label: Betaproteobacteria | NCBITaxon:28216 · TaxonMech · TraitMech |
PRIMARY_DEGRADER
PRIMARY_PRODUCER
|
DOMINANT |
|
|||
| Nitrospirae core floodplain members — ontology label: Nitrospira | NCBITaxon:1234 · TaxonMech · TraitMech |
PRIMARY_PRODUCER
|
N/A |
|
|||
| Acidobacteriota floodplain representatives — ontology label: Acidobacteriota | NCBITaxon:57723 · TaxonMech · TraitMech |
PRIMARY_DEGRADER
|
N/A |
|
|||
| Gemmatimonadota floodplain representatives — ontology label: Gemmatimonadota | NCBITaxon:142182 · TaxonMech · TraitMech |
PRIMARY_DEGRADER
|
N/A |
|
|||
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.
Core Floodplain Biogeochemical Potential Reservoir
The 2015 operational core comprises 42 representative genomes detected in at least 89 of 94 samples without a significant association to any one floodplain. Their gene inventories define biogeochemical potential, not measured activation or flux. Listed Betaproteobacteria and Gemmatimonadota participants are partial higher-level core groupings, not a complete roster or an assertion that every genome encodes every pathway. Widely represented capacities did not predict the later transcription snapshot.
Participating Taxa: Betaproteobacteria-dominated core floodplain microbiome, Gemmatimonadota floodplain representatives
Metabolites: thiosulfate (CHEBI:16094 · MediaIngredientMech · CMMMech), carbon dioxide (CHEBI:16526 · MediaIngredientMech · CMMMech)
Biological Processes:
- sulfur compound metabolic process (GO:0006790 · PathwayMech)
- carbon fixation (GO:0015977 · PathwayMech)
Evidence
-
PMID:34022966 - SUPPORT (COMPUTATIONAL)"Widely represented genetic capacities did not predict in situ activity at one time point, but rather they define a reservoir of biogeochemical potential available as conditions change."
-
PMID:34022966 - SUPPORT (COMPUTATIONAL)"Genomes affiliated with Acidobacteria, Bacteroidetes, and Chloroflexi were not part of the core floodplain microbiome"
Core Floodplain Aerobic and Sulfur Oxidation Capacity
The operational core genome set is enriched in capacities for aerobic respiration, aerobic CO or other small-molecule oxidation, and thiosulfate oxidation. This is comparative gene-content enrichment, not measured reaction rates, cooperation or niche partitioning. The two canonical participant groups are a partial core roster; no universal per-taxon pathway assignment or substrate specificity for every CODH-like homolog is implied.
Participating Taxa: Betaproteobacteria-dominated core floodplain microbiome, Gemmatimonadota floodplain representatives
Metabolites: thiosulfate (CHEBI:16094 · MediaIngredientMech · CMMMech)
Biological Processes:
- aerobic respiration (GO:0009060 · PathwayMech)
- sulfur compound metabolic process (GO:0006790 · PathwayMech)
Evidence
-
PMID:34022966 - SUPPORT (COMPUTATIONAL)"we identified a core floodplain microbiome that is enriched in capacities for aerobic respiration, aerobic CO oxidation, and thiosulfate oxidation with the formation of elemental sulfur."
Low-Organic-Carbon-Associated Gene Transcription in Floodplain L
In the September 2016 floodplain L RNA snapshot, lower organic carbon correlated with increased transcription of selected C1, sulfur, hydrogen and nitrogen redox genes and carbon-fixation genes. This is not a carbon manipulation, measured flux, a result independently sampled in all three floodplains or activation of the entire 2015 core. Betaproteobacteria are included only as a broad grouping linked to CBB carbon-fixation capacity/activity; their overall transcription favored higher organic carbon. Other low-carbon-active groups are not reliably represented by the canonical taxonomy, so this is explicitly a partial participant list.
Participating Taxa: Betaproteobacteria-dominated core floodplain microbiome
Metabolites: formate (CHEBI:15740 · MediaIngredientMech · CMMMech), carbon dioxide (CHEBI:16526 · MediaIngredientMech · CMMMech)
Biological Processes:
- nitrification (GO:0019329 · PathwayMech)
- carbon fixation (GO:0015977 · PathwayMech)
Evidence
-
PMID:34022966 - PARTIAL (COMPUTATIONAL)"Within all three meanders, low soil organic carbon correlated with high activity of genes involved in methanol, formate, sulfide, hydrogen, and ammonia oxidation, nitrite oxidoreduction, and nitrate and nitrite reduction."
-
PMID:34022966 - SUPPORT (COMPUTATIONAL)"the most highly transcribed genes were relatively rare amoCAB and nxrAB (for nitrification) genes, followed by genes involved in methanol and formate oxidation, and nitrogen and CO2 fixation."
-
PMID:34022966 - SUPPORT (COMPUTATIONAL)"we resampled floodplain L for metatranscriptomics and metagenomics"
-
PMID:34022966 - SUPPORT (COMPUTATIONAL)"Activity of the Calvin Benson Bassham (CBB) pathway for CO2 fixation is linked to Betaproteobacteria, Deltaproteobacteria, Gammaproteobacteria, and NC10"
Associated Datasets
| Dataset | Type | Repository | Accession |
|---|---|---|---|
|
East River floodplain metagenomes and metatranscriptomes
Umbrella BioProject for East River floodplain metagenome and metatranscriptome datasets. |
METAGENOMICS | NCBI_BIOPROJECT | PRJNA630765 |
|
East River representative genomes and environmental metadata
ESS-DIVE data package containing representative genomes and environmental metadata for East River floodplain microbiome analyses. |
GENOMICS | OTHER | doi:10.15485/1631979 |
Knowledge gaps & discussions (1)
KNOWLEDGE_GAP OPEN Which genomes and environmental mechanisms link conserved capacity to measured flux?
Core capacity enrichment is a part/whole description, not a causal consequence requiring an arrow. Gene inventories did not predict one-time expression, and the 2016 RNA study sampled only L. Direct flux and selective environmental perturbations are missing. The canonical Nitrospira genus ID cannot stand in for the paper's Nitrospirae phylum; Acidobacteriota are non-core and overall more transcriptionally active at higher organic carbon. Neither is assigned an unsupported graph link just to suppress disconnected warnings. Taxonomy and non-graph scope remain under #1421; no GTDB withholding policy is changed.
Attaches to: ecological_interactions#Core Floodplain Biogeochemical Potential Reservoir, ecological_interactions#Core Floodplain Aerobic and Sulfur Oxidation Capacity, ecological_interactions#Low-Organic-Carbon-Associated Gene Transcription in Floodplain L
Environmental Factors
| Factor | Value | Unit |
|---|---|---|
| East River meander-bound floodplain position | upper, middle, and lower East River floodplain soils | N/A |
|
||
| Soil organic carbon gradient | low soil organic carbon associated with increased chemolithotrophic and nitrogen-cycling activity | N/A |
|
||
Cross-Mech Suite Links
Explore related entities across the CultureBotAI X-Mech knowledge bases: