A natural, depth-resolved microbial community from a hillslope-to-riparian transect in the DOE-supported East River watershed near Crested Butte, Colorado. Metagenomic and geochemical analyses showed that distance from the East River, proximity to the groundwater table, and underlying weathered shale strongly structure microbial community composition and metabolic potential. Riparian-zone communities are compositionally distinct from hillslope communities and are functionally differentiated by capacities for carbon fixation, nitrogen fixation, sulfate reduction, Candidate Phyla Radiation bacteria in saturated sediments, and selenium reduction at depth.
Taxonomy
| Taxon | Ontology ID | Functional Roles | Abundance |
|---|---|---|---|
| East River hillslope-riparian transect microbiome — ontology label: cellular organisms | NCBITaxon:131567 · TaxonMech · TraitMech |
PRIMARY_DEGRADER
PRIMARY_PRODUCER
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N/A |
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| riparian zone microbial communities — ontology label: cellular organisms | NCBITaxon:131567 · TaxonMech · TraitMech |
PRIMARY_DEGRADER
PRIMARY_PRODUCER
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DOMINANT |
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| riparian saturated sediment Candidate Phyla Radiation bacteria — ontology label: Patescibacteria group | NCBITaxon:1783273 · TaxonMech · TraitMech |
CROSS_FEEDER
SYNTROPHIC_PARTNER
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N/A |
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| hillslope microbial communities — ontology label: cellular organisms | NCBITaxon:131567 · TaxonMech · TraitMech |
PRIMARY_DEGRADER
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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.
Hypothesized Groundwater and Weathered Shale Filtering
Across the September 2016 PLM transect, microbial composition and DNA-based metabolic potential covaried with depth, river proximity, groundwater and weathered shale. HYPOTHESIZED moisture, redox and substrate filtering may explain these patterns, but no selective groundwater, shale or nutrient perturbation isolated the drivers. Compartment participants retain distinct canonical labels despite sharing a broad cellular-organisms ID; they are not resolved taxa.
Participating Taxa: East River hillslope-riparian transect microbiome, riparian zone microbial communities, hillslope microbial communities
Metabolites: nitrate (CHEBI:17632 · MediaIngredientMech · CMMMech), sulfate (CHEBI:16189 · MediaIngredientMech · CMMMech)
HYPOTHESIZED - groundwater-associated low-redox conditions may favor organisms carrying anaerobic carbon, nitrogen and sulfur pathway genes, producing the observed riparian-versus-hillslope differences. Spatial gene abundance supports the model but does not isolate redox as the mediator or demonstrate flux.
HYPOTHESIZED - depth and water-table conditions may select compatible microorganisms and possible hosts, influencing candidate-phylum distributions. Observational detections support environmental filtering, but no host dependence or exclusive groundwater requirement was tested; deep hillslope exceptions remain.
HYPOTHESIZED - shale-derived selenium availability together with periodically reducing groundwater conditions may select selenate-respiring organisms and enrich srdA. Gene abundance and incomplete chemistry support this proposed mechanism, not experimentally demonstrated selenium reduction or export control.
Evidence
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PMID:31380022 - PARTIAL (COMPUTATIONAL)"proximity to groundwater and underlying weathered shale"
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PMID:31380022 - PARTIAL (COMPUTATIONAL)"strongly impact microbial community structure and metabolic potential"
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PMID:31380022 - PARTIAL (COMPUTATIONAL)"the proximity to sulfate and nitrate rich Mancos shale bedrock"
Riparian Carbon Nitrogen and Sulfur Genomic Potential
Riparian samples near and below the water table differed from hillslope samples in DNA abundances of genes associated with carbon fixation, nitrogen fixation and sulfur reduction. DsrD and other reductase signatures help interpret direction, but RNA was extracted for another study and no pathway flux was measured here. This comparison supports a putative functional zone, not demonstrated interspecies niche partitioning, complete redox cycling or equivalent metabolism in all compartments.
Participating Taxa: riparian zone microbial communities, hillslope microbial communities
Metabolites: carbon dioxide (CHEBI:16526 · MediaIngredientMech · CMMMech), sulfate (CHEBI:16189 · MediaIngredientMech · CMMMech)
Biological Processes:
- carbon fixation (GO:0015977 · PathwayMech)
- nitrogen fixation (GO:0009399 · PathwayMech)
- sulfate reduction (GO:0019420 · PathwayMech)
Evidence
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PMID:31380022 - SUPPORT (COMPUTATIONAL)"capacities for carbon and nitrogen fixation and sulfate reduction"
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PMID:31380022 - SUPPORT (COMPUTATIONAL)"functionally differentiated from hillslope communities"
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PMID:31380022 - SUPPORT (COMPUTATIONAL)"While RNA was extracted for the purpose of another study"
Depth-Enriched Uncultivated Bacterial Lineages
Non-CPR candidate phyla increased with sampling depth. CPR detections were concentrated near and below the PLM4 water table, with two Yanofskybacteria occurrences in deep hillslope samples near weathered shale. These are distinct patterns, not exclusive confinement of every uncultivated lineage to saturated riparian sediment. CPR dependency on unknown hosts is a literature-based hypothesis, not measured cross-feeding or syntrophy in this transect.
Participating Taxa: East River hillslope-riparian transect microbiome, riparian saturated sediment Candidate Phyla Radiation bacteria
Evidence
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PMID:31380022 - SUPPORT (COMPUTATIONAL)"consistently increase in abundance with increasing depth"
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PMID:31380022 - PARTIAL (COMPUTATIONAL)"riparian zone saturated sediments we found Candidate Phyla Radiation bacteria"
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PMID:31380022 - PARTIAL (COMPUTATIONAL)"Many are likely obligate symbionts, and as such they may often associate with anaerobic hosts"
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PMID:31380022 - SUPPORT (COMPUTATIONAL)"Other than the two occurrences of Yanofskybacteria species in deep samples close to the soil"
Deep Shale and Riparian Selenate Reduction Potential
DNA abundance of the srdA catalytic-subunit gene was elevated in groundwater-saturated riparian samples and deep weathered shale, consistent with selenate-reduction potential. The measured srdA-selenium association lacks chemistry at the deepest high-srdA sites. Actual selenate reduction rates, selenium removal, growth support and water-quality improvement were not measured; this is not direct evidence of selenite reduction by a named taxon.
Participating Taxa: riparian zone microbial communities, hillslope microbial communities
Metabolites: selenate (CHEBI:15075 · MediaIngredientMech · CMMMech)
Evidence
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PMID:31380022 - SUPPORT (COMPUTATIONAL)"Selenium reduction is prominent at depth"
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PMID:31380022 - SUPPORT (COMPUTATIONAL)"weathered shale and saturated riparian zone sediments"
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PMID:31380022 - SUPPORT (COMPUTATIONAL)"Selenate reductase encoded by the gene srdA, which is associated with selenate respiration"
Associated Datasets
| Dataset | Type | Repository | Accession |
|---|---|---|---|
|
East River hillslope metagenome BioProject example
NCBI BioProject record for a DOE JGI East River watershed hillslope metagenome sample associated with groundwater sediment microbial communities from the East River, Colorado. |
METAGENOMICS | NCBI_BIOPROJECT | PRJNA444173 |
Knowledge gaps & discussions (1)
KNOWLEDGE_GAP OPEN Which environmental mechanisms and organisms realize the inferred redox capacities?
Selective groundwater/redox/substrate perturbations and direct flux measurements are needed to distinguish the proposed drivers. DNA abundance is metabolic potential, not transcription or activity; selenium chemistry is missing at key deep high-srdA sites. CPR partners and exchanges are unknown, and candidate phyla are not synonymous with CPR. The three original arrows remain explicit hypotheses, not niche-partitioning facts. Non-graph role and activity wording remain under #1422.
Attaches to: ecological_interactions#Hypothesized Groundwater and Weathered Shale Filtering, ecological_interactions#Riparian Carbon Nitrogen and Sulfur Genomic Potential, ecological_interactions#Depth-Enriched Uncultivated Bacterial Lineages, ecological_interactions#Deep Shale and Riparian Selenate Reduction Potential
External Resources
| Name | Repository | Resource ID |
|---|---|---|
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Primary publication for the East River hillslope-riparian transect community
PubMed record for the East River hillslope-to-riparian transect metagenomic and geochemical community study. |
OTHER | PMID:31380022 |
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DOI landing page
DOI landing page for the Ecology and Evolution article. |
OTHER | doi:10.1002/ece3.5254 |
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DOE PAGES record
DOE PAGES record for the East River hillslope-riparian transect article. |
OTHER | OSTI:1560176 |
Environmental Factors
| Factor | Value | Unit |
|---|---|---|
| Hillslope-to-riparian transect position | depth-resolved hillslope to riparian zone transect | N/A |
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| Groundwater table proximity | proximity to groundwater table | N/A |
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| Weathered shale | underlying weathered shale | N/A |
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