East River Floodplain Core Microbiome

Community ID CommunityMech:000137

Ecological State STABLE

Environment floodplain soil
ENVO:00001998

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	NCBITaxon:28216	PRIMARY_DEGRADER PRIMARY_PRODUCER	DOMINANT
PMID:34022966 - SUPPORT (COMPUTATIONAL) "Betaproteobacteria was the group with the highest number of representative genomes (80) in all three floodplains." PMID:34022966 - SUPPORT (COMPUTATIONAL) "The core floodplain microbiome was dominated by Betaproteobacteria, with lower abundances of Nitrospirae, Rokubacteria, Gemmatimonadetes, Gammaproteobacteria, Deltaproteobacteria, and Candidatus Letescibacteria"
Nitrospirae core floodplain members	NCBITaxon:1234	PRIMARY_PRODUCER	N/A
PMID:34022966 - SUPPORT (COMPUTATIONAL) "the most highly transcribed genes were relatively rare amoCAB and nxrAB (for nitrification) genes"
Acidobacteriota floodplain representatives	NCBITaxon:57723	PRIMARY_DEGRADER	N/A
PMID:34022966 - SUPPORT (COMPUTATIONAL) "Other abundant taxa across floodplains included Deltaproteobacteria (27 representatives), Acidobacteria (21 representatives), Nitrospirae and Planctomycetes (both with 13 representatives)"
Gemmatimonadota floodplain representatives	NCBITaxon:142998	PRIMARY_DEGRADER	N/A
PMID:34022966 - SUPPORT (COMPUTATIONAL) "The core floodplain microbiome was dominated by Betaproteobacteria, with lower abundances of Nitrospirae, Rokubacteria, Gemmatimonadetes, Gammaproteobacteria, Deltaproteobacteria, and Candidatus Letescibacteria"

Ecological Interactions

Taxon

Cross-feeding

Mutualism

Syntrophy

Competition

Commensalism

Niche partitioning

Colonization facilitation

Strain competition

Predation

Core Floodplain Aerobic and Sulfur Oxidation Capacity

NICHE_PARTITIONING

Source Taxon: core floodplain bacteria

Metabolites: thiosulfate (CHEBI:16094)

Biological Processes:

aerobic respiration (GO:0009060)
oxidation-reduction process (GO:0055114)
sulfur compound metabolic process (GO:0006790)

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 Chemolithotrophic Activity

NICHE_PARTITIONING

Source Taxon: East River floodplain bacteria

Metabolites: formate (CHEBI:15740), carbon dioxide (CHEBI:16526)

Biological Processes:

nitrification (GO:0019329)
carbon fixation (GO:0015977)
oxidation-reduction process (GO:0055114)

Evidence

PMID:34022966 - SUPPORT (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."

Associated Datasets

Dataset	Type	Repository	Accession
East River floodplain metagenomes and metatranscriptomes Umbrella BioProject for East River floodplain metagenome and metatranscriptome datasets.	METAGENOME	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.	GENOME	OTHER	doi:10.15485/1631979

Environmental Factors

Factor	Value	Unit
East River meander-bound floodplain position	upper, middle, and lower East River floodplain soils	N/A
PMID:34022966 - SUPPORT (IN_VIVO) "We intensively sampled the microbiomes of floodplain soils located in the upper, middle, and lower reaches of the East River, Colorado."
Soil organic carbon gradient	low soil organic carbon associated with increased chemolithotrophic and nitrogen-cycling activity	N/A
PMID:34022966 - SUPPORT (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."