Metagenomic analysis of nitrogen-cycling genes in upper Mississippi river sediment with mussel assemblages

Ellen M Black; Michael S Chimenti; Craig L Just

doi:10.1002/mbo3.739

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Metagenomic analysis of nitrogen-cycling genes in upper Mississippi river sediment with mussel assemblages

Journal article

Open access

Peer reviewed

Metagenomic analysis of nitrogen-cycling genes in upper Mississippi river sediment with mussel assemblages

Ellen M Black, Michael S Chimenti and Craig L Just

MicrobiologyOpen (Weinheim), Vol.8(5), pp.e00739-n/a

05/2019

DOI: 10.1002/mbo3.739

PMCID: PMC6528593

PMID: 30270525

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https://doi.org/10.1002/mbo3.739View

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Abstract

We investigated the impact of native freshwater mussel assemblages (order Unionoida) on the abundance and composition of nitrogen-cycling genes in sediment of an upper Mississippi river habitat. We hypothesized that the genomic potential for ammonia and nitrite oxidation would be greater in the sediment with mussel assemblages, presumably due to mussel biodeposition products, namely ammonia and organic carbon. Regardless of the presence of mussels, upper Mississippi river sediment microbial communities had the largest genomic potential for nitrogen fixation followed by urea catabolism, nitrate metabolism, and nitrate assimilation, as evidenced by analysis of nitrogen cycling pathway abundances. However, genes encoding nitrate and nitrite redox reactions, narGHI and nxrAB, were the most abundant functional genes of the nitrogen cycling gene families. Using linear discriminant analysis (LDA), we found nitrification genes were the most important biomarkers for nitrogen cycling genomic potential when mussels were present, and this presented an opposing effect on the abundance of genes encoding nitric oxide reduction. The genes involved in nitrification that increased the most were amoA associated with comammox Nitrospira and nxr homologs associated with Nitrospira. On the other hand, the most distinctive biomarkers of microbial communities without mussels were norB and nrfA, as part of denitrification and dissimilatory nitrate reduction to ammonium pathways, respectively. Ultimately, this research demonstrates the impact of native mollusks on microbial nitrogen cycling in an aquatic agroecosystem.

Animals

Bivalvia - growth & development

Geologic Sediments - microbiology

Metabolic Networks and Pathways - genetics

Microbiota

Nitrogen Cycle

Nitrogen Fixation

Rivers - microbiology

Details

Title: Subtitle: Metagenomic analysis of nitrogen-cycling genes in upper Mississippi river sediment with mussel assemblages
Creators: Ellen M Black - University of Iowa
Michael S Chimenti - Institute of Human Genetics
Craig L Just - University of Iowa
Resource Type: Journal article
Publication Details: MicrobiologyOpen (Weinheim), Vol.8(5), pp.e00739-n/a
DOI: 10.1002/mbo3.739
PMID: 30270525
PMCID: PMC6528593
NLM abbreviation: Microbiologyopen
ISSN: 2045-8827
eISSN: 2045-8827
Grant note: P30 ES005605 / NIEHS NIH HHS
Language: English
Date published: 05/2019
Academic Unit: Civil and Environmental Engineering; IIHR--Hydroscience and Engineering; Iowa Institute of Human Genetics
Record Identifier: 9984197256102771

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