Sediments and Soils Act as Reservoirs for Taxonomic and Functional Bacterial Diversity in the Upper Mississippi River

In this study, we utilized Illumina next-generation sequencing of 16S rDNA to characterize the bacterial communities in water, sediments, and soils at four sites along the Mississippi River and Minnesota River, in Minnesota, in order to evaluate community exchanges between these habitats. Communities in water and sediment were hypothesized to show greater taxonomic similarity than those in soil, while microbial communities in sediment and soil would show greater functional similarity. Habitat-specific communities showed significant differences in phylogenetic structure and β-diversity (P < 0.001), but site-specific differences in community structures within a single habitat type did not differ greatly (P ≥ 0.083). Community exchange among habitats generally influenced < 5 % of the total community composition in a single sample, with the exception of the sediment community at the Minnesota River site, which contributed to a mean of 14 % of the microbial community in the water column. Communities from all habitat types were significantly correlated with each other (r = 0.44–0.64, P ≤ 0.004). Furthermore, approximately 33 % of the taxonomic units were found in all samples and comprised at least 40 % of the bacterial community. Functional annotation of shotgun sequencing data revealed similar functional profiles for sediment and soil communities that were distinct from those in the water. Results of this study suggest that sediments, when disturbed, contribute significantly to bacterial communities in the water and that a core bacterial community may be supported in the soils and sediments. Furthermore, a high degree of functional redundancy results in similar functional profiles in sediment and soil communities.