Light Penetration, Dissolved Oxygen, and Riparian Zone Extent Are Associated with the Structure, Gene Expression, and Lipid Production of Riverbed Microbial Communities

We analyzed riverbed microbiota structure, gene expression, and fatty acid production across several sites along Little Miami River in Ohio, United States. The sites varied in stream width, shading, surrounding land use, and the size of the riparian zone. Within each site, we observed strong concordance among microbial community composition, functional gene expression, and fatty acid signature. All microbial communities were dominated by the members of phylum Proteobacteria, class Planctomycetacia, and by algal and cyanobacterial cells. The measured concentrations of chlorophyll a, dissolved oxygen, and soluble phosphorus were the main environmental determinants of microbial community structure. These were in turn dependent on the level of penetrating sunlight and, to a lesser degree, on the width of the riparian zone. The level of sunlight affected the expression of light-harvesting complexes, methanogenesis genes, anaerobic respiratory reductases and fermentation pathways, as well as functions of denitrification, ammonification, and sulfate reduction. The expression of phosphorus scavenging and antibiotic resistance genes was highest at the site lacking a riparian zone and surrounded by farmland. Overall, our findings demonstrate that riverbed microbiota exhibit consistent structural and functional responses to interacting geochemical and anthropogenic gradients. Our data also provide support for the hypothesis that phototrophic microorganisms act as central organizers of benthic community metabolism.