Abstract: Hydrology and land use strongly influence aquatic ecosystems, with consequences for microbial communities and important processes (e.g., decomposition, phytoplankton productivity). The goal of our study was to examine variation in the microbial communities across systems that differ in these attributes. Water samples were collected from four sites in central Illinois on eight dates over the course of the summer, including the Illinois River and three backwater lakes connected to the river. Water levels at one site (Thompson Lake) were lowered via pumping during the season, allowing comparison of a site with modified hydrology to sites tied more to river hydrology. These sites also differ in historical and current land use impacts, including historical agriculture and mining activity. Water samples were filtered and DNA extracted for 3 size fractions ( >20 micron, 3-20 micron, and 0.22-3 micron). Sequencing data targeting different taxa (16S for bacteria, ITS for fungi) were generated using Illumina MiSeq. We found that microbial diversity and composition varied among sites and size fractions (p < 0.05), but not over time (p > 0.05). One notable pattern was that metrics of bacterial alpha diversity were significantly lower at a backwater lake associated with historical mining activity compared to other sites (p < 0.05). Differences among sites may arise from hydrological and other environmental factors, while differences among fractions suggest communities of particulate-associated microbes differ from free-living communities. Overall, our findings offer insights into variation in these microbial communities, with implications for ecosystem functioning and water quality.
