Metagenomic analysis of river microbial communities

As concern over the availability of freshwater increases, so does the interest in river microorganisms due to their importance in drinking water safety and signalling environmental contamination. However, foundational understanding of their variability in rivers is lacking, especially for viruses. Here, I present work to improve the understanding of planktonic microbial communities in rivers over time in the context of varying environmental conditions and contrasting land use. DNA-sequencing based metagenomic and phylogenetic marker gene (16S, 18S, g23) approaches were used to profile microbial communities, coupled with measures of environmental and chemical conditions. I analysed microbial community profiles from monthly samples collected over one year from three watersheds with agricultural, urban, or minimal land use. Viral, bacterial, and microeukaryotic planktonic communities were synchronous overall, but had contrasting geographic patterns and the strength of their synchrony, as well as their relationships with environmental conditions, were heterogenous across sampling sites. These differences illustrated that bacteria are important yet insufficient representatives of microbial community dynamics despite their prevalence in microbiome research. However, this emphasis on bacteria has produced richer reference databases, which enabled a gene-specific analysis. Using a reference-based approach, I found that communities with lower water quality due to agricultural activity had higher abundances of nutrient metabolism and bacteriophage gene families. Based on these water quality associated findings and on complementary analyses, I identified potential biomarkers to demonstrate that bacterial river metagenome data could feasibly support the development of new assays for water quality monitoring. To complement these studies of anthropogenic contamination, I studied bacteria in river biofilms across a natural gradient of metal concentrations at a potential mining site. Clear relationships among metal concentrations, pH, and microbiomes were evident and this study provided fundamental knowledge of microbial communities at a potential mine site before disruption from development. Throughout these studies, the scarcity of reference information for microbial communities in lotic freshwater provided an opportunity to identify weaknesses in popular microbiome analysis methods and present approaches better suited to poorly characterised environments. Overall, my work aims to improve the understanding of planktonic river microbial community variability, both for the advancement of basic science and to support future development of more effective water quality monitoring approaches.