Temporal and spatial changes in bacterial diversity in mixed use watersheds of the Great Lakes region

Environmental water monitoring is an important responsibility of municipal governments. In this study, we partnered with several municipalities in an extensive sampling program to investigate the effects of spatiotemporal and environmental factors on bacterial diversity in a complex watershed ecosystem containing specific environments including creeks, a river, canals, stormwater outfalls and freshwater lakes of the Niagara Peninsula. Samples were collected using standard municipal protocols and bacterial DNA extracted from these samples was sequenced using high-throughput DNA sequencing targeting the V3–V4 regions of the 16S rRNA gene. Average taxonomic richness and alpha diversity differed significantly between samples collected from lakes and creeks (P < 0.05), and between lakes and stormwater outfalls (P < 0.05). Beta diversity also differed significantly (P < 0.0001) between habitats suggesting that each of these habitats harbours distinct bacterial groups. Among the environmental factors examined, dissolved oxygen (DO) level was strongly associated (P < 0.001) with bacterial diversity. Using a Bayesian source tracking method, the proportional contribution of creeks, river, canals and stormwater outfall habitats in shaping lake bacterial community structure was quantified. Sequences associated with genera known to contain pathogens as well as fecal indicator bacteria were found in every habitat. This study demonstrates that DNA sequence analysis can augment traditional methods of watershed monitoring and management by providing additional information on bacteria of interest to water quality policy makers. Future work may integrate taxonomic and functional analyses to obtain a greater understanding of pathogen survival, nutrient cycling and microbial interactions in freshwater ecosystems.