Date of Award


Publication Type


Degree Name



Great Lakes Institute for Environmental Research


Agricultural non-point pollution, Bioindicators, Microbial genomics, Sediment


K.G. Drouillard


C. Weisener


Managing and mitigating point and non-point contamination to freshwater resources depends on reliable and sensitive monitoring of ecosystem health. Microorganisms in surface waters and sediments respond rapidly to anthropogenic disturbances, making them valuable bioindicators of human-induced landscape change. However, there lacks a baseline understanding of microbial community composition and function in industrially and agriculturally impacted regions of the Great Lakes. Without a reference state of microbial diversity and activity, future investigations seeking to integrate microorganisms into ecosystem assessments will lack context. Using genomic tools and measurements of chemical and nutrient contaminants, this thesis provides case studies of microbial community responses to persistent non-point stressors in lower Great Lakes watersheds.

In the first study, Detroit River bed sediments collected over a gradient of chemical contamination were analyzed for microbial gene expression via RNA-seq metatranscriptomics. Results showed that microbial communities exploit unique anabolic and catabolic pathways to derive and store energy from industrial organic contaminants, including nitrate reduction, beta-oxidation, and gluconeogenesis, while simultaneously recruiting stress-response and gene transfer mechanisms to cope with xenobiotic pressures. These observations prove that microbial function, as measured by RNA, is sensitive to legacy-contamination in freshwater sediments.

The following studies of this thesis focused on agricultural-impacted headwaters of Southern Ontario, with an emphasis on bed and suspended sediment microbial community responses to fertilizer practice. In an initial study, suspended sediment was collected and assessed for its potential as a carrier and indicator of riverine microbial taxa within Big Creek, Essex County. Results showed that time-integrated sampling using passive Phillips Tube (PT) samplers provided reliable and consistent collection of the suspended phases microbial community based on DNA-metabarcoding. However, it was observed that sampler precision was greatest during higher flow periods, and that deployment times exceeding two weeks resulted in dissolved oxygen depletion within the sampler apparatus, leading to shifts of the microbial community in-situ. These results show that passive sampling of suspended sediment can be supplementary to bed sediment microbiological investigations, so long as timeframes of collection are considered.

In the next study, Big Creek and two additional sites, Nissouri Creek and the Saugeen River, were assessed for Phosphorus (P) and Nitrogen (N) impacts and bed sediment microbial community response as a function of watershed-wide fertilizer practice. Big Creek, characterized by chemical fertilizer, showed historical and current day P concentrations in exceedance of guidelines, with suspended sediment identified as the primary carrier and release vector of internal P. Nissouri Creek, characterized by a manure- chemical fertilizer mix, showed greater N concentrations, with bed sediments being vulnerable to redox-driven internal P release. The Saugeen River was confirmed as an appropriate reference system that exhibited low nutrient concentrations and low internal P-release risk. Big Creek supported a more varied microbial community, while Nissouri Creek and the Saugeen River shared more similarities, despite their overarching nutrient differences. No sets of microbial taxa were found to be reliable indicators of sediment P-release across all sites, however, several genera showed high differential abundance during a notable P-source event during spring sampling at Nissouri Creek.

The final study applied microbial DNA and RNA-seq methods to bed sediments of Big Creek, Nissouri Creek, and the Saugeen River to associate function with community composition, and to strengthen evidence that metatranscriptomics can co-align with trends in anthropogenic non-point pollution stress. Results showed differences in N, P, and Sulfur (S) metabolism pathways, indicating that fertilizer practice can alter sediment microbial community biogeochemical cycling. Further, DNA and RNA-based amplicon sequencing of bed and suspended sediments, as well as surface water phase microbial communities revealed that RNA-based communities were lower in alpha diversity and represented a sub-set of the total DNA-based community across river substrates, with surface water showing a high proportion of non-active taxa inferred to be of allochthons origin.

This thesis work lays a foundation for pairing microbial genomics with assessments of industrial and agricultural non-point pollution to assess bottom-up ecosystem functioning in lower Great Lakes watersheds.