Date of Award


Publication Type


Degree Name



Great Lakes Institute for Environmental Research

First Advisor


Second Advisor


Third Advisor



Fecal indicator bacteria, Freshwater microbiology, Metatranscriptomics, Microbial source tracking, Recreational water, RT-qPCR



Creative Commons License

Creative Commons Attribution 4.0 International License
This work is licensed under a Creative Commons Attribution 4.0 International License.


Contamination of natural aquatic ecosystems is a serious global concern as populations increase and the environment is impacted by climate change. Nonpoint source (NPS) contamination of allochthonous materials, such as sediments, nutrients, and microorganisms, is commonly introduced to a body of water through runoff and wash-off which cumulates over a large area, and is subsequently transported to surface waters (e.g., rivers, streams, lakes) and shorelines. The principal form of microbial contamination of water resources is often from fecal pollution derived from humans, domesticated animals, or wildlife, and contains a variety of human pathogens. There are also numerous factors (with limited research) affecting pathogen survival, persistence, and growth in these environments, complicating research models and progress, and our overall understanding of the microbiology of natural waters. Thus, the potential for human health risk associated with recreational water use can be difficult to recognise and regulate without appropriate testing to identify and characterize the pathogenic profile in these environments. Traditional water quality assessments involve the use of an indicator organism (e.g., E. coli) as a proxy for fecal contamination in recreational waters. However, there are several limitations to these simplistic approaches which lead to unreliable water quality evaluations. These tests 1) are infrequent, time consuming, and nonrepresentative of in situ conditions; 2) target only one organism but omit other waterborne pathogens; 3) involve culture-based techniques or the use of environmental DNA, which cannot inform on microbial activity; 4) neglect to identify contamination origin or source; and perhaps the most significant shortcoming of these assessments is that they 5) overlook the sediment compartment, assuming pathogenic microbes only have planktonic lifestyles.

The research presented though this dissertation aims to address the knowledge gap regarding the concern for human health implications involving microbial contamination associated with recreational water use. A spatiotemporal microbial biosignature was first established for freshwater bed sediment in Laurentian Great Lakes beaches. This baseline allowed for focused mRNA-based metatranscriptomic and rRNA-based targeted transcriptomic assessments of both bed and suspended sediment fractions of the nearshore swimming zone. Results indicated significant microbial activity (through diverse metabolic functions as well as pathogenic-related gene expression) associated with both sediment fractions, suggesting freshwater sediment acts as a reservoir and secondary source for microorganisms (including waterborne pathogens) through sediment dynamics (e.g., erosion, resuspension, transport, deposition). Microbial biomass and activity were typically upregulated at low-energy, fine-grained locations, such as Belle River and Kingsville, Ontario beaches. Microbial source tracking (MST) evaluations determined avian sources (i.e., gulls and geese) to be the largest NPS of fecal indicator bacteria (FIB) associated with the sediment compartment along these freshwater shorelines. MST targets provided superior results over general FIB targets and traditional water quality assessments by exposing contamination source details.

The results obtained from this research significantly improve our understanding of freshwater ecosystems and human health implications in recreational water through microbial characterization (i.e., expansive community profiling and gene expression studies), MST, and sediment-microbe relationships.