Genomics-Based Characterization of the Microbial Community and Plasmidome of the Regina Wastewater Treatment Facility and the Surrounding Aquatic Environment
Wastewater produced from human activity contains high concentrations of contaminants like ammonia, pathogens, and organic compounds with high biological oxygen demand; all of which must be remediated with proper wastewater treatment prior to discharge into the environment. Most large-scale wastewater treatment plants (WWTPs) remove contaminants from wastewater using the activated sludge process, wherein wastewater is mixed with a flocculent slurry of microorganisms that use these contaminants for the production of energy or increasing microbial biomass. The activated sludge environment is a complex microbial ecosystem, containing stable populations of organisms adapted to activated sludge, as well as transient environmental and human gutassociated organisms. These microbial communities are subject to various selective pressures, including predation, fluctuating temperatures, sub-therapeutic levels of antibiotics, and heavy metals. Although microbial activity plays a large role in the functionality of these systems, there is limited information about the resident microbial communities within. In general, the bacteria in these systems are monitored through microscopy, staining, and culturing. While these tools are useful, they provide limited information about the microbial communities as a whole. Thus, this work aims to use higher resolution tools like high-throughput metagenomic sequencing and quantitative PCR to gain more information about the microbial communities in a wastewater treatment environment. This thesis focuses on three aspects of the microbial communities in the Regina WWTP: (1) the composition of the activated sludge microbial community and how it changes in response to seasonality (2) mobile genetic elements in untreated wastewater and activated sludge, and (3) the antimicrobial resistance (AMR) genes that are released into Wascana creek in the treated wastewater effluent. Samples of WWTP effluent, untreated wastewater, and activated sludge were collected from the Regina WWTP. DNA was extracted from all samples and used in high throughput sequencing to determine information about microbial community composition and mobile genetic elements, or quantitative PCR to quantify the AMR genes leaving the WWTP in the effluent. The results indicated that the Regina WWTP activated sludge system is primarily composed of the bacterial phyla, Proteobacteria and Actinobacteria. Although the composition of this microbial community varied seasonally at the genus level, the performance of the WWTP remained stable, suggesting that the functionality of this system is robust to some change within the microbial community. Quantification of functional genes revealed that denitrification genes were abundant, while nitrification genes were not, likely due to nitrifying organisms accounting for a very low proportion of the overall microbial biomass. In the recovered collection of mobile genetic elements, plasmids providing resistance to metals and antibiotics were abundant, which likely contribute to microbial adaptation to these environments. Additionally, quantification of antibiotic resistance genes in the treated effluent revealed that some of these genes are surviving the wastewater treatment process, suggesting that WWTPs may be contributing to the dissemination of antibiotic resistance in the environment.
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Faculty of Graduate Studies and Research, University of Regina