Abstract

Freshwater bacterial communities play important roles in global biogeochemical cycling and aquatic food webs, yet bacterial diversity, community composition, and community metabolism in freshwater ecosystems remain less explored compared to terrestrial and marine
ecosystems. In this thesis work, I investigated bacterial communities in hundreds of lakes located across Canada, a country that contains millions of lakes. Utilizing 16S rRNA and metagenomic techniques, this research explores diversity patterns, community composition and functional
capabilities of lake bacterial communities and links variation in these three components to human-mediated alterations, specifically watershed land use types within lake watersheds.

In the first research chapter, I performed an investigation of communities in 403 lakes from seven ecozones. I identified distinct bacterial diversity patterns between western (Semi-Arid Plateaux, Prairies, and
Boreal Plains ecozones) and eastern (Boreal Shield, Mixedwood Plains, Atlantic Maritimes, and Atlantic Highlands ecozones) Canada. The identified pattern was primarily influenced by lake physicochemistry including productivity, ion concentration, and lake depth. Bacterial community structure was influenced particularly by lake pH and trophic state.

In the next research chapter, I expanded the study to 621 lakes across 12 ecozones and explored variation in diversity and community composition patterns in relation to water quality and land use. Total phosphorus (TP)
was identified as a key variable shaping community composition, with notable shifts occurring at 110 μg/L TP. Variation in bacterial communities within the Prairies ecozone were driven by agriculture while urbanisation played a role in structuring community composition within the
Pacific Maritimes ecozone.

In the final research chapter, I investigated bacterial functional capabilities using gene-centric metagenomics. Physicochemical parameters emerged as top predictors of variation in functional gene composition, with xenobiotics biodegradation and metabolism notably influenced. Overall, the research presented in this thesis demonstrates that bacterial diversity, community composition, and community function exhibit variations across continental and regional scales that can be attributed to within-lake conditions and watershed land use types.