Expanding the frontiers of microbial diversity and function

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Microbial communities govern biogeochemical cycling of carbon and nutrients, impact the fertility of soils and aquatic environments, maintain the healthy function of human bodies, play an important role in the food industry, and offer countless applications in biotechnology. The profound influence of microorganisms on human life and the global climate underlines the value of studying the biogeography of microorganisms in the environment, exploring the vast resource of genes associated with uncultured microbial life, and expanding our knowledge of most microbial species on earth: those present at low relative abundance. Although technical limitations have hindered the ability of microbial ecologists to quantify microbial diversity and adequately characterize microbial communities, this is no longer the case. My research program leverages advances in next-generation sequencing and computational biology to explore microbial biogeography in terrestrial and aquatic environments. In doing so, we target and recover novel microbial species that will expand our knowledge of the tree of life and enable us to mine genomes for scientific breakthroughs and industrial benefit.The long-term goals of my research program are to identify factors that influence microbial community composition and diversity, link specific microbial groups to environmental parameters, discover novel microorganisms present at low abundance in terrestrial and aquatic environments, and investigate key microorganisms involved in the production and attenuation of carbon and nitrogen. My research program will continue to offer insight into the principles of soil and freshwater microbial ecology, producing predictive datasets that will guide the discovery of new organisms and enzymes of value to research and industry for many years to come.My specific short-term objectives include: 1) Characterise microbial biogeography and the rare biosphere of the rare Charitable Research Reserve (Cambridge, Ontario), 2) Generate a comprehensive microbial map of the Grand River watershed, and 3) Explore the metabolism and ecological significance of ammonia-oxidizing archaea (AOA; our model rare biosphere members) within engineered freshwater environments. This proposal includes a plan for genomic and metabolic characterization of highly novel AOA that we have enriched to near purity over the past two years: Candidatus Nitrosofontus exaquare and Candidatus Nitrosopura aquariensis. Together, the proposed research program will develop quantitative models of community structure and reveal rare microorganisms that have not yet been discovered. Identifying patterns governing microbial diversity enables strong predictive approaches for soil and water management practices and assists in focused cultivation- and metagenomics-based discovery of organisms of relevance for both biogeochemical cycling and potential industrial applications.