Genomic studies of microbial dark matter in extreme ecosystems of Canada

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Extraction and sequencing of DNA from natural environments has revealed a vast biodiversity of microbes. Estimates of total microbial diversity based on these studies range from a few million to over a trillion species. However, only a few thousand of these have been grown in a laboratory, so it is clear that microbiologists have a very limited ability to assess biodiversity via cultivation. A major goal of microbial ecology is to better understand the genetic and ecological diversity of the uncultured microbial majority. This goal can be achieved in two ways: by applying improved cultivation methods to obtain more cultured isolates from across the Tree of Life, or by using DNA-based methods that deliver information about the genetic capabilities of microbes without the need for cultivation. Key molecular techniques for this goal include metagenomics (sequencing the DNA of an entire community) and single-cell genomics (sequencing the DNA of a single cell). These can be used to piece together the genomes of uncultured microbes and make hypotheses about their physiologies. My research program combines cultivation-independent and cultivation-dependent methods to study microbial life in extreme ecosystems of Canada. The proposed research will first describe microbial communities in previously unstudied extreme habitats, including thermal (>50oC) and acid (pH -1 to 5) springs located in Canada's North. The goal of these environmental studies is twofold: to test how the taxonomic and metagenomic compositions of these communities vary with environmental parameters such as pH, and to identify sites rich in novel bacterial lineages that can then be studied in more depth. Metagenomes from these sites will be screened for genes of known functions, particularly genes that encode the key enzyme in ammonia and methane oxidation and therefore are critical for global biogeochemical cycles of C and N. Application of further methods like stable isotope probing and single cell genomics will identify the physiologies of bacteria possessing these genes. Finally, we will attempt to isolate and physiologically characterize new bacterial lineages that previous students have genomically characterized and determined how to enrich in the laboratory. This research will combine biodiversity surveys of previously unstudied environments with in-depth, hypothesis-based examination of how bacterial communities respond to extreme environmental conditions. Cataloguing the uncultured microbial majority will help us to better understand how global biogeochemical cycles operate, and may uncover new genetic resources for biotechnology. This work will also help to describe the full scope of biodiversity in unique ecosystems of Canada's North, and may include the description of new species or even phyla (kingdoms) of life.