Genomic studies of microbial dark matter in extreme ecosystems of Canada

从自然环境中提取和测序DNA揭示了微生物的巨大生物多样性。基于这些研究的总微生物多样性估计范围从数百万到超过一万亿种。然而，只有几千个这样的细菌在实验室中被培育出来，因此很明显，微生物学家通过培养来评估生物多样性的能力非常有限。微生物生态学的一个主要目标是更好地了解未培养微生物的遗传和生态多样性。这一目标可以通过两种方式实现：应用改进的培养方法从整个生命之树中获得更多的培养分离物，或者使用基于dna的方法，在不需要培养的情况下提供有关微生物遗传能力的信息。实现这一目标的关键分子技术包括宏基因组学（对整个群落的DNA进行测序）和单细胞基因组学（对单个细胞的DNA进行测序）。这些可以用来拼凑未培养微生物的基因组，并对它们的生理机能做出假设。

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.