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。根据这些研究，对微生物多样性总量的估计从几百万到一万多亿种不等。然而，只有几千个在实验室中生长，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大多数的遗传和生态多样性。这一目标可以通过两种方式实现：通过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株，或者通过使用基于DNA的方法，无需培养即可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的微生物的基因组，并对它们的生理学做出假设。 我的研究项目结合了独立培养和依赖培养的方法来研究加拿大极端生态系统中的微生物生命。这项拟议中的研究将首先描述以前未研究过的极端栖息地中的微生物群落，包括位于加拿大北部的热泉（> 50 ℃）和酸性泉（pH值-1至5）。这些环境研究的目标是双重的：测试这些社区的分类和宏基因组组成如何随环境参数（如pH值）而变化，并确定富含新细菌谱系的地点，然后可以更深入地研究。来自这些位点的宏基因组将筛选已知功能的基因，特别是编码氨和甲烷氧化中的关键酶的基因，因此对C和N的全球生物地球化学循环至关重要。进一步的方法，如稳定同位素探测和单细胞基因组学的应用将确定具有这些基因的细菌的生理学。最后，我们将尝试分离和生理特性的新细菌谱系，以前的学生已经基因组特征，并确定如何在实验室中丰富。 这项研究将结合联合收割机生物多样性调查以前未研究的环境，深入，假设为基础的检查细菌群落如何应对极端的环境条件。对大多数未培养的微生物进行编目将有助于我们更好地了解全球生物地球化学循环的运作方式，并可能为生物技术发现新的遗传资源。这项工作还将有助于描述加拿大北部独特生态系统中生物多样性的全部范围，并可能包括对新物种甚至生命门（王国）的描述。

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.