Genomic studies of microbial dark matter in extreme ecosystems of Canada

从自然环境中提取DNA并进行测序，揭示了微生物的巨大生物多样性。根据这些研究估计的微生物总多样性从几百万种到超过一万亿种不等。然而，其中只有几千种是在实验室中培养出来的，所以很明显，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大多数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：通过应用改进的培养方法，从整个生命树获得更多有培养的分离物，或者通过使用基于DNA的方法，在不需要培养的情况下传递关于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元基因组学(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经培养的微生物的基因组，并对它们的生理做出假设。 我的研究项目结合了独立于栽培和依赖于栽培的方法来研究加拿大极端生态系统中的微生物生命。这项拟议的研究将首先描述以前未被研究的极端栖息地中的微生物群落，包括位于加拿大北部的温泉(&gt；50oC)和酸泉(pH-1至5)。这些环境研究的目标有两个：测试这些群落的分类和元基因组组成如何随着环境参数(如pH)的变化，以及确定富含新细菌谱系的地点，以便进行更深入的研究。来自这些位点的超基因组将被筛选出已知功能的基因，特别是编码氨氧化和甲烷氧化关键酶的基因，因此对全球碳和氮的生物地球化学循环至关重要。应用进一步的方法，如稳定同位素探测和单细胞基因组学，将识别拥有这些基因的细菌的生理。最后，我们将尝试分离和生理表征以前的学生已经在基因组学上表征并确定如何在实验室中丰富的新的细菌谱系。 这项研究将结合对以前未被研究的环境的生物多样性调查，以及对细菌群落如何对极端环境条件做出反应的深入、基于假设的检查。对未培养的大多数微生物进行分类将有助于我们更好地了解全球生物地球化学循环是如何运作的，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全面描述加拿大北部独特生态系统中的生物多样性，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.