Genomic studies of microbial dark matter in extreme ecosystems of Canada

加拿大极端生态系统中微生物暗物质的基因组研究

• 批准号: RGPIN-2019-06265
• 负责人: Dunfield, Peter
• 金额: $ 4.23万
• 依托单位: University of Calgary
• 依托单位国家: 加拿大
• 项目类别: Discovery Grants Program - Individual
• 财政年份: 2021
• 资助国家: 加拿大
• 起止时间: 2021-01-01 至 2022-12-31
• 项目状态: 已结题
• 来源: https://www.nserc-crsng.gc.ca/ase-oro/Details-Detailles_eng.asp?id=738808
• 关键词: Genomic; studies; microbial; dark; matter

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.

自然环境中DNA的提取和测序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的估计值范围从数百万到超过万亿种。但是，其中只有几千种在实验室中生长的，因此很明显，微生物学家通过培养评估生物多样性的能力非常有限。微生物生态学的主要目标是更好地了解未养殖微生物多数的遗传和生态多样性。可以通过两种方式实现此目标：通过应用改进的培养方法，从整个生命树中获得更多培养的分离株，或者使用基于DNA的方法来提供有关微生物遗传能力而无需培养的信息。该目标的关键分子技术包括宏基因组学（整个社区的DNA测序）和单细胞基因组学（测序单细胞的DNA）。这些可用于将未培养的微生物的基因组拼凑在一起，并假设其生理。我的研究计划结合了与培养无关和培养依赖性方法，用于研究加拿大极端生态系统中的微生物寿命。拟议的研究将首先描述以前未研究的极端栖息地的微生物群落，包括位于加拿大北部的热（> 50oc）和酸（pH -1至5）弹簧。这些环境研究的目的是双重的：测试这些群落的分类学和元基因组组成如何随环境参数（例如pH）而变化，并确定富含新型细菌谱系的地点，然后可以更深入地研究这些谱系。这些位点的元素将筛选为已知功能的基因，尤其是编码氨和甲烷氧化中的关键酶的基因，因此对于C的全球生物地球化学周期至关重要。最后，我们将尝试隔离和生理表征以前学生在基因组中表征并确定如何富含实验室的新细菌谱系。 这项研究将结合对以前未研究的环境的生物多样性调查，并基于深入的假设研究细菌群落对极端环境条件的反应。分类未培养的微生物多数将有助于我们更好地了解全球生物地球化学周期的运作方式，并可能发现生物技术的新遗传资源。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，并可能包括对生命的新物种甚至门（王国）的描述。