Using Phylogenetic Structure to Clarify the Evolutionary Ecological Distribution of Microorganisms

利用系统发育结构阐明微生物的进化生态分布

• 批准号: 1557192
• 负责人: Thomas Sharpton
• 金额: $ 73.18万
• 依托单位: Oregon State University
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-04-01 至 2021-03-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1557192&HistoricalAwards=false
• 关键词: Using; Phylogenetic; Structure; Clarify; Evolutionary

Microscopic organisms, or microbes, are fascinating creatures because they exhibit an unparalleled diversity, can be found virtually everywhere in nature, and are responsible for critical ecosystem services. Advances in DNA sequencing technology have transformed how scientists study these evolutionary and ecological aspects of microbial life by providing genetic insight into which types of microbes live in specific environments. However, less is understood about how microbes have evolved the ability to thrive in these environments. This research project uses innovative methods to integrate evolutionary and ecological information about microbes to determine how they have evolved in particular environments and to discover evolutionary groups of microbes that are essential to the ecosystem. This work is important because (1) it will provide researchers with the tools needed to understand how evolutionary and ecological forces influence microbial biodiversity, (2) it will facilitate effective preservation of microbial ecosystems and their services, and (3) is will provide a means of efficiently engineering communities of microbes that are industrially valuable. Further, this research will provide valuable, fundamental insights regarding the mechanisms by which microbes evolve within the context of their ecosystem. In terms of broader impacts, this work is valuable because the tools generated will benefit future investigators in developing more quantitative analyses and research plans. The research team will also convene an annual bioinformatics workshop intended to bring in more under-represented and first-generation students.This project will develop a set of eco-phylogenetic methods for assessing how and why specific groups of microbes diversify. Specifically, this approach analyzes phylogenies assembled from a set of microbial communities and profiles the presence and abundance of each evolutionary group (clade) in each community. It then identifies clades whose phylogenetic and ecological distributions indicate that specific evolutionary or ecological mechanisms have influenced their diversification. This includes development of statistical and model-based procedures to assess the likelihood that non-random processes created the observed patterns in community composition, diversification and relatedness. Finally, it will apply these methods to the study of mammalian gut and plant leaf associated microbial communities to determine which microbial clades are critical to the structure of these communities, co-evolving with their host, and subject to evolutionarily conserved interactions with other microbial clades.

微观生物或微生物是引人入胜的生物，因为它们表现出无与伦比的多样性，几乎可以在自然界中任何地方找到，并且负责关键的生态系统服务。 DNA测序技术的进步已经改变了科学家如何通过提供遗传洞察微生物在特定环境中生活的遗传学洞察，如何研究微生物生命的这些进化和生态方面。但是，关于微生物如何发展在这些环境中繁荣发展的能力的理解较少。该研究项目使用创新方法来整合有关微生物的进化和生态信息，以确定它们在特定环境中的进化并发现生态系统必不可少的微生物的进化组。这项工作很重要，因为（1）它将为研究人员提供了解进化和生态力量如何影响微生物生物多样性所需的工具，（2）它将有助于有效地保存微生物生态系统及其服务，并且（3）将提供一种有效地工程工业有价值的微生物的手段。此外，这项研究将为微生物在其生态系统的背景下发展的机制提供宝贵的基本见解。在更广泛的影响方面，这项工作是有价值的，因为生成的工具将使未来的研究人员在制定更定量的分析和研究计划中受益。研究团队还将召集年度生物信息学研讨会，旨在引入更多代表性和第一代学生。该项目将开发一系列生态生态学方法，用于评估如何以及为什么特定的微生物多样化。具体而言，这种方法分析了从一组微生物群落组装的系统发育，并概述了每个社区中每个进化组（进化枝）的存在和丰度。然后，它确定了其系统发育和生态分布的进化枝表明特定的进化或生态机制影响了它们的多样化。这包括开发基于统计和模型的程序，以评估非随机过程创建社区组成，多元化和相关性中观察到的模式的可能性。最后，将这些方法应用于哺乳动物肠道和植物叶相关的微生物群落的研究，以确定哪些微生物进化枝对于这些群落的结构至关重要，与宿主共同发展，并与其他微生物进化枝的进化相互作用。