Collaborative Research: Untangling the Deep Genealogy of Microbial Dark Matter

这项突破性的技术能够从单个细胞中快速测序整个基因组，将用于解开生命早期进化和谱系的秘密。在这一突破之前，许多生命最早的分化谱系无法被分析，因为它们不能在实验室培养中生长。细菌和古细菌群中不可培养的“微生物暗物质”（MDM）构成了地球上大多数生物物种多样性和生物质量，现在可以通过单扩增基因组（sag）测序来揭示这一点。在这个前所未有的研究项目中，许多新的基因组，编码了不同生物体的蓝图，可以并且将被分析，以阐明(1)这些古老微生物物种的谱系，(2)它们起源的相对时间，以及(3)远亲之间的水平基因转移可能在新物种和新生活方式的起源中发挥的作用。此外，将在世界各地未开发的地下环境中进行广泛的MDM采样，加强对科学新生命形式的发现和理解。一个合作的科学家团队将分析100多个富含mdm的野外样本，这些样本来自多个研究地点，包括南非Kaapvaall克拉通的前寒武纪盾状环境，通过南达科他州桑福德地下研究设施获得的前寒武纪变质杂岩，以及与第三纪火山区相关的断层相关泉水和内华达州死亡谷区域流系统的寒武纪沉积岩。广泛的背景资料（环境和生物元数据）也将纳入这些抽样工作。研究任务首先从已知或怀疑包含大量MDM的站点收集现场样本和元数据。然后，通过测序其小亚单位（SSU） rRNA基因iTags来调查所收集样品内的微生物群落组成。根据iTag数据，选择20个最符合本项目目标的样本，并从中测序12600个单扩增基因组（SAGs）。然后，通过SSU rRNA基因对SAGs进行鉴定，800个最符合本项目目标的MDM SAGs将被进一步注释、排列并与各种公开可用的数据集结合，用于细菌和古细菌全面系谱的详细、统计系统发育重建。如上所述，将对系谱推断和其他对理解MDM进化很重要的数据层（包括地球化学、地理空间、微生物群落组成和微生物生理学数据）进行汇编，并用于解决项目的一般进化问题。分析还将解决地球深层地下环境作为细菌和古生菌早期进化史储存库的潜力。该项目通过美国能源部联合基因组研究所向研究人员提供现有的主要奖励，以支付测序费用。该项目有非常丰富的教育和推广组成部分，面向本科生和研究生，博士后研究人员和高中教师的研究经验。还计划为公众设计吸引人的外展活动和媒体。此外，该项目产生的实验室和计算工具以及大量基因组数据将为广泛的研究界提供主要资源，并可能为生物技术工业提供主要资源。

Breakthrough technology enabling rapid sequencing of whole genomes from single cells, will be used in this project to unlock secrets of life's early evolution and genealogy. Prior to this breakthrough, many of life's earliest diverging lineages could not be analyzed because they cannot be grown in laboratory cultures. This unculturable "Microbial Dark Matter" (MDM) within the groups Bacteria and Archaea constitutes the majority of biological species diversity and biological mass on Earth, and this can now be brought to light by the sequencing of single amplified genomes (SAGs). In this unprecedented research project, many new genomes, encoding the blueprints for disparate organisms, can and will be analyzed to illuminate (1) the genealogy of these ancient microbial species, (2) the relative timing of their origins, and (3) the role that horizontal gene transfer among distant relatives may have played in the origins of new species and novel ways of living. Further, extensive MDM sampling will be done from unexplored subterranean environments around the world, enhancing the discovery and understanding of life forms that are new to science. A team of collaborating scientists will analyze over 100 MDM-rich field samples, collected from multiple study sites, including Precambrian shield environments from the Kaapvaall Craton of South Africa, a Precambrian metamorphic complex accessed via the Sanford Underground Research Facility in South Dakota, and fault-associated springs associated with Tertiary volcanic areas and Cambrian-aged sedimentary rocks of the Death Valley Regional Flow System in Nevada. Extensive contextual information (environmental and biological metadata) will also be incorporated in these sampling efforts. The research tasks begin with the collection of field samples and metadata from sites known or suspected to contain a high proportion of MDM. Then, the microbial community composition within the collected samples is surveyed by sequencing their small sub-unit (SSU) rRNA gene iTags. Based on the iTag data, 20 samples that best meet the objectives of this project are selected, and 12,600 single amplified genomes (SAGs) from them will be sequenced. The SAGs will then be identified by their SSU rRNA genes, and 800 MDM SAGs that best meet the objectives of this project will be further annotated, aligned and combined with various publicly-available data sets for use in detailed, statistical phylogenetic reconstruction of a comprehensive genealogy for Bacteria and Archaea. The genealogical inferences, in combination with other data layers important to understanding MDM evolution (including geochemical, geospatial, microbial community composition, and microbial physiology data) will be compiled and used in addressing the project's general evolutionary questions, as noted above. Analyses will also address the potential for the deep subsurface environments of Earth to serve as a repository for the early evolutionary history of Bacteria and Archaea. This project leverages an existing major award to the researchers through the DOE Joint Genome Institute to cover sequencing costs. The project has a very rich educational and outreach component, geared toward research experiences for undergraduate and graduate students, postdoctoral researchers and high school teachers. Engaging outreach activities and media designed for the general public are also planned. Further, the laboratory and computational tools and the massive genomic data produced by this project will provide a major resource to the broad research community and, potentially, to the biotechnology industry.