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对整个基因组进行测序，将在这个项目中用于揭开生命早期进化和系谱的秘密。在这一突破之前，许多最早的生命分化谱系无法分析，因为它们不能在实验室培养中生长。细菌和古生物群中的这种不可培养的“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量，现在可以通过单扩增基因组(SAGs)的测序来揭示这一点。在这项史无前例的研究项目中，许多编码不同生物体蓝图的新基因组能够并将被分析，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所起的作用。此外，将从世界各地尚未探索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从多个研究地点收集的100多个富含MDM的野外样本，包括南非Kaapvaall克拉通的前寒武纪盾牌环境，通过南达科他州的Sanford地下研究设施进入的前寒武纪变质杂岩，以及与第三纪火山区有关的断层泉水，以及内华达州死亡谷区域流动系统的寒武纪沉积岩。广泛的背景信息(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含有高比例MDM的地点收集实地样本和元数据。然后，通过对其小亚基(SSU)rRNA基因iTags进行测序，调查收集样本中的微生物群落组成。根据ITAG的数据，选择了20个最符合本项目目标的样本，并将对其中的12,600个单扩增基因组(SAG)进行测序。然后，将通过SSU rRNA基因确定SAG，对最符合本项目目标的800个MDM SAG进行进一步注释、比对并与各种公开可用的数据集结合，用于详细、统计地重建细菌和古生菌的全面谱系。如上所述，谱系推论将与对了解MDM进化很重要的其他数据层(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)结合起来，并用于解决该项目的一般进化问题。分析还将探讨地球深层地下环境作为细菌和古生物早期进化史的储存库的潜力。该项目利用现有的通过能源部联合基因组研究所授予研究人员的主要奖项来支付测序费用。该项目有非常丰富的教育和推广部分，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。还计划开展面向公众的宣传活动和媒体。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，并可能为生物技术行业提供重要资源。

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.