Collaborative research: Untangling the Deep Genealogy of Microbial Dark Matter

突破性的技术，使整个基因组的快速测序从单细胞，将用于该项目，以解开生命的早期进化和家谱的秘密。在这一突破之前，许多生命最早的分化谱系无法被分析，因为它们无法在实验室培养中生长。这种不可培养的“微生物暗物质”（MDM）在细菌和微生物群中构成了地球上大部分的生物物种多样性和生物质量，现在可以通过对单个扩增基因组（SAG）进行测序来揭示这一点。在这个前所未有的研究项目中，许多新的基因组，编码不同生物的蓝图，可以并将被分析以阐明（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发挥的作用。此外，将从世界各地未探索的地下环境中进行广泛的MDM采样，以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，包括来自南非Kaapvaall地区的前寒武纪盾牌环境，这是一个通过南达科他州桑福德地下研究设施访问的前寒武纪变质杂岩，与第三纪火山区和寒武纪有关的断层伴生泉-内华达州死亡谷区域流动系统的年代沉积岩。在这些取样工作中还将纳入广泛的背景信息（环境和生物元数据）。研究任务开始从已知或怀疑含有高比例MDM的地点收集现场样本和元数据。然后，通过对其小亚单位（SSU）rRNA基因iTags进行测序，调查所收集样品中的微生物群落组成。根据iTag数据，选择最符合本项目目标的20个样本，并对其中的12，600个单扩增基因组（SAG）进行测序。然后将通过其SSU rRNA基因鉴定SAG，并将最符合本项目目标的800个MDM SAG进一步注释，对齐并与各种公开可用的数据集结合，用于细菌和细菌的全面谱系的详细统计系统发育重建。系谱推断，结合其他数据层的重要理解MDM演变（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）将被编译和用于解决该项目的一般进化问题，如上所述。分析还将涉及地球深层地下环境作为细菌和细菌早期进化历史的储存库的潜力。该项目通过美国能源部联合基因组研究所利用现有的主要奖项来支付测序费用。该项目有一个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，实验室和计算工具以及该项目产生的大量基因组数据将为广泛的研究界提供重要资源，并可能为生物技术产业提供重要资源。

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.