Deep Trench Single-cell Genomics

深沟单细胞基因组学

• 批准号: 0827051
• 负责人: Douglas Bartlett
• 金额: $ 65.8万
• 依托单位: University of California-San Diego Scripps Inst of Oceanography
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-09-01 至 2014-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0827051&HistoricalAwards=false
• 关键词: Deep; Trench; Single; cell; Genomics

Microbial diversity in deep-sea environments is high, where microbial evolution and distribution have been influenced by extreme factors such as high pressure, low temperature, low carbon and no light. Scientists from the University of California San Diego and University of Puerto Rico-Mayaguez will explore the biodiversity of microorganisms of particularly extreme deep-sea environments - deep-sea trenches - by focusing on one site, the Puerto Rico Trench, the deepest part of the Atlantic Ocean. Deep trench prokaryotes (bacteria and archaea) are expected to possess novel enzymes and cell properties which allow them to survive and grow under these extreme conditions. One major goal of this project is to study the genomes of these microorganisms to understand what capabilities they have evolved to live in this harsh environment. Another goal is to evaluate the extent and diversity of novel protein families in the genomes of these deep trench microbes. Water samples collected from the trench and maintained under very high pressure (80 MPa or 11,000 psi), will be examined using single-cell genomic technology. A careful sorting procedure will be developed to avoid contamination, chimeras (hybridization of two or more different genomes) and other artifacts of sample handling. These researchers will collect two hundred individual cells from the water sample by micromanipulation and amplify their genomic DNA in nanoliter volume microfluidic chambers. They will perform 16S rDNA (universal marker gene) sequencing on each sample as an independent genetic identifier. They will then select genomic DNA candidates with novel phylogenetic characteristics for further full genome sequencing. The closed and assembled genome sequences will be annotated to assign gene function. These researchers will compare these genome sequences with sequences from various marine metagenomic datasets and will also compare the extent and diversity of novel protein families in these genomes to the large number of protein families identified in the Global Ocean Survey dataset. These researchers expect to discover anticipated as well as unexpected properties of deep sea microorganisms in this manner. Their outreach activities will include multiple workshops with the deep sea microbiology community and the development of an international conference on High Pressure Bioscience and Biotechnology. The genome sequences will also become a rare community resource since microbial samples from deep sea trenches are very difficult to obtain.

深海环境微生物多样性高，微生物的演化和分布受到高压、低温、低碳、无光等极端因素的影响。来自加州大学圣地亚哥分校和波多黎各大学-马亚圭斯分校的科学家将专注于大西洋最深处的波多黎各海沟，探索特别极端深海环境-深海海沟-微生物的生物多样性。深沟原核生物(细菌和古细菌)有望拥有新的酶和细胞特性，使它们能够在这些极端条件下生存和生长。这个项目的一个主要目标是研究这些微生物的基因组，以了解它们进化出了什么能力来在这种恶劣的环境中生活。另一个目标是评估这些深沟微生物基因组中新蛋白质家族的范围和多样性。从海沟收集并在非常高的压力(80兆帕或11,000磅/平方英寸)下保持的水样将使用单细胞基因组技术进行检测。将制定仔细的分选程序，以避免污染、嵌合体(两个或更多不同基因组的杂交)和其他样品处理的人工制品。这些研究人员将通过显微操作从水样中收集200个单个细胞，并在纳升体积的微流体室中放大它们的基因组DNA。他们将对每个样本进行16S rDNA(通用标记基因)测序，作为一个独立的遗传识别符。然后，他们将选择具有新的系统发育特征的候选基因组DNA进行进一步的全基因组测序。封闭和组装的基因组序列将被注释以分配基因功能。这些研究人员将把这些基因组序列与各种海洋元基因组数据库中的序列进行比较，并将这些基因组中新蛋白质家族的范围和多样性与全球海洋调查数据集中确定的大量蛋白质家族进行比较。这些研究人员希望通过这种方式发现深海微生物的预期和意想不到的特性。它们的外联活动将包括与深海微生物界举办多个讲习班，以及举办一次高压生物科学和生物技术国际会议。基因组序列也将成为一种稀有的群落资源，因为从深海海沟获取微生物样本非常困难。