Ocean's dark energy: Global inventory of chemoautotrophs in the aphotic realm

黑暗的海洋，定义为透光层以下的水柱，包含地球上最大的微生物群落之一，由活跃和代谢多样的微生物组成。这些生物群影响着当地的进程和全球碳循环，例如，通过进行大部分海洋有机物的生物矿化。越来越多的证据表明，在黑暗的海洋中的化学自养也可能是显着的，与潜在的重大影响，黑暗的海洋的微生物生态学和生物地球化学。然而，它仍然在很大程度上没有回答的能源和代谢途径是用来支持这种微生物驱动的暗碳固定和微生物分类群体在黑暗的海洋中拥有化能自养代谢途径。该项目的总体目标是通过大规模微生物单细胞基因组学，辅以宏基因组学和元转录组学测序，获得黑暗海洋中化学自养生物的全面全球清单。研究人员将解决以下一般假设：1。在暗海中发现的多个原核生物分类群具有化能自养代谢途径.已知的和以前未被认识的化能自养途径都存在于暗海的原核生物中.暗洋化能自养生物在地球仪上广泛分布，其地理分布格局取决于水团的等密度线运动、水团年龄和有机物质的向下通量.在项目实施过程中，将从地球仪周围所有主要的中层和深层水团中产生单一扩增基因组（SAG），代表已知存在于黑暗海洋中的细菌和古菌的所有主要分类群。将分析这些SAG的特异性化学自养指示基因。将对SAG的子集进行全基因组测序，从而能够详细注释化能自养途径。宏基因组学和后转录组学片段募集将用于确定化能自养生物分布和化能自养途径表达的全球模式。这一雄心勃勃的项目之所以成为可能，是因为毕格罗实验室最近开发了从单个细胞中高通量回收基因组DNA的技术和设施，美国能源部联合基因组研究所提供了基因组测序支持，以及在许多领先的黑暗海洋微生物学家之间建立了广泛的合作网络。一个开始的研究人员将参与这个项目作为一个共同PI，提供第一手接触到赠款写作，项目管理和本科生导师。 该项目将产生大量独特的参考材料，为今后研究暗海洋微生物奠定坚实的基础，包括207个微生物基因组，代表暗海洋细菌和古菌的所有主要分类群，多个宏基因组，元转录组和pyrotag数据集，以及来自不同原核生物分类群的约2，000个单个细胞的基因组DNA，水体和地理位置。这项工作将提高我们对全球碳循环的理解，与气候变化研究直接相关。单细胞基因组技术及其可及性的进一步改进可能会有利于人类健康相关研究（例如人类微生物组和癌症研究）以及新能源和天然产品的生物勘探。

The dark ocean, defined as the water column below the photic, contains one of the largest microbial biomes on earth, composed of active and metabolically diverse microorganisms. These biota impact local processes and the global carbon cycling, e.g. by conducting a large fraction of marine organic matter remineralization. An increasing body of evidence suggests that chemoautotrophy in the dark ocean may also be significant, with potentially major implications to the dark ocean's microbial ecology and biogeochemistry. However, it remains largely unanswered what energy sources and metabolic pathways are used to support this microbial-driven dark carbon fixation and which microbial taxonomic groups possess chemoautotrophic metabolic pathways in the dark ocean.Intellectual Merit. The overall goal of this project is to obtain a comprehensive, global inventory of chemoautotrophs in the dark ocean through large-scale microbial single cell genomics, supplemented with metagenomic and metatranscriptomic sequencing. The investigators will address the following general hypotheses:1. Multiple prokaryote taxonomic groups found in the dark ocean contain chemoautotrophic metabolicpathways.2. Both known and previously unrecognized chemoautotrophy pathways are present in dark ocean'sprokaryotes.3. Dark ocean chemoautotrophs are broadly distributed around the globe, with biogeographic patternsdetermined by the isopycnal movement of water masses, water mass age, and the downward flux oforganic matter.4. Diverse chemoautotrophy pathways are expressed in the dark ocean.During the course of the project, single amplified genomes (SAGs) will be generated from all major intermediate and deep water masses around the globe, representing all major taxonomic groups of bacteria and archaea that are known to be present in the dark ocean. These SAGs will be analyzed for specific chemoautotrophy-indicative genes. Whole genome sequencing will be performed on a subset of SAGs, enabling detailed annotation of chemoautotrophy pathways. Metagenomic and metatranscriptomic fragment recruitment will be used to determine global patterns of chemoautotroph distribution and chemoautotrophy pathway expression. This ambitious project is made possible by the recent development of techniques and facilities for high-throughput genomic DNA recovery from individual cells at Bigelow Laboratory, genomic sequencing support provided by the U.S. Department of Energy Joint Genome Institute, and the establishment of a broad network of collaborations among many leading dark ocean microbiologists.Broader Impacts. One beginning researcher will be involved in this project as a co-PI, providing first-hand exposure to grant writing, project management and undergraduate student mentorship. The project will generate a large quantity of unique reference materials, laying a solid foundation for future studies of dark ocean microorganisms, including 207 microbial genomes, representing all major taxonomic groups of bacteria and archaea from the dark ocean, multiple metagenomes, metatranscriptomes and pyrotag data sets, as well as genomic DNA from ~2,000 individual cells from diverse prokaryote taxonomic groups, water masses and geographic locations. The work will improve our understanding of the global carbon cycle, with direct relevance to climate change studies. Further improvements in single cell genomics technology and its accessibility will likely benefit human health-related studies (e.g. human microbiome and cancer research) and bioprospecting for new energy sources and natural products.