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

黑暗的海洋，定义为光柱以下的水柱，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。这些生物群影响局部过程和全球碳循环，例如通过引导大部分海洋有机物再矿化。越来越多的证据表明，暗海中的化学自养可能也很重要，对暗海的微生物生态和生物地球化学有潜在的重大影响。然而，哪些能量来源和代谢途径是用来支持这种微生物驱动的暗碳固定的，哪些微生物分类群在暗海洋中具有化学自养代谢途径，这些问题在很大程度上仍然没有答案。知识价值。该项目的总体目标是通过大规模微生物单细胞基因组学，并辅以宏基因组和亚转录组测序，获得黑暗海洋中化学自养生物的全面全球清单。调查人员将解决以下一般假设：1。在深海中发现的多个原核生物分类类群都含有化学自养代谢途径。已知的和以前未被认识的化学自养途径都存在于黑暗海洋的原核生物中。暗洋化学自养生物在全球分布广泛，其生物地理格局由水体的等平运动、水体年龄和有机物的向下通量决定。不同的化学自养途径在暗海洋中表达。在项目过程中，单扩增基因组（sag）将从全球所有主要的中间和深水群中产生，代表已知存在于黑暗海洋中的所有主要细菌和古细菌分类群。这些sag将被用于分析特定的化学自养指示基因。将对sag的一个子集进行全基因组测序，以便对化学自养途径进行详细注释。宏基因组和亚转录组片段募集将用于确定化学自养分布和化学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，得益于毕格罗实验室（Bigelow Laboratory）最近开发的从单个细胞中提取高通量基因组DNA的技术和设备，美国能源部联合基因组研究所（U.S. Department of Energy Joint Genome Institute）提供的基因组测序支持，以及许多领先的暗海微生物学家之间建立的广泛合作网络。更广泛的影响。一名初级研究人员将作为共同负责人参与该项目，提供第一手的资助写作，项目管理和本科生指导。该项目将产生大量独特的参考材料，为今后暗海微生物的研究奠定坚实的基础，包括代表暗海细菌和古细菌所有主要分类类群的207个微生物基因组，多个宏基因组、元转录组和热标记数据集，以及来自不同原核生物分类类群、水体和地理位置的约2000个单个细胞的基因组DNA。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。单细胞基因组学技术的进一步改进及其可及性可能有利于与人类健康有关的研究（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.