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

黑暗的海洋，定义为光层以下的水柱，包含地球上最大的微生物群落之一，由活跃的和代谢多样化的微生物组成。这些生物群影响当地进程和全球碳循环，例如通过进行很大一部分海洋有机物质再矿化。越来越多的证据表明，黑暗海洋中的化学自养也可能是重要的，对黑暗海洋的微生物生态和生物地球化学具有潜在的重大影响。然而，在很大程度上仍然没有回答什么能源和代谢途径用来支持这种微生物驱动的暗碳固定，以及哪些微生物分类群在黑暗海洋中拥有化学自养代谢途径。该项目的总体目标是通过大规模微生物单细胞基因组学，辅以元基因组和后转录测序，获得黑暗海洋中全面的、全球的化学自养生物清单。研究人员将解决以下一般假设：1.在黑暗海洋中发现的多个原核生物分类群包含化学自养代谢途径。在黑暗海洋的原核生物中，既有已知的和以前未知的化学自养途径。暗海化学自养生物广泛分布于全球各地，其生物地理格局由水团的等周期运动、水团年龄和有机质向下的通量决定。在黑暗海洋中表达了不同的化学自养途径。在该项目的过程中，将从全球所有主要的中深层水团中产生单一扩增基因组(SAGs)，代表已知存在于黑暗海洋中的所有主要的细菌和古菌分类群。这些SAG将被分析为特定的化学自养指示基因。全基因组测序将在SAG的子集上进行，从而能够对化学自养途径进行详细的注释。后基因组和后转录片段募集将被用来确定化学自养细胞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，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，以及许多领先的黑暗海洋微生物学家建立了广泛的合作网络。一名初级研究员将作为合作PI参与这个项目，提供第一手的资金撰写、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，为今后对暗海洋微生物的研究奠定坚实的基础，其中包括207个微生物基因组，代表来自黑暗海洋的细菌和古菌的所有主要分类组，多个元基因组、后转录组和焚烧标签数据集，以及来自不同原核生物分类组、水团和地理位置的约2,000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及其可获得性的进一步改进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)以及对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.