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

Bigelow Laboratory For Ocean Sciences, East Boothbay ME

Investigators

Abstract

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 metabolic pathways. 2. Both known and previously unrecognized chemoautotrophy pathways are present in dark ocean's prokaryotes. 3. Dark ocean chemoautotrophs are broadly distributed around the globe, with biogeographic patterns determined by the isopycnal movement of water masses, water mass age, and the downward flux of organic 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.