Our main goal is to explore the metabolic and genomic diversity of deep subsurface sediment communities underlying oligotrophic ocean gyres. It has become apparent that in contrast to well-studied ocean margin sediments, oxygen (O2) and nitrate (NO3-), two powerful oxidants of organic carbon, penetrate deeply into the sediment in vast areas of the ocean underlying oligotrophic gyres. Nitrogen cycling, including subsurface N2-fixation, and thus new input of nitrogen may support deeply buried microbial communities in carbon-lean sediments underlying oligotrophic ocean gyres. Active cells persist throughout the sediment column even in the most carbon-starved sediments in the center of the South Pacific Gyre. The nature of the microbial communities and their metabolic potentials are largely unknown and might be very different from communities in continental margin setting. We obtained samples (whole core rounds) from both the South Pacific Gyre (329) and the North Pond (336) expedition, and developed a method for extracting intact cells from large sediment volumes by density centrifugation, similar to the procedure used for extracting cells for subsurface cell enumerations. DNA extraction and subsequent shotgun metagenome sequencing was highly successful. Assembly of metagenomic data followed by differential binning yielded high genomic sequence coverage and recovery of >280 distinct genomes.
The objectives of this proposal therefore are: 1) Analyzing the metagenomic data on the community and organism level with a specific focus on nitrogen metabolisms. 2) Validating the metabolic potential, for example nitrogen fixation, with incubation experiments and determining the rates of nitrogen fixation and denitrification.
We propose to analyze these data in two distinct ways: i) a functional analysis of core capabilities in each sample (Community level) and ii) a comparative genomic approach using almost complete genomes and analyzing the physiological ability of each individual member (Organism level) of the deep subsurface microbiome, thus shining light on interdependencies of microorganisms. Our metagenomic sequencing approach will give unprecedented insight into the deep subsurface microbiome of ultra oligotrophic gyres.