Microbial Diversity and Function in Shallow Subsurface Sediment and Oceanic Lithosphere of the Atlantis Massif.

The marine lithospheric subsurface is one of the largest biospheres on Earth; however, little is known about the identity and ecological function of microorganisms found in low abundance in this habitat, though these organisms impact global-scale biogeochemical cycling. Here, we describe the diversity and metabolic potential of sediment and endolithic (within rock) microbial communities found in ultrasmall amounts (101 to 104 cells cm-3) in the subsurface of the Atlantis Massif, an oceanic core complex on the Mid-Atlantic Ridge that was sampled on International Ocean Discovery Program (IODP) Expedition 357. This study used fluorescence-activated cell sorting (FACS) to enable the first amplicon, metagenomic, and single-cell genomic study of the shallow (<20 m below seafloor) subsurface of an actively serpentinizing marine system. The shallow subsurface biosphere of the Atlantis Massif was found to be distinct from communities observed in the nearby Lost City alkaline hydrothermal fluids and chimneys, yet similar to other low-temperature, aerobic subsurface settings. Genes associated with autotrophy were rare, although heterotrophy and aerobic carbon monoxide and formate cycling metabolisms were identified. Overall, this study reveals that the shallow subsurface of an oceanic core complex hosts a biosphere that is not fueled by active serpentinization reactions and by-products. IMPORTANCE The subsurface rock beneath the ocean is one of the largest biospheres on Earth, and microorganisms within influence global-scale nutrient cycles. This biosphere is difficult to study, in part due to the low concentrations of microorganisms that inhabit the vast volume of the marine lithosphere. In spite of the global significance of this biosphere, little is currently known about the microbial ecology of such rock-associated microorganisms. This study describes the identity and genomic potential of microorganisms in the subsurface rock and sediment at the Atlantis Massif, an underwater mountain near the Mid-Atlantic Ridge. To enable our analyses, fluorescence-activated cell sorting (FACS) was used as a means to concentrate cells from low biomass environmental samples for genomic analyses. We found distinct rock-associated microorganisms and found that the capacity for microorganisms to utilize organic carbon was the most prevalent form of carbon cycling. We additionally identified a potential role for carbon monoxide metabolism in the subsurface.

Single cell genomics yields a wide diversity of small planktonic protists across major ocean ecosystems.

Marine planktonic protists are critical components of ocean ecosystems and are highly diverse. Molecular sequencing methods are being used to describe this diversity and reveal new associations and metabolisms that are important to how these ecosystems function. We describe here the use of the single cell genomics approach to sample and interrogate the diversity of the smaller (pico- and nano-sized) protists from a range of oceanic samples. We created over 900 single amplified genomes (SAGs) from 8 Tara Ocean samples across the Indian Ocean and the Mediterranean Sea. We show that flow cytometric sorting of single cells effectively distinguishes plastidic and aplastidic cell types that agree with our understanding of protist phylogeny. Yields of genomic DNA with PCR-identifiable 18S rRNA gene sequence from single cells was low (15% of aplastidic cell sorts, and 7% of plastidic sorts) and tests with alternate primers and comparisons to metabarcoding did not reveal phylogenetic bias in the major protist groups. There was little evidence of significant bias against or in favor of any phylogenetic group expected or known to be present. The four open ocean stations in the Indian Ocean had similar communities, despite ranging from 14°N to 20°S latitude, and they differed from the Mediterranean station. Single cell genomics of protists suggests that the taxonomic diversity of the dominant taxa found in only several hundreds of microliters of surface seawater is similar to that found in molecular surveys where liters of sample are filtered.