Evaluating the distribution and genomic content of novel microbes in deep-sea sediments

Marine sediments harbor an estimated 50% of all microbes on earth. However, the identity, distribution, and metabolism of deep-sea benthic microbes are poorly understood. In this study, we collected sediment cores at 8 sites across a 300km transect off the San Francisco Coast spanning 100-4500m water depth and 0-30cm sediment depth. Using amplicon sequencing of 16S rDNA, we investigated trends in microbial community composition across distinct physicochemical parameters, and evaluated the sequence novelty of detected microbes. Canonical correspondence analysis showed microbial communities clustered by water and sediment depth, correlating to changes in pressure, temperature and oxygen concentrations of the overlying water, as well as pore water ammonium, phosphate, and nitrate concentrations. Many microbes were from potentially novel lineages: an average of 34% of the operational taxonomic units (OTUs) present in each sample were <90% similar to the 16S rRNA gene of any representative genome in GenBank, and up to 13% of OTUs found in one sample were <70% similar to representatives. To investigate the metabolic capabilities of these uncharacterized lineages, we sequenced a metagenome from surface sediment at 3500m water depth using a novel assembly method that combines 10X genomics technology and barcoded short reads. This approach resulted in higher quality metagenome assembled genomes (MAGs) and, specifically, more MAGs containing a 16S rRNA gene sequence than conventional assembly methods. We obtained 24 MAGs with >70% completion, <10% contamination, and a 16S rRNA gene. Of these, the 9 most complete MAGs had average amino acid identities <65% to their closest 16S rRNA match from representative genomes, These potentially novel MAGs include organisms capable of sulfate and sulfite reduction, as well as nitrification and general heterotrophic growth. These results suggest that microorganisms distantly related to those previously characterized, dominated our sediment samples and are mediating important conversions in carbon, sulfur, and nitrogen cycles in this environment.