May 31, 2018
Dr. Alma Parada, Stanford University
Evaluating the diversity and distribution of novel microbes across physical and geochemical gradients in deep-sea sediments
Marine sediments harbor an estimated 50% of all microbes on earth. Despite this numerical importance, the factors controlling the diversity, metabolism, and distribution of these benthic microbes, especially in representative deep-sea sediments, are poorly understood. In this study, we collected sediment cores at 8 sites across a 300km transect off the coast of San Francisco spanning 100-4500m water depths and 0-30cm sediment depths. Using Illumina sequencing of the 16S rRNA gene and transcripts, we characterized the microbial community to compare changes in the physical and chemical parameters of the sediment to changes in the microbial community and metabolic potential. Canonical correspondence analysis indicated site, pressure, temperature and oxygen concentrations of the overlying water was correlated to stratification of the microbial community water depth, while pore water ammonium and nitrate concentrations correlated to differences in the communities across sediment depths. Interestingly, 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 the GenBank database. To investigate the metabolic capabilities of these uncharacterized lineages, we sequenced a metagenome from surface sediment at 3500m water depth and used a novel assembly method that combines 10X genomics technology and barcoded reads. We obtained 24 metagenome assembled genomes (MAGs) with >70% completion, <10% contamination, and a 16S rRNA gene. Of these, 13 (~55%) MAGs had 16S rRNA genes <90% similar to representative genomes in GenBank. OTUs with a percent identity of 99-100% to the 16S of these MAGs were widely distributed and active across the transect. The widespread presence of potentially novel organisms in sediments at depths representative of the majority of ocean indicates the importance of previously uncharacterized microbes in global carbon and biogeochemical cycles.
Dr. Parada received a B.S. in Biology from the University of La Verne. She attended graduate school at the University of Southern California, working in Dr. Jed Fuhrman’s laboratory studying the temporal and spatial variability of marine archaea at the San Pedro Ocean Time-series station, ~10 km off the coast of the Los Angeles Port. She received her Ph.D. in Marine Biology and Biological Oceanography. She is currently a C-DEBI postdoctoral fellow at Stanford University in Dr. Anne Dekas’ lab. Her work focuses on studying the diversity, distribution and role of benthic archaea in the carbon cycle using a combination of molecular and stable isotope probing techniques.