Genomics of marsh microbes

With funding from my NSF CAREER award, and led by grad student Joe Vineis, we are exploring multiple aspects of the functional roles of microbes in salt marsh sediments. One way that we can learn more about the unique microbial metabolisms in salt marshes is by reconstructing their genomes from metagenomic sequencing data. We have these reconstructed genomes from both flow through reactor experiments (Bulseco et al. 2019, 2020) and from deep sediment cores that represent thousands of years of salt mash organic matter accumulation.  We are sorting our way through thousands of genomes to better understand the connections between carbon, nitrogen, and sulfur cycling in these complex habitats.

For example, one of the more interesting organisms that are super abundant in nitrate enriched marsh sediments is this Chlorobium species. These bacteria have an incredibly diverse metabolic repertoire. They have the genetic capacity for both carbon fixation and for decomposition of organic carbon.  They can also fix nitrogen and they can reduce sulfate. It is through reconstructing these genomes that we can begin to connect the dots between the important biogeochemical processes that underly marsh ecosystem functioning.