Active Research Projects

Bacterial Roles in the Ocean Sulfur Cycle - Dimethylsulfide (DMS) released from ocean surface waters is the predominant natural source of sulfur to the atmosphere, where it plays a critical role in Earth’s climate through aerosol formation and cloud cover. Marine bacterioplankton use two primary pathways to degrade DMSP, one of which produces DMS and the other of which leads to biosynthesis of sulfur-containing amino acids, yet little is known about environmental conditions that regulate these pathways. We are identifying bacterial genes for DMSP transformation through molecular biology, genomic, and functional genomic studies with model marine bacteria; investigating interactions between bacteria and phytoplankton in laboratory systems; conducting field research with coastal bacterial and phytoplankton communities; and working with researchers at the Monterey Bay Aquarium Research Institute to capture real-time gene expression of DMSP genes in the ocean. Our long-term goal is to understand the role of marine bacterioplankton in sulfur-mediated global temperature regulation.

Environmental Transcriptomics - By sequencing mRNAs retrieved directly from seawater, we can ‘eavesdrop’ on the activities of natural bacterial communities. The gene expression data acquired provides a direct link between the genetic potential of a community and their biogeochemical activities. We are applying this approach to understand diel, seasonal, and interannual changes in activities of bacteria in coastal and open ocean environments.

Coastal Carbon Cycling - Bacterioplankton control the flux of dissolved organic carbon (DOC) into the microbial food web and influence the release of inorganic carbon to atmospheric and offshore reservoirs. Yet when and how organic carbon is decomposed in coastal waters is still a matter of considerable controversy, at least in part because the thousands of compounds making up the DOC pool are processed by hundreds of different bacterial taxa. Our research is focused on assembling the functional network for bacterioplankton communities processing marine DOC: the bioreactive components, the metabolic pathways used to transform them, and the partitioning of ecological niches. We are coupling molecular biology approaches (metagenomics, metatranscriptomics, metabolomics) with high-resolution chemical analyses of DOC composition and turnover to resolve patterns of carbon transformation, and ultimately to model and predict biogeochemical activities of coastal bacterioplankton in a changing ocean. More details are available on the SIMCO website (

Roseobacter Model Organism System Development - Almost 60 genome sequences are available for cultured members of the marine Roseobacter lineage. Since this group is a dominant member of most coastal seawater communities, the sequenced strains provide a powerful system to understanding the activities of their wild relatives. We have been developing genetic systems, functional genomics approaches, culturing protocols, and bioinformatics resources ( to facilitate discoveries of the ecological and biogeochemical roles of these ubiquitous marine bacterioplankton.

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