Active Research Projects

Sulfur Cycle Gene Discovery - 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 regulate DMS flux by converting the precursor compound DMSP (dimethylsulfoniopropionate) either to DMS or to other sulfur compounds that are not climatically active. We are identifying bacterial genes for DMSP transformation through molecular biology, genomic, and functional genomic studies with model marine bacteria and natural bacterial communities. We have found that marine bacterioplankton in several taxonomic groups harbor genes for DMSP degradation, although we do not yet know the taxonomic identity of many. At least half the cells in ocean surface water have the genetic capability to degrade DMSP, and we are developing a real-time ocean monitoring assay for DMSP-relevant gene abundance and expression (in collaboration with Drs. C. Scholin and C. Preston of MBARI). 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. Total RNA is collected from the environment, rRNA is selectively removed, mRNA is linearly amplified, and cDNA is synthesized and sequenced by pyrosequencing.  We are applying this approach to understand diel changes in activities of autotrophic and heterotrophic bacteria at Station ALOHA, a deep-water ocean monitoring site near Hawaii (in collaboration with Drs. J. Zehr and I. Hewson), and to track seasonal patterns of carbon flow through a nearshore bacterial community at Sapelo Island, Georgia. Our goal is to use patterns of bacterioplankton gene expression to better understand the flux and fate of organic matter in the ocean.

Assigning Bacterial Roles - Little information exists on the specific metabolic functions of each marine bacterioplankton taxon, despite their importance in assimilating and mineralizing carbon and nutrients in seawater. We are coupling flow cytometry to metagenomics in order to address this issue, which physically separates bacterial cells capable of metabolizing individual compounds and then directly determines their metabolic abilities through metagenomic sequencing. Ecological theory predicts that heterogeneous environments, such as coastal oceans, should favor the establishment of generalist bacterial species with broad ecological niches; our recent studies agree with this prediction. We do not yet fully understand how the various genes in ocean bacteria are packaged together, but obtaining this information is critical for modeling and predicting biogeochemical activities of coastal bacterioplankton in a changing ocean.

Roseobacter Model Organism System Development - Over 30 genome sequences are available for cultured members of the marine Roseobacter group. Since this bacterial group is often a dominant member of coastal seawater communities, the sequenced strains provide a powerful system to understanding the activities of their wild relatives. We have been developing genetic systems, microarrays, culturing protocols, and bioinformatics resources (www.roseobase.org) to facilitate discoveries of the ecological and biogeochemical roles of marine bacterioplankton. Roseobacter model systems are a key thrust in our ongoing efforts to understand coastal ocean biogeochemistry.