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		Brian Palenik's Research Marine Genomics Research The DOE-funded Joint Genome Institute has completed the genomes of several marine cyanobacteria. This allows an unprecedented opportunity to understand the process of carbon fixation in these marine organisms, how it is regulated, and how these organisms respond to environmental stresses that may constrain their growth and carbon fixation rates. Genome of Synechococcus Image: P Chain, SIO We have been involved in annotating the genome of Synechococcus sp. strain WH8102 in collaboration with Bianca Brahamsha at SIO and others. In collaboration with the Brahamsha lab we are now characterizing the transporters in this genome, using our ability to make genetic mutations in WH8102. Since two-component regulatory systems are a family of regulatory elements that play an important role in environmental sensing by bacteria, we are currently characterizing these in WH8102 as well. Recently our genomics research is also expanding into characterizing the genome of a marine diatom. Collaborators Bianca Brahamsha Ian Paulsen, The Institute for Genomic Research (TIGR) Genomes to Life, Developing Computational Capabilities to Understand Complex Biological Systems Mark Hildebrand, Scripps Institution for Oceanography Phytoplankton Diversity In marine ecosystems, gradients of light, temperature and nutrients occur horizontally (coastal to offshore) and vertically. The extent to which microorganisms acclimate or speciate in response to these gradients is under active investigation. We have been characterizing the diversity of marine cyanobacteria using multiple approaches including strain isolation, environmental DNA clone libraries using rpoC1 (RNA polymerase) sequences, and physiology experiments to characterize cyanobacterial diversity in marine environments from estuaries to the open ocean. We have found that Synechococcus is a group with multiple species (perhaps genera) and particular isolates can be repeatedly found and cultured from specific environments. Our results indicate that cyanobacterial communities are highly structured (see Ferris and Palenik, 1998). We are currently investigating what processes have created this structure. We have also begun characterizing the diversity of small eukaryotic phytoplankton as well. These organisms likely compete with marine cyanobacteria for resources. Phytoplankton-Environment Interactions Phytoplankton must respond to changes in their environment. These could be changes in light intensity, light quality, nutrient concentrations, or toxicants. We are currently characterizing proteins induced by environmental change, characterizing their regulation in laboratory experiments, and then characterizing their presence in field samples to actually demonstrate phytoplankton responses in situ (see for example Dyhrman and Palenik 1999). We are currently focusing on copper stress in diatoms and nitrogen and phosphorus limitation in a coccolithophorid Emiliania huxleyi. In addition to genomic and other approaches to understanding phytoplankton diversity, we are also involved in field research to simply characterize phytoplankton abundance in space and time. In particular we have characterized phytoplankton abundance at the SIO pier (over several years) and in the larger CalCOFI study area. We are beginning to combine this work with the other approaches discussed above. New Research Directions Scientific research always takes new directions depending on recent discoveries and graduate student interests. As these develop we will discuss them here. References S. T. Dyhrman and B. Palenik, 1999. Phosphate stress in cultures and field populations of the dinoflagellate Prorocentrum minimum detected by a single cell alkaline phosphatase assay. Appl. Environ. Microbiol. 65:3205-3212. M.J. Ferris and B. Palenik, 1998. Niche adaptation in ocean cyanobacteria. Nature. 396:226-228.

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