UC San Diego

Metagenomic studies of marine ecosystems have provided a wealth of molecular data with which to aid in the understanding of taxonomic diversity, potential abundances and putative functional roles in biogeochemical cycles. A metagenomics investigation of surface ocean microbial communities within the Southern California Bight and adjacent California Current Ecosystem was initiated in order to improve understanding of the impact of upwelling. These data show that the community composition of bacteria within the 0.1-0.8[Mu]m size class is tightly coupled to position within the upwelling mosaic; and therefore correlated with oceanographic metadata such as nutrient availability, chlorophyll, temperature, and salinity. However, evaluation of bacteria among the larger size classes (0.8-200[Mu]m) reveals a relatively consistent community regardless of position. These organisms are predicted to have larger genome sizes and a greater metabolic repertoire. One site within aged-upwelled waters exhibited a peak in Planctomycete abundance, indicative of a bloom that corresponded with diatom sequence abundance. Among the marine virioplankton community, novel accessory genes involved in nitrogen metabolism were identified, and potentially reflect adaptation of CCE virioplankton to host community shifts that result from pulses of high nutrients. Additionally, high abundances of sequences related to known virioplankton from CC waters, Roseophage SIO1, were identified; however, gaps in genome coverage were identified and possibly refelct a novel Roseophage strain. Also, analysis of viral sequences from the cellular fraction (>0.1[Mu]m) suggests that viruses infecting cyanobacteria and phytoplankton are relatively more abundant compared to the viral fraction (<0.1[Mu]m), indicating a need to evaluate >0.1[Mu]m fraction material in order to obtain a complete picture of the marine virioplankton community. A new method was developed to bridge the gap between metagenomic and genomic studies of marine virioplankton. This method relied on the isolation and characterization of single viral particles