OM43 is a clade of uncultured beta-proteobacteria that is commonly found in environmental nucleic acid sequences from productive coastal ocean ecosystems, and some freshwater environments, but is rarely detected in ocean gyres. Ecological studies associate OM43 with phytoplankton blooms, and evolutionary relationships indicate that they might be methylotrophs. Here we report on the genome sequence and metabolic properties of the first axenic isolate of the OM43 clade, strain HTCC2181, which was obtained using new procedures for culturing cells in natural seawater. We found that this strain is an obligate methylotroph that cannot oxidize methane but can use the oxidized C1 compounds methanol and formaldehyde as sources of carbon and energy. Its complete genome is 1304 428 bp in length, the smallest yet reported for a free-living cell. The HTCC2181 genome includes genes for xanthorhodopsin and retinal biosynthesis, an auxiliary system for producing transmembrane electrochemical potentials from light. The discovery that HTCC2181 is an extremely simple specialist in C1 metabolism suggests an unanticipated, important role for oxidized C1 compounds as substrates for bacterioplankton productivity in coastal ecosystems.

A quantitative PCR assay for the SAR11 clade of marine Alphaproteobacteria was applied to nucleic acids extracted from monthly depth profiles sampled over a 3-year period (2004-2007) at the open-ocean Station ALOHA (A Long-term Oligotrophic Habitat Assessment; 22 degrees 45'N, 158 degrees 00'W) in the oligotrophic North Pacific Ocean. This analysis revealed a high contribution (averaging 36% of 16S rRNA gene copies) of SAR11 to the total detected 16S rRNA gene copies over depths ranging from the surface layer to 4000 m, and revealed consistent spatial and temporal variation in the relative abundance of SAR11 16S rRNA gene copies. On average, a higher proportion of SAR11 rRNA gene copies were detected in the photic zone (< 175 m depth; mean = 38%) compared with aphotic (> 175 m depth; mean = 30%), and in the winter months compared with the summer (mean = 44% versus 33%, integrated over 175 m depth). Partial least square to latent structure projections identified environmental variables that correlate with variation in the absolute abundance of SAR11, and provided tools for developing a predictive model to explain time and depth-dependent variations in SAR11. Moreover, this information was used to hindcast temporal dynamics of the SAR11 clade between 1997 and 2006 using the existing HOT data set, which suggested that interannual variations in upper ocean SAR11 abundances were related to ocean-climate variability such as the El Niño Southern Oscillation.

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The exploration of bacterial diversity in the global ocean has revealed new taxa and previously unrecognized metabolic potential; however, our understanding of what regulates this diversity is limited. Using terminal restriction fragment length polymorphism (T-RFLP) data from bacterial small-subunit ribosomal RNA genes we show that, independent of depth and time, a large fraction of bacterioplankton co-occurrence patterns are non-random in the oligotrophic North Pacific subtropical gyre (NPSG). Pair-wise correlations of all identified operational taxonomic units (OTUs) revealed a high degree of significance, with 6.6% of the pair-wise co-occurrences being negatively correlated and 20.7% of them being positive. The most abundant OTUs, putatively identified as Prochlorococcus, SAR11, and SAR116 bacteria, were among the most correlated OTUs. As expected, bacterial community composition lacked statistically significant patterns of seasonality in the mostly stratified water column except in a few depth horizons of the sunlit surface waters, with higher frequency variations in community structure apparently related to populations associated with the deep chlorophyll maximum. Communities were structured vertically into epipelagic, mesopelagic, and bathypelagic populations. Permutation-based statistical analyses of T-RFLP data and their corresponding metadata revealed a broad range of putative environmental drivers controlling bacterioplankton community composition in the NPSG, including concentrations of inorganic nutrients and phytoplankton pigments. Together, our results suggest that deterministic forces such as environmental filtering and interactions among taxa determine bacterioplankton community patterns, and consequently affect ecosystem functions in the NPSG.