Analysis of marine cyanobacteria and proteobacteria genomes has provided a profound understanding of the life strategies of these organisms and their ecotype differentiation and metabolisms. However, a comparable analysis of the Bacteroidetes, the third major bacterioplankton group, is still lacking. In the present paper, we report on the genome of Polaribacter sp. strain MED152. On the one hand, MED152 contains a substantial number of genes for attachment to surfaces or particles, gliding motility, and polymer degradation. This agrees with the currently assumed life strategy of marine Bacteroidetes. On the other hand, it contains the proteorhodopsin gene, together with a remarkable suite of genes to sense and respond to light, which may provide a survival advantage in the nutrient-poor sun-lit ocean surface when in search of fresh particles to colonize. Furthermore, an increase in CO2 fixation in the light suggests that the limited central metabolism is complemented by anaplerotic inorganic carbon fixation. This is mediated by a unique combination of membrane transporters and carboxylases. This suggests a dual life strategy that, if confirmed experimentally, would be notably different from what is known of the two other main bacterial groups (the autotrophic cyanobacteria and the heterotrophic proteobacteria) in the surface oceans. The Polaribacter genome provides insights into the physiological capabilities of proteorhodopsin-containing bacteria. The genome will serve as a model to study the cellular and molecular processes in bacteria that express proteorhodopsin, their adaptation to the oceanic environment, and their role in carbon-cycling.Bacteroidetes ͉ marine bacteria ͉ whole-genome analysis ͉ heterotrophic CO2 fixation

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We used mesocosm experiments to study the bacterioplankton community in a highly dynamic coastal ecosystem during four contrasting periods of the seasonal cycle: winter mixing, spring phytoplankton bloom, summer stratification and autumn upwelling. A correlation approach was used in order to measure the degree of coupling between the dynamics of major bacterial groups, heterotrophic carbon cycling and environmental factors. We used catalysed reporter deposition-fluorescence in situ hybridization to follow changes in the relative abundance of the most abundant groups of bacteria (Alphaproteobacteria, Gammaproteobacteria and Bacteroidetes). Bacterial carbon flux-related variables included bacterial standing stock, bacterial production and microbial respiration. The environmental factors included both, biotic variables such as chlorophyll-a concentration, primary production, phytoplankton extracellular release, and abiotic variables such as the concentration of dissolved inorganic and organic nutrients. Rapid shifts in the dominant bacterial groups occurred associated to environmental changes and bacterial bulk functions. An alternation between Alphaproteobacteria and Bacteroidetes was observed associated to different phytoplankton growth phases. The dominance of the group Bacteroidetes was related to high bacterial biomass and production. We found a significant, non-spurious, linkage between the relative abundances of major bacterial groups and bacterial carbon cycling. Our results suggest that bacteria belonging to these major groups could actually share a function in planktonic ecosystems.

To investigate the effects of mesoscale eddies on prokaryotic assemblage structure and activity, we sampled two cyclonic eddies (CEs) and two anticyclonic eddies (AEs) in the permanent eddy-field downstream the Canary Islands. The eddy stations were compared with two far-field (FF) stations located also in the Canary Current, but outside the influence of the eddy field. The distribution of prokaryotic abundance (PA), bulk prokaryotic heterotrophic activity (PHA), various indicators of single-cell activity (such as nucleic acid content, proportion of live cells, and fraction of cells actively incorporating leucine), as well as bacterial and archaeal community structure were determined from the surface to 2000 m depth. In the upper epipelagic layer (0-200 m), the effect of eddies on the prokaryotic community was more apparent, as indicated by the higher PA, PHA, fraction of living cells, and percentage of active cells incorporating leucine within eddies than at FF stations. Prokaryotic community composition differed also between eddy and FF stations in the epipelagic layer. In the mesopelagic layer (200-1000 m), there were also significant differences in PA and PHA between eddy and FF stations, although in general, there were no clear differences in community composition or single-cell activity. The effects on prokaryotic activity and community structure were stronger in AE than CE, decreasing with depth in both types of eddies. Overall, both types of eddies show distinct community compositions (as compared with FF in the epipelagic), and represent oceanic 'hotspots' of prokaryotic activity (in the epi-and mesopelagic realms).

We used catalysed reported deposition - fluorescence in situ hybridization (CARD-FISH) to analyse changes in the abundance of the bacterial groups Alphaproteobacteria, Gammaproteobacteria and Bacteroidetes, and of hydrocarbon-degrading Cycloclasticus bacteria in mesocosms that had received polycyclic aromatic hydrocarbons (PAHs) additions. The effects of PAHs were assessed under four contrasting hydrographic conditions in the coastal upwelling system of the Rías Baixas: winter mixing, spring bloom, summer stratification and autumn upwelling. We used realistic additions of water soluble PAHs (approximately 20-30 microg l(-1) equivalent of chrysene), but during the winter period we also investigated the effect of higher PAHs concentrations (10-80 microg l(-1) chrysene) on the bacterial community using microcosms. The most significant change observed was a significant reduction (68 +/- 5%) in the relative abundance of Alphaproteobacteria. The magnitude of the response of Cycloclasticus bacteria (positive with probe CYPU829) to PAHs additions varied depending on the initial environmental conditions, and on the initial concentration of added PAHs. Our results clearly show that bacteria of the Cycloclasticus group play a major role in low molecular weight PAHs biodegradation in this planktonic ecosystem. Their response was stronger in colder waters, when their background abundance was also higher. During the warm periods, the response of Cycloclasticus was limited, possibly due to both, a lower bioavailability of PAHs caused by abiotic factors (solar radiation, temperature), and by inorganic nutrient limitation of bacterial growth.

To decipher the response of mesopelagic prokaryotic communities to input of nutrients, we tracked changes in prokaryotic abundance, extracellular enzymatic activities, heterotrophic production, dark dissolved inorganic carbon (DIC) fixation, community composition (16S rRNA sequencing) and community gene expression (metatranscriptomics) in 3 microcosm experiments with water from the mesopelagic North Atlantic. Responses in 3 different treatments amended with thiosulfate, ammonium or organic matter (i.e., pyruvate plus acetate) were compared to unamended controls. The strongest stimulation was found in the organic matter enrichments, where all measured rates increased >10-fold. Strikingly, in the organic matter treatment, the dark DIC fixation rates—assumed to be related to autotrophic metabolisms—were equally stimulated as all the other heterotrophic-related parameters. This increase in DIC fixation rates was paralleled by an up-regulation of genes involved in DIC assimilation via anaplerotic pathways. Alkaline phosphatase was the metabolic rate most strongly stimulated and its activity seemed to be related to cross-activation by nonpartner histidine kinases, and/or the activation of genes involved in the regulation of elemental balance during catabolic processes. These findings suggest that episodic events such as strong sedimentation of organic matter into the mesopelagic might trigger rapid increases of originally rare members of the prokaryotic community, enhancing heterotrophic and autotrophic carbon uptake rates, ultimately affecting carbon cycling. Our experiments highlight a number of fairly unstudied microbial processes of potential importance in mesopelagic waters that require future attention.