Rising concentrations of atmospheric carbon dioxide are acidifying the world's oceans. Surface seawater pH is 0.1 units lower than pre-industrial values and is predicted to decrease by up to 0.4 units by the end of the century. This change in pH may result in changes in the physiology of ocean organisms, in particular, organisms that build their skeletons/shells from calcium carbonate, such as corals. This physiological change may also affect other members of the coral holobiont, for example, the microbial communities associated with the coral, which in turn may affect the coral physiology and health. In the present study, we examined changes in bacterial communities in the coral mucus, tissue and skeleton following exposure of the coral Acropora eurystoma to two different pH conditions: 7.3 and 8.2 (ambient seawater). The microbial community was different at the two pH values, as determined by denaturing gradient gel electrophoresis and 16S rRNA gene sequence analysis. Further analysis of the community in the corals maintained at the lower pH revealed an increase in bacteria associated with diseased and stressed corals, such as Vibrionaceae and Alteromonadaceae. In addition, an increase in the number of potential antibacterial activity was recorded among the bacteria isolated from the coral maintained at pH 7.3. Taken together, our findings highlight the impact that changes in the pH may have on the coral-associated bacterial community and their potential contribution to the coral host.

This study examined the abundance, cell size, and activity of Bacteria and Archaea in the Chukchi Sea and the Canada Basin of the western Arctic Ocean in the spring (May-June) and summer (July-August) of 2002 and 2004. Data from fluorescence in situ hybridization (FISH) analyses indicate that bacterial abundance as a percent of total prokaryotes decreased with depth, whereas in contrast, Crenarchaeota increased from about 10% of prokaryotes in surface waters to as much as 40% in samples from 100 to 200 m. Euryarchaeota were detectable in only a few samples. Relative abundance of Crenarchaeota, expressed as a percent of total prokaryotes, correlated with ammonium concentrations, but relative bacterial abundance did not. Crenarchaeota cells were significantly larger than Bacteria by 1.5-to 2-fold in the upper 200 m. Data collected from a combination of FISH and microautoradiography indicate that often the fraction of both Bacteria and Crenarchaeota assimilating organic compounds was high (up to 55%), and both microbial groups were more active in assimilating amino acids than other compounds. However, Crenarchaeota were usually less active than Bacteria in assimilating amino acids and glucose, but were nearly as active as Bacteria in assimilating protein and diatom extracellular polymers. The fraction of Bacteria and Crenarchaeota assimilating CO 2 in surface waters was higher than expected by anaplerotic fixation alone, suggesting that many of these microbes are chemoautotrophic. These data add to a growing body of evidence indicating how the roles of Archaea and Bacteria differ in biogeochemical cycles of the oceans.The abundances of Archaea and Bacteria vary differently with depth in the oceans examined to date, and these differences provide one of the first clues that the two prokaryotic domains are regulated by different factors in marine environments. Data from fluorescence in situ hybridization (FISH) studies indicate that Archaea make up a larger fraction of total prokaryote abundance in the mesopelagic and bathypelagic zones than in surface waters of the North Pacific Ocean (Karner et al. 2001). In fact, Crenarchaeota are nearly as abundant as Bacteria at about 1,000-m depth in the North Pacific but are near detection limits in surface waters where Bacteria dominate (Karner et al. 2001). There is some evidence of a similar depth distribution for Archaea and Bacteria in the North Atlantic Ocean (Herndl et al. 2005;Teira et al. 2006).Unlike temperate oceans, Archaea may be abundant even in the surface layer of the polar oceans (DeLong et al. 1994). Probing of ribonucleic acid (RNA) blots has suggested that Archaea make up, depending on the season and location, 1-17% of the picoplankton in surface waters around Antarctica (Massana et al. 1998;Murray et al. 1999). FISH studies with polyribonucleotide probes have confirmed the high abundance of Archaea, mainly Crenarchaeota, especially in winter surface waters near the Antarctic Peninsula (Church et al. 2003). Total archaeal abundance also appears to ...

We measured N2 fixation rates from oceanic zones that have traditionally been ignored as sources of biological N2 fixation; the aphotic, fully oxygenated, nitrate (NO−3)-rich, waters of the oligotrophic Levantine Basin (LB) and the Gulf of Aqaba (GA). N2 fixation rates measured from pelagic aphotic waters to depths up to 720 m, during the mixed and stratified periods, ranged from 0.01 nmol N L−1 d−1 to 0.38 nmol N L−1 d−1. N2 fixation rates correlated significantly with bacterial productivity and heterotrophic diazotrophs were identified from aphotic as well as photic depths. Dissolved free amino acid amendments to whole water from the GA enhanced bacterial productivity by 2–3.5 fold and N2 fixation rates by ~2-fold in samples collected from aphotic depths while in amendments to water from photic depths bacterial productivity increased 2–6 fold while N2 fixation rates increased by a factor of 2 to 4 illustrating that both BP and heterotrophic N2 fixation were carbon limited. Experimental manipulations of aphotic waters from the LB demonstrated a significant positive correlation between transparent exopolymeric particle (TEP) concentrations and N2 fixation rates. This suggests that sinking organic material and high carbon (C): nitrogen (N) micro-environments (such as TEP-based aggregates or marine snow) could support high heterotrophic N2 fixation rates in oxygenated surface waters and in the aphotic zones. Indeed, our calculations show that aphotic N2 fixation accounted for 37 to 75% of the total daily integrated N2 fixation rates at both locations in the Mediterranean and Red Seas with rates equal or greater to those measured from the photic layers. Moreover, our results indicate that that while N2 fixation may be limited in the surface waters, aphotic, pelagic N2 fixation may contribute significantly to new N inputs in other oligotrophic basins, yet it is currently not included in regional or global N budgets.

Members of the SAR11 clade often dominate the composition of marine microbial communities, yet their contribution to biomass production and the flux of dissolved organic matter (DOM) is unclear. In addition, little is known about the specific components of the DOM pool utilized by SAR11 bacteria. To better understand the role of SAR11 bacteria in the flux of DOM, we examined the assimilation of leucine (a measure of biomass production), as well as free amino acids, protein, and glucose, by SAR11 bacteria in the Northwest Atlantic Ocean. We found that when SAR11 bacteria were >25% of total prokaryotes, they accounted for about 30 to 50% of leucine incorporation, suggesting that SAR11 bacteria were major contributors to bacterial biomass production and the DOM flux. Specific growth rates of SAR11 bacteria either equaled or exceeded growth rates for the total prokaryotic community. In addition, SAR11 bacteria were typically responsible for a greater portion of amino acid assimilation (34 to 61%) and glucose assimilation (45 to 57%) than of protein assimilation (<34%). These data suggest that SAR11 bacteria do not utilize various components of the DOM pool equally and may be more important to the flux of low-molecular-weight monomers than to that of high-molecular-weight polymers.The SAR11 clade is one of the most abundant bacterial phylogenetic groups in the ocean. About 25% of the 16S rRNA gene sequences retrieved from uncultured marine bacteria belong to the SAR11 bacteria (13), and representatives of the SAR11 clade have been found in clone libraries from around the world (28). Investigations using fluorescence in situ hybridization (FISH) confirm that SAR11 bacteria often make up 25 to 35% of the total prokaryotic community in the surface waters of both coastal and open-ocean systems (22,24). The high abundance and global distribution of SAR11 bacteria suggest that they mediate a significant fraction of the dissolved organic matter (DOM) flux in the ocean. As with most marine bacterial groups, however, little is known about the contribution of SAR11 bacteria to the flux of DOM.The uptake of some DOM components by SAR11 bacteria was examined previously in the Gulf of Maine and the Sargasso Sea. Malmstrom el al. (22) found that the SAR11 clade dominated the assimilation of dissolved free amino acids and dimethylsulfoniopropionate, supporting the hypothesis that SAR11 bacteria mediate a large portion of the DOM flux. However, the assimilation of high-molecular-weight (HMW) DOM, which is a major source of C for bacterial communities (2), was not examined. In the Delaware Bay, Cottrell and Kirchman (5) found differences between the assimilation of low-molecular-weight (LMW) monomers and that of HMW polymers by the alpha-proteobacteria. The SAR11 bacteria, which are an abundant subgroup of the alpha-proteobacteria (13), may also contribute differently to the fluxes of LMW and HMW components of the DOM pool. To better understand their contribution to the flux of DOM, the assimilation of LMW monomers and HMW polymers ...