Bacterioplankton communities play a crucial role marine biogeochemical cycles because they mediate the flux of dissolved organic matter (DOM), which is equal to about half of primary production in the ocean. These bacterial communities are also known to be incredibly diverse and comprised of bacteria from several different phylogenetic groups. However, the relationship between microbial diversity and biogeochemical cycling remains unclear. My dissertation focused on determining the contributions of abundant bacterial phylogenetic groups to the biogeochemical flux of DOM in the ocean. One specific goal if this dissertation was the identification and quantification of bacteria that assimilate the organic sulfur compound dimethylsulfoniopropionate (DMSP). DMSP can be hydrolyzed to produce dimethylsulfide (DMS), a sulfurous gas hypothesized to moderate changes in global temperature. However, most dissolved DMSP is assimilated into bacterial biomass, a process that satisfies nearly all of the bacterial S demand in the surface waters of the ocean. Since the biogeochemical fate of DMSP can affect either climate regulation or S transfer through marine food webs, it is important to identify bacteria that metabolize DMSP. To identify and quantify bacteria assimilating DMSP, I used a combination of micro-autoradiography and fluorescence in situ hybridization (Micro-FISH) to follow 35 S-DMSP assimilation into marine bacterial communities. In addition to DMSP flux, I also investigated the ecological activity of SAR11 bacteria. Gene sequences belonging to the SAR11 clade typically dominate 16S rRNA clone libraries from the ocean, and investigations with fluorescence in situ hybridization confirm that SAR11 bacteria often make up 25--35% of bacterioplankton communities. (Abstract shortened by UMI.).

The current study added to the growing information regarding the composition of bacterial community in aquatic environments and the role of specific bacterial groups in DOM assimilation. In particular, this study was the first to unfold the relation between structure and function of the bacterial community in the Arctic Ocean, the only cold environment studied in that aspect to date. The molecular study of GH5 revealed the potential of the community for polysaccharides degradation, however, more need to be done to broaden our understanding of the mineralization of these compounds in the marine environment.

The flux of dissolved organic matter (DOM) through aquatic bacterial communities is a major process in carbon cycling in the oceans and other aquatic systems. Our work addressed the general hypothesis that the phylogenetic make-up of bacterial communities and the abundances of key types of bacteria are important factors influencing the processing of DOM in aquatic ecosystems. Since most bacteria are not easily cultivated, the phylogenetic diversity of these microbes has to be assessed using culture-independent approaches. Even if the relevant bacteria were cultivated, their activity in the lab would likely differ from that under environmental conditions. This project found variation in DOM uptake by the major bacterial groups found in coastal waters. In brief, the data suggest substantial differences among groups in the use of high and molecular weight DOM components. It also made key discoveries about the role of light in affecting this uptake especially by cyanobacteria. In the North Atlantic Ocean, for example, over half of the light-stimulated uptake was by the coccoid cyanobacterium, Prochlorococcus, with the remaining uptake due to Synechococcus and other photoheterotrophic bacteria. The project also examined in detail the degradation of one organic matter component, chitin, which is often said to be the second most abundant compound in the biosphere. The findings of this project contribute to our understanding of DOM fluxes and microbial dynamics supported by those fluxes. It is possible that these findings will lead to improvements in models of the carbon cycle that have compartments for dissolved organic carbon (DOC), the largest pool of organic carbon in the oceans.

Bacterioplankton communities play a crucial role in marine biogeochemical cycles because they mediate the flux of dissolved organic matter (DOM), which is equal to about half of primary production in the ocean. These bacterial communities are also known to be very diverse and are comprised of bacteria from several different phylogenetic groups. Most biogeochemical studies of marine environments use the dichotomy of grouping microorganisms into two boxes, photoautotrophs and heterotrophs. My dissertation is about organisms and processes not described by these two boxes. An important component of my research work was the identification and quantification of organic matter uptake by marine cyanobacteria Prochlorococcus and Synechococcus. The goal of the first part of my dissertation was to identify the microbial groups responsible for light-dependent leucine incorporation and to examine the effect of light on the uptake of amino acids added at tracer levels. My hypothesis was that stimulation of bacterial production by light was due to photoheterotrophy by Prochlorococcus. My results indicated that this was in fact the case, but other groups of photoheterotrophic bacteria contributed to the light effect as well. The uptake of essential elements in reduced organic forms could provide an additional source of macronutrients to be used in protein synthesis, and help explain the success of Prochlorococcus and Synechococcus in oligorophic environments. These marine cyanobacteria are capable of accessing a wide variety of organic compounds. These results allowed me to hypothesize that these marine cyanobacteria take up dissolved organic matter for limiting elements like nitrogen and phosphorus. To determine if these cyanobacteria were also capable of assimilating non-limiting organic compounds without nitrogen or phosphorus, uptake rates of amino acids and glucose by Prochlorococcus, Synechococcus and heterotrophic bacteria were determined in the Sargasso Sea in May and September of 2008 using flow cytometry. This study revealed that glucose uptake by Synechococcus was significantly higher than uptake by both Prochlorococcus and heterotrophic bacteria in all samples, while uptake by Prochlorococcus and heterotrophic bacteria was similar. These results suggested that coccoid cyanobacteria are competitive at assimilating dissolved organic compounds without nitrogen or phosphorus, though these microbes accounted for a small fraction of total uptake. Phosphorus potentially limits the growth and productivity of microbial communities in many oligotrophic oceans. Both dissolved inorganic phosphorus (DIP) and dissolved organic phosphorus (DOP) could be an important resource in these regimes. Assimilation rates of inorganic and organic phosphorus by marine cyanobacteria and heterotrophic bacteria in the oligotrophic ocean are not well quantified. For the last chapter of my dissertation, I used radioisotope tracers of orthophosphate and ATP combined with flow cytometry sorting to quantify assimilation by heterotrophic bacteria, Prochlorococcus and Synechococcus during the fall of 2007 and 2008 and the spring of 2009 in the western Sargasso Sea. Phosphate and ATP uptake rates were 50-fold and 80-fold higher for Synechococcus compared to the other two groups. However, there was no significant difference between ATP and phosphate uptake by Prochlorococcus and heterotrophic bacteria. Total uptake of phosphate and ATP was dominated by heterotrophic bacteria, while uptake by Prochlorococcus and Synechococcus was a smaller fraction of the total. This coincided with the lower abundance of these cyanobacteria (25% and 2.5% of total prokaryotes respectively) compared to heterotrophic bacteria during my study. Phosphate and ATP turnover was surprisingly similar for the three groups analyzed, suggesting P uptake by marine cyanobacteria is not that different from uptake by heterotrophic bacteria. Collectively, these data suggest that inorganic and organic P play an important role in the ecological success of marine cyanobacteria in the Sargasso Sea. The current study added to the growing information regarding the role of specific bacterial groups, such as cyanobacteria, in DOM assimilation. In particular, this study was the first to unfold the contribution of photoheterotrophic microbes to leucine assimilation in the North Atlantic Ocean. My results not only provided new evidence of carbon uptake by phototrophic picoplankton, they lay the foundation for a number of new interesting questions regarding these extremely successful microorganisms.

Microbial communities dominate the fluxes of organic material in the ocean, in part due to their high abundance. To determine the amount of carbon processed by bacteria, bulk properties, such as production, abundance, biomass, and respiration, are measured for the total community. Phylogenetic analyses of bacteria are used to describe the structure within microbial communities. However, neither bulk activity measurements nor phylogenetic identification alone can determine which bacterial groups respond to certain environmental conditions or which bacterial groups use certain organic compounds. The goal of this dissertation was to assess the responses of different bacterial taxa to environmental conditions and available substrates. A basic characteristic of microbes is cell size. The size of microbial cells affects ecological interactions with other organisms and may be related to rates of biomass production. Using a protein stain, I analyzed the biovolume of microbial communities in Arctic, Antarctic, and temperate waters. Microbes in higher latitudes were on average 30% larger than cells from temperate waters. The abundance of bacterial taxa varied among geographic regions, and the size of some bacterial groups also differed among regions. Gammaproteobacteria and members of the Sphingobacteria-Flavobacteria (SF) group were larger in high latitude waters. In each environment, SF cells were larger than other bacteria by about 15%, while Gammaproteobacteria were intermediate in size and Alphaproteobacteria did not differ in size from the average bacterial cell. In addition to varying in size, bacterial taxa differ in the use of organic material. I used microautoradiography and fluorescent in situ hybridization to identify bacteria incorporating organic compounds. In the Delaware estuary and mid- Atlantic bight, about 30% of all cells incorporated leucine and other amino acids, while only 10% incorporated protein. Using light and dark treatments, I found that light affected single-cell activity in about 20% of cases, but there was no net effect of light on bulk bacterial production. Light did not affect Gamma - and Alphaproteobacteria differently. However, 25% more bacteria in the SAR11 clade used leucine in the light than the total community. Other environmental conditions besides light also correlated with the abundance and activity of bacterial groups. Gammaproteobacterial abundance correlated with bacterial production and concentrations of dissolved organic carbon and nitrogen, and a higher fraction of Gammaproteobacteria used leucine in the summer than in the fall. There is also geographic variation in abundance and activity of specific bacterial taxa. I examined the abundance and single-cell activity of dominant bacterial clades in waters off the west Antarctic peninsula. More bacteria used leucine (40%) than used a mixture of amino acids or protein (12-22%). Gammaproteobacteria were a large fraction (20%) of the community in this region, and using a new probe I assessed the ecological role of the Ant4D3 gammaproteobacterial clade. The Ant4D3 clade constituted 10% of the total community, and while the active fraction of this clade did not differ among various compounds, Ant4D3 dominated the incorporation of amino acids. The use of organic material varied among the Polaribacter, SAR11, and Ant4D3 clades. Polaribacter contributed the most to protein uptake. Though dominated by different bacterial taxa, the activity of this Antarctic microbial community was comparable to that of temperate communities. The research presented in Chapter 4 is the first description of the single-cell activity of bacterial groups in coastal Antarctic waters. The research described in this dissertation details the abundance of specific bacterial groups along with bacterial cell size (Chapter 2), light effects on bacterial activity (Chapter 3), and bacterial activity in polar waters (Chapter 4). Generally the approach taken was to divide the "black box" of all microbes into broad phylogenetic groups, which display characteristic differences yet are abundant as cohesive units in the microbial community. Assessing microbial communities at this scale, I found variation of broad bacterial taxa in size, activity, and response to environmental factors. The combination of single-cell methods with genomic approaches will enable us to move toward quantifying bacterial contribution to global processes and predicting the response of bacterial groups to environmental change.