Structure and function of microbial communities processing dissolved organic matter in marine environments
Heterotrophic bacteria are important participants in the global carbon cycle as they process about 50% of the fixed carbon in the oceans. Since the amount of primary production in the ocean is equal to that in terrestrial environments, the need to understand these processes is obvious. Various measurements are used to assess the amount of carbon that is processed through bacteria, including bacterial production, bacterial respiration, dissolved organic matter (DOM) concentrations and fluxes. However, none of these methods reveal which bacterial groups use specific compounds in the DOM pool. The aim of this dissertation was to address some of these issues. Microautoradiography combined with fluorescence in situ hybridization (Micro-FISH) was used to evaluate which bacterial groups assimilate common DOM components, and whether this assimilation can be related to other environmental factors. In the Delaware Estuary the assimilation of glucose and extracellular polymeric substances (EPS) was dominated by the abundant bacterial groups. In the freshwater end of the estuary Actinobacteria and Betaproteobacteria were the dominant groups, while in the saline part of the estuary Alphaproteobacteria and Cytophaga-like bacteria contributed the most to DOM uptake. Only 35-50% of the assimilation could be explained by bacterial group abundance. In addition, groups that had more assimilating cells were not necessarily more abundant. Therefore, it seems that the bacterial community in the Delaware Estuary might be affected equally by "bottom-up" (DOM availability) and "top-down" (predation and viral lysis) factors. In contrast, the oligotrophic environment of the Western Arctic Ocean displayed a different pattern. Most of the assimilation (90-99%) could be explained by abundance in the Arctic Ocean. These data suggest that the microbial community in this environment is mostly controlled by DOM availability. Perhaps the most interesting observation of this study was the level of activity detected in the Arctic environment. Up to 50% of all prokaryotes assimilated amino acids, followed by EPS and proteins. Glucose, however, was the least assimilated compound. The contribution to assimilation of DOM was different among the bacterial groups. The contribution to DOM assimilation by Cytophaga-like bacteria decreased between the Chukchi Sea shelf and the Canada Basin. In contrast, Alphaproteobacteria contributed the most in the slope region. This group also contributed more to the assimilation of low molecular weight (LMW) DOM, while Cytophaga-like bacteria contributed more to the assimilation of high molecular weight (HMW) DOM. The last part of this dissertation dealt with the molecular mechanism of the degradation of polysaccharides, which is an important part of the labile DOM pool in the marine environment. The Carbohydrate-Active enZymes (CAZy) and the Sargasso Sea whole-shotgun databases were searched for the common endoglucanases in the marine environment. One sub-group of glycosyl hydrolases, family 5 (GH5), was identified as a potential important enzyme in the marine environment. Two GH5 gene-libraries were constructed from the Mid-Atlantic Bight and the Sargasso Sea. The two libraries were different from each other. The sequences in these libraries were also different from sequences known from cultured bacteria. Translation of the amplified fragment indicated that the important residues for activity are present, and therefore these are potentially active endoglucanases. GH5 abundance in surface water of the North Atlantic, as measured with quantitative PCR (Q-PCR), fluctuated between 10 copies to 200 copies per nanogram DNA. The abundance of GH5 correlated to chlorophyll concentrations in the eastern part of the sampled region and in one depth profile. 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.