| dc.description.abstracteng | Marine Bacteria and Archaea represent the major part of the total biodiversity on Earth. They are main drivers of biogeochemical cycles in marine environments and play an integral role in ecosystem structuring. Therefore, the understanding how marine prokaryotic communities are structured and how these communities react towards altered environmental conditions is of fundamental importance. In this thesis, the diversity and ecology of Bacteria and Archaea in the pelagic realm of the North Sea was studied using different culture-independent approaches. In particular, the abundance and ecological role of the Roseobacter clade was analyzed. Moreover, the response of the investigated prokaryotic communities to changing environmental conditions was examined.
One objective was to analyze active archaeal and bacterial community structures in the southern North Sea. Moreover, the impact of a phytoplankton bloom on prokaryotic community composition and diversity was elucidated. For this purpose, 14 marine water samples were collected in May 2010 in the German Bight in and outside of a phytoplankton bloom. Community structures were assessed by pyrotag sequencing of 16S rRNA transcripts. A total of 62,045 and 211,769 16S rRNA sequences were used to examine archaeal and bacterial community composition and diversity, respectively. Different marine lineages of the Gamma- and Alphaproteobacteria including the SAR92 clade and the Roseobacter clade affiliated (RCA) cluster dominated the bacterial community. The archaeal community mainly composed of Halobacteria as well as minor proportions of Thermoplasmata and members of the Marine Group I.
Both archaeal and bacterial community structures were influenced by the presence of the examined phytoplankton bloom. In addition to structural changes, the bacterial richness was reduced in bloom presence indicating that only certain bacteria could thrive during the bloom. To exploit the impact of the phytoplankton bloom on gene expression, environmental mRNA from three samples was extracted, enriched, and sequenced resulting in a total of 988,022 sequences for all three samples. Changes in various metabolic pathways including photosynthesis and protein metabolism were recorded as response to the bloom. The observed changes were induced either directly by the bloom or indirectly by altered environmental parameters as most of these parameters were significantly correlated to bloom presence.
Another objective was to assess the structure and diversity of total and active bacterial communities along a latitudinal gradient ranging from the German Bight to the Norwegian coast. For this purpose, surface water samples were taken in July 2011 on board of the research vessel Heincke. Community structures were examined by pyrotag sequencing of 16S rRNA genes and transcripts. A total of 382,507 16s rRNA gene sequences were used to assess bacterial community structures. These communities were dominated by different groups affiliated to the Bacteroidetes and Alphaproteobacteria including the marine groups NS5, NS7, and NS9, different subclusters of the Roseobacter clade, and members of the SAR116 clade. Moreover, Cyanobacteria were found in minor abundance with Synechococcus as the dominant genus.
Total and active bacterial community structures were significantly altered along the latitudinal gradient whereas the bacterial richness was unaffected. The abundance of certain marine groups such as the Roseobacter CHAB-I-5 and NAC11-7 clusters either decreased or increased with rising latitude. The recorded changes in bacterial community structures along the studied gradient might be explained by changing environmental conditions which are probably caused by the different water currents found along the gradient. Additionally, the composition of the Rhodobacteraceae in the free-living and in the particle-associated fraction in different depths as well as in the sediment along the latitudinal gradient was investigated. The composition of this family significantly varied between the different fractions.
In addition to the overall bacterial community structure, the ecological contribution of an abundant member of the RCA cluster, Planktomarina temperata, to nutrient cycling in the pelagic realm of the North Sea was analyzed. This cluster exhibited more than 20% relative abundance in samples derived from the first sampling. Consequently, the largest mRNA dataset of this cruise and a metagenome obtained by direct sequencing of gDNA from the same sample was mapped on its genome. Around one million pyrosequencing reads were mapped in total. Large parts of the genome were retrieved by the mapping approach with approximately 86% of the genome transcribed. Active features included the photosynthetic operon, the two CO dehydrogenase systems, and the assimilatory sulfate reduction pathway.
In addition to marine ecosystems, the diversity of other prokaryotic communities in three non-marine habitats was examined. In the first survey, we studied the prokaryotic community in two hyperthermal springs on the Azores. Environmental DNA was extracted from two sediment samples and further analyzed using different metagenomic methods. The first spring was dominated by heterotrophic bacterial genera including Caldicellulosiruptor, Dictyoglomus, and Fervidobacterium as well as by the chemolithoautotrophic genus Sulfurihy-drogenibium. The archaeal community comprised Crenarchaeota with Thermo-proteaceae and Desulfurococcaceae as the dominant families. The bacterial community in the other spring was mainly composed of the heterotrophic genus Acidicaldus and the chemolithoautotrophic genus Acidithiobacillus.
In the second study, the diversity and genomic potential of a bacterial biofilm associated with two freshwater algae, Chlorella vulgaris and Scenedesmus obliquus, in a photobioreactor was investigated. DNA was extracted from collected biofilm samples and analyzed using different metagenomic approaches. The recorded community size was rather limited with approximately 30 bacterial species. The majority of the observed Bacteria were affiliated to Alphaproteobacteria, Betaproteobacteria, and Bacteroidetes. Analysis of the genomic potential revealed a high metabolic diversity with respect to the utilization of polymers, aromatic, and non-aromatic compounds.
In the third study, the bacterial endophytic community structures in three agricultural important grasses, Dactylis glomerata, Festuca rubra, and Lolium perenne, was examined. Moreover, the response of these communities to fertilizer application, mowing frequency, and seasonal changes over two consecutive years was investigated. Endophytic community structures were studied by DGGE-based analysis of 16S rRNA genes amplified from plant DNA. The communities were dominated by different members of the Firmicutes and Proteobacteria with Bacillus and Pseudomonas as the predominate genera. The studied management regimes significantly altered the endophytic communities in L. perenne and F. rubra but not in D. glomerata. On the other hand, season significantly affected the community structures in all three grasses. Moreover, as community structures were subjected to seasonal variations, the recorded impact of management regimes differed between the two investigated years. | de |