Diversity and Ecology of the Roseobacter Clade and other Marine Microbes as revealed by Metagenomic and Metatranscriptomic Approaches

Abstract

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.