ena-STUDY-MPI BREMEN-22-10-2013-13:02:30:723-93
Illumina and 454-based metatranscriptomic analyses of a diatom-induced bacterioplankton bloom in the North Sea
Planktonic bacteria from marine pelagic coastal zones are much more diverse than in the open ocean and consist of members with distinct ecological niches. In this study we investigated bacterioplankton communities that were sampled during a diatom-dominated spring phytoplankton bloom near the North Sea island Helgoland (about 40 km off the German coast). Sequencing of total community RNA allowed simultaneous detection of the community composition via 16S ribosomal RNA analyses, and the expressed functional genes via messenger RNA analyses. As most prominent community members, Flavobacteria (Ulvibacter, Formosa, Polaribacter), Alphaproteobacteria (SAR11 clade and Rhodobacteraceae) and Gammaproteobacteria (Reinekea spp. and SAR92 clade) could be identified down to genus level, which was confirmed by 16S rRNA gene amplicon ('pyrotag') sequencing of the same samples. These samples were also sequenced in a metagenome approach, assembled and taxonomically classified. Mapping of the transcripts on the metagenomes allowed investigation of the expression profiles of the prominent taxa. Members of the Flavobacteria, Alphaproteobacteria and Gammaproteobacteria exhibited distinct expression profiles of uptake transporters and carbohydrate-active enzymes, indicating a specialization on different nutrients. Members of the flavobacterial genera Formosa and Polaribacter acted as major polymer degraders, whereas members of the alphaproteobacterial Rhodobacteraceae and the gammaproteobacterial Reinekea exhibited a less specialized behavior, enabling them to rapidly adapt to changing nutrient conditions. Complementary sequencing effort using 454 pyrosequencing and Illumina enabled a comprehensive picture of the dominant metabolic processes down to genus level. This helped to identify the strategies of how members of the bacterioplankton evade extinction in a seemingly homogenous habitat.
Planktonic bacteria from marine pelagic coastal zones are much more diverse than in the open ocean and consist of members with distinct ecological niches. In this study we investigated bacterioplankton communities that were sampled during a diatom-dominated spring phytoplankton bloom near the North Sea island Helgoland (about 40 km off the German coast). Sequencing of total community RNA allowed simultaneous detection of the community composition via 16S ribosomal RNA analyses, and the expressed functional genes via messenger RNA analyses. As most prominent community members, Flavobacteria (Ulvibacter, Formosa, Polaribacter), Alphaproteobacteria (SAR11 clade and Rhodobacteraceae) and Gammaproteobacteria (Reinekea spp. and SAR92 clade) could be identified down to genus level, which was confirmed by 16S rRNA gene amplicon ('pyrotag') sequencing of the same samples. These samples were also sequenced in a metagenome approach, assembled and taxonomically classified. Mapping of the transcripts on the metagenomes allowed investigation of the expression profiles of the prominent taxa. Members of the Flavobacteria, Alphaproteobacteria and Gammaproteobacteria exhibited distinct expression profiles of uptake transporters and carbohydrate-active enzymes, indicating a specialization on different nutrients. Members of the flavobacterial genera Formosa and Polaribacter acted as major polymer degraders, whereas members of the alphaproteobacterial Rhodobacteraceae and the gammaproteobacterial Reinekea exhibited a less specialized behavior, enabling them to rapidly adapt to changing nutrient conditions. Complementary sequencing effort using 454 pyrosequencing and Illumina enabled a comprehensive picture of the dominant metabolic processes down to genus level. This helped to identify the strategies of how members of the bacterioplankton evade extinction in a seemingly homogenous habitat.