Project area A - Ecology and Evolution
In project area A “Ecology and Evolution” the Roseobacter clade is investigated at the community and population level in various marine ecosystems in the water column and in sediments, applying culture-dependent and -independent (metagenomic and metatranscriptomic) methods.
Important questions address the diversity and biogeochemical role, function and activity of key players of this clade and their genome organisation. These questions can only be addressed and answered on the basis of a profound knowledge of the taxonomy, phylogenomics and evolutionary relationships and the core- and pan-genome of this clade. Consequently, the latter points will be addressed as well in this project area.
Project area B - Genetics and Physiology
Project area B ”Genetics and Physiology” constitutes the natural bridge between investigation of Roseobacter clade bacteria in their full diversity and natural habitats down to the examination of the metabolic and regulatory principles of selected strains.
Here, the two selected model organisms Dinoroseobacter shibae and Phaeobacter gallaeciensis are investigated in connection with other thematically appropriate strains. Closely interconnected projects are analysing the energy metabolism and corresponding gene regulatory network of D. shibae with a broad spectrum of physiological, genetic and molecular biology methods.
Further, the pathways of secondary metabolite production with focus on antibiotic or signalling function are of central interest. Roseobacter clade-wide genome based searches and functional investigations will be combined with genetic and chemical studies using the two model systems D. shibae and P. gallaeciensis. Closely related are the questions for quorum sensing compounds and their biological function. The deduction of general principles for the versatile employment of metabolic strategies is envisaged.
Project area C - Systems Biology
The project area C “Systems Biology” focuses on the two model organisms D. shibae and P. gallaeciensis.
The final goal here is the generation of bioinformatics models which allow for the prediction of metabolic and gene regulatory adaptation processes. In order to generate the necessary data for model building a strictly coordinated experimental effort is conducted. Highly standardized and reproducible growth conditions in a chemostat provide the basis for the integrated analysis of transcriptome, proteome, metabolome and the dynamic fluxome in response to defined growth changes or genetic variations.
Obtained data are used to generate and iteratively optimize genome based metabolic and gene regulatory models. Data from closely related B area projects will be integrated. The long-term goal is the integration of the various models in complex systems biology models for the prediction of multi-level adaptation processes. Based on the genome information of other Roseobacter clade bacteria the established bioinformatics models will be used to predict and understand their strain specific adaptation strategies to their habitats. These systems biology analyses of roseobacters in their environment closes the circuit to project area A.
Project area Z - Central Facilities
Integrated Research Training GroupThe Integrated Research Training Group (IRTG) aims at internationally attracting highly talented young scientists from biology, chemistry and bioinformatics to the interdisciplinary research programme of the proposed SFB/TR. An initial orientation and qualification phase will be provided in a structured PhD programme. This includes a thesis work within one of the projects, an accompanying study programme with soft skill qualifications, and an outer-university training phase with a stay abroad or in appropriate partner institutions. This way the IRTG will develop the students´ personality as independent researchers and boost their chances on the job market.
Information Infrastructure, Database & Bioinformatics Tool Development
The bioinformatics platform provides and establishes a central analysis pipeline of important software tools and databases within the proposed SFB/TR. Furthermore, it enables a systems biology platform for model integration, simulation and visualization. The platform assures data retrieval, integration and analysis in a standardized and uniform way. It offers information systems and communication platforms for experience and data exchange. This platform is necessary for the interoperability and data storage on a sustained basis within and beyond the consortium. It also offers technical support and education to all members of the SFB/TR.
Central Administrative Tasks
This project will provide the central platform for the scientific and administrative management of the SFB/TR. It will be located at ICBM and thus benefit from the centralized administration and infrastructure of ICBM. Besides budget administration, important tasks include organisation of workshops, stays of guest scientists, help in planning and organising research cruises and support for the Integrated Research Training Group. This project will be independent of the INF-project which will be located in Braunschweig and be mainly responsible for data management and providing software tools for the SFB/TR.