Im Sonderforschungsbereich "Roseobacter" untersuchen Forschende der Universität Oldenburg und der TU Braunschweig gemeinsam mit weiteren Verbundpartnern die Ökologie, Physiologie und Molekularbiologie des Bakteriums Roseobacter. Ziel ist ein systembiologisches Verständnis dieser global relevanten Gruppe von Meeresbakterien.
Presseinformationen:
Förderungsdauer:
3. Förderperiode. 2018-2021
Projektpartner:
Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH
Georg-August-Universität Göttingen
Rheinische Friedrich-Wilhelms-Universität Bonn
Vertreter der Roseobacter-Gruppe gehören zu den häufigsten Prokaryoten in marinen Ökosystemen. Diese Bakterien sind physiologisch äußerst vielseitig und spielen für die globalen Stoffkreisläufe der Meere eine wichtige Rolle. Im TRR-51 werden die evolutionären, genetischen und physiologischen Prinzipien untersucht, welche die Grundlage des Erfolges dieser Bakterien sind. Dazu wird die Roseobacter-Gruppe angefangen vom Ökosystem bis hin zur Systembiologie von Modellorganismen bezüglich wichtiger biogeochemischer und Stoffwechselprozesse und deren genetischen und genomischen Grundlagen betrachtet.
Das übergeordnete Ziel dieses Transregionalen Sonderforschungsbereichs TRR51 „Roseobacter“ ist ein umfassendes Verständnis des evolutionären und Anpassungserfolges der Roseobacter-Gruppe in marinen Ökosystemen. Vertreter dieser Gruppe sind global verteilt und vielfach prominente Komponenten von Bakteriengemeinschaften oder leisten spezielle Stoffwechselprozesse im gegebenen ökologischen Zusammenhang. Vertreter dieser Gruppe zeichnen sich zudem durch sehr unterschiedliche und vielseitige Physiologien aus. Die Mission des TRR51 besteht darin, die Roseobacter-Gruppe hinsichtlich ihrer Evolution und Phylogenie und die Struktur und den Gehalt der Genome bezüglich der vielseitigen Physiologie und Ökologie zu untersuchen. Diese Untersuchungen beinhalten Umwelt- und biogeografische Studien auf der Gemeinschaftsebene sowie detaillierte Arbeiten über die Physiologie einzelner Organismen und systembiologische Studien von zwei Modellorganismen, Dinoroseobacter shibae und Phaeobacter inhibens. Die Untersuchungen in der dritten Antragsphase werden fokussiert auf Interaktionen dieser Organismen, hauptsächlich mit zwei kosmopolitischen Algen aus Küstenmeeren, Thalassiosira rotula und Prorocentrum minimum. Des Weiteren sind Interaktionen mit und die Bedeutung von Phagen ein weiterer Untersuchungsschwerpunkt.
Die Arbeiten sind nach wie vor gegliedert in den Projektbereich A mit Schwerpunkt Ökologie und Evolution, den Projektbereich B mit Schwerpunkt Genetik und Physiologie und den Projektbereich C mit Schwerpunkt auf der Systembiologie der beiden Modellorganismen.
Die Umweltuntersuchungen, hauptsächlich im Projektbereich A beheimatet, werden die Analysen der Proben und Daten abschließen, die während zweier Fahrten mit dem Forschungsschiff Sonne im Pazifik auf einem Transekt entlang des 180. Längengrades zwischen den Wassermassen der südlichen Polarfront bei 52°S und subarktischen Gebieten in der Beringsee bei 59°N gesammelt wurden. Die Arbeiten umfassten die Beprobung der Wassersäule und des Oberflächensedimentes für Messungen der Aktivität und Zusammensetzung der Bakteriengemeinschaften, metagenomische, -transkriptomische, -proteomische und geometabolomische Untersuchungen. Diese Untersuchungen zielen auf eine umfassende und synoptische Analyse dieser Daten zusammen mit Daten von früheren Fahrten im Atlantik und Südpolarmeer, um ein synoptisches Vorhersagemodell der funktionellen Rolle der pelagischen und benthischen Roseobacter-Vertreter zu etablieren.
Untersuchungen mit den Modellorganismen D. shibae und P. inhibens, beheimatet in allen drei Projektbereichen, konzentrieren sich auf Interaktionen mit den beiden Modellalgen T. rotula und P. minimum. Die Genome beider Algen werden sequenziert. Themen umfassen den Einfluss der Interaktionen auf das Endo- und Exometabolom beider Partner, die Rolle von spezifischen Metaboliten auf das Wachstum der Algen, die Rolle von Quorum Sensing, dem Sauerstoffpartialdruck, Eisen und der Temperatur auf die Wachstumsregulation und den Metabolitenaustausch und die Bedeutung der extrachromosomalen Elemente. Die unterschiedlichen Effekte der direkten physikalischen Interaktionen und der nur über Austausch von gelösten Verbindungen vermittelten Interaktionen werden speziell untersucht. Transkriptions- und proteomische Ansätze sollen in den meisten der vorgesehenen Untersuchungen eingesetzt werden, ebenso wie die Modellierung der metabolischen Interaktionen beider Partner.
27.-28.11.2019 Workshop for SFB-PhD students|Bremen|Link
28.-30.08.2019 MarBio2019|Alter Landtag, Oldenburg|Link
13.-14.06.2019 15th Status Seminar|Alter Landtag, Oldenburg|
30.11.2018 14th Status Seminar|BRICS,Braunschweig|
16.-18.10.2018 Workshop for SFB-PhD students|Spiekeroog|Program
11.-14.09.2018 YOUMARES 9 Oldenburg I Homepage
05.-07.06.2018 13th Status Seminar|Oldenburg|
18.-19.09.2017 Evaluation of SFB/TRR51, 3rd funding period|Oldenburg|
13.-15.09.2017 YOUMARES 8|Kiel|
08.06.2017 Tag des Meeres with conference: "Career Path in Marine Sciences"|ICBM Oldenburg|Poster
23.03.2017 1st ICBM PhD Day|ICBM Wilhelmshaven|
28.01.-27.02.2017 Sonne Research cruise PoriBacNewZ The goal of this expedition is a comprehensive investigation of the structural and functional biodiversity of bacteria communities in the water column, in the sediment and in sponges in the biogeographic provinces of the Southwest Pacific. Auckland, Neuseeland - Southwest Pacific - Auckland, Neuseeland|Homepage, Blog
13.-15.10.2016 Workshop for SFB-PhD students "State of your research in the CRC Roseobacter - you scientific career and what comes next?" Additional: research funding opportunitie Neuwerk, Cuxhaven|Program
11.-13.09.2016 YOUMARES 7|Hamburg|
23.-24.6.2016 12th Status Seminar|Alter Landtag, Oldenburg|Program
27.05.2016 2nd Graduate Symposium - Career Paths in Marine and Climate Sciences Climate Sciences Haus der Wissenschaft, Bremen|Poster
01.05.-03.06.2016 Sonne Research cruise BacGeoPac The scientists will investigate, besides the hydrography and biooptics of the water, the composition and significance of the bacterial communities and the dissolved organic nutrients in the various climatic regions of the Pacific. Auckland, Neuseeland - Dutch Harbor, Alaska, USA Homepage, Blog
09. 11. 2015 11th Status Seminar|HZI, Braunschweig|Program
16. 10. 2015 Tag des Meeres with conference: "Career Path in Marine Sciences" with conference: "Career Path in Marine Sciences" ICBM, Oldenburg|Program
16.-18.09.2015 YOUMARES 6|Bremen|Flyer
1.-3. 6. 2015 Workshop for SFB-PhD students "Young scientists meet industry,enterprises, scientific management and institutes"|Hamburg|Program
7.-8. 5. 2015 10th Status Seminar|Alter Landtag, Oldenburg|Final Agenda
20. 11. 2014 9th Status Seminar|HZI, Braunschweig|
23. 5. 2014 Graduate Symposium "Career Path in Marine and Climate Science"|Bremen|Flyer
8.-9. 5. 2014 8th Status Seminar|Oldenburg|Program
11.-13. 09. 2013 YOUMARES 4Oldenburg|Oldenburg|Flyer
5.-6. 9. 2013 Evaluation of SFB/TRR51, 2nd funding period|Braunschweig|Final Agenda
24.-26. 6. 2013 International Symposium, major outcome of 1st phase|HWK, Delmenhorst
22. 5. 2013 Science Slam 2013|Oldenburg, Exerzierhalle|Flyer
14.-15. 2. 2013 PI Meeting|Wolfenbüttel|Final Agenda
3. 11. 2012 Conference "Career ways in marine science"|ICBM, Oldenburg|Program, Conference book
15.-16. 10. 2012 7th Status Seminar|HZI, Braunschweig|Final Agenda
12.-14. 9. 2012 YOUMARES 3.0|Lübeck|Flyer
7.-9. 9. 2012 Workshop for SFB-PhD students|AWI-Wattenmeerstation, Sylt|Program
5. 6. 2012 6th Status Seminar|HZI, Braunschweig|Final Agenda
6. 2. 2012 5th Status Seminar|HZI, Braunschweig|Final Agenda
15. 9. 2011 4th Status Seminar|HZI, Braunschweig|Final Agenda
7.-9. 9. 2011 YOUMARES 2.0|Dt. Schifffahrtsmuseum, Bremerhafen|Flyer
23. 8. 2011 Science Slam|Polyester, Oldenburg|Flyer
16.-17. 5. 2011 3rd Status Seminar|HWK, Delmenhorst|Final Agenda
10. 2. 2011 2nd Status Seminar|University, Oldenburg|Final Agenda
26.-28. 11. 2010 Workshop for SFB-PhD students|Wattstation, Carolinensiel|Invitation
21 10. 2010 1st Status Seminar|HZI, Braunschweig|Final Agenda
17. 9. 2010 Info-Hour: Research Training Group|ICBM-Terramare, Wilhelmshaven
15. 9. 2010 Info-Hour: Research Training Group|TU Braunschweig
12. 8. 2010 Info-Hour: Research Training Group|ICBM, Oldenburg
20. 7. 2010 Info-Hour: Research Training Group|ICBM, Oldenburg
13.-15. 6. 2010 Kick Off Symposium|HWK, Delmenhorst|Program
The Roseobacter clade is a major lineage of the family Rhodobacteraceae of Alphaproteobacteria. Its members form one of the most abundant and successful groups of non-obligately phototrophic prokaryotes in the marine environment. In contrast to the high ecological importance the knowledge of this clade and of its key players in the marine environment is still surprisingly limited. Consequently, in the framework of this proposed SFB/TR marine microbial ecologists, bacterial physiologists, biochemists, natural product chemists, geneticists and computer scientists from Braunschweig and Oldenburg join forces to investigate the Roseobacter clade from the ecosystem level down to systems biology of model organisms with respect to important metabolic processes.
The major goal is the understanding of evolutionary, genetic and physiological principles which constitute the secret of success for these bacteria. How is the genetic configuration of these bacteria successfully employed for rapid evolutionary adaptations to multiple habitats at the level of metabolic and related regulatory networks? This question is the driver for the following projects:
Project area A - Ecology and Evolution
Project area B - Genetics and Physiology
Project area C - Systems Biology
Project area Z - Central Facilities
Speaker:
Prof. Dr. Meinhard Simon
E-Mail: m.simon(at)icbm.de Tel: +49(0)441-798-5361 Fax:+49(0)441-798-3438
Deputy Speaker:
Prof. Dr. Dieter Jahn
E-Mail: d.jahn(at)tu-bs.de Tel: +49(0)531-391-5801 Fax: +49(0)531-391-5854
Deputy Speaker:
Prof. Dr. Thorsten Dittmar
E-Mail: thorsten.dittmar@uni-oldenburg.de Tel: +49(0)441-798-3602 Fax: +49(0)441-798-
Prof. Dr. Irene Wagner-Döbler
E-Mail: irene.wagner-doebler(at)helmholtz-hzi.de Tel: +49(0)531-6181-3080 Fax: +49(0)531-6181-3096
Prof. Dr. Stefan Schulz
E-Mail: stefan.schulz(at)tu-bs.de Tel: +49(0)531-391-7353 Fax: +49(0)531-5272
Name | Working Group | Project | |
Prof. Dr. Bernd Blasius | blasius@icbm.de | Institute for Chemistry and Biology of the Marine Environment University of Oldenburg | C7 |
PD Dr. Thorsten Brinkhoff | thorsten.brinkhoff@icbm.de | Biology of Geological Processes Institute for Chemistry and Biology of the Marine Environment University of Oldenburg | A1, B2 |
PD Dr. Rolf Daniel | rdaniel@gwdg.de | Genomic and Applied Microbiology Institute for Microbiology and Genetics University of Göttingen | Z02 |
Dr. Jeroen Dickschat | j.dickschat@uni-bonn.de | Kekulé-Institut for Organic Chemistry and Biochemie Universität Bonn | B7 |
Prof. Dr. Thorsten Dittmar | thorsten.dittmar@uni-oldenburg.de | Institute for Chemistry and Biology of the Marine Environment University of Oldenburg | A8 |
Dr. Bert Engelen | bert.engelen@icbm.de | Paleomicrobiology Institute for Chemistry and Biology of the Marine Environment University of Oldenburg | A2 |
Dr. Ferdinand Esser | ferdinand.esser@uni-oldenburg.de | Institute for Chemistry and Biology of the Marine Environment University of Oldenburg | GRAD |
Dr. Heike Freese | heike.freese@dsmz.de | Microbial Ecology and Diversity Research German Collection of Microorganisms and Cell Cultures Braunschweig | A7 |
PD Dr. Markus Göker | markus.goeker@dsmz.de | Phylogenomic and functional phenotyping German Collection of Microorganisms and Cell Cultures Braunschweig | A6 |
Dr. Elisabeth Härtig | e.haertig@tu-braunschweig.de | Institute of Microbiology Technische Universität Braunschweig | B5 |
Prof. Dr. Karsten Hiller | karsten.hiller@tu-braunschweig.de | Institute of Bioinformatics and Biochemistry Technische Universität Braunschweig | C3 |
Prof. Dr. Dieter Jahn | d.jahn@tu-braunschweig.de | AG Prof. Dr. Dieter Jahn Institute of Microbiology Technische Universität Braunschweig | B5, INF |
Dr. Christina Moraru | liliana.christina.moraru@uni-oldenburg.de | Institute for Chemistry and Biology of the Marine Environment University of Oldenburg | B6 |
Dr. Jutta Niggemann | jutta.niggemann@uni-oldenburg.de | Institute for Chemistry and Biology of the Marine Environment University of Oldenburg | A8 |
Prof. Dr. Jörg Overmann | joerg.overmann@dsmz.de | Molecular Ecology ans Systematics German Collection of Microorganisms and Cell Cultures Braunschweig | A7 |
PD Dr. Jörn Petersen | jpe07@dsmz.de | Molecular Ecology ans Systematics German Collection of Microorganisms and Cell Cultures Braunschweig | A5 |
Dr. Silke Pradella | spr05@dsmz.de | Molecular Ecology ans Systematics German Collection of Microorganisms and Cell Cultures Braunschweig | A5 |
Prof. Dr. Ralf Rabus | rabus@icbm.de | General and Molecular Microbiology Institute for Chemistry and Biology of the Marine Environment University of Oldenburg | C1, C5 |
Dr. Kerstin Schmidt-Hohagen | k.schmidt-hohagen@tu-braunschweig.de | Department of Bioinformatics and Biochemistry Institute of Biochemistry and Biotechnology Technische Universität Braunschweig | C3 |
Prof. Dr. Stefan Schulz | stefan.schulz@tu-braunschweig.de | Chemical Communication Institute of Organic Chemistry Technische Universität Braunschweig | C2 |
Prof. Dr. Meinhard Simon | m.simon@icbm.e | Biology of Geological Processes Institute for Chemistry and Biology of the Marine Environment University of Oldenburg | A1, B2, Z |
Prof. Dr. Irene Wagner-Döbler | irene.wagner-doebler@helmholtz-hzi.de | Microbial Communication Helmholtz Centre for Infection Research | B4, C5 |
Dr. Lars Wöhlbrand | lars.woehlbrand@uni-oldenburg.de | General and Molecular Microbiology Institute for Chemistry and Biology of the Marine Environment University of Oldenburg | C1 |
PD Dr. Jörg Grunenberg, Joerg.Grunenberg(at)tu-bs.de, Computational Chemistry Institute of Organic Chemistry, Technische Universität Braunschweig B3, C2
Dr. Johannes Klein johannes.klein(at)tu-bs.de, AG Computational Microbiology Institute of Microbiology, Technische Universität Braunschweig,INF
Dr. Richard Münchr.muench(at)tu-bs.de, AG Computational Microbiology Institute of Microbiology, Institute of Microbiology, Technische Universität Braunschweig, INF
Dr. Bernd Nörtemann, b.noertemann(at)tu-braunschweig.de, Institute of Biochemical Engineering, Technische Universität Braunschweig, C4
Dr. Ulrich Papke, u.papke(at)tu-bs.de, Institute of Organic Chemistry, Technische Universität Braunschweig, C4
Dr. Petra Tielen, p.tielen(at)tu-bs.de, AG Tielen, Institute of Mikrobiology, Technische Universität Braunschweig, B5
Dr. Sonja Voget, svoget(at)uni-goettingen.de, Genomic and Applied Mikrobiology, Institute for Microbiology and Genetics, University of Göttingen, A3/Z
Name | Institute | Project | |
Lukas Birmes | lub17@dsmz.de | Deutschen Sammlung von Mikroorganismen und Zellkulturen | A5 |
Miriam Becker | miriam.becker@tu-braunschweig.de | Institut für Mikrobiologie TU Braunschweig | B5 |
Maren Behringer | m.behringer@tu-braunschweig.de | Institut für Mikrobiologie TU Braunschweig | B5 |
Nicole Beier | nicole.beier@helmholtz-hzi.de | Mikrobielle Proteomik TU Braunschweig | C6 |
Nelli Bill | nbill@web.de | Abteilung Bioinformatik & Biochemie TU Braunschweig | C3 |
Vera Bischoff | vera.bischoff@uol.de | Institut für Chemie und Biologie des Meeres Universität Oldenburg | B6 |
Trần QuốcDen | denhaugiang@gmail.com | Institut für Chemie und Biologie des Meeres Universität Oldenburg | A1 |
Tim Harig | t.harig@tu-braunschweig.de | Institut für Organische Chemie TU Braunschweig | C2 |
Juliane Hartlich | juliane.hartlich@tu-braunschweig.de | Institut für Mikrobiologie TU Braunschweig | INF |
Kristin Kalvelage | kerstin.kalvelage@uol.de | Institut für Chemie und Biologie des Meeres Universität Oldenburg | C1 |
Diana Koteska | d.koteska@tu-braunschweig.de | Institut für Organische Chemie TU Braunschweig | C2 |
Janina Leinberger | janina.leinberger@uni-oldenburg.de | Institut für Chemie und Biologie des Meeres Universität Oldenburg | B2 |
Florian Lenk | flenk@gwdg.de | Institut für Mikrobiologie und Genetik Universität Göttingen | A3 |
Johannes Mansky | j.mansky@tu-braunschweig.de | Institut für Mikrobiologie TU Braunschweig | B4 |
Elisabeth Majer | e.majer@tu-braunschweig.de | Institut für Bioinformatik und Biochemie Universität Braunschweig | C3 |
Felix Milke | felix.milke@uol.de | Institut für Chemie und Biologie des Meeres Universität Oldenburg | A1 |
Mohammed Mozzamil | Institut für Chemie und Biologie des Meeres Universität Oldenburg | C7 | |
Lisa Plötzky | l.ploetzky@tu-braunschweig.de | Institut für Mikrobiologie TU Braunschweig | B5 |
Marion Pohlner | marion.pohlner@uni-oldenburg.de | Institut für Chemie und Biologie des Meeres Universität Oldenburg | A2 |
Carsten Reuse | c.reuse@tu-braunschweig.de | Institut für Bioinformatik und Biochemie Universität Braunschweig | C3 |
Selene Sanchez | selene.sanchez@gmail.com | Institut für Mikrobiologie TU Braunschweig | C5 |
Carmen Scheuner | carmen.scheuner@dsmz.de | Deutschen Sammlung von Mikroorganismen und Zellkulturen | A6 |
Sujatha Srinivas | sujatha.srinivas@uol.de | Institut für Chemie und Biologie des Meeres Universität Oldenburg | B2 |
Dennis Tebbe | dennis.tebbe@uol.de | Institut für Chemie und Biologie des Meeres Universität Oldenburg | A2 |
Arne Weiten | arne.ruediger.weiten@uni-oldenburg.de | Institut für Chemie und Biologie des Meeres Universität Oldenburg | C1 |
Laura Wolter | laura.wolter@uni-oldenburg.de | Institut für Chemie und Biologie des Meeres Universität Oldenburg | B2 |
Daniel Wünsch | daniel.wuensch@uni-oldenburg.de | Institut für Chemie und Biologie des Meeres Universität Oldenburg | C1 |
Falk Zucker | falk.zucker@uol.de | Institut für Chemie und Biologie des Meeres Universität Oldenburg | B6 |
Insa Bakenhus, Institut für Chemie und Biologie des Meeres Universität Oldenburg, A1
Pascal Bartling, Deutschen Sammlung von Mikroorganismen und Zellkulturen, A5
Annekathrin Bartsch, Institut für Bioverfahrenstechnik, TU Braunschweig, C4
Paul Beyersmann, Institut für Chemie und Biologie des Meeres, Universität Oldenburg, B2
Sara Billerbeck, Institut für Chemie und Biologie des Meeres, Universität Oldenburg, A1
Sven Breider, Institut für Chemie und Biologie des Meeres, Universität Oldenburg, B2
Nelson L. Brock, Institut für Organische Chemie, TU Braunschweig, B3
Hilke Bruns, Institut für Organische Chemie, TU Braunschweig, C2
Ina Buchholz, Arbeitsgruppe Mikrobielle Kommunikation, HZI Braunschweig, B4
Christian Citron, Institut für Organische Chemie, TU Braunschweig, B3
Marco Dogs, Institut für Chemie und Biologie des Meeres, Universität Oldenburg, B2
Matthias Ebert, Institut für Mikrobiologie, TU Braunschweig, B5
Anne Fiebig, Deutschen Sammlung von Mikroorganismen und Zellkulturen, A6
Oliver Frank, Deutschen Sammlung von Mikroorganismen und Zellkulturen, A5
Michael Hensler, Abteilung Bioinformatik & Biochemie, TU Braunschweig, C3
Steffi Heyber, Institut für Mikrobiologie, TU Braunschweig, C5
Jenny Jacobs, Institut für Mikrobiologie, TU Braunschweig, B5
Palani Kannan, Deutschen Sammlung von Mikroorganismen und Zellkulturen, A6
Saranya Kanukollu, Institut für Chemie und Biologie des Meeres, Universität Oldenburg, A2
Christian Kirchhoff, Institut für Chemie und Biologie des Meeres, Universität Oldenburg, B1
Sarah Kleist, Abteilung Bioinformatik & Biochemie, TU Braunschweig, C3
Arne Klingner, Institut für Bioverfahrenstechnik, TU Braunschweig, C4
Sebastian Koßmehl, Institut für Chemie und Biologie des Meeres, Universität Oldenburg. C1
Sebastian Laaß, Institut für Mikrobiologie, TU Braunschweig, B5
Ann-Kathrin Ludewig, Deutschen Sammlung von Mikroorganismen und Zellkulturen, A5
Michael Maczka, Institut für Organische Chemie, TU Braunschweig, C2
Mathias Milici, Arbeitsgruppe Mikrobielle Kommunikation, HZI Braunschweig, B4
Maike Narten, Institut für Mikrobiologie, TU Braunschweig, B5
Alexander Neumann, Institut für Organische Chemie, TU Braunschweig, C2
Beatriz Elizabeth Noriega Ortega, Institut für Chemie und Biologie des Meeres, Universität Oldenburg, A8
Diana Patzelt, Arbeitsgruppe Mikrobielle Kommunikation, HZI Braunschweig, B4
Tanja Piekarski, Institut für Mikrobiologie, TU Braunschweig, B5
Rene Rex, Abteilung Bioinformatik & Biochemie, TU Braunschweig, C3
Nora Roesky, Deutschen Sammlung von Mikroorganismen und Zellkulturen, A5
Hanna Ruppersberg, Institut für Chemie und Biologie des Meeres, Universität Oldenburg, C1
Maya Soora, Institut für Chemie und Biologie des Meeres, Universität Oldenburg, B1
Sonja Voget, Institut für Mikrobiologie und Genetik, Universität Göttingen, A3
John Vollmers, Institut für Mikrobiologie und Genetik, Universität Göttingen, A3
Hui Wang, Arbeitsgruppe Mikrobielle Kommunikation, HZI Braunschweig, C5
Heidi Wichmann, Institut für Chemie und Biologie des Meeres, Universität Oldenburg, B1
Katharina Wiegemann, Institut für Chemie und Biologie des Meeres, Universität Oldenburg, C1
Gerrit Wienhausen, Institut für Chemie und Biologie des Meeres, Universität Oldenburg, A8
Sabine Will, Abteilung Bioinformatik & Biochemie, TU Braunschweig, C3
Lisa Zieschke, Institut für Organische Chemie, TU Braunschweig, C2
Course program Grad PhD Programme 2018
Objective
The scientific world requires highly qualified young scientists. The Research Training Group integrated into the CRC Roseobacter wants to attract the most promising young scientists from across the world with majors in biology, biotechnology, biochemistry, chemistry and bioinformatics. The group supports the education of the PhD students through providing an excellent research environment and offering introductory and advanced training courses. This comprehensive concept improves the qualifications of the doctoral students and facilitates their development into leading researchers of the future.
The aims of the Research Training Group are
The Research Training Group is based on the following pillars:
Specialized scientific knowledge
The PhD students broaden and deepen their scientific knowledge in their area of specialization by:
Communicative competences
The PhD students improve their communication and presentation techniques and get expertise in knowledge transfer by:
Interdisciplinary competences / Soft skills
The PhD students can develop strategies and expertise for their scientific career. The main issues focus on:
Structured PhD programme
The aim of the structured PhD programme is to promote the research independence and additional qualifications of young scientists. The programme includes the following procedure:
The holder of a Master/Diplom in biology, biotechnology, biochemistry, chemistry or bioinformatics applies at the University. Application for admission Form OL (ger)
The applicant registers as PhD student at Faculty V. Application for PhD admission Form OL (ger), Application for Initiation of procedure Form OL (ger)
The PhD student applies at the Graduate School Science and Technology. Application Form OL (en), Admission Order OL (ger), Application Form BS (en)
A dissertation agreement on the rights and duties of the PhD student is signed. Dissertation Agreement OL (en)
A thesis concept paper is prepared by the PhD student and discussed with the thesis committee. Guidelines Concept Paper (en)
The PhD student selects a primary supervisor and additional experienced scientists to form a thesis committee. Guidelines Thesis Committee (en), Minutes Thesis Committee (en)
The PhD student prepares a thesis work and attends the Intergrated Research Training Group (IRTG). The work also includes:
The PhD student receives the doctoral degree and a certificate for successfully completing the IRTG. PhD Order OL (08/2009, ger), PhD Order OL (01/2013, ger), PhD Order BS (ger)
Mentoring Programme: "Conflict management and communication" COURSES for the PhD students of the SFB Roseobacter | 31. August - 01. September 2017 9 - 17, ICBM Oldenburg |
YOUMARES 8 Oceans across boundaries: Learning from each other | 13.-15. September 2017 Kiel |
2nd ICBM PhD Day | 09. October 2017, 9 - 19 ICBM Oldenburg |
Mentoring Programme: Networking strategies and creative ways for career strategies – Closing Symposium with Mentors | 15. November 2017, 9 -16 ICBM Oldenburg |
Curriculum of the structured PhD Programme for PhD students enrolled in the Graduate School 'Science and Technology', PhD program 'Environmental Sciences and Biodiversity' of the University Oldenburg
The following courses are especially organised for the PhD students of the SFB Roseobacter:
Course Overview
Course programme 2017
Course Programme 2016
Course Programme 2015
Course Programme 2014
Workshop "Introduction to Next Generation Sequencing"; 10.-12. July 2017, Course announcement
Workshop: "GIS for environmental scientists"
Basic course: 22. February 2016, ICBM Oldenburg
Advanced course: 07.-09. March 2016, ICBM Oldenburg
Oldenburg: "Prokaryotic Genomics & Bioinformatics"; 26.-27. November 2015, Course announcement
Workshop: Societal relevance of (Coastal) biodiversity change, Young scientists meet industry, enterprises, scientific management and institutes, including the workshop "fundraising at DFG Bonn", 26.-30. September 2016, Terramare, Wilhelmshaven, PDF
International Workshop: Geo-metabolomics “First steps towards a systems biology understanding of organic matter cycling in aquatic systems”; 24.–28. November 2014, Hanse Institute for Advanced Study, Delmenhorst, Germany, Agenda
Scientific Image Processing and Analysis:
Oldenburg: Seminar + tutorial (Engl); Dr. Jan Brocher, BioVoxxel, 23. + 24. April 2013
Career Day "Re-Search your future – Sea what comes next" at the World Oceans Day, 08. June 2017, Poster
Graduate Syposium: "Career Paths in Marine and Climate Sciences" 27. May 2016, Poster
Career Day for Marine Scientists at the ICBM, 16. October 2015, 13 - 18 Uhr, Programme
Graduate Symposium: „Career Path in Marine and Climate Sciences" 23. May 2014, Flyer
Conference: "Career ways in marine sciences" 03. November 2012
Good scientific practice
04. Februar 2016, Course announcement
06. November 2015, Course announcement
09. June 2015, Course annoncement
10. Dezember 2014, Course announcement
23. April 2014, Course announcement
17. October 2013, Course announcement
Statistics and Software R
Braunschweig: Seminar + tutorial; Münch, Roselius, Heyber, Brötje, 15.-17. July 2015
Oldenburg: Seminar + tutorial (Engl); Münch, Klein; Roselius, 19.-21. November 2012
Braunschweig: Seminar + tutorial (Engl); Münch, Klein, Roselius, 21.+23.-25. November 2011
MatLab programming course
Oldenburg: Seminar + tutorial (Engl); Christoph Feenders, 27. - 31. March 2017, Course announcement
Systems Biology of Promoters
Braunschweig: Seminar + tutorial; Dr. Alexander Kel, Dr. Jeannette Koschmann, 29.-30. November 2016, Course Announcement
Colloquium
Microbial Colloquium at the ICBM
ICBM Summer School
Summer School: Introduction to Data Analysis and Ecosystem Modeling, 30. July – 12. August 2017
Summer School: Water column processes from coast to ocean, 4 - 18 July 2015
Summer School: "Biogeochemistry of tidal flats and beaches of the southern North Sea coast (Wadden Sea)", 10.- 24. August 2013
Summer School: "Coastal Systems", 22. August - 02. September 2011
ICBM PhD Day
1st ICBM PhD Day, 23. March 2017
PhD Workshop
"State of your research in the CRC Roseobacter – your Scientific Career and what comes next?", 13.-15. October 2016, Neuwerk
“Young scientists meet industry, enterprises, scientific management and institutes” including the workshop “Science communication - How to turn science into a story", 01.-03. June 2015, Hamburg
"My contribution to the CRC Roseobacter – my Scientific Network", 25.-27. September 2014, Nationalpark-Haus Wittbülten, Spiekeroog
Workshop: "Erfolgsfaktor Persönlichkeit und Stimme - überzeigend auftreten - sicher sprechen - glaubwürdig präsentieren" Teil 2, 15. April 2016, ICBM Oldenburg
Workshop: "Erfolgsfaktor Persönlichkeit und Stimme - überzeigend auftreten - sicher sprechen - glaubwürdig präsentieren" Teil 1, 01. April 2016, ICBM Oldenburg
Workshop: "Durchboxtraining", 02.-03. November 2015, TU Braunschweig
Workshop: "Arroganz-Training", 06.-07. November 2014, TU Braunschweig
Workshop: "How to present at international scientific conferences?"
Oldenburg: Workshop (Engl); Tress & Tress GbR "How to present at international scientific conferences?" 24.-26. November 2014, ICBM
Oldenburg: Workshop (Engl); Tress & Tress GbR, 9.-11. January 2013, ICBM, Oldenburg
Seminar organisation of "conference career ways in marine science" ICBM Oldenburg 1. Juni - 7. September 2012 (guided by F.Esser)
Project Management
Oldenburg: Seminar "Basics of Project Management", 25.-26. June 2015
Oldenburg: Seminar "Basic in project management"; Dr. F. Esser; 12.-13. August 2014; ICBM University of Oldenburg
Mentoring
Oldenburg: Mentoring programme 2016-2017 for young researchers
Oldenburg: Mentoring programme 2014-2015 for young researchers
Oldenburg: Mentoring programme 2014-2015 for young researchers. Kick-off meeting
Career planning
Oldenburg Seminar: Methods of career planning: "Creative ways getting your dream job" - "Kreative Wege zum Traumjob"; Dr. F. Esser; 15. March 2016, ICBM, University of Oldenburg
Braunschweig: „Bewerbungstraining", Dr. Sylvia Lorenz, October 19.-20. October 2015; TU Braunschweig
Oldenburg Seminar: „Methods of career planning” Part II: “You only go further if you are prepared to learn from others” – Benefit of mentoring, how to learn from a mentor; Dr. F. Esser; 11. July 2014, ICBM, University of Oldenburg
Oldenburg Seminar: „Methods of career planning" Part 1: "Only those in a networt go further" - Network strategies to reach your personal objecives; Dr. F. Esser; 17. June 2014, ICBM, University of Oldenburg
Oldenburg Seminar: „Methods of career planning” Part I: “Only those in a network go further” – Network strategies to reach your personal objectives; Dr. F. Esser; 28. November 2013, ICBM, University of Oldenburg
Oldenburg Seminar: „Methods of career planning” Part II: “You only go further if you are prepared to learn from others” – Benefit of mentoring, how to learn from a mentor; Dr. F. Esser; 11. July 2014, ICBM, University of Oldenburg
Oldenburg Seminar: „Methods of career planning” Part II: “You only go further if you are prepared to learn from others” – Benefit of mentoring, how to learn from a mentor; Dr. F. Esser; 12. December 2013, ICBM, University of Oldenburg
Oldenburg: Seminar "Creative ways getting your dream job"; Dr. F. Esser; 10. May 2013, ICBM University of Oldenburg
Scientific Writing "How to publish in peer-reviewed journals?"
Oldenburg: Workshop (Engl); Tress & Tress GbR, 17.-19. November 2015, ICBM, Oldenburg
Oldenburg: Workshop (Engl); Tress & Tress GbR, 7. - 9. January 2015, ICBM, Oldenburg
Oldenburg: Workshop (Engl); Tress & Tress GbR, 24.-26. November 2014, ICBM, Oldenburg, Programm
Braunschweig: Workshop (Engl); Tress & Tress GbR, 10.-12. January 2012, TU Braunschweig
Oldenburg: Workshop (Engl); Tress & Tress GbR, 14.-16. December 2011, ICBM-Terramare, Wilhelmshaven
Fundraising
Braunschweig: Workshop "Erfolgreich Drittmittel einwerben", 25. November 2014, TU Braunschweig
Leadership competencies
Braunschweig: Workshop "Führung: Kompetenzen und Konzepte", 22. September 2016, TU Braunschweig
Zeitmanagement
Braunschweig: Seminar "Zeitmanagement", 25. - 26. July 2015
Carl von Ossietzky Universität Oldenburg
Courses offered by the Graduate Academy
Courses and Events by the Graduate School 'Science and Technology' OLTECH
Technische Universität Braunschweig
Courses and Events by the Graduate Academy GradTUBS
University didactics and innovative teaching methods: Teach4TU
Basic IT: Gauß-IT-Zentrum
Language Center
Personalentwicklung
Application, networking and career orientation: Career Service
Business start-ups and self-employment: Technology Transfer
Gender equality: Equal Opportunities Office
Braunschweig University Library: Coffee Lectures
The doctoral students passing the structured PhD programme will get 150 credit points (CP) for their research work and 30 CPs for successfully completing the programme of the Research Training Group.
Specialised scientific knowledge | at least 12 CP |
Communicative competences | at least 6 CP |
Interdisciplinary competences/ Soft skills | at least 6 CP |
Type of course, project or event | Effort | CP |
Specialised scientific knowledge | ||
Summer School | 1-2 weeks + report | 3 |
Congress or Workshop (national, international) | 1 week + oral presentation/poster | 3 |
Lab visit abroad | at least 3 weeks + report | 6 |
Trip on research vessel | at least 3 weeks + report | 6 |
Lecture, seminar, practical training | 2 hours per week (semester) + participation/exam | 1,5/3 |
International colloquium | 1 semester + active participation | 3 |
Colloquium in respective area | 1 semester + active participation | 3 |
Communication competences | ||
Guiding students during practical course | 4 weeks + preparation/organisation | 6 |
Forum of advanced Master students and PhD students | 1 semester + organisation/participation | 3 |
Advanced presentation techniques | 1 day + active participation | 0,5 |
Communication (e.g. conflict managment) | 1 day + active participation | 0,5 |
Didactics | 1 day + active participation | 0,5 |
Interdisciplinary competences / Soft skills | ||
Literature survey | 1 day + active participation | 0,5 |
Scientific English | 2 hours per week (semester) + contribution | 3 |
Statistics | 5 days + active participation | 3 |
Scientific writing | 3 days + concept of manuscript | 3 |
Proposal writing | 2 days + concept of proposal | 1 |
Journal club | 1 hour per week (semester) | 3 |
Project management | 2 days | 1 |
Time management | 2 days | 1 |
Career strategies | 1 day | 0,5 |
Bakenhus I, Wemheuer B, Akyol P, Giebel HA, Dlugosch L, Daniel R, Simon M (2019) Distinct relationships between fluorescence in situ hybridization- and rRNA gene- and amplicon-based sequencing data of bacterioplankton lineages. System Appl Microbiol 42/5: article 126000 (doi.org/10.1016/j.syapm.2019.06.005).
Bischoff V, Bunk B, Meier-Kolthoff J, Spröer C, Poehlein A, Dogs M, Nguyen M, Petersen J, Daniel R, Overmann J, Göker M, Simon M, Brinkhoff T, Moraru C (2019) Cobaviruses – a new globally distributed phage group infecting Rhodobacteraceae in marine ecosystems. ISME J: 13, 1404–1421.
Czech L, Hoeppner A, Kobus S, Seubert A, Riclea R, Dickschat J, Heider J, Smits SH, Bremer E (2019) Illuminating the catalytic core of ectoine synthase through structural and biochemical analysis. Sci Reports 9: 364. DOI: 10.1038/s41598-018-36247-w.
Giebel HA, Wolterink M, Brinkhoff T, Simon M (2019) Complementary energy acquisition via aerobic anoxygenic photosynthesis and carbon monoxide oxidation by Planktomarina temperata of the Roseobacter group. FEMS Microb Ecol 95/5: fiz050.
Hansen CT, Niggemann J, Giebel H-A, Simon M, Bach W, Dittmar T (2019) Biodegradability of hydrothermally altered deep-sea dissolved organic matter. Mar Chem 217: Article 103706 (https://doi.org/10.1016/j.marchem.2019.103706).
Koch H, Dürwald A, Schweder T, Noriega-Ortega B, Vidal-Melgosa S, Hehemann J-H, Dittmar T, Freese HM, Becher D, Simon M, Wietz M (2019) Biphasic cellular adaptations and ecological implications of Alteromonas macleodii degrading a mixture of algal polysaccharides. ISME 13/1: 92-103.
Koch H, Freese HM, Hahnke RL, Simon M, Wietz M (2019) Adaptations of Alteromonas sp. 76-1 to polysaccharide degradation: A CAZyme plasmid for ulvan degradation and two alginolytic systems. Front Microbiol 10: Article 504.
Koppenhöfer S, Wang H, Scharfe M, Kaever V, Wagner-Döbler I, Tomasch J. (2019) Integrated transcriptional regulatory network of quorum sensing, replication control, and SOS response in Dinoroseobacter shibae. Front Microbiol 10: 803. doi: 10.3389/fmicb.2019.00803.
Majzoub M, Beyersmann P, Simon M, Thomas T, Brinkhoff T, Egan S (2019) Phaeobacter inhibens controls bacterial community assembly on a marine diatom. FEMS Microb Ecol 95/6: fiz060.
Meier-Kolthoff JP, Goeker M (2019) TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nature Comm 10: 2182. DOI: 10.1038/s41467-019-10210-3.
Barrero-Canosa J, Moraru C (2019) PhageFISH for monitoring phage infections at single cell level. In: Methods in molecular biology (Clifton, N.J.) Volume 1898: 1-26. DOI:10.1007/978-1-4939-8940-9_1.
Noriega-Ortega BE, Wienhausen, Mentges A, Dittmar T, Simon M, Niggemann J (2019) Does the chemodiversity of bacterial exometabolomes sustain the chemodiversity of marine dissolved organic matter? Front Microbiol 10: Article 215.
Petersen J, Vollmers J, Ringel V, Brinkmann H, Ellebrandt-Sperling C, Sproeer C, Howat AM, Murrell JC, Kaster AK (2019) A marine plasmid hitchhiking vast phylogenetic and geographic distances. Proc Natl Acad Sci US 116/41: 20568-20573. DOI: 10.1073/pnas.1905878116.
Pohlner M, Dlugosch L, Wemheuer B, Mills H, Engelen B, Reese BK (2019) The majority of active Rhodobacteraceae in marine sediments belongs to uncultured genera: A molecular approach to link their distribution to environmental conditions. Front Microbiol 10:659, doi.org/10.3389/fmicb.2019.00659.
Steinert G, Wemheuer B, Janussen D, Erpenbeck D, Daniel R, Simon M, Brinkhoff T, Schupp P (2019) Prokaryotic diversity and community patterns in Antarctic continental shelf sponges. Front Mar Sci 6: Article 297.
Wemheuer F, von Hoyningen-Huene AJE, Pohlner M, Degenhardt J, Engelen B, Daniel R, Wemheuer B (2019) Primary production in the water column as major structuring element of the biogeographical distribution and function of Archaea in deep-sea sediments of the central Pacific Ocean. Archaea, vol. 2019, Article ID 3717239, doi.org/10.1155/2019/3717239.
Wünsch D, Tautwein K, Scheve S, Hinrichs C, Feenders C, Blasius B, Schomburg D, Rabus R (2019) Amino acid and sugar catabolism in the marine bacterium Phaeobacter inhibens DSM 17395 from an energetic viewpoint. Appl Environ Microbiol 85/24: e02095-19. doi: 10.1128/AEM.02095-19.
Ziesche L, Wolter L, Wang H, Brinkhoff T, Pohlner M, Engelen B, Wagner-Döbler I, Schulz S (2019) An unprecedented medium-chain diunsaturated N-acylhomoserine lactone from marine Roseobacter group bacteria, Mar Drugs 17: E20. doi: 10.3390/md17010020.
Bakenhus I, Dlugosch L, Giebel HA, Beardsley C, Simon M, Wietz M (2018) Distinct biogeographic patterns of bacterioplankton composition and single-cell activity between the subtropics and Antarctica. Environ Microbiol 20/8, Special Issue: 3100-3108.
Bakenhus I, Voget S, Poehlein A, Brinkhoff T, Daniel R, Simon M (2018) Genome sequence of Planktotalea frisia type strain (SH6-1T), a representative of the Roseobacter group isolated from the North Sea during a phytoplankton bloom. Stand Gen Sci 13: 7, doi.org/10.1186/s40793-018-0311-5.
Bartling P, Vollmers J, Petersen J (2018) The first world swimming championships of roseobacters - Phylogenomic insights into an exceptional motility phenotype. System Appl Microbiol 41/6: 544-554. DOI: 10.1016/j.syapm.2018.08.012
Brinkmann H, Goeker M, Koblizek M, Wagner-Doebler I, Petersen J (2018) Horizontal operon transfer, plasmids, and the evolution of photosynthesis in Rhodobacteraceae. ISME J 12/8: 1994-2010. DOI: 10.1038/s41396-018-0150-9
Bruns H, Herrmann J, Müller R, Wang H, Wagner-Döbler I, Schulz S (2018) Oxygenated N-Acyl Alanine Methyl Esters (NAMEs) from the marine bacterium Roseovarius tolerans EL-164. J Nat Prod 81: 131-139. doi: 10.1021/acs.jnatprod.7b00757
Bruns H, Ziesche L, Taniwal NK, Wolter L, Brinkhoff T, Herrmann J, Müller R, Schulz S (2018) N-Acylated amino acid methyl esters from marine Roseobacter group bacteria. Beilstein J Org Chem 14: 2964-2973. doi: 10.3762/bjoc.14.276
Daniel R, Simon M, Wemheuer B (2018) Editorial: Molecular ecology and genetic diversity of the Roseobacter clade. Front Microbiol 9: Article 1185.
Eckweiler D, Dudek D, Hartlich J, Broetje D, Jahn D (2018) PRODORIC2: the bacterial gene regulation database in 2018. Nucleic Acids Res 46/D1: D320-326. DOI: 10.1093/nar/gkx1091
Kirchhoff C, Ebert M, Jahn D, Cypionka H (2018) Chemiosmotic energy conservation in Dinoroseobacter shibae: Proton translocation driven by aerobic respiration, denitrification and photosynthetic light reaction. Front Microbiol doi:10.3389/fmicb.2018.00903
Klotz F, Brinkhoff T, Freese HM, Wietz M, Teske A, Simon M, Giebel HA (2018) Tritonibacter horizontis gen. nov., sp. nov., a member of the Rhodobacteraceae, isolated from the Deepwater Horizon oil spill. Int J Syst Evol Microbiol 68: 736-744. DOI 10.1099/ijsem.0.002573
Kopejtka K, Tomasch J, Bunk B, Spröer C, Wagner-Döbler I, Koblížek M (2018) The complete genome sequence of Rhodobaca barguzinensis alga05 (DSM 19920) documents its adaptation for life in soda lakes. Extremophiles 22(6): 839-849. doi: 10.1007/s00792-018-1041-8.
Schlawis C, Kern S, Kudo Y, Grunenberg J, Moore B, Schulz S (2018) Structural elucidation of trace components combining GC/MS, GC/IR, DFT-calculation and synthesis - Salinilactones, unprecedented bicyclic lactones from Salinispora bacteria. Angew Chem Int Ed 57: 14921-14925. doi: 10.1002/anie.201807923: Angew Chem 130: 15137-15141. doi: 10.1002/ange.201807923
Tomasch J, Wang H, Hall ATK, Patzelt D, Preusse M, Petersen J, Brinkmann H, Bunk B, Bhuju S, Jarek M, Geffers R, Lang AS, Wagner-Döbler I (2018) Packaging of Dinoroseobacter shibae DNA into Gene Transfer Agent particles is not random. Genome Biol Evol 10(1): 359-369. doi: 10.1093/gbe/evy005.
Trautwein K, Hensler M, Wiegmann K, Skorubskaya E, Wöhlbrand L, Wünsch D, Hinrichs C, Feenders C, Müller C, Schell, K, Ruppersberg HS, Vagts J, Koßmehl S, Steinbüchel A, Schmidt-Kopplin P, Wilkes H, Hillebrand H, Blasius B, Schomburg D and Rabus R (2018) The marine bacterium Phaeobacter inhibens secures external ammonium by rapid buildup of intracellular nitrogen stocks. FEMS Microbiol Ecol 94/10: fiy154. doi: 10.1093/femsec/fiy154
Ziesche L, Rinkel J, Dickschat JS, Schulz S (2018) Acyl-group specificity of AHL synthases involved in quorum-sensing in Roseobacter group bacteria. Beilstein J Org Che. 14: 1309-1316. doi: 10.3762/bjoc.14.112
Ebert, M., Schweyen, P., Bröring, M., Laass, S., Härtig, E. & Jahn, D. (2017) Heme and nitric oxide binding by the transcriptional regulator DnrF from the marine bacterium Dinoroseobacter shibae increases napDpromoter affinity. J. Biol. Chem., in press
Beyersmann PG, Tomasch J, Son K, Stocker R, Göker M, Wagner-Döbler I, Simon M, Brinkhoff T (2017) Dual function of tropodithietic acid as antibiotic and signaling molecule in global gene regulation of the probiotic bacterium Phaeobacter inhibens. Sci Rep 7: 730. 10.1038/s41598-017-00784-7 [doi];10.1038/s41598-017-00784-7 [pii].
Bill N, Tomasch J, Riemer A, Müller K, Kleist S, Schmidt-Hohagen K, Wagner-Döbler I, Schomburg D (2017) Fixation of CO2 using the ethylmalonyl-CoA pathway in the photoheterotrophic marine bacterium Dinoroseobacter shibae. Environ Microbiol doi:10.1111/1462-2920.13746.
Blasenovic I, Kind T, Torbasinovic H, Obrenovic S, Mehta SS, Tsugawa H, Wermuth T, Schauer N, Jahn M, Biedendieck R, Jahn D (2017) Comprehensive comparison of in silico MS/MS fragmentation tools of the CASMI contest: database boosting is needed to achieve 93% accuracy. J Cheminform) 9: 32.
Breider S, Freese HM, Spröer C, Simon M, Overmann J, Brinkhoff T (2017) Phaeobacter porticola sp. nov., an antibiotic producing bacterium isolated from a harbor in the southern North Sea. Int J Syst Evol Microbiol. In press.
Burkhardt I, Lauterbach L, Brock NL, Dickschat JS (2017) Chemical Differentiation of Three DMSP Lyases from the Marine Roseobacter group. Org Biomol Chem (published online, doi: 10.1039/C7OB00913E).
Celik E, Maczka M, Bergen N, Brinkhoff T, Schulz S, Dickschat JS (2017) Metabolism of 2,3-dihydroxypropane-1-sulfonate by marine bacteria. Org Biomol Chem 15: 2919-2922.
Dogs M, Wemheuer B, Wolter L, Bergen N, Daniel R, Simon M, Brinkhoff T (2017) Rhodobacteraceae on the marine brown alga Fucus spiralis are predominant and show physiological adaptation to an epiphytic lifestyle. Syst Appl Microbiol, in press.
Ebert M, Laass S, Thürmer A, Roselius L, Eckweiler D, Daniel R, Härtig E, Jahn D (2017) FnrL and three Dnr regulators are used for the metabolic adaptation to low oxygen tension in Dinoroseobacter shibae. Frontiers in Microbiology 8:642
Kirchhoff C, Cypionka H (2017) Boosted membrane potential as bioenergetic response to anoxia in Dinoroseobacter shibae. Front Microbiol, 8:695, https://doi.org/10.3389/fmicb.2017.00695
Kleist S, Ulbrich M, Bill N, Schmidt-Hohagen K, Geffers R, Schomburg D (2017) Dealing with salinity extremes and nitrogen limitation - an unexpected strategy of the marine bacterium Dinoroseobacter shibae. Environ Microbiol 19: 894–908. doi:10.1111/1462-2920.13266.
Meier-Kolthoff JP, Göker M. (2017) Genome-based phylogeny and classification of bacteriophages. Bioinformatics, accepted.
Milici M, Vital M, Tomasch J, Badewien TH, Giebel H-A, Plumeier I, Wang H, Pieper DH, Wagner-Döbler I, Simon M. (2017) Diversity and community composition of particle-associated and free-living bacteria in mesopelagic and bathypelagic Southern Ocean water masses: evidence of dispersal limitation in the Bransfield strait. Limnol Oceanogr 62: 1080-1095.
Petersen J, Wagner-Döbler I (2017) Plasmid transfer in the ocean - a case study from the Roseobacter group. Front Microbiol, accepted.
Pohlner M, Marshall I, Schreiber L, Cypionka H, Engelen B (2017) Draft genome sequence of Pseudoruegeria str. SK021, a representative of the marine Roseobacter group, isolated from North Sea sediment. Genome Anouncements (in press).
Ruppersberg HS, Goebel MR, Kleinert SI, Wünsch D, Trautwein K, Rabus R (2017) Photometric determination of ammonium and phosphate in seawater medium using a microplate reader. J Mol Microbiol Biotechnol 27:73-80
Schneider D, Wemheuer F, Pfeiffer B, Wemheuer B (2017) Extraction of total DNA and RNA from marine filter samples and generation of a universal cDNA as universal template for marker gene studies. Methods in Molecular Biology 1539:13-22.
Shang Y, Sikorski J, Bonkowski M, Fiore-Donno A-M, Kandeler E, Boeddinghaus R, Marhan S, Solly E, Schrumpf M, Schöning I, Tesfaye W, Buscot F, Overmann J (2017) Inferring interactions in complex microbial communities from nucleotide sequence data and environmental parameters. PLoS One 12: e0173765. https://doi.org/10.1371/journal.pone.0173765
Simon C, Daniel R (2017) Construction of small-insert and large-insert metagenomic libraries. Methods in Molecular Biology 1539:1-12
Simon M, Scheuner C, Meier-Kolthoff JP, Brinkhoff T, Wagner-Döbler I, Ulbrich M, Klenk HP, Schomburg D, Petersen J, Göker M. (2017) Phylogenomics of Rhodobacteraceae reveals evolutionary adaptation to marine and non-marine habitats. ISME 11: 1483-1499.
Trautwein K, Feenders C, Hulsch R, Ruppersberg HS, Strijkstra A, Kant M, Vagts J, Wünsch D, Michalke B, Maczka M, Schulz S, Hillebrand H, Blasius B, Rabus R (2017) Non-Redfield, nutrient synergy, and flexible internal elemental stoichiometry in a marine bacterium. FEMS Microbiol Ecol doi: 10.1093/femsec/fix059
Will SE, Neumann-Schaal M, Heydorn RL, Bartling P, Petersen J, Schomburg D (2017) The limits to growth – energetic burden of the endogenous tropodithietic acid in Phaeobacter inhibens DSM 17395. PLoS ONE 12(5): e0177295. https://doi.org/10.1371/journal.pone.0177295 .
Wöhlbrand L, Wemheuer B, Feenders C, Ruppersberg HS, Hinrichs C, Blasius B, Daniel R, Rabus R (2017a) Complementary metaproteomic approaches to assess the bacterioplankton response toward a phytoplankton spring bloom in the Southern North Sea. Front Microbiol 8:442
Wöhlbrand L, Rabus R, Blasius B, Feenders C (2017b) Influence of nanoLC column- and gradient-length as well as MS/MS frequency and sample complexity on shotgun protein identification of marine bacteria. J Mol Microbiol Biotechnol accepted
Billerbeck S, Wemheuer B, Voget S, Poehlein A, Giebel HA, Brinkhoff T, Gram L, Jeffrey WH, Daniel R, Simon M (2016) Biogeography and environmental genomics of the Roseobacter group affiliated pelagic CHAB-I-5 lineage. Nature Microbiol. 1: Article no. 16063 (DOI: 10.1038/NMICROBIOL.2016.63).
Crenn K, Serpin D, Lepleux C, Spröer C, Bunk B, Overmann J, Jeanthon C (2016) Silicimonas algicola gen. nov., sp. nov., a novel member of the Roseobacter clade isolated from the cell surface of the marine diatom Thalassiosira delicatula. Int. J. Syst. Evol. Microbiol. 66: 4580-4588
Giebel HA, Klotz F, Voget S, Poehlein A, Grosser K, Teske A, Brinkhoff T (2016) Draft genome sequence of the marine Rhodobacteraceae strain O3.65, cultivated from oil-polluted seawater of the Deepwater Horizon oil spill. Stand Genomic Sci 11:81-93.
Gomez-Consarnau L, Gonzalez JM, Riedel T, Jaenicke S, Wagner-Döbler I, Sanudo-Wilhelmy SA, Fuhrman JA (2016) Proteorhodopsin light-enhanced growth linked to vitamin-B1 acquisition in marine Flavobacteria. ISME J 10: 1102-1112. ismej2015196 [pii];10.1038/ismej.2015.196 [doi].
Kanukollu S, Voget S, Pohlner M, Vandieken V, Petersen J, Kyrpides NC, Woyke T, Shapiro N, Göker M, Klenk H-P, Cypionka H, Engelen B (2016) Genome sequence of Shimia sp. SK013, a representative of the Roseobacter group isolated from marine sediment. Standards in Genomic Sciences 11: 25 (doi:10.1186/s40793-016-0143-0).
Kanukollu S, Wemheuer B, Herber J, Billerbeck S, Lucas J, Daniel R, Simon M, Cypionka H, Engelen B (2016) Distinct compositions of free-living, particle-associated and benthic communities of the Roseobacter group in the North Sea. FEMS Microbiol Ecol. 92/1: fiv145, doi: 10.1093/femsec/fiv145.
Lucas J, Koester I, Wichels A, Niggemann J, Dittmar T, Callies U, Wiltshire KH, Gerdts G (2016) Short-term dynamics of North Sea bacterioplankton-dissolved organic matter coherence on molecular level. Front Microbiol 7: 321.
Michael V, Frank O, Bartling P, Scheuner C, Göker M, Brinkmann H, Petersen J. (2016) Biofilm plasmids with a rhamnose operon are widely distributed determinants of the “swim-or-stick” lifestyle in roseobacters. ISME J 10: 2498-2513.
Milici M, Deng ZL, Tomasch J, Decelle J, Wos-Oxley ML, Wang H, Jauregui R, Plumeier I, Giebel HA, Badewien TH, Wurst M, Pieper DH, Simon M, Wagner-Döbler I (2016) Co-occurrence Analysis of Microbial Taxa in the Atlantic Ocean Reveals High Connectivity in the Free-Living Bacterioplankton. Front Microbiol 7: 649. 10.3389/fmicb.2016.00649 [doi].
Milici M, Tomasch J, Wos-Oxley M, Decelle J, Jáuregui R, Wang H, Deng ZL, Plumeier I, Giebel HA, Badewien T, Wurst M, Pieper DH, Simon M, Wagner-Doebler I (2016) Bacterioplankton biogeography in the Atlantic Ocean: a case study of the distance-decay relationship. Frontiers Microbiol. 7: Article 570.
Milici M, Tomasch J, Wos-Oxley ML, Wang H, Jauregui R, Camarinha-Silva A, Deng ZL, Plumeier I, Giebel HA, Wurst M, Pieper DH, Simon M, Wagner-Döbler I (2016) Low diversity of planktonic bacteria in the tropical ocean. Sci Rep 6: 19054. srep19054 [pii];10.1038/srep19054 [doi].
Mitulla M, Dinasquet J, Guillemette R, Simon M, Azam F, Wietz M (2016) Response of bacterial communities from California coastal waters to alginate particles and an alginolytic Alteromonas macleodii strain. Environ Microbiol 18: 4369–4377 (doi:10.1111/1462-2920.13314).
Moran MA, Kujawinski EB, Stubbins A, Fatland R, Aluwihare LI, Buchan A, Crump BC, Dorrestein PC, Dyhrman ST, Hess NJ, Howe B, Longnecker K, Medeiros PM, Niggemann J, Obernosterer I, Repeta DJ, Waldbauer JR (2016) Deciphering ocean carbon in a changing world. PNAS 113: 3143-3151.
Osterholz H, Singer G, Wemheuer B, Daniel R, Simon M, Niggemann J, Dittmar T (2016) Deciphering associations between dissolved organic molecules and bacterial communities in a pelagic marine system. ISME J 7: 1717-1730.
Overmann J, Lepleux C (2016) Marine Bacteria and Archaea: Diversity, Adaptations, and Culturability. In: Stal LJ, and Cretoiu MS (eds.) The Marine Microbiome. Chapter 2. Springer International Publishing, Switzerland. p. 21- 55
Patzelt D, Michael V, Päuker O, Ebert M, Tielen P, Jahn D, Tomasch J, Petersen J, Wagner-Döbler I (2016) Gene flow across genus barriers - Conjugation of Dinoroseobacter shibae’s 191-kb killer plasmid into Phaeobacter inhibens and AHL-mediated expression of type IV secretion systems. Front Microbiol 7: 742.
Segev E, Wyche TP, Kim KH, Petersen J, Ellebrandt C, Vlamakis H, Barteneva N, Pauson JN, Chai L, Clardy J, Kolter R (2016) Dynamic metabolic exchange governs a marine algal-bacterial interaction. eLife 5: e17473.
Trautwein K, Will SE, Hulsch R, Maschmann U, Wiegmann K, Hensler M, Michael V, Ruppersberg H, Wünsch D, Feenders C, Neumann-Schaal M, Kaltenhäuser S, Ulbrich M, Schmidt-Hohagen K, Blasius B, Petersen J, Schomburg D, Rabus R (2016) Native plasmids restrict growth of Phaeobacter inhibens DSM 17395. Energetic costs of plasmids assessed by quantitative physiological analyses. Environ Microbiol 18: 4817-4829.
Wagner-Döbler I (2016) Biofilm transplantation in the deep sea. Mol Ecol 25: 1905-1907. 10.1111/ mec.13612 [doi].
Wichmann H, Brinkhoff T, Simon M, Richter-Landsberg C (2016) Dimethylsulfoniopropionate promotes process outgrowth in neural cells and exerts protective effects against tropodithietic acid. Marine Drugs 14: 89 (doi:10.3390/md14050089).
Widderich N, Kobus S, Höppner A, Riclea R, Seubert A, Dickschat JS, Heider J, Smits SHJ, Bremer E (2016b) Biochemistry and Crystal Structure of Ectoin Synthase: a Metal-Containing Member of the Cupin Superfamily. PLoS ONE 11:e0151285.
Widderich N, Czech L, Elling FJ, Könneke M, Stöveken N, Pittelkow M, Riclea R, Dickschat JS, Heider J, Bremer E (2016a) Strangers in the archaeal world: Osmostress-responsive biosynthesis of ectoine and hydroxyectoine by the marine thaumarchaeon Nitrosopumilus maritimus. Environ Microbiol 18:1227-1248.
Zhan Y, Huang S, Voget S, Simon M, Chen F (2016) A novel Roseobacter phage possesses features of podoviruses, siphoviruses, prophages and gene transfer agents. Scientific Reports 6: 30372 (DOI: 10.1038/srep30372).
Ashauer KP, Wemheuer B, Daniel R, Meinicke P (2015) Tax4Fun: predicting functional profiles from metagenomics 16S rRNA data. Bioinformatics 31:2882-2884
Billerbeck S, Orchard J, Tindall BJ, Giebel HA, Brinkhoff T, Simon M (2015) Description of Octadecabacter temperatus sp. nov., isolated from the southern North Sea, emended description of the genus Octadecabacter and reclassification of Octadecabacter jejudonensis Park & Yoon 2014 as Pseudooctadecabacter jejudonensis gen. nov., comb. nov. Internat J System Evol Microbiol 65: 1967–1974.
Broy S, Chen C, Hoffmann T, Brock NL, Nau-Wagner G, Jebbar M, Smits SHJ, Dickschat JS, Bremer E (2015) Abiotic Stress Protection by Ecologically Abundant DMSP and its Natural and Synthetic Derivatives: Insights from Bacillus subtilis. Environ Microbiol 17:2362-2378.
Dickschat JS, Rabe P, Citron C (2015) The chemical biology of dimethylsulfoniopropionate. Org Biomol Chem 13:1954-1968.
Frank O, Göker M, Pradella S, Petersen J (2015) Ocean's twelve: Flagellar and biofilm chromids in the multipartite genome of Marinovum algicola DG898 exemplify functional compartmentalization. Environmental Microbiology 17: 4019-4034 (doi:10.1111/1462-2920.12947).
Frank O, Michael V, Päuker O, Boedeker C, Jogler C, Rohde M, Petersen J (2015) Plasmid curing and the loss of grip - The 65-kb replicon of Phaeobacter inhibens DSM 17395 is required for biofilm formation, motility and the colonization of marine algae. Syst Appl Microbiol 38: 120–127.
Gram L, Rasmussen B, Wemheuer B, Bernbom N, Yin Ng Y, Porsby CH, Breider S, Brinkhoff T (2015) Phaeobacter inhibens from the Roseobacter-clade has an environmental niche as surface colonizer in harbours. Syst Appl Microbiol 7: 483-493.
Hofner B, Boccuto L, Göker M (2015) Controlling false discoveries in high-dimensional situations: Boosting with stability selection. BMC Bioinformatics 16: 144 (doi:10.1186/s12859-015-0575-3).
Klingner A, Bartsch A, Dogs M, Wagner-Döbler I, Jahn D, Simon M, Brinkhoff T, Becker J, Wittmann C (2015) Large-scale 13C flux profiling reveals conservation of the Entner-Doudoroff pathway as a glycolytic strategy among marine bacteria that use glucose. Appl Environ Microbiol 81/7: 2408-2422.
Lau SC, Riedel T, Fiebig A, Han J, Huntemann M, Petersen J, Ivanova NN, Markowitz V, Woyke T, Göker M, Kyrpides NC, Klenk H-P, Qian P-Y (2015) Genome sequence of the pink-pigmented marine bacterium Loktanella hongkongensis type strain (UST950701-009PT), a representative of the Roseobacter group. Stand Genomic Sci 10: 51.
Neumann AM, Balmonte JP, Berger M, Giebel HA, Arnosti C, Voget S, Simon M, Brinkhoff T, Wietz M (2015) Different utilization of alginate and other algal polysaccharides by marine Alteromonas macleodii ecotypes. Environ Microbiol 17/10: 3857-3868.
Osterholz H, Niggemann J, Giebel H-A, Simon M, Dittmar T (2015) Inefficient microbial production of refractory dissolved organic matter in the ocean. Nature Commun 6: 7422.
Riedel T, Spring S, Fiebig A, Scheuner C, Petersen J, Göker M (2015) Genome sequence of the Roseovarius mucosus type strain (DSM 17069T), a bacteriochlorophyll a -containing representative of the marine Roseobacter group isolated from the dinoflagellate Alexandrium ostenfeldii. Stand Genomic Sci 10: 17.
Schulz S, Hötling S (2015) The use of the lactone motif in chemical communication. Nat Prod Rep 32:1042–1066.
Soora M, Tomasch J, Wang H, Michael V, Petersen J, Engelen B, Wagner-Döbler I, Cypionka H (2015) Oxidative stress and starvation in Dinoroseobacter shibae: The role of extrachromosomal elements. Front Microbiol 6: 233.
Voget S, Billerbeck, Simon, M, Daniel R (2015). Closed genome sequence of Octadecabacter temperatus SB1, the first mesophilic species of the genus Octadecabacter. Genome Announc 3(5): e01051-15. doi:10.1128/genomeA.01051-15.
Voget S, Bruns H, Wagner-Döbler I, Schulz S, Daniel R (2015) Draft Genome Sequence of Roseovarius tolerans EL-164, a Producer of N-Acylated Alanine Methyl Esters and N-Acylhomoserine Lactones. Genome Announcement 3(5):15.
Voget S, Valerio SMD, von Hoyningen-Huene AJE, Nattramilarasu PK, Vollheyde K, Xiao S, Daniel R (2015) Genome sequence of Jannaschia aquimarina GSW-M26, a member of the Roseobacter clade. Genome Announcements 3:e00353-15
Voget S, Wemheuer B, Brinkhoff T, Vollmers J, Dietrich S, Giebel HA, Beardsley C, Sardemann C, Bakenhus I, Billerbeck S, Daniel R, Simon M (2015) Adaptation of an abundant Roseobacter RCA organism to pelagic systems revealed by genomic and transcriptomic analyses. ISME J 9: 371-384.
Wang H, Tomasch J, Michael V, Bhuju S, Jarek M, Petersen J, Wagner-Döbler I (2015) Identification of genetic modules mediating the Jekyll and Hyde interaction of Dinoroseobacter shibae with the dinoflagellate Prorocentrum minimum. Front Microbiol 6: 1262.
Wemheuer B, Wemheuer F, Hollensteiner J, Meyer F-D, Voget S, Daniel R (2015) The green impact: bacterioplankton response towards a phytoplankton spring bloom in the southern North Sea assessed by comparative metagenomic and metatranscriptomic approaches. Front. Microbiol. 6:805.
Wichmann H, Vocke F, Brinkhoff T, Simon M, Richter-Landsberg C (2015) Cytotoxic effects of tropodithietic acid on mammalian clonal cell lines of neuronal and glial origin. Marine Drugs 13: 7113–7123.
Wietz M, Wemheuer B, Simon H, Giebel HA, Seibt MA, Daniel R, Brinkhoff T, Simon M (2015) Polysaccharides initiate distinct responses of bacterial communities from the Southern and Atlantic Oceans. Environ Microbiol 17/10: 3822-3831.
Ziesche L, Bruns H, Dogs M, Wolter L, Mann F, Wagner-Döbler I, Brinkhoff T, Schulz S (2015) Homoserine lactones, methyl oligohydroxybutyrates and other extracellular metabolites of macroalgae associated bacteria of the Roseobacter clade: Identification and function. ChemBioChem. 16: 2094-2107.
Breider S, Scheuner C, Schumann P, Fiebig A, Petersen J, Pradella S, Klenk H-P, Brinkhoff T, Göker M (2014) Genome-scale data suggest reclassifications in the Leisingera-Phaeobacter cluster including proposals for Sedimentitalea gen. nov. and Pseudophaeobacter gen. nov. Front Microbiol 5: 416.
Breider S, Teshima H, Petersen J, Fiebig A, Chertkov O, Dalingault H, Chen A, Pati A, Goodwin LA, Chain P, Detter JC, Ivanova NN, Lapidus A, Rohde M, Tindall BJ, Kyrpides NC, Woyke T, Simon M, Göker M, Klenk HP, Brinkhoff T (2014) Complete genome sequence of Leisingera nanhaiensis strain DSM 24252T isolated from marine sediment. Standards in Genomic Sciences 9: 687-703 (doi:10.4056/sigs.3828824).
Brock NL, Nikolay A, Dickschat JS (2014) Biosynthesis of the Antibiotic Tropodithietic Acid by the Marine Bacterium Phaeobacter inhibens. ChemComm 50:5487-5489.
Brock NL, Menke M, Klapschinski TA, Dickschat H (2014) Marine bacteria from the Roseobacter clade produce sulfur volatiles via amino acid and dimethylsulfoniopropionate catabolism. Org Biomol Chem 12: 4318-4323.
Drüppel K, Hensler M, Trautwein K, Koßmehl S, Wöhlbrand L, Schmidt-Hohagen K, Ulbrich M, Bergen N, Meier-Kolthoff JP, Göker M, Klenk H-P, Schomburg D, Rabus R (2014) Pathways and substrate-specific regulation of amino acid degradation in Phaeobacter inhibens DSM 17395 (archetype of the marine Roseobacter clade). Environ Microbiol 16: 218–238. doi:10.1111/1462-2920.12276.
Frank O, Pradella S, Rohde M, Scheuner C, Klenk H-P, Göker M, Petersen J (2014) Complete genome sequence of the Phaeobacter gallaeciensis type strain CIP 105210T (= DSM 26640T = BS107T). Stand Genomic Sci 9: 914–932.
Laass S, Kleist S, Bill N, Drüppel K, Kossmehl S, Wöhlbrand L, Rabus R, Klein J, Rohde M, Bartsch A, Wittmann C, Schmidt-Hohagen K, Tielen P, Jahn D, Schomburg D (2014) Gene regulatory and metabolic adaptation processes of Dinoroseobacter shibae DFL12T during oxygen depletion. J Biol Chem 289: 13219–13231. doi:10.1074/jbc.M113.545004.
Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M (2014) Highly parallelized inference of large genome-based phylogenies. Concurrency and Computation: Practice and Experience 26: 1715-1729 (doi:10.1002/cpe.3112
Petersen J, Ludewig AK, Michael V, Bunk B, Jarek M, Baurain D, Brinkmann H (2014) Chromera velia, endosymbioses and the Rhodoplex hypothesis - Plastid evolution in cryptophytes, alveolates, stramenopiles, and haptophytes (CASH lineages). Genome Biol Evol 6: 666–684.
Rabe P, Klapschinski TA, Brock NL, Citron CA, D'Alvise P, Gram L, Dickschat JS (2014) Synthesis and Bioactivity of Analogs of the Marine Antibiotic Tropodithietic Acid. Beilstein J Org Chem 10: 1796-1801.
Riedel T, Fiebig A, Han J, Huntemann M, Spring S, Petersen J, Ivanova NN, Markowitz V, Woyke T, Göker M, Kyrpides NC, Klenk H-P (2014b) Genome sequence of the Wenxinia marina type strain (DSM 24838T), a representative of the Roseobacter group isolated from oilfield sediments. Stand Genomic Sci 9: 855–865.
Riedel T, Spring S, Fiebig A, Petersen J, Göker M, Klenk H-P. (2014a) Genome sequence of the pink to light reddish-pigmented Rubellimicrobium mesophilum type strain (DSM 19309T), a representative of the Roseobacter group isolated from soil, and emended description of the species. Stand Genomic Sci 9: 902–913.
Riedel T, Spring S, Fiebig A, Petersen J, Kyrpides NC, Göker M, Klenk H-P (2014c) Genome sequence of the exopolysaccharide-producing Salipiger mucosus type strain (DSM 16094T), a moderately halophilic member of the Roseobacter clade. Stand Genomic Sci 9: 1331–1343.
Roselius, L., Langemann, D., Müller, J., Hense, B., Filges, S., Jahn, D. & Münch, R. (2014) Modeling and analysis of a gene-regulatory feed-forward loop with basal expression of the second regulator. J Theoret Biol., 363:290–299
Wang H, Tomasch J, Jarek M, Wagner-Döbler I (2014) A dual-species co-cultivation system to study the interactions between Roseobacters and dinoflagellates. Front Microbiol 5: 311. 10.3389/ fmicb.2014.00311 [doi].
Wang H, Ziesche L, Frank O, Michael V, Martin M, Petersen J, Schulz S, Wagner-Döbler I, Tomasch J (2014) The CtrA phosphorelay integrates differentiation and communication in the marine alphaproteobacterium Dinoroseobacter shibae. BMC Genomics 15: 130.
Wemheuer B, Güllert S, Billerbeck S, Giebel H-A, Voget S, Simon M, Daniel R (2014) Impact of a phytoplankton bloom on the diversity of the active bacterial community in the southern North Sea as revealed by metatranscriptomic approaches. FEMS Microbiol Ecol 87: 378-389 (DOI: 10.1111/1574-6941.12230).
Wiegmann K, Hensler M, Wöhlbrand L, Ulbrich M, Schomburg D, Rabus R (2014) Carbohydrate catabolism in Phaeobacter inhibens DSM 17395, member of the marine Roseobacter clade. Appl Environ Microbiol 80:4725-4737
Beyersmann PG, Chertkov O, Petersen J, Fiebig A, 11 co-authors, Simon M, Göker M, Klenk HP, Brinkhoff T (2013) Genome sequence of Phaeobacter caeruleus type strain (DSM 24564T), a surface-associated member of the marine Roseobacter clade. Stand Genomic Sci 8: 403-419.
Breider S, Teshima H, Petersen J, Fiebig A, 12 co-authors, Simon M, Göker M, Klenk HP, Brinkhoff T (2013) Complete genome sequence of Leisingera nanhaiensis strain DSM 24252T isolated from marine sediment. Stand Genomic Sci, 9: 687-703.
Brock NL, Citron CA, Zell C, Berger M, Wagner-Döbler I, Petersen J, Brinkhoff T, Simon M, Dickschat JS (2013) Isotopically Labeled Sulfur Compounds and Synthetic Selenium and Tellurium Analogs to Study Sulfur Metabolism in Marine Bacteria. Beilstein J Org Chem 9:942-950.
Bruns H, Thiel V, Voget S, Patzelt H, Daniel R, Wagner-Döbler I, Schulz S (2013) N-Acylated Alanine Methyl Esters from Roseovarius tolerans, Structural Analogs of Quorum-Sensing Autoinducers, N-Acylhomoserine Lactones. Chem Biodiversity: 10/9: 1559-1573.
Buddruhs N, Chertkov O, Fiebig A, Petersen J, 10 co-authors, Göker M, Brinkhoff T, Klenk HP (2013) Complete genome sequence of the marine methyl-halide oxidizing Leisingera methylohalidivorans type strain (DSM 14336T), a member of the Roseobacter clade. Stand Genomic Sci, 9(1):128-41 (doi: 10.4056/sigs.4297965).
Buddruhs N, Pradella S, Göker M, Päuker O, Michael V, Pukall R, Spröer C, Schumann P, Petersen J, Brinkhoff T (2013) Biological non-identity of Phaeobacter gallaeciensis type-strain deposits revealed by sequence and phenotypic analysis. Int J Syst Evol Microbiol 63: 4340-4349.
Dogs M, Teshima H, Petersen J, Fiebig A, 13 co-authors, Simon M, Klenk HP, Göker M, Brinkhoff T (2013) Genome sequence of Phaeobacter daeponensis type strain (DSM 23529T), a facultatively anaerobic bacterium isolated from marine sediment, and emendation of Phaeobacter daeponensis. Stand Genomic Sci 9: 142-159.
Dogs M, Voget S, Teshima H, Petersen J, Fiebig A, 12 co-authors, Simon M, Klenk HP, Göker M, Brinkhoff T (2013) Genome sequence of Phaeobacter inhibens type strain (T5T), a secondary-metabolite producing member of the marine Roseobacter clade, and emendation of the species Phaeobacter inhibens. Stand Genomic Sci, 9: 334-350 DOI:10.4056/sigs.4448212).
Ebert M, Laaß S, Burghartz M, Petersen J, Rabus R, Wöhlbrand L, Tielen P, Jahn D. (2013) Chromosomal and plasmid encoded genes are essential for the anaerobic growth of the marine bacterium Dinoroseobacter shibae. J.Bacteriol, 195/20: 4769-4777.
Fiebig A, Pradella S, Petersen J, Michael V, Päuker O, Rohde M, Göker M, Klenk HP, Wagner-Döbler I (2013b) Genome of the marine alphaproteobacterium Hoeflea phototrophica type strain (DFL-43T). Stand Genomic Sci 7:440-444.
Fiebig A, Pradella S, Petersen J, Päuker O, Michael V, Lünsdorf H, Göker M, Klenk HP, Wagner-Döbler I (2013a). Genome of the R-body producing marine alphaproteobacterium Labrenzia alexandrii type strain (DFL-11T). Stand Genomic Sci 7: 413-426.
Freese H, Dalingault H, Petersen J, Pradella S, Fiebig A, 12 co-authors, Brinkhoff T, Göker M, Overmann J, Klenk HP (2013) Genome sequence of the phage-gene rich marine Phaeobacter arcticus type strain DSM 23566T. Stand Genomic Sci 8(3): 450–464.
Giebel HA, Kalhoefer D, Gahl-Janssen R, Choo YJ, Lee K, Cho JC, Tindall BJ, Rhiel E, Beardsley C, Aydogmus ÖO, Voget S, Daniel R, Simon M, Brinkhoff T (2013) Planktomarina temperata gen. nov., sp. nov., belonging to the globally distributed RCA cluster of the marine Roseobacter clade, isolated from the German Wadden Sea. Int J System Evol Microbiol, 63: 4207–4217.
Göker M, Klenk HP (2013) Phylogeny-driven target selection for genome-sequencing (and other) projects. Stand Genomic Sci, 8(2): 360–374.
Groenhagen U, Baumgartner R, Bailly A, Gardiner A, Eberl L, Schulz S, Weisskopf L (2013) Production of bioactive volatiles by various Burkholderia ambifaria strains. J. Chem. Ecol: 39/10: 1343-1345
Hahnke S, Brock NL, Zell C, Simon M, Dickschat JS, Brinkhoff T (2013) Physiological diversity of Roseobacter clade bacteria co-occurring during a phytoplankton bloom in the North Sea. Syst Appl Microbiol 36:39-48.
Hahnke S, Sperling M, Langer T, Wichels A, Gerdts G, Beardsley C, Brinkhoff T, Simon M (2013b) Distinct seasonal growth patterns of the bacterium Planktotalea frisia in the North Sea and specific interactions with phytoplankton algae. FEMS Microbiol Ecol, 86: 185-199.
Kielkowsky P, Brock NL, Dickschat JS, Hocek M (2013) Nucleobase Protection Strategy for Gene Cloning and Expression. ChemBioChem, 14:801-804.
Koßmehl S, Wöhlbrand L, Drüppel K, Feenders C, Blasius B, Rabus R (2013) Subcellular protein localization (cell envelope) in Phaeobacter inhibens DSM 17395. Proteomics 13/18-19 SI: 2743-2760
Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 14: 60.
Neumann A, Patzelt, D, Wagner-Döbler, I, Schulz, S. (2013). Identification of New N-Acylhomoserine Lactone Signalling Compounds of Dinoroseobacter Shibae DFL-12 by Overexpression of LuxI Genes. Chembiochem 14/17: 2355-2361.
Patzelt, D., Wang, H., Buchholz, I., Rohde, M., Gröbe, L., Pradella, S., Neumann, A., Schulz, S., Heyber, S., Münch, K., Münch, R., Jahn, D. ,Wagner-Döbler, I. & Tomasch, J. 2013. You are what you talk: Quorum sensing induces individual morphologies and cell division modes in Dinoroseobacter shibae. ISME J 12: 2274-2286.
Penesyan A, Breider S, Schumann P, Tindall BJ, Egan S, Brinkhoff T (2013) Epibacterium ulvae gen. nov., sp. nov., epibiotic bacteria isolated from the surface of a marine alga. Int J Syst Evol Microbiol 63: 1589 - 1596.
Petersen J, Frank O, Göker M, Pradella S (2013) Extrachromosomal, extraordinary and essential--the plasmids of the Roseobacter clade. Appl Microbiol Biotechnol 97: 2805-2815.
Rabus R (2013) Environmental Microbial Proteomics: New avenues for a molecular understanding of the functional role of microorganisms in the natural environment. Proeomics 13/18-19 SI: 2697-2699.
Rex R, Bill N, Schmidt-Hohagen K, Schomburg D (2013) Swimming in light: A large-scale computational analysis of the metabolism of Dinoroseobacter shibae.PLOS Comp Biol, 9/10 Article e1003224.
Riedel T, Fiebig A, Petersen J, Gronow S, Göker M, Klenk HP (2013a) Genome sequence of the Litoreibacter arenae type strain (DSM 19593T), a member of the Roseobacter clade isolated from sea sand. Stand Genomic Sci, 9(1): 117–127..
Riedel T, Gomez-Consarnau L, Tomasch J, Martin M, Jarek M, Gonzalez JM, Spring S, Rohlfs M, Brinkhoff T, Cypionka H, Göker M, Fiebig A, Klein J, Goesmann A, Fuhrman JA, Wagner-Döbler I. 2013a. Genomics and physiology of a marine flavobacterium encoding a proteorhodopsin and a xanthorhodopsin-like protein. PLoS One 8:e57487.
Riedel T, Rohlfs M, Buchholz I, Wagner-Döbler I, Reck M. 2013b. Complete sequence of the suicide vector pJP5603. Plasmid 69:104-107.
Riedel T, Teshima H, Petersen J, Fiebig A, 16 co-authors, Göker M, Brinkhoff T, Klenk HP (2013c) Genome sequence of the Leisingera aquimarina type strain (DSM 24565T), a member of the marine Roseobacter clade rich in extrachromosomal elements. Stand Genomic Sci, 8: (3):389-402.
Riemer SA, Rex R, Schomburg D (2013) A metabolite-centric view on flux distributions in genome-scale metabolic models. BMC Syst Biol 7: 33.
Soora M, Cypionka H (2013) Light enhances survival of Dinoroseobacter shibae during long-term starvation. PLoS ONE 8:e83960. doi:10.1371/journal.pone.0083960
Spring S, Riedel T, Spröer K, Yan S, Harder J, Fuchs BM. 2013. Taxonomy and evolution of bacteriochlorophyll a-containing members of the OM60/NOR5 clade of marine gammaproteobacteria: Description of Luminiphilus syltensis gen. nov., sp. nov., reclassification of Haliea rubra as Pseudohaliea rubra gen. nov., comb. nov., and emendation of Chromatocurvus halotolerans. BMC Microbiol 13: Article Number: UNSP 118.
Spring S, Riedel T. 2013. Mixotrophic growth of bacteriochlorophyll a-containing members of the OM60/NOR5 clade of marine gammaproteobacteria is carbon-starvation independent and correlates with the type of carbon source and oxygen availability. BMC Microbiol 13: Article number 117.
Vaas LAI, Sikorski J, Hofner B, Buddruhs N, Fiebig A, Klenk HP, Göker M (2013) opm: An R package for analysing OmniLog® Phenotype MicroArray Data. Bioinformatics, 29(14):1823-4.
Vollmers J, Voget S, Dietrich S, Gollnow K, Smits M, Meyer K, Brinkhoff T, Simon M, Daniel R (2013) Poles apart: arctic and antarctic Octadecabacter strains share high genome plasticity and a new type of xanthorhodopsin. PLoS One 8:e63422.
Wöhlbrand L, Trautwein K, Rabus R (2013) Proteomic tools for environmental microbiology – a roadmap from sample preparation to protein identification and quantification. Proteomics 13/18-19 SI: 2700-2730
Zech H, Echtermeyer C, Wöhlbrand L, Blasius B, Rabus R (2011) Biological versus technical variability in 2D DIGE experiments with environmental bacteria. Proteomics 11: 3380-3399.
Zech H, Hensler M, Koßmehl S, Drüppel K, Wöhlbrand L, Trautwein K, Hulsch R, Maschmann U, Colby T, Schmidt J, Reinhardt R, Schmidt-Hohagen K, Schomburg D, Rabus R (2013a) Adaptation of Phaeobacter gallaeciensis DSM 17395 to growth with complex nutrients. Proteomics doi:10.1002/pmic.201200513
Zech H, Hensler M, Koßmehl S, Drüppel K, Wöhlbrand L, Trautwein K, Colby T, Schmidt J, Reinhardt R, Schmidt-Hohagen K, Schomburg D, Rabus R (2013b) Dynamics of amino acid utilization in Phaeobacter inhibens DSM 17395. Proteomics doi:10.1002/pmic.201200560.
Berger M, Brock NL, Liesegang H, Dogs M, Preuth I, Simon M, Dickschat JS, Brinkhoff T (2012) Genetic analysis of the upper phenylacetate catabolic pathway in the production of tropodithietic acid by Phaeobacter gallaeciensis. Appl Environ Microbiol 78: 3539-3551.
Klein, J., Leupold, S., Biegler, I., Biedendieck, R., Münch, R. & Jahn D. (2012) TLM-Tracker: software for cell segmentation, tracking and lineage analysis in time-lapse microscopy movies. Bioinformatics 28:2276-2277.
Petersen J, Brinkmann H, Bunk B, Michael V, Päuker O, Pradella S (2012) Think pink: photosynthesis, plasmids and the Roseobacter clade. Environ Microbiol 14: 2661-2672.
Riclea R, Gleitzmann J, Bruns H, Junker C, Schulz B, Dickschat JS (2012) Algicidal Lactones from the Marine Roseobacter Clade Bacterium Ruegeria pomeroyi. Beilstein J Org Chem 8:941-950.
Riedel T, … Rohde M, Tindall BJ, Göker M, Klenk HP, and 27 authors. 2012a. Genome sequence of the Antarctic rhodopsins-containing flavobacterium Gillisia limnaea type strain (R-8282T). Standards in Genomic Sciences 7:117-119.
Riedel T, … Rohde M, Tindall BJ, Göker M, Klenk HP, and 27 authors. 2012b. Genome sequence of the orange-pigmented sea-water bacterium Owenweeksia hongkongensis type strain (UST20020801 T ). Standards in Genomic Sciences 7:120-130.
Shevchuk, O., Roselius, L., Günther, G., Klein, J., Jahn, D., Steinert, M. & Münch R. (2012) InFiRe - a novel computational method for the identification of insertion sites in transposon mutagenized bacterial genomes. Bioinformatics 28:306-310.
Simon M, Billerbeck S, Kessler D, Selje N, Schlingloff A (2012) Bacterioplankton communities in the Southern Ocean:Composition and growth response to various substrate regimes. Aquat Microb Ecol 68:13–28.
Thole S, Kalhoefer D, Voget S, Berger M, Engelhardt T, Lliesegang H, Wollherr A, Kjelleberg S, Daniel R, Simon M, Thomas T, Brinkhoff T (2012) Phaeobacter gallaeciensis genomes from globally opposite locations reveal high similarity of adaptation to surface life. ISME Journal 6: 2229-2244.
Vaas LAI, Sikorski J, Michael V, Göker M, Klenk HP (2012) Visualization and curve-parameter estimation strategies for efficient exploration of Phenotype Microarray kinetics. PLoS ONE 7: e34846.
Wemheuer B, Wemheuer F, Daniel R (2012) RNA-based assessment of diversity and composition of active archaeal communities in the German Bight. Archaea 2012: 695826.
Bartsch, A., Bunk, B., Haddad, I., Klein, J., Münch, R., Johl, T., Kärst, U., Jänsch, L., Jahn, D., & Retter, I. (2011) GeneReporter-sequence-based document retrieval and annotation. Bioinformatics 27:1034-1035
Berger M, Neumann A, Schulz S, Simon M, Brinkhoff T (2011) Tropodithietic acid production in Phaeobacter gallaeciensis is regulated by N-acyl homoserine lactone-mediated quorum sensing. J. Bacteriol. 193: 6576–6585.
Jaramillo-Colorado B, Olivero-Verbel, J, Stashenko, EE, Wagner-Döbler, I, Kunze, B. (2011). Anti-Quorum Sensing Activity of Essential Oils From Colombian Plants. Nat Prod Res 26(12):1075-86.
Kalhoefer D, Thole S, Voget S, Lehmann R, Liesegang H, Wollher A, Daniel R, Simon M, Brinkhoff T (2011) Comparative genome analysis and genome-guided physiological analysis of Roseobacter litoralis. BMC Genomics. DOI: 10.1186/1471-2164-12-324.
Lemme A, Gröbe, L, Reck, M, Tomasch, J, Wagner-Döbler, I. (2011). Subpopulation-Specific Transcriptome Analysis of Competence-Stimulating-Peptide-Induced Streptococcus Mutans. J Bacteriol 193(8):1863-77.
Münch, R., Klein J. & Jahn D. (2011) Prediction and Analysis of Gene Regulatory Networks in Prokaryotic Genomes. (Yang N., Ed.).Systems and Computational Biology - Molecular and Cellular Experimental Systems. 149-162.
Petersen J (2011) Phylogeny and compatibility: plasmid classification in the genomics era. Arch Microbiol 193: 313-321.
Petersen J, Brinkmann H, Berger M, Brinkhoff T, Päuker O, Pradella S (2011) Origin and evolution of a novel DnaA-like plasmid replication type in Rhodobacterales. Mol Biol Evol 28: 1229-1240.
Simon C, Daniel R (2011) Metagenome analyses: past and future trends. Applied and Environmental Microbiology 77: 1153–1161.
Tomasch J, Gohl, R, Bunk, B, Diez, MS, Wagner-Döbler, I. (2011). Transcriptional Response of the Photoheterotrophic Marine Bacterium Dinoroseobacter Shibae to Changing Light Regimes. ISME J 5(12):1957-68.
Prof. Dr. Meinhard Simon
Carl von Ossietzky Universität Oldenburg
Biologie Geologischer Prozesse
+49-(0)441-798-5361
E-Mail: m.simon(at)icbm.de
Prof. Dr. Dieter Jahn
Technische Universität Braunschweig
Institut für Mikrobiologie
+49 531-391-55101
Email: d.jahn@tu-braunschweig.de
Katinka Hoppe
Carl von Ossietzky Universität Oldenburg
Institute for Chemistry and Biology of the Marine Environment (ICBM)
Carl von Ossietzky Str. 9-11 D-26129 Oldenburg
Tel.: +49(0)441-798 3306