Projekte

Principal investigators: Prof. Dr. Meinhard Simon, apl. Prof. Dr. Thorsten Brinkhoff

Post docs: Dr. Helge-Ansgar Giebel, Dr. Sara Billerbeck, Dr. Cristina Moraru

PhD students: Insa Bakenhus

Objective

The overall goal of this project is to elucidate the significance and function of the Roseobacter group in marine pelagic ecosystems of coastal and oceanic surface waters. During the first funding period we focus on the temperate, subpolar and polar zone and apply culture-dependent and culture-independent molecular approaches to assess the diversity and abundance, activity and functional response of relevant subclusters of this group.

The main research questions of project A1 are:

• What is the phylogenetic diversity of the Roseobacter group in pelagic ecosystems?
• What is the quantitative significance of this group and subclusters in these ecosystems and relative to other bacterioplankton groups?
• Are the Roseobacter subclusters and populations metabolically more active than other bacterioplankton groups and if so, under which environmental conditions?
• What are specific biogeochemical and metabolic functions of subclusters of this group in these ecosystems?
• What is the quantitative significance of Roseobacter-specific biogeochemical functions in pelagic ecosystems? (CO oxidase, AAP)
• Do specific interactions of distinct Roseobacter populations with distinct algal populations exist and if so, what kind of interactions?

Projects

• Biogeography of pelagic Roseobacter subcluster (S. Billerbeck, I. Bakenhus)
• Isolation and characterisation of pelagic Roseobacter strains (H.-A. Giebel / S. Billerbeck)
• Genome sequencing of pelagic roseobacters (H.-A. Giebel, S. Billerbeck, I. Bakenhus; in cooperation with project A3/Z02)
• Aerobic, anoxygenic photosynthesis in Planktomarina temperata (H.-A. Giebel)

Methods

• Sampling the water column and mesocosm experiments onboard different reserch vessels
• PCR with primers specific for the Roseobacter group and relevant subclusters to analyse their distribution in global oceans
• Cluster Analysis of DGGE gels to determine the diversity of the Roseobacter group
• 454 – Pyrosequencing / Illumina sequencing to get an insight in the diversity and abundance of Roseobacter subclusters (in cooperation with A3/Z02)
• (CARD-, MAR-, BrdU-) FISH for quantitative analyses on group or species level of bacteria or roseobacters and to link that to substrate specific activities
• Flow Cytometry is used for cell counting of bacterial and algal cells of in situ or culture samples and for analyses of their population dynamics
• Isolation of new pelagic roseobacters via dilution cultures with different minimal media
• Genome analysis of newly isolated roseobacters

Hydrographic and Biogeochemical parameters analysed during the cruises

• CTD (salinity, temperature, depth, fluorescence, turbidity)
• Chla, phaeopigments
• DOC, TDN, DOM
• Nutrients (NO_x,NO₂, PO₄, SiO₄)
• POC, PON
• Amino acids (DAA, TAA)
• Carbohydrates (DFCHO, TCHO)
• Phytoplankton quantitative
• Phytoplankton autofluorescence
• Bacterial cell numbers (live measurement onboard by flow cytometry)
• Bacterial DNA, RNA
• (CARD-/MAR-/BrdU-) FISH
• Grazing of specific bacterial groups
• Bacterial production, substrate turnover rates

Expeditions:

DateExpedition

26.01.-27.02.2017 RV Sonne (SO254), Southwest Pacific, Auckland (New Zealand) - Auckland (more information)

01.05.-03.06.2016 RV Sonne (SO248), Pacific transect, Auckland (New Zealand) - Dutch Harbour (Alaska)

23.05.-06-06.2014 RV Heincke (HE425), North Sea transect

10.4.-15.5.2012 RV Polarstern (ANT-XVIII/5), Atlantic transect, Punta Arenas (Chile) - Bremerhaven (Cruise report)

14.3.-9.4. 2012 RV Polarstern (ANT-XXVIII/4), Southern Ocean, Punta Arenas (Chile) - Antarctic Penninsula and back (Cruise report)

3.12.2011-5.1.2012 RV Polarstern (ANT-XXVIII/2), Southern Ocean, Kapstadt (South Afrika) - Neumeyer-Station and back (Cruise report)

12.-29.7. 2011 RV Heincke (HE361), North Sea transect

25.-31. 5. 2010 RV Heincke (HE327), German Bight

International Cooperations

• Prof. Jang-Cheon Cho, Inha University, Incheon, Korea
• Prof. Dr. Feng Chen, University of Maryland, Baltimore USA
• Dr. Sijun Huang, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
• Prof. Lone Gram, National Food Institute, Technical University of Denmark, Lyngby, Denmark
• Prof. Wade Jeffrey, Center for Environmental Diagnostics and Bioremediation, University of West Florida, Pensacola, United States of America

Bachelor, Master and PhD theses

• Klotz, Franziska (Master, 2016). Characterization of "Tritonibacter horizontis", isolated from seawater after the Deepwater Horizon oil spill.

• Billerbeck, Sara (PhD, 2016). The pelagic clusters of the Roseobacter group: Global distribution, genome analysis and physiological characterization.

• Dlugosch, Leon (Master, 2016). Bacterioplankton community composition and growth activity during early summer in the North Sea.

• Orchard, Julia (Master, 2014). Physiological Characterization of "Candidatus Octadecabacter temperatus" SB1.

• Jongmans, Elanor (Master, 2014). Phylogeny-based evaluation of pufM gene specific primer systems.

• Milke, Felix (Bachelor, 2014). Hydrographic, chemical and microbial characterization of the pelagic North Sea in early summer.

• Tran, Quoc Den (Master, 2014). Quantification of DNA-synthesizing cells in bacterial communities of the North Sea by BrdU-FISH.

• Hahnke, Sarah (PhD, 2012). Physiological characterization and molecular ecological investigation of diverse organisms of the Roseobacter clade isolated from the North Sea.

• Kalhöfer, Daniela (PhD, 2012). Genome analysis and comparative genomics of host-associated bacteria of the marine Roseobacter clade.

• Aydogmus, Ozan (Master, 2011). Development of specific molecular biological detection systems for a distinct population of a pelagic Roseobacter isolate (SH36).

• Bakenhus, Insa (Bachelor, 2011). Quantifizierung von aktiven Roseobacter spp. in der Nordsee mittels Bromodesoxyuridin Inkorporation und Fluoreszenz in situ Hybridisierung (BrdU-FISH).

• Wienhausen, Gerrit (Bachelor, 2011). Vorkommen von Untergruppen der Roseobacter-Gruppe in der Deutschen Bucht.

• Pockels, Lina (Bachelor, 2010). Biogeografische Verteilung der Gattung Roseobacter und Taurinverwertung durch Roseobacter litoralis.

Publications

2017

• Bakenhus I, Voget S, Poehlein A, Brinkhoff T, Daniel R, Simon M (2017). Genome sequence of Planktotalea frisia type strain (SH6-1^T), a representative of the Roseobacter group isolated from the North Sea during a phytoplankton bloom. Stand Gen Sci (submitted).

• 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.

• 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.

2016

• Billerbeck S, Wemheuer B, Voget S, Poehlein A, Giebel H-A, Brinkhoff T, Gram L, Jeffrey W H, Daniel R, Simon M (2016). Biogeography and environmental genomics of the Roseobacter-affiliated pelagic CHAB-I-5 lineage. Nat. Microbiol. Article 16063.

• 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.

• 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: Article fiv145.

• 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.

• Milici M, Deng1 ZL, Tomasch J, Decelle J, Wos-Oxley M, Wang H, Jáuregui R, Plumeier I, Giebel H-A, Badewien H, Wurst M, Pieper P, Simon M, Wagner-Doebler I (2016) Co-occurrence analysis of microbial taxa in the Atlantic Ocean reveals high connectivity in the free-living bacterioplankton. Frontiers Microbiol. 7: Article 649.

• Milici M, Tomasch J, Wos-Oxley M, Decelle J, Jáuregui R, Wang H, Deng ZL, Plumeier I, Giebel H-A, 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 590.

• Milici M, Tomasch J, Wos-Oxley ML, Wang H, Jáuregui R, Camarinha-Silva A, Deng ZL, Plumeier I, Giebel H-A, Wurst M, Pieper DH, Simon M, Wagner-Döbler I (2016) Low diversity of planktonic bacteria in the tropical ocean. Scientific Reports 6: Article 19054.

• 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, online first (doi:10.1111/1462-2920.13314).

• 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.

• 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). 

2015

• Billerbeck S, Orchard J, Tindall B J, Giebel H-A, 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. Int. J. Syst. Evol. Microbiol. 1967–1974.

• Voget S, Wemheuer B, Brinkhoff T, Vollmers J, Dietrich S, Giebel H-A, 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.

• Voget S, Billerbeck S, 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).

• 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.

• Neumann AM, Balmonte JP, Berger M, Giebel H-A, 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 Comm 6: 7422.

• Schwedt A, Seidel M, Dittmar T, Simon M, Bondarev V, Romano S, Lavik G, Schulz-Vogt HN (2015) Substrate use of Pseudovibrio sp. growing in ultraoligotrophic seawater, PLOS One, 10(3): e0121675 (doi:10.1371/journal.pone.0121675).

• Wietz M, Wemheuer B, Simon H, Giebel H-A, 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.

2014

• 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).

2013

• Hahnke S, Brock NL, Zell C, Simon M, Dickschat JS, Brinkhoff T (2013a). Physiological diversity of Roseobacter clade bacteria co-occurring during a phytoplankton bloom in the North Sea. System. 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.

• Giebel H-A, Kalhoefer D, Gahl-Janssen R, Choo YJ, Lee K, Cho JC, Tindall BJ, Rhiel E, Beardsley C, Aydogmus Ö O, 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. Inter. J. System. Evol. Microbiol. 63: 4207–4217.
• Vollmers J, Voget S, Dietrich S, Gollnow K, Smits M, Meyer K, Brinkhoff T, Simon M, Daniel R (2013) Poles apart: Extreme genome plasticity and a new xanthorhodopsin-like gene family in the genomes of Octadecabacter arcticus 238 and Octadecabacter antarcticus 307. PLoS One 8(5): e63422PLoS One.

2012

• 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.

2011

• Kalhoefer D, Thole S, Voget S, Lehmann R, Liesegang H, Wollher A, Daniel R, Simon M, Brinkhoff T (2011). Comparative genome analysis and enhanced physiological description of Roseobacter litoralis. BMC Genomics 12: 324.

Other Publications

• Beardsley C, 12 co-authors, Simon M (2012) The Roseobacter clade and the dissolved organic matter (DOM) composition in the Atlantic sector of the Southern Ocean. In: Kattner G (ed) The expedition of the Research Vessel "Polarstern" to the Antarctic in 2012 (ANT-XXVIII/2) Reports on Polar and Marine Research 646: 36-39.
• Simon M, and 13 co-authors (2012) In: Bumke K (ed) The expedition of the Research Vessel "Polarstern" to the Antarctic in 2012 (ANT-XXVIII/5) Reports on Polar and Marine Research 654: 30-35.
• Simon, M, and 11 co-authors (2012) Composition and activity of the bacterioplankton communities in the Drake Passage and Antarctic Peninsula region with a special emphasis on the Roseobacter clade and dissolved organic matter. In: Lucassen M (ed) The expedition of the Research Vessel "Polarstern" to the Antarctic in 2012 (ANT-XXVIII/4) Reports on Polar and Marine Research 653: 49-54.

Presentations at national and international symposia

• Bakenhus, I., Wietz, M., Giebel, H.-A., Beardsley, C., Simon, M. 2016. Bacterioplankton biogeography and activity patterns in the Southern Ocean. Symposium of the International Society for Microbial Ecology (ISME) Montreal, Canada, 22-26.August (talk).

• Billerbeck S., Voget S., Wemheuer B., Poehlein A., Giebel H.-A., Brinkhoff T., Daniel R., Simon M. 2016. Biogeography and environmental genomics of the Roseobacter group affiliated CHAB-I-5 lineage. Symposium of the International Society for Microbial Ecology (ISME), Montreal, Canada, 22-26.August (poster).

• Bakenhus, I., Giebel, H.-A., Wemheuer, B., Wietz, M., Dlugosch, L., Simon, M. 2015. Bacterioplankton community composition and activity patterns across a latitudinal transect from Antarctica (70°S) to the North Atlantic (47°N). Symposium on Aquatic Microbial Ecology (SAME), Uppsala (talk).

• Giebel, H.-A., Schlingloff, A., Simon, M., Brinkhoff, T. 2015. Physiological vs. genomic features of the Roseobacter clade affiliated (RCA) cluster: What we can learn from cultivation-approaches with Planktomarina temperata. Symposium on Aquatic Microbial Ecology (SAME), Uppsala (poster).

• Bakenhus, I., Giebel, H.-A., Wurst, M., Beardsley, C., Simon, M., Wietz, M. 2015. Bacterioplankton biogeography and activity in the Southern Ocean. Annual Meeting of the German Society of General and Applied Microbiology (VAAM), Marburg (poster).

• Giebel, H.-A., B. Wemheuer, S. Voget, R. Daniel and M. Simon. 2014. The abundant Roseobacter clade affiliated (RCA) cluster: Metabolic traits of its model organism Planktomarina temperata RCA23. 17th Ocean Sciences Meeting (OSM, co-sponsored by the American Society of Limnology and Oceanography (ASLO)), Honolulu, Hawaii, USA, February 23-28. (book of abstracts, p. 118, poster).

• Simon, M., B. Wemheuer, H.-A. Giebel, S. Billerbeck, M. Wurst, R. Daniel. 2014. Highly productive and active bacterioplankton communities in the southern ocean in austral fall. 17th Ocean Sciences Meeting (OSM, co-sponsored by the American Society of Limnology and Oceanography (ASLO)), Honolulu, Hawaii, USA, February 23-28. (book of abstracts, p. 79, talk).

• Busch, M., F. Peiffer, Giebel, H.-A., H. Hillebrand, S. Moorthi. 2014. Effects of nutrient concentrations, phagotrophic feeding and alleopathy on bloom dynamics of potentially harmful dinoflagelates. 17th Ocean Sciences Meeting (OSM, co-sponsored by the American Society of Limnology and Oceanography (ASLO)), Honolulu, Hawaii, USA, February 23-28. (book of abstracts, p. 140, talk).

• Giebel, H.-A., B. Wemheuer, S. Voget and M. Simon. 2013. Benefits of aerobic anoxygenic photosynthesis for the Roseobacter clade affiliated (RCA) cluster. 1st EMBO conference on Aquatic Microbial Ecology (SAME13), Stresa, Italy, 8-13 September 2013. (book of abstracts, p. 219, poster).

• Simon, M. et al. (2013). Progress report and future perspectives of project A1. 7^th status semimar of TRR 51, HWK Delmenhorst, Germany, 15-66 October 2013. (talk).

• Billerbeck, S., B. Wemheuer, H.-A. Giebel, R. Daniel and M. Simon. 2013. Distribution and abundance of clusters of the Roseobacter clade in the North Sea. 1^st EMBO conference on Aquatic Microbial Ecology (SAME13), Stresa, Italy, 8-13 September 2013. (book of abstracts, p. 225, poster).

• M. Simon, B. Wemheuer, H.-A. Giebel, T. Brinkhoff, C. Beardsley, I. Bakenhus, R. Daniel and S. Voget. 2013. Major role of photoheterotrophic and CO oxidizing Roseobacter RCA population in the ocean. 1^st EMBO conference on Aquatic Microbial Ecology (SAME13), Stresa, Italy, 8-13 September 2013. (book of abstracts, p. 69, talk).

• Giebel, H-A. et al. (2013). Benefits of aerobic anoxygenic photosynthesis for growth of Cand. Planktomarina temperata of the Roseobacter clade affiliated (RCA) cluster. International Symposium: Research highlights and reports of the first funding period of TRR 51, HWK Delmenhorst, Germany, 24-26 June 2013, (talk).

• Simon, M. et al. (2013). Progress report. International Symposium: Research highlights and reports of the first funding period of TRR 51, HWK Delmenhorst, Germany, 24-26 June 2013, (talk).

• Giebel, H.-A., B. Wemheuer, S. Voget, and M. Simon. 2013. Turn on the lights: Benefits of aerobic anoxygenic photosynthesis for the Roseobacter clade affiliated (RCA) cluster. Annual Meeting of the German Society of General and Applied Microbiology (VAAM) together with KNVM, Bremen, Germany, May 10-13. (book of abstracts, p. 176, poster).

• Simon, M. , T. Brinkhoff, B. Wemheuer, H.-A. Giebel, C. Beardsley, I. Bakenhus, R. Daniel and S. Voget. 2013. Major role of photoheterotrophic and CO oxidizing Roseobacter RCA population in the ocean. Annual Meeting of the German Society of General and Applied Microbiology (VAAM) together with KNVM, Bremen, Germany, May 10-13. (book of abstracts, p. 163, talk).

• Billerbeck, S., H.-A. Giebel, T. Brinkhoff, C. Beardsley, L. Gram, W.H. Jeffrey and M. Simon. 2013. Distribution of clusters of the Roseobacter clade in global oceans. Annual Meeting of the German Society of General and Applied Microbiology (VAAM) together with KNVM, Bremen, Germany, May 10-13. (book of abstracts, p. 164, talk).

• Simon, M. (2012). A1 Progress report and future perspectives. 7^th Status Seminar of the Transregio 51, Oktober 15-16, HWK Delmenhorst, Germany (talk).

• Simon, M. 2012. The Roseobacter clade and its potential significance for the microbial carbon pump. Workshop SCOR WG 134: The Microbial Carbon Pump in the Ocean, Delmenhorst, Germany, August 26-28.

• Giebel, H.-A., B. Wemheuer, S. Voget, and M. Simon. 2012. The Roseobacter clade affiliated (RCA) cluster: Do these microbes conduct aerobic anoxygenic photosynthesis? 14^th Symposium of the International Society for Microbial Ecology (ISME), The power of the small, Copenhagen, Denmark, August 19-24. (book of abstracts, poster).

• Simon, M., T. Brinkhoff, B. Wemheuer, H.-A. Giebel, C. Beardsley, I. Bakenhus, R. Daniel and S. Voget. 2012. Evidence for ocean-wide distribution of an abundant photoheterotrophic and CO oxidizing RCA roseobacter population in the North Sea and North Atlantic. 14^th Symposium of the International Society for Microbial Ecology (ISME), The power of the small, Copenhagen, Denmark, August 19-24. (book of abstract, talk).

• Simon, M., B. Wemheuer, H.-A. Giebel, T. Brinkhoff, C. Beardsley, R. Daniel and S. Voget. 2012. Genomic features and distribution of an abundant photoheterotrophic and CO oxidizing RCA isolate in the North Sea and North Atlantic. Gordon Research Conferences (GRC), Marine Microbes - Bridging the Gaps from Genomes to Biomes, Lucca (Barga), Italy, June 24-29. (book of abstract, poster).

• Billerbeck, S., H.-A. Giebel and M. Simon. 2012. Occurence of Roseobacter subclusters in the North Sea. Gordon Research Conferences (GRC), Marine Microbes - Bridging the Gaps from Genomes to Biomes, Lucca (Barga), Italy, June 24-29. (book of abstract, poster).

• Giebel, H-A. (2012). Science and life on board the RV Polarstern during cruises ANT-XXVIII/4&5. 6^th Status Seminar of the Transregio 51, 5^th June 2012, HZI Braunschweig, Germany (talk).

• Simon, M. (2012). Polarstern cruise from Punta Arenas to the Southern Ocean and across the Atlantic back to Bremerhaven, 14 Mar – 15 May 2012 – report and first results. 6^th Status Seminar of the Transregio 51, 5^th June 2012, HZI Braunschweig, Germany (talk).

• Giebel, H-A. and J. Vollmers (2012). Sampling of roseobacters in the Southern Ocean - cience and life on board the RV Polarstern cruise ANT-XXVIII/2 -report and first results. 5^th Status Seminar of the Transregio 51, 6^th June 2012, HZI Braunschweig, Germany (talk).

• Giebel, H.-A., B. Wemheuer, S. Voget, and M. Simon. 2011. First hints for conducting aerobic anoxygenic photosynthesis by bacteria of the Roseobacter clade affiliated (RCA) cluster. 12^th Symposium on Aquatic Microbial Ecology (SAME), Rostock-Warnemünde, Germany, August 28-September 2. (book of abstracts, p. 225, poster).

• Billerbeck, S., H.-A. Giebel, and M. Simon. 2011. Occurrence of Roseobacter subclusters in the German Bight of the North Sea. 12^th Symposium on Aquatic Microbial Ecology (SAME), Rostock-Warnemünde, Germany, August 28-September 2. (book of abstracts, p. 138, poster).

• Simon, M., S. Hahnke, H.-A. Giebel, S. Simon, H. Osterholz, and T. Brinkhoff. 2011. Physiology and interactions of phytoplankton-assosiated roseobacters. 12^th Symposium on Aquatic Microbial Ecology (SAME), Rostock-Warnemünde, Germany, August 28-September 2. (book of abstracts, p. 113, talk).

• Beardsley, C. 2011. International workshop: Fluorescence in situ hybridisation (1^st FISH camp), MPI, Bremen, Germany, June 14-24.

• Billerbeck, S., H.-A. Giebel and M. Simon. 2011. Occurrence of Roseobacter subclusters in the German Bight of the North Sea. Annual Meeting of the German Society of General and Applied Microbiology (VAAM), Karlsruhe, Germany, April 3-6. (book of abstracts, p. 110, poster).

• Langer, T., S. Hahnke, T. Brinkhoff and M. Simon. 2011. Response of the Roseobacter clade to an experimentally-induced Phaeocystis bloom. Annual Meeting of the German Society of General and Applied Microbiology (VAAM), Karlsruhe, Germany, April 3-6. (book of abstracts, p. 171, poster).

• Simon, M. 2011. Decomposition of humic acids by estuarine and marine bacterial communities. Ocean Science Meeting (co-sponsored by the American Society of Limnology and Oceanography (ASLO)), San Juan, Puerto Rico, February 19-20.

• Billerbeck, S. (2010). Ecological significance, biogeography and physiology of the Roseobacter group in pelagic systems. 1^st Status Seminar of the Transregio 51, 21^st October 2010, HZI Braunschweig, Germany (talk).

• Simon, M., Giebel, H.-A., Voget, S., Kalhoefer, D., Daniel, R. and T. Brinkhoff. 2010. The Roseobacter RCA cluster in the North Sea - population dynamics, physiological and genomic properties. 13^th Symposium of the International Society for Microbial Ecology (ISME), Stewards of a changing planet, Seattle, WA, USA, August 22-27. (book of abstracts, poster).

• Giebel, H.-A., D. Kalhoefer, S. Voget, T. Brinkhoff and M. Simon. 2010. Distribution of Roseobacter RCA and SAR11 lineages in the Southern Ocean and North Sea and characteristics of an abundant RCA isolate. Gordon Research Conferences (GRC), Marine Microbes: From Genes To Global Cycles, Tilton, NH, USA, July 4-9. (book of abstracts, poster).

• Giebel, H.-A., D. Kalhoefer, H. Osterholz, S. Voget, T. Brinkhoff and M. Simon. 2010. The Roseobacter clade affiliated (RCA) cluster: Its occurence, diversity and potential significance in marine habitats. Transregional Collaborative Research Center (TRR-51) Kick-off Symposium: Ecology, Physiology and Molecular Biology of the Roseobacter clade: Towards a Systems Biology Understanding of a Globally Important Clade of Marine Bacteria, Delmenhorst, Germany, June 13-15. (book of abstracts, talk).

• Hahnke, S., H.-A. Giebel, M. Sperling, H. Osterholz, M. Simon and T. Brinkhoff. 2010. Physiology and biogeography of phytoplankton-associated roseobacters. Transregional Collaborative Research Center (TRR-51) Kick-off Symposium: Ecology, Physiology and Molecular Biology of the Roseobacter clade: Towards a Systems Biology Understanding of a Globally Important Clade of Marine Bacteria, Delmenhorst, Germany, June 13-15. (book of abstracts, talk).

• Giebel, H.-A., D. Kalhoefer, H. Osterholz, S. Voget, T. Brinkhoff and M. Simon. 2010. The Roseobacter clade affiliated (RCA) cluster: Its occurence, diversity and potential significance. International workshop: The microbial view of marine biogeochemical cycles, Banyuls-sur-Mer, France, May 19-21. (book of abstracts, talk).

• Simon, M., S. Hahnke, H.-A. Giebel, H. Osterholz and T. Brinkhoff. 2010. Drivers of organic matter turnover in the sea - some examples from the Roseobacter clade. International workshop: The microbial view of marine biogeochemical cycles, Banyuls-sur-Mer, France, May 19-21. (book of abstracts, talk).

Principal investigators: PD Dr. Bert Engelen 

PostDoc: Dr. Marion Pohlner

PhD student: Benedikt Heyerhoff, Dennis Tebbe

Former PhD students: Judith Lucas, Dr. Saranya Kanukollu

Former master students: Julius Degenhardt, Janina Herber, Nawras Ghanem

Objective: 

Roseobacter-affiliated bacteria represent a numerically significant part not only of pelagic, but also of benthic microbial communities. Thus, we want to understand their biogeography, distribution, abundance and main activities in marine sediments. So far, we have analyzed samples from the North Sea (Heincke cruise HE361), the Antarctic Peninsula (Polarstern cruise ANT28/4) and the Pacific Ocean (Sonne cruises SO248 and SO254) to identify regional differences and a putative overlap between free water, particles and the sediment surface. In order to identify the metabolic activity of roseobacters, ribosomal RNA based analyses are performed by Digoxygenin-labeled UTP incorporation. Here, we will identify the factors that affect their occurrence and their metabolic response to changes at the oxic/anoxic transition zone. These experiments are currently running with special emphasis on their sulfur metabolism.

Methods:

Cultivation

• Original samples obtained directly from various sites are transferred in media amended with DMS, DMSP and DMSO. All cultivations are  performed in serial dilutions (MPN)

Diversity and distribution of the Roseobacter group

• Total cell counts (original and MPN enrichments) with SYBR Green I quantification.
• CARD-FISH by using both, EUB388 and ROS536R probes
• qPCR by using Bacteria and Roseobacter-specific primers
• Cluster analysis of DGGE gels
• 454- and Illumina-Sequencing

Metabolic activity tests

• Quantitative (real-time) PCR
• In vivo labeling of bacterial rRNA by incorporating DIG-11-UTP and separation by magnetic beads
• Parallel verification of the results by stable isotope probing (SIP)

Expeditions:

• Expedition SO254 (RV Sonne, February 2017): Functional diversity of bacterial communities and the metabolome in the water column, sediment and in sponges in the southwest Pacific around New Zealand - Microbial abundance, diversity and activity in Pacific Deep Sea sediments
• Expedition SO248 (RV Sonne, May 2016): Ductional diversity of bacterial communities and the geometabolome in the central and north Pacific - Microbial abundance, diversity and activity in Pacific Deep Sea sediments
• Expedition ANT28/4 (RV Polarstern, March-April 2012): The Roseobacter clade and the DOM composition in the Drake Passage and the Antarctic Peninsula region of the Southern Ocean
• Expedition HE361 (RV Heincke, June 2011): Sampling two transects along the German/Danish coast and the Norwegian channel

Contributions at (inter)national conferences:

• VAAM conference (17–20 March 2019, Mainz): Abundance and diversity of Bacteria and Archaea within deep-sea sediments along a Pacific transect from New Zealand to Alaska (Presentation)
• VAAM conference (15–18 April 2018, Wolfsburg): The distribution of benthic Roseobacter group members in the Pacific is shaped by nutrient availability at the seafloor and productivity in the water column (Poster)
• ISME conference (21-26 August 2016, Montreal): The Roseobacter group in marine sediments - abundance, diversity and metabolic potential (Poster)
• VAAM conference (13–16 March 2016, Jena): Defining unknown members of the Roseobacter group in marine sediments (Poster)
• VAAM conference (01-04 March 2015, Marburg): Distinctive distribution of free-living, particle-associated and benthic Roseobacter populations (Presentation) and Identification of metabolically active microbial communities in sediments by two independent RNA-based in vivo labeling techniques (Poster) 
• ISME conference (24-29 August 2014, Seoul): Specific distribution of Roseobacter populations from the water column down to the sediments of a coastal sea (Poster)
• VAAM conference (10-13 March 2013, Bremen): Spatial distribution and diversity of the Roseobacter clade in temperate and permanently cold marine sediments (Poster)

International collaboration:

• Brandi Kiel-Reese, Texas A&M University - Corpus Christi, Texas, USA
• Heath Mills, University of Houston - Clear Lake, Texas, USA
• Hendrik Schäfer, University of Warwick, United Kingdom

Master thesis:

• Degenhardt, Julius (March 2017): Abundance and diversity of the Roseobacter group within deap-sea sediments along a transect from Nez Zealand to Alaska
• Ghanem, Nawras (April 2013): Adundance and distribution of Roseobacter-affiliated bacteria in Antarctic sediments
• Herber, Janina (November 2012): Abundance and diversity of Roseobacter-affiliated bacteria in sediment and water samples of the North Sea

PhD thesis:

• Pohlner, Marion (2019): Contribution of the Roseobacter group to the abundance, distribution and activity of microbial communities in marine sedimentsThe metabolic potential and the distribution of the Roseobacter group in marine sediments
• Kanukollu, Saranya (2016): The metabolic potential and the distribution of the Roseobacter group in marine sediments

Publications:

• Kanukollu S, Ghanem N, Wemheuer B, Erlmann N, Schnetger B, Köster J, Pohlner M, Daniel R, Cypionka H, Engelen B The seafloor around the South Shetland Islands exhibits a shift in diversity of benthic bacteria and the Roseobacter group with increasing water and sediment depth (to be resubmitted to Polar Research)
• Pohlner M, Dlugosch L, Wemheuer B, Mills H, Engelen B, Reese BK (2019) The Majority of Active Rhodobacteraceae in Marine Sediments Belong to Uncultured Genera: A Molecular Approach to Link Their Distribution to Environmental Conditions. Front Microbiol 10:659, https://doi.org/10.3389/fmicb.2019.00659.
• 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, Article ID 3717239, https://doi.org/10.1155/2019/3717239.
• 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 2019, 17:1, https://doi.org/10.3390/md17010020.
• Pohlner M, Degenhardt J, von Hoyningen-Huene A, Wemheuer B, Erlmann N, Schnetger B, Engelen B (2017) The biogeographical distribution of benthic Roseobacter group members along a Pacific transect is linked to oceanic provinces with comparable nutrient composition. Front Microbiol 8: 2550, https://doi.org/10.3389/fmicb.2017.02550.
• Pohlner M, Marshall I, Schreiber L, Cypionka H, Engelen B (2017) Draft genome sequence of Pseudoruegeria sp. SK021, a representative of the marine Roseobacter group, isolated from North Sea sediment. Genome A 5:e00541-17, https://doi.org/10.1128/genomeA.00541-17.
• Harig T, Schlawis C, Ziesche L, Pohlner M, Engelen B, Schulz S (2017) Nitrogen-containing volatiles from marine Salinispora pacifica and Roseobacter-group bacteria. J Nat Prod, https://doi.org/10.1021/acs.jnatprod.7b00789.
• 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. SIGS 11:1-10, https://doi.org/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, https://doi.org/10.1093/femsec/fiv145.
• 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, https://doi.org/10.3389/fmicb.2015.00233.
• Sass H, Köpke B, Rütters H, Feuerlein T, Dröge S, Cypionka H, Engelen B (2010) Tateyamaria pelophila sp. nov. a facultatively anaerobic Alphaproteobacterium isolated from tidal-flat sediments, and emended descriptions of the genus Tateyamaria and of Tateyamaria omphalii. Int J Sys Evol Microbiol 60: 1770-1777, https://doi.org/10.1099/ijs.0.013524-0.

Principal Investigators: Prof. Dr. Rolf Daniel

Post-Doc: Birgit Pfeiffer

PhD student: Florian Lenk

Associated scientists: Dr. Anja Poehlein, Dr. Bernd Wemheuer

Objective

In this subproject, the genomic potential and important functions of Roseobacter populations will be analyzed by culture-independent metagenomic and metatranscriptomic approaches. To identify indigenous gene- and taxon-specific patterns and key metabolic functions comparative metabolic and functional profiling of representative samples from the North Sea, the Southern Ocean, biofilms, and mesocosms will be performed by employing large-scale pyrosequencing. The mesocosm experiments will be focused on the effect of addition of organic sulfur compounds, defined phytoplankton algae, or organic compounds on the functional and phylogenetic structure of the community. The influence of incubation at light and dark as well as different salinities and pH values will be also evaluated. For metagenomic sequence analysis and for metatranscriptomic analyses, DNA and RNA, respectively, will be isolated from all samples, simultaneously. In addition, metagenomic libraries are constructed and screened for important functions such as genes involved in quorum sensing, energy metabolism, production of secondary metabolites and the corresponding regulatory networks. The large-insert libraries are also screened for phylogenetic anchors such as 16S rRNA genes. Recombinant fosmids harbouring 16S rRNA genes are sequenced. In this way, a phylogenetic marker is linked to other genes of the same organisms. This approach will be extended to other marker genes and gene clusters. These studies in close cooperation with the results of the systems biology approaches to model organism allow a partial genome characterization of uncultivated roseobacters via comparison to the data obtained for the cultivated Roseobacter strains. The distribution and variability of certain genes and pathways in environmentally abundant members of the Roseobacter group are mirrored. In this way, generated systems biology models from other subprojects can be extended to uncultivated Roseobacter clade bacteria.

Role in the CRC/General Methods

Together with A5, A6, and A7, we concentrate on different aspects of genomic research (Fig. 1). In A3, we focus on metagenomics.

We apply different metagenomic and metatranscriptomic approaches to study the Roseobacter clade in situ (Fig. 2). In addition, we also analyse the genome of certain Roseobacter isolates (with focus on the genus Octadecabacter and differernt members of so far underreprestend subclusters).

Cruises and sampling campaigns:

2017:

1. RV SONNE, Pacific Ocean (SO254)

2016

1. RV Sonne, Pacific Ocean (SO248)

2014

1. RV Heincke, North Sea (HE425)

2012

1. Jyllinge Habour, Jyllinge, Dänemark: Phaeobacter gallaeciensis (Cooparation with project B2 and Lone Gram (DTU))
2. RV Polarstern, ANTXXVII/5: Atlantic transect (Punta Arenas - Bremerhaven)
3. RV Polarstern, ANTXXVII/4: Drake Passage and Southern Ocean (Punta Arenas - Antarktis)
4. RV Meteor, Ausfahrt M86/4: Mediterranean Sea transect (Dubrovnik - Palma de Mallorca)

2011

1. RV Polarstern, ANT-XXVII/2, Southern Ocean (Cape Town - Neumeyer Station)
2. RV Heincke, North Sea (HE361)

2010

1. RV Heincke, North Sea (HE327)

Relevant publications:

2017

1. 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 (abstract).
2. Ebert M, Laass S, Thürmer A, Roselius L, Eckweiler D, Daniel R, Härtig E and Jahn D (2017) FnrL and three Dnr regulators are used for the metabolic adaptation to low oxygen tension in Dinoroseobacter shibae. Front Microbiol 8:642 (abstract).
3. 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 (abstract).
4. Simon C, Daniel R (2017) Construction of small-insert and large-insert metagenomic libraries. Methods in Molecular Biology 1539:1-12 (abstract).
5. 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 (abstract).

2016

1. Billerbeck S, Wemheuer B, Voget S, Poehlein A, Giebel H-A, Brinkhoff T, Gram L, Jeffrey WH, Daniel R, Simon M (2016) Biogeography and environmental genomics of the Roseobacter-affiliated pelagic CHAB-I-5 lineage. Nature Microbiol 1:16063 (abstract).
2. Giebel H-A, 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 (abstract).
3. 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:fiv137 (abstract).
4. Kanukollu S, Voget S, Pohlner M, Vandieken V, Petersen J, Kyrpides NC, Woyke T, Shapiro N, Göker M, Klenk HP, Cypionka H, Engelen B (2016) Genome sequence of Shimia str. SK013, a representative of the Roseobacter group isolated from marine sediment. Stand Genomic Sci 11:25 (abstract).
5. 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 1-14 (abstract).

2015

1. Aßhauer KP, Wemheuer B, Daniel R, Meinicke P (2015) Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data. Bioinformatics 31:2882-2884 (abstract).
2. Daniel R (2015) Mikrobielle Genomforschung - Schlüsseltechnologie der Lebenswissenschaften. BIOspektrum 21:28-29 (abstract).
3. Gram L, Rasmussen BB, Wemheuer B, Bernbom N, Ng YY, Porsby CH, Breider S, Brinkhoff T (2015) Phaeobacter inhibens from the Roseobacter clade has an environmental niche as a surface colonizer in harbors. Syst Appl Microbiol 38:483-493 (abstract).
4. 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 17:3857-3868 (abstract).
5. Voget S, Wemheuer B, Brinkhoff T, Vollmers J, Dietrich S, Giebel H.-A., 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 (abstract).
6. 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 Announc 3:e00353-15 (abstract).
7. Voget S, Billerbeck S, Simon M, Daniel R (2015) Closed genome sequence of Octadecabacter temperatus SB1, the first mesophilic species of the genus Octadecabacter. Genome Announc 3:e01051-15 (abstract).
8. 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 Announc 3:e01096-15 (abstract).
9. 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 (abstract).
10. Wietz M, Wemheuer B, Simon H, Giebel HA, Seibt MA, Daniel R, Brinkhoff T, Simon M (2015) Bacterial community dynamics during polysaccharide degradation at contrasting sites in the Southern and Atlantic Oceans. Environ Microbiol 17:3822-3831 (abstract).

2014

1. Nacke H, Daniel R (2014) Approaches in metagenome research - progress and challenges. In: Encyclopedia of Metagenomics. SpringerReference (Ed: Nelson, K.). Springer-Verlag Berlin Heidelberg SpringerReference_363415 (abstract).
2. Thürmer A (2014) Next Generation Sequencing in der mikrobiellen (Meta)Genomforschung. BIOspektrum 2.14:168-171 (abstract).
3. Voget S, Göker M, Brinkhoff T (2014) Genomik: Grundlage zum Verständnis des Erfolgs der Roseobacter-Gruppe. BIOspektrum 3.14:279-282 (abstract).
4. 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 Microbiology Ecology 87:378-389 (abstract).

2013

1. Bruns H, Thiel V, Voget S, Patzelt D, Daniel R, Wagner-Döbler I, Schulz S (2013) N-Acylated alanine methyl esters (NAMEs) from Roseovarius tolerans, structural analogs of quorum-sensing autoinducers, N-acylhomoserine lactones. Chemistry & Biodiversity 10:1559-1573 (abstract).
2. Dogs M, Voget S, Teshima H, Petersen J, Davenport K, Dalnigault H, Chen A, Pati A, Ivanova N, Goodwin LA, Chain P, Detter JC, Standfest S, Rohde M, Gronow S, Kyrpides NC, Woyke T, Simon M (2013) Genome sequence of Phaeobacter inhibits type strain (T5T), a secondary metabolite producing member of the marine Roseobacter clade, and emendation of the species description of Phaeobacter inhibits. Stand Genomic Sci 9:142-159.
3. Giebel H-G, Kalhoefer D, Gahl-Janssen R, Choo Y-J, Lee K, Cho J-C, 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 Syst Evol Microbiol 63:4207–4217 (abstract).
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 (abstract).

2012

1. Berger M, Brock N, Liesegang H, Dogs M, Preuth I, Simon M, Dickschat J, Brinkhoff T (2012) Genetic analysis of the upper phenylacetate catabolic pathway in the production of tropodithietic acid by Phaeobacter gallaeciensis. Appl Environ Microbiol 78:3539-51 (abstract).
2. Brinkhoff T, Fischer D, Vollmers J, Voget S, Beardsley C, Thole S, Mussmann M, Kunze B, Wagner-Döbler I, Daniel R, Simon M (2012) Biogeography and phylogenetic diversity of a cluster of exclusively marine myxobacteria. ISME J 6:1260-1272 (abstract).
3. Thole S, Kalhoefer D, Voget S, Berger M, Engelhardt T, Liesegang 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 J 6:2229-2244 (abstract).
4. Wemheuer B, Wemheuer F, Daniel R (2012) RNA-based assessment of diversity and composition of active archaeal communities in the German Bight. Archaea 2012: Article ID 695826 (abstract).

2011

1. 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 12:324 (abstract).
2. Simon C, Daniel R (2011) Metagenomic analyses: past and future trends. Appl Environ Microbiol 77(4):1153-1161 (abstract).

2010

1. Wagner-Döbler I, Ballhausen B, Berger M, Brinkhoff T, Buchholz I, Bunk B, Cypionka H, Daniel R, Drepper T, Gerdts G, Hahnke S, Han C, Jahn D, Kalhoefer D, Kiss H, Klenk HP, Kyrpides N, Liebl W, Liesegang H, Meincke L, Pati A, Petersen J, Piekarski T, Pommerenke C, Pradella S, Pukall R, Rabus R, Stackebrandt E, Thole S, Thompson L, Tielen P, Tomasch J, von Jan M, Wanphrut N, Wichels A, Zech H, Simon M (2010) The complete genome sequence of the algal symbiont Dinoroseobacter shibae: a hitchhiker's guide to life in the sea. ISME J 4(1):61-77 (abstract).
2. Simon C, Daniel R (2010) Construction of small-insert and large-insert metagenomic libraries. Methods in Molecular Biology 668: 39-50

Other Publications

• Beardsley C, 12 co-authors, Simon M (2012) The Roseobacter clade and the dissolved organic matter (DOM) composition in the Atlantic sector of the Southern Ocean. In: Kattner G (ed) The expedition of the Research Vessel "Polarstern" to the Antarctic in 2012 (ANT-XXVIII/2) Reports on Polar and Marine Research 646: 36-39.
• Simon M, and 13 co-authors (2012) In: Bumke K (ed) The expedition of the Research Vessel "Polarstern" to the Antarctic in 2012 (ANT-XXVIII/5) Reports on Polar and Marine Research 654: 30-35.
• Simon, M, and 11 co-authors (2012) Composition and activity of the bacterioplankton communities in the Drake Passage and Antarctic Peninsula region with a special emphasis on the Roseobacter clade and dissolved organic matter. In: Lucassen M (ed) The expedition of the Research Vessel "Polarstern" to the Antarctic in 2012 (ANT-XXVIII/4) Reports on Polar and Marine Research 653: 49-54.

Presentations at national and international symposia (selection)

Talks:

1. Wemheuer B et al. (2016). Driving forces of bacterioplankton community structure, diversity and function in the North Sea. Functional Metagenomics 2016 in Inderøy, Norway
2. Wemheuer et al. (2015). The green impact – bacterioplankton response towards a phytoplankton spring bloom in the southern North Sea assessed by comparative metagenomic and metatranscriptomic approaches. Annual Conference of the Association for General and Applied Microbiology (VAAM) 2015 in Marburg, Germany.
3. Wemheuer B (2013). Metagenomics and metatranscriptomics at the Goettingen Genomics Laboratory. German Conference on Bioinformatics (GCB) 2013 in Goettingen, Germany.

Bachelor, Master und PhD theses:

Running

1. Florian Lenk (PhD thesis)

2017

1. Avril von Hoyningen-Huene (Master): "Structural and functional characterization of microbial communities in the ocean"

2016

1. Pinar Akyol (Master): "Bacterioplankton community structures and functions along geographical gradients in the North Sea"
2. Dirk Berkelmann (Master): "From order to chaos – bacterial community dynamics under different environmental regimes in a simulated marine ecosystem"

2015

1. Ines Friedrich (Bachelor): "Development of novel Escherichia coli mutants for funtional screenings of metagenomic libraries."
2. Katharina Smaluch (Master): "Impact of phytoplankton blooms and other environmental parameterson bacterioplankton communities
3. Carl Simon Strittmatter (Bachelor): "Characterization of metagenomes derived from aquatic habitats"

2014

1. Bernd Wemheuer (PhD): "Diversity, ecology and physiology of the Roseobacter clade and other marine microorganisms in the North Sea as revealed by culture-independent approaches"

2013

1. Peggy Klempert (Diplom): "Characterization of marine microbial communites applying culture-indipendent appraoches"
2. Florian Lenk (Master): "Metagenomic analysis of antarctic se ice samples"
3. John Vollmers (PhD): "Genomic comparisation and molecular characterization of selected members of the Roseobacter-clade"

2012

1. Simon Güllert (Master): "Phylogenetic and functional characterization of microbial communities derived from the German Bight"
2. Dimitri Meier (Master): "Phylogenetic and functional characterization of microbial communities derived from the North Sea along a North-South gradient from Germany to Norway"
3. Katja Meyer (Master): "Distribution and Function of selected Rhodopsin Families"

2011

1. Pinar Akyol (Bachelor): "Purification and Characterization of a metagenome-derived Peptidase"
2. Maike Smits (Bachelor): "Functional and comparative Analyses of Rhodopsins from selected polar Roseobacter strains"

Contact

Address

Georg-August University Göttingen
Institute of Microbiology and Genetics
Department of Genomic and Applied Microbiology and Göttingen Genomics Labratory
Grisebachstr. 8, 37077 Göttingen, Germany

eMail                                rdaniel(at)gwdg.de

Phone                            +49 (0)551 39-33827

Phone (Secratary)          +49 (0)551 39-33842

Fax                                   +49 (0)551 39-1218

URL                                    http://appmibio.uni-goettingen.de/

The Roseobacter ‘plasmid’ team 2017:

Principal investigators: PD Dr. Jörn Petersen, Dr. Silke Pradella

Research Associate: Dr. Henner Brinkmann

PhD student: Pascal Bartling

Technical assistance: Claire Ellebrandt, Victoria Michael, Orsola Päuker

Master students: Lukas Birmes, Sandra Hacke

Introduction

Research in our team is focused on the evolution and function of extrachromosomal replicons (ECRs or ‘plasmids’), which are highly abundant in Roseobacter genomes.

As other Alphaproteobacteria typical representatives of the Roseobacter group own multipartite genomes. These are composed of a single chromosome and a variable number of ECRs. For example, twelve ECRs were detected in the Roseobacter species Marinovum algicola. This number is even unsurpassed within the Proteobacteria and the ECRs of this species account for about one-third of the total genomic information. Important functions have been assigned to Roseobacter plasmids, including aerobic anoxygenic photosynthesis (Fig. 1), motility, biofilm formation and synthesis of the antibiotic tropodithietic acid (TDA). It is hypothesized that ECRs mediate the horizontal gene transfer of privotal functions and might thus allow to the rapid adaptions of roseobacters to changing environments.

Due to the conspicuous wealth of Roseobacter ECRs and the availability of an exceptional amount of genome data (> 450 Rhodobacteraceae genomes have been sequenced [01/2017]) the Roseobacter group constitutes an ideal platform for the investigation of alphaproteobacterial plasmids.

As main goals of our project A5 we aim to reveal:

1.  Evolutionary aspects

• Plasmid abundance, distribution and relevance in the Roseobacter group

• A natural classification scheme for Roseobacter plasmids based on the phylogeny of plasmid replication and partitioning genes

• The genetic basis for compatibility and the host-range of alphaproteobacterial plasmids

• The role of the extrachromosomal replicons ECRs in the dynamics of Roseobacter genomes

2.  Functional aspects

• The functional consequences of plasmid loss (via curing) or plasmid gain (via conjugation) in Roseobacter strains

• The role of ECRs in symbiotic associations of roseobacters with marine micro- and macroalgae

Outcome (2010-2017)

1.  Genomics of roseobacters

1.1  Think Pink! – Complete photosynthesis gene clusters are plasmid-encoded!

• As a highlight of the first funding period we showed that a complete photosynthesis gene cluster (45 kb) is located on the 118 kb plasmid of Sulfitobacter guttiformis^T (Fig. 2) and hypothesized that the horizontal gene transfer of extrachromosomal replicons drives evolution in the Roseobacter group.

1.2  Genome sequencing of plasmid-rich roseobacters (Rhodobacteraceae) and relatives

• Dinoroseobacter shibae DSM 16493^T: 5 plasmids (72 to 191 kb; in cooperation with project B4; Wagner-Döbler et al. 2010)

• Marinovum algicola DG898 (DSM 27768): 11 plasmids (6 to 255 kb, Pradella et al. 2010). We completely sequenced the genome of this strain in order to understand the molecular basis for maintaining a multipartite genome organization (Frank et al. 2015a; Fig. 3).

• Phaeobacter gallaeciensis DSM 26640^T: 7 plasmids (40 to 255 kb; Frank et al. 2015b; Buddruhs & Pradella et al. 2013)
• Others: Shimia str. SK013 (Kanukollu et al. 2016), Loktanella hongkongensis^T (Lau et al. 2015), Roseovarius mucosus^T (Riedel et al. 2015), Rubellimicrobium mesophilum^T (Riedel et al. 2014), Wenxinia marina^T (Riedel et al. 2014), Salipiger mucosus^T (Riedel et al. 2014), Hoeflea phototrophica^T (Fiebig et al. 2013b), Labrenzia alexandrii^T (Fiebig et al. 2013a)

2.  Classification and compatibility of plasmids in the Roseobacter group

• We developed a robust classification scheme for Roseobacter plasmids based on the phylogeny of the plasmidal replicase and partitioning genes (Petersen et al. 2009, Petersen 2011). Our phylogenetic plasmid data base is continuously updated with incoming Roseobacter genome sequences.
• On basis of the thitherto unknown DnaA-like replicase a novel plasmid-type was identified in Rhodobacterales (Petersen et al. 2011).
• Our phylogeny-based plasmid classification allowed predictions about the plasmid compatibility and was a prerequisite to develop a target-orientated plasmid curing strategy (see below; Petersen et al. 2011).

3.  Target-orientated plasmid curing to reveal plasmid functions

• In order to reveal the function of specific plasmids, we designed a target-oriented plasmid curing strategy for Roseobacter strains (Petersen et al. 2013). Various cured Roseobacter plasmid mutants, including mutants of CRC 51 model strains, were generated:
• Phaeobacter inhibens DSM 17395 (3 native plasmids): The complete set of mutants cured from all native plasmids in every combination was obtained (Trautwein et al. 2016).
• Dinoroseobacter shibae DFL-12 (5 plasmids): 3 plasmid mutants - Δ191 kb, Δ86 kb, Δ72 kb
• Other mutans derived from: Marinovum algicola DG898 (DSM 27768; Frank et al 2015a), Marinovum algicola DSM10251^T, Phaeobacter inhibens DSM 24588, Phaeobacter gallaeciensis DSM 26640^T, Pseudophaeobacter arcticus DSM 23566^T (Michael et al. 2016)

4.  Essential functions of ECRs demonstrated by target-orientated plasmid curing

• Roseobacter wildtype strains and the corresponding plasmid mutants were compared in the laboratory experiments and the “loss of function” of the mutant strain was revealed.

   Dinoroseobacter shibae DFL-12^T:

• The 191 kb “killer” plasmid is essential for the anaerobic growth of D. shibae DFL-12 (Ebert et al. 2013) and cell density dependent killing effect of this strain on the dinoflagellate Prorocentrum minimum (in cooperation with project B4; Wang et al. 2015).
• The 72 kb plasmid is pivotal for adaptation to starvation and oxidative stress (in cooperation with project B1; Soora et al. 2015).

•    Phaeobacter inhinbens DSM 17395:

• The 65 kb plasmid is required for biofilm formation, motility and colonization of marine algae (Frank et al. 2015b, Fig. 4). Biofilm plasmids of this type are widely distributed among the Roseobacter group and are essential for the sessile mode of life in many of these strains (Michael et al. 2016).
• Systems biology of the Phaeobacter inhibens DSM 17395 plasmid mutants. Based on the complete set of plasmid curing mutants derived from Phaeobacter inhibens DSM 17395, the physiological and energetic consequences of plasmid carriage were investigated. Maintenance of the large TDA-encoding 262 kb plasmid was shown to be extremely costly for our model strain Phaeobacter inhibens DSM 17395 (in cooperation with projects C1 and C3; Trautwein et al. 2016)!

• Marinovum algicola DG 898:

• The 52 kb plasmid represented a biofilm plasmid and is required for surface attachment (Frank et al. 2015a).
• A complete flagellum gene cluster is located on the 143 kb plasmid of strain DG898. In contrast to the wildtype, the cured plasmid mutant D143 kb is immotile (Frank et al. 2015a)

5.  Conjugation

• The conjugative transfer of ECRs between Dinoroseobacter shibae DFL-12 as donor and Phaeobacter inhibens DSM 17395 as recipient was proven (in cooperation with project B4; Patzelt et al. 2016; Fig. 5).

6.  Transposon mutagenesis

• A transoposon library of Phaeobacter inhibens DSM 17395 containing 5500 quality checked mutants was established.

Current projects

• Plasmid transfer between roseobacters and rhizobia: We determine the host range of RepABC-type plasmids.

• Detection of novel DnaA-like I photosynthesis plasmids

• Evolution of photosynthesis in Rhodobacteraceae

• Identification of a novel promiscuous plasmid type RepL in roseobacters

• Comparative genomics of Marinovum algicola strains. We compare the genome sequences of the closely related Marinovum algicola strains in order to reveal the genome dynamics in this plasmid-rich species (in cooperation with projects A6 and A7).

• Plasmid flux and horizontal gene transfer in the genus of Phaeobacter (in cooperation with project A7)

• Dinoroseobacter shibae DFL-12 – The sixth element. Pulsed-field gel electrophoresis analyses of different glycerol stock cultures showed that our completely sequenced model organism D. shibae DSM 16493^T lost two plasmids in the course of cryoconservation. We isolated and sequenced a sixth plasmid of Dinoroseobacter shibae DFL-12 (in cooperation with project A3). The 102 kb replicon is dominated by genes that assumingly confer resistance to a broad spectrum of heavy metals. We performed several physiological tests to differentiate between the two D. shibae plasmid mutants and determine the gene expression of the sixth element by comparative transcriptome analysis.

• The archaetypal type I flagellar system of Rhodobacteraceae. The three flagellar systems of Rhodobacteraceae are analyzed.

• Bacterial communities in non-axenic algal cultures. We analyze the composition of the bacterial communities associated with 23 xenic algae cultures from marine and brackish environments. Culture-independent methods, i.e. barcoded partial 16S rRNA gene 454-pyrosequencing and cultivation are used in order to quantify the amount of the bacterial epibionts and to reveal specific associations (in cooperation with project A3).

• Algal tumors of the red alga Ceramium rubrum: Are roseobacters involed in the gall formation? The bacterial community of algal galls is analyzed by culture- independent and -dependent methods.

Methods

• Cultivation, isolation and characterization of bacteria
• Cultivation of microalgae
• Broad spectrum of molecular methods (DNA and RNA isolation, PCR, cloning, hybridization)
• Pulsed-field gel electrophoresis for Roseobacter genome structure analyses
• Target-orientated plasmid curing to generate plasmid mutants
• Transposon Mutagenesis
• Next generation sequencing and genome finishing (Illumina, PacBio)
• Transcriptome analyses using the Illumina technology
• Phylogenetic and phylogenomic analyses
• Comparative genomics
• Phenotype MicroArray technology (Biolog)
• Bacterial community analysis of xenic algal cultures using 16S rDNA amplicon sequencing

International Cooperations

• Baurain Denis, Université of Liège, Liège, Belgium
• Gram Lone, TU Denmark, Lyngby, Denmark
• Green David, Scottish Marine Institute, Oban, UK
• Jogler Christian, Radboud University, Nijmegen, The Netherlands
• Kaster Anne-Kristin, DSMZ Braunschweig, Germany
• Klenk Hans-Peter, Newcastle University, UK
• Kolter Roberto, Harvard Medical School, Boston, USA
• Philippe Hervé, CNRS Moulis, France
• Santini Joanne, University College London, UK
• Segev Einat, Harvard Medical School, Boston, USA
• Summers Anne, University of Georgia, USA
• Wichard Thomas, Uni Jena, Germany

Publications

Second funding period (2014-2017)

• Bartling P, Brinkmann H, Bunk B, Overmann J, Göker M, Petersen J (2017). The composite 259-kb plasmid of Martelella mediterranea DSM 17316T – A natural replicon with functional RepABC modules from Rhodobacteraceae and Rhizobiaceae. Front Microbiol in press (DOI: 10.3389/fmicb.2017.01787).
• Dickschat J, Rinkel J, Klapschinski T, Petersen J (2017). Characterisation of the L-cystine b-lyase PatB from Phaeobacter inhibens, an enzyme involved in the biosynthesis of the marine antibiotic tropodithietic acid. ChemBioChem in press (DOI:10.1002/cbic.201700358).
• Petersen J, Wagner-Döbler I (2017). Plasmid transfer in the ocean - a case study from the Roseobacter group. Front Microbiol: 8: 1350 (DOI: 10.3389/fmicb.2017.01350).
• 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 J 11: 1483-1499 (DOI: 10.1038/ismej.2016.198).
• 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: e0177295 (DOI: 10.1371/journal.pone.0177295).
• 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 (DOI: 10.7554/eLife.17473).
• 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 (DOI: 10.1038/ismej.2016.30).
• 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 (DOI: 10.1111/1462-2920.13381).
• 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 (DOI: 10.3389/fmicb.2016.00742).
• Kanukollu S, Voget S, Pohlner M, Vandieken V, Petersen J, Kyrpides NC, Woyke T, Shapiro N, Göker M, Klenk H, Cypionka H, Engelen B (2016). Genome sequence of Shimia str. SK013, a representative of the Roseobacter group isolated from marine sediment. Stand Genomic Sci 11: 25 (DOI: 10.1186/s40793-016-0143-0).
• 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 (DOI: 10.3389/fmicb.2015.01262).
• 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. Environ Microbiol 17: 4019–4034 (DOI: 10.1111/1462-2920.12947).
• Lau CKS, 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 (DOI: 10.1186/s40793-015-0050-9).
• 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 (DOI: 10.3389/fmicb.2015.00233).
• 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 (DOI: 10.1016/j.syapm.2014.12.001).
• Riedel T, Spring S, Fiebig A, Scheuner C, Petersen J, Göker M (2015). Genome sequence of the Roseovarius mucosus type strain (DSM 17069^T), a bacteriochlorophyll a-containing representative of the marine Roseobacter group isolated from the dinoflagellate Alexandrium ostenfeldii. Stand Genomic Sci 10: 17 (DOI: 10.1186/1944-3277-10-17).
• 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 (DOI: 10.3389/fmicb.2014.00416).
• 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 24252^T isolated from marine sediment. Stand Genomic Sci 9: 687-703 (DOI: 10.4056/sigs.3828824).
• 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 (DOI: 10.1093/gbe/evu043).
• 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 (DOI: 10.1186/1471-2164-15-130).
• 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 105210^T (= DSM 26640^T = BS107^T). Stand Genomic Sci 9: 914–932 (DOI: 10.4056/sigs.5179110).
• Riedel T, Spring S, Fiebig A, Petersen J, Göker M, Klenk H-P (2014). Genome sequence of the pink to light reddish-pigmented Rubellimicrobium mesophilum type strain (DSM 19309^T), a representative of the Roseobacter group isolated from soil, and emended description of the species. Stand Genomic Sci 9: 902–913 (DOI: 10.4056/sigs.5621012).
• 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 (2014). Genome sequence of the Wenxinia marina type strain (DSM 24838^T), a representative of the Roseobacter group isolated from oilfield sediments. Stand Genomic Sci 9: 855–865 (DOI: 10.4056/sigs.5601028).
• Riedel T, Spring S, Fiebig A, Petersen J, Kyrpides NC, Göker M, Klenk H-P (2014). Genome sequence of the exopolysaccharide-producing Salipiger mucosus type strain (DSM 16094^T), a moderately halophilic member of the Roseobacter clade. Stand Genomic Sci 9: 1331–1343 (DOI: 10.4056/sigs.4909790).

First funding period (2010-2013)

• Buddruhs N*, Pradella S*, Göker M, Päuker O, Pukall R, Spröer C, Schumann P, Petersen J, Brinkhoff T (2013). Molecular and phenotypic analyses reveal the non-identity of the Phaeobacter gallaeciensis type strain deposits CIP 105210^T and DSM 17395. Int J Syst Evol Microbiol 63: 4340-4349. (*contributed equally) (DOI: 10.1099/ijs.0.053900-0).
• 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 14336^T), a member of the Roseobacter clade. Stand Genomic Sci 9:128-41 (DOI: 10.4056/sigs.4297965).
• 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 (DOI: 10.3762/bjoc.9.108).
• 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 24564^T), a surface-associated member of the marine Roseobacter clade. Stand Genomic Sci 8: 403-419 (DOI: 10.4056/sigs.3927626).
• 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 23529^T), a facultatively anaerobic bacterium isolated from marine sediment, and emendation of Phaeobacter daeponensis. Stand Genomic Sci 9: 9:9010142 (DOI: 10.4056/sigs.4287962)
• 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 (T5^T), 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, Koßmehl S, Wöhlbrand L, Rabus R, Wittmann C, Tielen P, Jahn D (2013). Transposon mutagenesis identified chromosomal and plasmid genes essential for adaptation of the marine bacterium Dinoroseobacter shibae to anaerobic conditions. J Bacteriol 195: 4769-4777 (DOI: 10.1128/JB.00860-13).
• Fiebig A, Pradella S, Petersen J, Päuker O, Michael V, Lünsdorf H, Göker M, Klenk H-P, Wagner-Döbler I (2013). Genome of the R-body producing marine alphaproteobacterium Labrenzia alexandrii type strain (DFL-11^T). Stand Genomic Sci 7: 413-426 (DOI: 10.4056/sigs.3456959).
• Fiebig A, Pradella S, Petersen J, Michael V, Päuker O, Rohde M, Göker M, Klenk H-P, Wagner-Döbler I (2013). Genome of the marine alphaproteobacterium Hoeflea phototrophica type strain (DFL-43^T). Stand Genomic Sci 7: 440-448 (DOI: 10.4056/sigs.3486982).
• 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 23566^T. Stand Genomic Sci 8: 450–464 (DOI: 10.4056/sigs.383362).
• Patzelt D, Wang, H, Buchholz, I, Rohde, M, Gröbe, L, Pradella S, Neumann A, Schulz S, Heyber S, Muench K, Muench 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 7/12: 2274-2286 (DOI: 10.1038/ismej.2013.107).
• 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 (DOI: 10.1007/s00253-013-4746-8).
• Riedel T, Fiebig A, Petersen J, Gronow S, Göker M, Klenk HP (2013). Genome sequence of the Litoreibacter arenae type strain (DSM 19593^T), a member of the Roseobacter clade isolated from sea sand. Stand Genomic Sci 9: 117–127.
• Riedel T, Teshima H, Petersen J, Fiebig A, 16 co-authors, Göker M, Brinkhoff T, Klenk HP (2013). Genome sequence of the Leisingera aquimarina type strain (DSM 24565^T), a member of the marine Roseobacter clade rich in extrachromosomal elements. Stand Genomic Sci 8: 389-402 (DOI: 10.4056/sigs.3858183).
• 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 (DOI: 10.1111/j.1462-2920.2012.02806.x).
• 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 (DOI: 10.1093/molbev/msq310).
• Petersen J (2011). Phylogeny and compatibility: plasmid classification in the genomics era. Arch Microbiol 193: 313-321 (DOI: 10.1007/s00203-011-0686-9).
• Wagner-Döbler I, Ballhausen B, Berger M,..., Petersen J, ..., Pradella S, et al. (2010). The complete genome sequence of the algal symbiont Dinoroseobacter shibae: a hitchhiker's guide to life in the sea. ISME J 4: 61-77 (DOI: 10.1038/ismej.2009.94).
• Pradella S, Päuker O, Petersen J (2010). Genome organisation of the marine Roseobacter clade member Marinovum algicola. Arch Microbiol 192: 115-126 (DOI: 10.1007/s00203-009-0535-2).

Relevant previous work

• Petersen J, Brinkmann H, Pradella S (2009). Diversity and evolution of repABC type plasmids in Rhodobacterales. Environ Microbiol 11: 2627-2638 (DOI: 10.1111/j.1462-2920.2009.01987.x).
• Pradella S, Allgaier M, Hoch C, Päuker O, Stackebrandt E, Wagner-Döbler I (2004). Genome organization and localization of the pufLM genes of the photosynthesis reaction center in phylogenetically diverse marine Alphaproteobacteria. Appl Environ Microbiol 70: 3360-3369 DOI: 10.1128/AEM.70.6.3360-3369.2004).

Contributions to symposia and seminars

Second funding period (2014-2017)

• Petersen J (2017). Foreign affairs – Plasmid transfer between bacterial genera reprograms the gene expression of the new host. Colloquium, 13. June 2017, Nijmegen, Netherlands (talk).
• Petersen J (2017). Foreign affairs – Plasmid transfer between bacterial genera reprograms the gene expression of the new host. BAGECO 14, Bacterial Genetics and Ecology, 4-8 June 2017, Aberdeen, Scotland (talk).
• Bartling P, Bunk B, Overmann J, Brinkmann H, Petersen, J (2017). Foreign affairs: Plasmid transfer between roseobacters and rhizobia. 5^th Joint Conference of the DGHM & VAAM. VAAM Annual Meeting 2017 and 69^th Annual Meeting of the DGHM, Würzburg, Germany, March 05-07.
• Petersen J (2016). Microbial ecology from a plasmid perspective. Harvard Medical School, Boston, USA, October 07^th (talk).
• Petersen J. (2016). Verknüpfung von Grundlagenforschung und Sammlungsaktivität am Beispiel der Roseobacter-Gruppe. Scientist‘s Meeting at DSMZ, Braunschweig, Germany, August 22^th.
• Petersen J (2016). Evolutionary plug and play-plasmid-mediated horizontal transfer of photosynthesis in Rhodobacteraceae. Workshop: Photosynthesis: plug and play? Leiden, The Netherlands, August 15-18 (invited talk).
• Petersen J (2016). Highlights beyond plasmids. 12^th Status Seminar of the CRC 51, Oldenburg, Germany, June 23-24 (talk).
• Petersen J (2016). Extrachromosomal, extraordinary and essential - the mobilome of the Roseobacter group. 12^th Status Seminar of the CRC 51, Oldenburg, Germany, June 23-24 (talk).
• Brinkmann H, Petersen J (2016). RpoB-phylogeny of genome-sequenced Rhodobacteraceae. 12^th Status Seminar of the CRC 51, Oldenburg, Germany, June 23-24 (poster).
• Pradella S, Wemheuer B, Päuker O, Frank O, Daniel R, Petersen J (2016). The bacterial diversity of the phycosphere. Annual Meeting of the German Society of General and Applied Microbiology (VAAM), Jena, Germany, March 13-16 (poster).
• Bartling P, Ellebrandt C, Petersen J (2016). Swimming motility of Phaeobacter inhibens DSM 17395 and the regulation of the archetypal flagellum of Rhodobacteraceae. Annual Meeting of the German Society of General and Applied Microbiology (VAAM), Jena, Germany, March 13-16 (poster).
• Petersen J. (2015). Dinoroseobacter shibae - a genetic nightmare? 11^th Status Seminar of the CRC 51, Braunschweig, Germany, December 9^th (talk).
• Pradella S, Michael V, Ellebrandt C, Päuker O, Bartling P, Frank O, Müller S, Brinkmann H, Petersen J (2015). Significance of plasmids in the Roseobacter group. 11^th Status Seminar of the CRC 51, Braunschweig, Germany, December 9^th (poster).
• Frank O, Göker M, Pradella S, Petersen J (2015). Oceans´s twelve: Flagellar and biofilm chromids in the multipartite genome of Marinovum algicola DG898. Prokkagenomics 2015. 6^th European Conference on Procaryotic an Fungal Genomics, Göttingen, Germany, September 29^th-October 2^nd (poster).
• Pradella S (2015). Oceans´s twelve: Flagellar and biofilm chromids in the multipartite genome of Marinovum algicola DG898. 10^th Status Seminar of the CRC 51, Oldenburg, Germany, May 8^th (talk).
• Petersen J, Bartling P (2015). Transposon mutants of Phaeobacter inhibens DSM 17395. 10^th Status Seminar of the CRC 51, Oldenburg, Germany, May 8^th (talk).
• Petersen J (2015). The sixth element – a 102-kb plasmid of Dinoroseobacter shibae modulates chromosomal gene expression. Annual Meeting of the German Society of General and Applied Microbiology (VAAM), Marburg/Lahn, Germany, March 1-4 (talk).
• Müller S, Hahnke RL, Tegtmeyer HE, Moosmann P, Petersen J, Erb TJ, Strous M (2015). Paracoccus denitrificans and nitrite: 500 generations – problem solved. Annual Meeting of the German Society of General and Applied Microbiology (VAAM), Marburg/Lahn, Germany, March 1-4 (talk).
• Petersen J (2015). One, two, three - Plasmid Curing in Phaeobacter inhibens. Microbiological Seminar at the Institute for Chemistry and Biology of the Marine Environment (ICBM), Oldenburg, Germany, January 21^th (talk).
• Petersen J (2014). Generation of 4,000 Transposon Mutants from Phaeobacter inhibens DSM 17395. 9^th Status Seminar of the CRC 51, Braunschweig, Germany, November 20^th (talk).
• Petersen J (2014). The Sixth Element: The 102-kb Plasmid of Dinoroseobacter shibae modulates chromosomal gene expression. 9^th Status Seminar of the CRC 51, Braunschweig, Germany, November 20^th (talk).
• Petersen J (2014). Plasmid curing and the loss of grip – RepA-I type replicons of the Roseobacter group are essential for biofilm formation, motility and the colonization of marine algae. Annual Meeting of the German Society of General and Applied Microbiology (VAAM), Dresden, Germany, October 05-08 (talk).
• Michael V, Päuker O, Sikorski J, Pradella S, Petersen J (2014). So much more than a souvenir - The relevance of plasmids in roseobacters exemplified for Phaeobacter inhibens DSM 17395. Annual Meeting of the German Society of General and Applied Microbiology (VAAM), Dresden, Germany, October 05-08 (poster).
• Petersen J (2014). Chromera velia, endosymbioses and the rhodoplex hypothesis. XVI. Annual Meeting of the International Society of Endocytobiology German Section (ISE-G). Herzogenhorn, Germany, July 21-24 (talk).
• Ludewig A-K (2014). Apicomplexans and the fate of plastids. XVI. Annual Meeting of the International Society of Endocytobiology German Section (ISE-G). Herzogenhorn, Germany, July 21-24 (talk).
• Petersen J (2014). From malaria to sparkling of the sea - Evolution of complex algae and alveolates. Symposium: Photosynthesis as we don't know it. Düsseldorf, Germany, March 27^th (talk).
• Petersen J (2014). Photosynthesis and plasmid-mediated horizontal gene transfer among roseobacters. Liège, Belgium, February 19^th (talk).
• Brinkmann H (2014). Origin and spread of photosynthesis in proteobacteria. Liège, Belgium, February 19^th (talk).
• Ludewig A-K (2014). Chromerids- connecting link in alveolate evolution. Liège, Belgium, February 19^th (talk).

First funding period (2010-2013)

• Frank O (2013). The plasmid wealth of Marinovum algicola opens new perspectives on multipartite genomes. International Symposium of the CRC 51, Delmenhorst, Germany, October 24-26 (talk).
• Patzelt D, Wang H, Buchholz I, Rohde M, Gröbe L, Neumann A, Schulz S, Pradella S, Münch R, Jahn D Wagner-Döbler I, Tomasch J (2013). You are what you talk: Quorum sensing induces individualisation of the algal symbiont Dinoroseobacter shibae DFL-12. Annual Meeting of the German Society of General and Applied Microbiology (VAAM), Bremen, Germany, March 10-13 (poster).
• Petersen J (2013). Transposon Mutagenesis: Experimental distinction of the essential and the dispensable gene pool of Phaeobacter inhibens DSM17395. Retreat of the CRC 51, Wolfenbüttel, Germany, February 15^th (talk).
• Petersen J (2013). Plasmids: Extrachromosomal, extraordinary and essential: The mobilome of the Roseobacter clade. Retreat of the CRC 51, Wolfenbüttel, Germany, February 14^th (talk).
• Petersen J (2012). Transposon Mutagenesis – New project ideas. 7^th Status Seminar of the CRC 51, Delmenhorst, Germany, October 16^th (talk).
• Petersen J (2012). Plasmids – Project A5 Progress report and future perspectives. 7^th Status Seminar of the CRC 51, Delmenhorst, Germany, October 15^th (talk).
• Pradella S (2012). Dinoroseobacter shibae – Plasmide und Plasmid-Curing. Dinoroseobacter shibae seminar, TU Braunschweig, Germany, July 2^nd (talk).
• Frank O, Petersen J, Päuker O, Pradella S (2011). Genome sequence of Marinovum algicola - meet the marine mobilome. ProkaGENOMICS - 5^th European Conference on Prokaryotic and Fungal Genomics, Göttingen, Germany, September 18-21 (poster).
• Petersen J (2011). Think pink: photosynthesis, plasmids and the Roseobacter clade. 3^rd Status Seminar of the CRC 51, HZI, Braunschweig, Germany, September 15^th (talk).
• Buddruhs N, Frank O, Pradella S, Petersen J (2011). Brown becomes white – phenotypical changes of Phaeobacter gallaeciensis through the loss of its major plasmid. MIMAS (Microbial Interactions in Marine Systems) Symposium, Greifswald, Germany, August 6-8 (poster).
• Frank O, Petersen J, Päuker O, Pradella S (2011). Meet the marine mobilome: plasmid classification and the partitioned genome of Marinovum algicola. MIMAS (Microbial Interactions in Marine Systems) Symposium, Greifswald, Germany, August 6-8 (poster).
• Petersen J (2011). Think pink: roseobacters, plasmids and their classification in the genomics era. Julius Kühn Institute, Braunschweig, Germany, June 7^th (invited talk).
• Buddruhs N, Frank O, Michael V, Päuker O, Pradella S, Petersen J (2011). Comparative phenomics of the wild type Phaeobacter gallaeciensis and its 65 kb plasmid knock-out mutant. Annual Meeting of the German Society of General and Applied Microbiology (VAAM), Karlsruhe, Germany, April 3-6 (poster).
• Frank O, Buddruhs N, Michael V, Päuker O, Pradella S, Petersen J (2011). A novel approach for alphaproteobacterial plasmid classification. Annual Meeting of the German Society of General and Applied Microbiology (VAAM), Karlsruhe, Germany, April 3-6 (poster).
• Petersen J (2011). Compatibility and phylogeny – plasmid classification in the genomics era. Annual Meeting of the German Society of General and Applied Microbiology (VAAM), Karlsruhe, Germany, April 6^th (talk).
• Pradella S, Petersen J (2010). Evolution and significance of plasmids within the Roseobacter clade. 1^st Status Seminar of the CRC 51, Braunschweig, Germany, October 21^th (talk).
• Petersen J (2010). Dinoflagellates - The bizarre world of unicellular individualists, Biologische Anstalt Helgoland, Germany, September 20^th (talk).
• Petersen J (2010). The intriguing abundance of plasmids in the Roseobacter clade – a novel approach for their classification. Transregional Collaborative Research Center (CRC-51) Kick-off Symposium: Ecology, Physiology and Molecular Biology of the Roseobacter clade: Towards a Systems Biology Understanding of a Globally Important Clade of Marine Bacteria, HWK, Delmenhorst, Germany, June 14^th (talk).

Knowledge transfer

• Brinkmann H (2011). Guest scientist at the DSMZ, December 2011
• Brinkmann H (2013). Guest scientist at the DSMZ, January 2013
• Michael V (2011). Isolation and cultivation of fastidious dinoflagellates; guest technician hosted by C. Dungan and K. Reece, Virginia, USA, August 2011
• Ludewig A-K (2013). Exchange student hosted by H. Philippe and H. Brinkmann, Université de Montréal, Canada, May to June 2013

Excursions

• Petersen J, Frank O, Michael V (2013). Collection of macro-algae, Helgoland, Germany, June 4-6.
• Frank O (2011). Practical course in marine microbiology at the Biologische Anstalt Helgoland, Germany, September 2011.

Roseobacter plasmids in the media

• DSMZ Press Release (2016). „ Microorganisms Getting a Grip - Plasmids Control Marine Biofilm Formation”, Leibniz-Institute DSMZ, Braunschweig, Germany, March 11^th (DSMZ Press Release Roseobacter 2016).
• DSMZ Press Release (2015). „Cleverer Propellertausch bei Meeresbakterien - Flagellen bei Roseobacter über spezielle Plasmide vererbt“, Leibniz-Institute DSMZ, Braunschweig, Germany, June 22^th (DSMZ Press Release Roseobacter 2015).
• Laborjournal (2012). „Gen-Geflüster - Jörn Petersen fand bei pinken Meeresbakterien eine besondere Form der Kommunikation über Plasmide“, December 11^th (Laborjournal 2012).
• DRadio Wissen (2012). Interview with Jörn Petersen concerning our „Think Pink!“ publication (Petersen et al. 2012), broadcast July 17^th, news id=115268.
• DSMZ Press Release 8/12 (2012). „Think pink! Success of pink bacteria in oceans of the world”, Leibniz-Institute DSMZ, Braunschweig, Germany, July 16^th (DSMZ Press Release Roseobacter 2012).
• DSMZ Press Release (2010). „Rosa: die Trendfarbe für niedersächsische Forscher. Sonderforschungsbereich Roseobacter in Niedersachsen etabliert“, Leibniz-Institute DSMZ, Braunschweig, Germany, October 6^th (DSMZ Presse Realease Roseobater 2010).

Former Members

• Dr. Ann-Kathrin Ludewig-Klingner (*formerly Ann-Kathrin Ludewig)
• Dr. Stefanie Hahnke (*formerly Dr. Stefanie Müller)
• Oliver Frank
• Nora Buddruhs

Principal investigator(s): Markus Göker (formerly also Hans-Peter Klenk)
Postdocs: Dr. Jan P. Meier-Kolthoff
PhD students: Anne Fiebig, Palani Kannan Kandavel
Assistants: Carmen Scheuner, Marina García-Lopez
Student assistants: Lisa Weinhold, Ana Ilieva, Tugce Kaman

Objective

The main goal of this project is to improve our knowledge on the evolution of the Roseobacter clade with the aim to create a reliable genome-informed taxonomy that also considers the phenotypic features of clade members. For this purpose we conduct comparative, functional (phenotyping) and (phylo-)genomic studies. Separation of genealogy-defining information from non-phylogenetic signals in the genomic data allows us to use the latter for the investigation of correlations to ecological conditions and/or geographic origin of the members of the clade, with its ecologically diverse and geographically widespread organisms.

Methods and Results

We are currently genome-sequencing the majority of the Rhodobacteraceae type strains in the course of the KMG-2 project in conjunction with the Joint Genome Institute. These data are phylogenetically analysed using whole-genome bioinfomatic methods, similar to those to infer species boundaries from genome sequences. Phenotypic data are comprehensively collected from the literature to assist in taxonomic reclassifications and comparisons with the phylogeny. Selected genomic features are compared using phylogeny-aware methods with relevant ecological and phenotypic features such as the habitat. For instance, our recent study revealed the genomic adaptations of Rhodobacteraceae to marine environments. We also showed that the so-called "Roseobacter clade" might not be monophyletic and thus should rather not be called a clade. Since bacteriophages are of great interest in marine ecosystems in general and for Rhodobacteraceae in particular, we have developed the web service VICTOR for phage phylogeny and classification. Our earlier work within the SFB-TRR 51 yielded the R package opm for analysising phenotype microarray data.

Publications

Manuscripts in press

Bartling, P., Brinkmann, H., Bunk, B., Overmann, J., Göker, M., Petersen, J. The composite 259-kb plasmid of Martelella mediterranea DSM 17316T – A natural shuttle vector for horizontal gene transfer between Rhodobacteraceae and Rhizobiaceae. Frontiers in Microbiology, in press.

Publications 2014-2017

Breider, S., Scheuner, C., Schumann, P., Fiebig, A., Petersen, J., Pradella, S., Klenk, H.-P., Brinkhoff, T., Göker, M. Genome-scale data suggest reclassifications in the Leisingera-Phaeobacter cluster including proposals for Sedimentitalea gen. nov. and Pseudophaeobacter gen. nov. Frontiers in Microbiology 5: 416, 2014 (doi:10.3389/fmicb.2014.00416).

Breider, S., Teshima, H., Petersen, J., Fiebig, A., Chertkov, O., Dalingault, H., Chen, A., Pati, A., Goodwin, L.A., Chain, P., Detter, J.C., Ivanova, N.N., Lapidus, A., Rohde, M., Tindall, B.J., Kyrpides, N.C., Woyke, T., Simon, M., Göker, M., Klenk, H.-P., Brinkhoff, T. Complete genome sequence of Leisingera nanhaiensis strain DSM 24252^T isolated from marine sediment. Standards in Genomic Sciences 9: 687-703, 2014 (doi:10.4056/sigs.3828824).

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].

Drüppel, K., Hensler, M., Trautwein, K., Koßmehl, S., Wöhlbrand, L., Schmidt-Hohagen, K., Ulbrich, M., Bergen, N., Meier-Kolthoff, J.P., Göker, M., Klenk, H.-P., Schomburg, D., Rabus, R.A. Pathways and substrate-specific regulation of amino acid degradation in Phaeobacter inhibens DSM 17395 (archetype of the marine Roseobacter clade). Environmental Microbiology 16: 218-138, 2014 (doi:10.1111/1462-2920.12276).

Frank, O., Pradella, S., Rohde, M., Scheuner, C., Klenk, H.-P., Göker, M., Petersen, J. Complete genome sequence of the Phaeobacter gallaeciensis type strain CIP 105210^T (= DSM 26640^T = BS107^T). Standards in Genomic Sciences 9: 914-932, 2014 (doi:10.4056/sigs.5179110).

Frank, O., Göker, M., Pradella, S., Petersen, J. Ocean's twelve: Flagellar and biofilm chromids in the multipartite genome of Marinovum algicola DG898 exemplify functional compartmentalization. Environmental Microbiology 17: 4019-4034, 2015 (doi:10.1111/1462-2920.12947).

Hofner, B., Boccuto, L., Göker, M. Controlling false discoveries in high-dimensional situations: Boosting with stability selection. BMC Bioinformatics 16: 144, 2015 (doi:10.1186/s12859-015-0575-3).

Kanukollu, S., Voget, S., Pohlner, M., Vandieken, V., Petersen, J., Kyrpides, N.C., Woyke, T., Shapiro, N., Göker, M., Klenk, H.-P., Cypionka, H., Engelen, B. Genome sequence of Shimia sp. SK013, a representative of the Roseobacter group isolated from marine sediment. Standards in Genomic Sciences 11: 25, 2016 (doi:10.1186/s40793-016-0143-0).

Lau, S.C.K., Riedel, T., Fiebig, A., Han, J., Huntemann, M., Petersen, J., Ivanova, N.N., Markowitz, V., Woyke, T., Göker, M., Kyrpides, N.C., Klenk, H.-P., Qian, P-Y. Genome sequence of the pink-pigmented marine bacterium Loktanella hongkongensis type strain (UST950701-009P^T), a representative of the Roseobacter group. Standards in Genomic Sciences 10: 51, 2015 (doi:10.1186/s40793-015-0050-9).

Meier-Kolthoff JP, Göker M. (2017) Genome-based phylogeny and classification of bacteriophages. Bioinformatics 2017: 1-9, 2017 (doi:10.1093/bioinformatics/btx440).

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

Michael, V., Frank, O., Bartling, P., Scheuner, C., Göker, M., Brinkmann, H., Petersen, J. Biofilm-plasmids with a rhamnose operon are essential determinants of the “swim-or-stick” lifestyle in roseobacters. The ISME Journal 2016: 1-16, 2016 (doi:10.1038/ismej.2016.30).

Riedel, T., Spring, S., Fiebig, A., Scheuner, C., Petersen, J., Göker, M., Klenk, H.-P. Genome sequence of the Roseovarius mucosus type strain (DSM 17069^T), a bacteriochlorophyll a-containing representative of the marine Roseobacter group isolated from the dinoflagellate Alexandrium ostenfeldii. Standards in Genomic Sciences 10: 17, 2015 (doi:10.1186/1944-3277-10-17).

Riedel, T., Fiebig, A., Göker, M., Klenk, H.-P. Complete genome sequence of the bacteriochlorophyll a-containing Roseibacterium elongatum type strain (DSM 19469^T), a representative of the Roseobacter clade isolated from Australian coast sand. Standards in Genomic Sciences 9: 840-854, 2014 (doi:10.4056/sigs.5541028).

Riedel, T., Fiebig, A., Han, J., Huntemann, M., Spring, S., Petersen, J., Ivanova, N.N., Markowitz, V., Woyke, T., Göker, M., Kyrpides, N.C., Klenk, H.-P. Genome sequence of the Wenxinia marina type strain (DSM 24838^T), a representative of the Roseobacter clade isolated from oilfield sediments. Standards in Genomic Sciences 9: 855-865, 2014 (doi:10.4056/sigs.5601028).

Riedel, T., Spring, S., Fiebig, A., Petersen, J., Göker, M., Klenk, H.-P. Genome sequence of the pink to light reddish-pigmented Rubellimicrobium mesophilum type strain (DSM 19309^T), a representative of the Roseobacter clade isolated from soil, and emended description of the species. Standards in Genomic Sciences 9: 902-913, 2014 (doi:10.4056/sigs.5621012).

Riedel, T., Spring, S., Fiebig, A., Petersen, J., Kyrpides, N.C., Göker, M., Klenk, H.-P. Genome sequence of the exopolysaccharide-producing Salipiger mucosus type strain (A3^T), a moderately halophilic member of the Roseobacter clade. Standards in Genomic Sciences 9: 1331-1343, 2014 (doi:10.4056/sigs.4909790).

Simon, M., Scheuner, C., Meier-Kolthoff, J.P., Brinkhoff, T., Wagner-Döbler, I., Ulbrich, M., Klenk, H.-P., Schomburg, D., Petersen, J., Göker, M. Phylogenomics of Rhodobacteraceae reveals evolutionary adaptation to marine and non-marine habitats. The ISME Journal 2017, 1-17, 2017 (doi:10.1038/ismej.2016.198).

Voget, S., Göker, M., Brinkhoff, T. Genomik: Grundlage zum Verständnis des Erfolgs der Roseobacter-Gruppe. BIOSpektrum 20: 279-282, 2014.

Publications 2011-2013

Beyersmann, P.G., Chertkov, O., Petersen, J., Fiebig, A., Chen, A., Pati, A., Ivanova, N.N., Lapidus, A., Goodwin, L.A., Chain, P., Detter, J.C., Rohde, M., Gronow, S., Kyrpides, N.C., Woyke, T., Simon, M., Göker, M., Klenk, H.-P., Brinkhoff, T. Genome sequence of Phaeobacter caeruleus type strain (DSM 24564^T), a surface-associated member of the marine Roseobacter clade. Standards in Genomic Sciences 8: 403-419, 2013 (doi:10.4056/sigs.3927623).

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 24252^T isolated from marine sediment. Stand Genomic Sci, 9: 687-703.

Buddruhs, N., Chertkov, O., Petersen, J., Fiebig, A., Chen, A., Pati, A., Ivanova, N.N., Lapidus, A., Goodwin, L.A., Chain, P., Detter, J.C., Gronow, S., Kyrpides, N.C., Woyke, T., Göker, M., Brinkhoff, T., Klenk, H.-P. Complete genome sequence of the marine methyl-halide oxidizing Leisingera methylohalidivorans type strain (DSM 14336^T), a member of the Roseobacter clade. Standards in Genomic Sciences 9: 128-141, 2013 (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. Molecular and phenotypic analyses reveal the non-identity of the Phaeobacter gallaeciensis type strain deposits CIP 105210^T and DSM 17395. International Journal of Systematic and Evolutionary Microbiology 63: 4340-4349, 2013 (doi:10.1099/ijs.0.053900-0).

Dogs, M., Teshima, H., Petersen, J., Fiebig, A., Chertkov, O., Dalingault, H., Chen, A., Pati, A., Goodwin, L.A., Chain, P., Detter, J.C., Ivanova, N.N., Lapidus, A., Rohde, M., Gronow, S., Kyrpides, N.C., Woyke, T., Simon, M., Klenk, H.-P., Göker, M., Brinkhoff, T. Genome sequence of Phaeobacter daeponensis type strain (DSM 23529^T), a facultatively anaerobic bacterium isolated from marine sediment, and emendation of Phaeobacter daeponensis. Standards in Genomic Sciences 9: 142-159, 2013 (doi:10.4056/sigs.4287962).

Dogs, M., Voget, S., Teshima, H., Petersen, J., Fiebig, A., Davenport, K.W., Dalingault, H., Chen, A., Pati, A., Ivanova, N.N., Goodwin, L.A., Chain, P., Detter, J.C., Rohde, M., Gronow, S., Kyrpides, N.C., Woyke, T., Simon, M., Klenk, H.-P., Göker, M., Brinkhoff, T. Genome sequence of Phaeobacter inhibens type strain (T5^T), a secondary-metabolite producing member of the marine Roseobacter clade, and emendation of the species Phaeobacter inhibens. Standards in Genomic Sciences 9: 334-350, 2013 (doi:10.4056/sigs.4448212).

Drüppel K, Hensler M, Trautwein K, Koßmehl S, Wöhlbrand L, Schmidt-Hohagen K, Ulbrich M, Bergen N, Meier-Kolthoff J, Göker M, Klenk HP, Schomburg D, Rabus, AR (2013) Pathways and substrate-specific regulation of amino acid degradation in Phaeobacter inhibens DSM 17395 (archetype of the marine Roseobacter clade). Environ Microbiol, submitted.

Fiebig, A., Pradella, S., Petersen, J., Michael, V., Päuker, O., Rohde, M., Göker, M., Klenk, H.-P., Wagner-Döbler, I. Genome of the marine alphaproteobacterium Hoeflea phototrophica type strain (DFL-43^T). Standards in Genomic Sciences 7: 440-444, 2013 (doi:10.4056/sigs.3486982).

Fiebig, A., Pradella, S., Petersen, J., Päuker, O., Michael, V., Lünsdorf, H., Göker, M., Klenk, H.-P., Wagner-Döbler, I. Genome of the R-body producing marine alphaproteobacterium Labrenzia alexandrii type strain (DFL-11^T). Standards in Genomic Sciences 7: 413-426, 2013 (doi:10.4056/sigs.3456959).

Fiebig, A., Riedel, T., Gronow, S., Klenk, H.-P., Göker, M. Genome sequence of the reddish-pigmented Rubellimicrobium thermophilum type strain (DSM 16684^T), a member of the Roseobacter clade. Standards in Genomic Sciences 8: 480-490, 2013 (doi:10.4056/sigs.4247911).

Freese, H., Dalingault, H., Petersen, J., Pradella, S., Fiebig, A., Davenport, K.W., Teshima, H., Chen, A., Pati, A., Ivanova, N.N., Goodwin, L.A., Chain, P., Detter, J.C., Rohde, M., Gronow, S., Kyrpides, N.C., Woyke, T., Brinkhoff, T., Göker, M., Overmann, J., Klenk, H.-P. Genome sequence of the phage-gene rich marine Phaeobacter arcticus type strain DSM 23566^T. Standards in Genomic Sciences 8: 450-464, 2013 (doi:10.4056/sigs.383362).

Göker, M., Klenk, H.-P. Phylogeny-driven target selection for genome-sequencing (and other) projects. Standards in Genomic Sciences 8: 360-374, 2013 (doi:10.4056/sigs.3446951).

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.

Petersen, J., Frank, O., Göker, M., Pradella, S. Extrachromosomal, Extraordinary and Essential – The Plasmids of the Roseobacter Clade. Applied Microbiology and Biotechnology 97: 2805-2815, 2013.

Riedel, T., Fiebig, A., Petersen, J., Gronow, S., Göker, M., Klenk, H.-P. Genome sequence of the Litoreibacter arenae type strain (DSM 19593^T), a member of the Roseobacter clade isolated from sea sand. Standards in Genomic Sciences 9: 117-127, 2013 (doi:10.4056/sigs.4258318).

Riedel, T., Teshima, H., Petersen, J., Fiebig, A., Davenport, K.W., Dalingault, H., Erkkila, T., Gu, W., Munk, A.C., Xu, Y., Chen, A., Pati, A., Ivanova, N.N., Goodwin, L.A., Chain, P., Detter, J.C., Rohde, M., Gronow, S., Kyrpides, N.C., Woyke, T., Göker, M., Brinkhoff, T., Klenk, H.-P. Genome sequence of the Leisingera aquimarina type strain (DSM 24565^T), a member of the marine Roseobacter clade rich in extrachromosomal elements. Standards in Genomic Sciences 8: 389-402, 2013 (doi:10.4056/sigs.3858183).

Sikorski, J., Göker, M., Vaas, L.A.I. Analyse von Hochdurchsatzdaten – Struktur und Umfang eines neu entwickelten Software-Pakets. GIT Labor-Fachzeitschrift 56: 528-530, 2012.

Vaas, L.A.I., Sikorski, J., Hofner, B., Buddruhs, N., Fiebig, A., Klenk, H.-P., Göker, M. opm: An R package for analysing OmniLog® Phenotype MicroArray Data. Bioinformatics 29: 1823-1824, 2013 (doi:10.1093/bioinformatics/btt291).

Vaas, L.A.I., Sikorski, J., Michael, V., Göker, M., Klenk, H.-P. Visualization and curve-parameter estimation strategies for efficient exploration of Phenotype Microarray kinetics. PLoS ONE 7: e34846, 2012 (doi:10.1371/journal.pone.0034846).

Principal investigator: Prof. Dr. Jörg Overmann
Scientist: Dr. Heike M. Freese

Aim

Bacteria of the Roseobacter clade represent an abundant but also phylogenetically and physiologically diverse group of marine bacteria. The evolutionary mechanisms underlying this high diversity (such as selective forces) have remained so far unknown. Therefore, we will identify the intraspecific population structure of the model organisms Phaeobacter inhibens and P. gallaeciensis in order to identify the specific evolutionary forces that are responsible for diversification of this important bacterial group.

A collection of 88 available Phaeobacter inhibens and P. gallaeciensis strains is investigated. The 16S rRNA genes of these strains show a close similarity of 99.5%. Comparisons of the complete internal transcribed spacer sequences and MALDI-TOF profiles showed that the strains fall in distinct subgroups. For a comprehensive analysis of the population structure of Phaeobacter inhibens and P. gallaeciensis, the genomes of representative strains were sequenced and are currently being analyzed.

In parallel, high-throughput isolation strategies are applied to enrich additional Phaeobacter-strains from the environment. Phaeobacter-related bacteria were successfully enriched. Variations in the phylogenetic composition among the different habitats suggest a habitat preference of the different lineages of the Roseobacter clade.

Methods

The Phaeobacterstrains are grown in appropriate media (Fig. 1) and their DNA extracted. For genome-sequencing, Illumina and PacBio-technology are employed. The two sequence types are separately assembled de novo and the created contigs are co-assembled afterwards. Then, the population structure is analysed (e.g. by split decomposition-analysis) and population genetics parameters (such as recombination rate : mutation rate r/n, effective population size, dN/dS) are determined from genes and genomes. Results will be compared with habitat parameters but also with the phenotypic characteristics of the strains.

In order to isolate Phaeobacter sp. from the environment, samples were taken at the North Sea coast in Neuharlingersiel (Fig. 2) and also during cruises of RV Sonne to the Pacific Ocean. Liquid and biofilm-specific high-throughput cultivation are performed using defined media. Success of cultivation is checked via specific screening PCR and sequencing.

Expeditions

Expedition SO254 (RV Sonne, February 2017, Southwest Pacific, Auckland (New Zealand) - Auckland): Functional diversity of bacterial communities and the metabolome in the water column, sediment and in sponges in the southwest Pacific around New Zealand – Population structure and divergence in the Roseobacter group

Expedition SO248 (RV Sonne, May 2016, Pacific transect, Auckland (New Zealand) - Dutch Harbour (Alaska)): Functional diversity of bacterial communities and the geometabolome in the central and north Pacific – Population structure and divergence in the Roseobacter group

Publications

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.

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. 67: 2153-2159.

Freese HM, Methner A, Overmann J (2017) Adaptation of biofilm bacteria to the open ocean: A genomically distinct subpopulation of Phaeobacter gallaeciensis colonizes Pacific mesozooplankton. Front Microbiol 8: 1659.

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.

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

Sonnenschein EC, Broughton C, Phippen W, Nielsen KF, Mateiu RV, Melchiorsen J, Gram L, Overmann J, Freese HM (2017) Phaeobacter piscinae sp. nov., a novel species of the roseobacter group and potential aquaculture probiont. Int J Syst Evol Microbiol. In press.

Principal investigators: Prof. Dr. Thorsten Dittmar, Dr. Jutta Niggemann, Prof. Dr. Meinhard Simon

Post docs:

PhD students:

Project outline:

Scientific questions

Marine dissolved organic matter (DOM) plays a vital role for life on Earth. It links organic matter production and decay in the water column because algal products can only be taken up by prokaryotic consumers as small dissolved molecules. Most of DOM is turned over by heterotrophic prokaryotes within hours and days after production. A small fraction of DOM, however, resists prokaryotic degradation. This refractory fraction of DOM has persisted in the ocean for thousands of years, and has accumulated to the largest pool of organic carbon in the ocean, approx. 30 times larger than the pool of particulate organic carbon. DOM remains arguably the most mysterious carbon pool on earth. It is an enigma how reduced organic molecules persist for millennia in an oxygen- and nutrient-rich environment in the deep ocean. Heterotrophic prokaryotes can acquire chemical energy and essential elements, such as nitrogen and phosphorous, from the oxidation of DOM, and most of the DOM is small enough in molecular size to be directly taken up by heterotrophic prokaryotes. In this project we aim at a better understanding of DOM in two aspects: 1 - The reasons behind millennium-scale stability of DOM, and 2 - Molecular interactions between prokaryotes and DOM in marine systems. The well characterized Roseobacter clade provides us with the unique opportunity to test hypotheses under well-constrained settings in the laboratory and in the field.

The advent of ultrahigh-resolution mass spectrometry via the Fourier transform ion cyclotron resonance technique (FT-ICR MS) has allowed unprecedented insights into the molecular composition of marine DOM. Over the past few years we identified >10,000 molecular formulae of compounds in DOM. The structural isomers behind these formulae are unknown, but in a recent study we estimated that there are more than 10¹⁵ different molecules in each liter of seawater. The concentration of individual compounds is so low that molecular diffusion limits uptake by microorganisms which is probably the main reason for the persistence of DOM in the ocean.

We hypothesize that part of the enormous molecular diversity in DOM is already present in the exometabolome of a single species. The expression of different metabolic pathways due to different growth or substrate conditions further increases the molecular diversity. In addition, each bacterial species has a specific molecular fingerprint. The interplay of species further increases the complexity of the exometabolome. This is also true for members of the Roseobacter clade and, therefore, relevant members of pelagic subclusters of this clade are involved in shaping the exometabolome of a given situation in pelagic ecosystems.

Aims, work program and methods

In order to understand the specific role and function of relevant members of pelagic subclusters of the Roseobacter clade (RCA, CHABI-5, NAC11-6, SH6-1, Octadecabacter) for shaping the marine exometabolome we will carry out growth experiments with model organisms of these subclusters and examine their exometabolome at typical situations of their growth cycle, initial conditions, mid-exponential growth phase, early and late stationary phase. The model organisms will be grown on defined single carbon sources, on algal exudates, at varying growth conditions (dark, light-dark, enhanced CO partial pressure, different temperatures). Further, selected experiments will be done with mixed cultures with one organism of the Roseobacter clade, utilizing preferentially low molecular weight compounds, and one Flavobacterium, rich in hydrolytic enzyme activities and thus capable of breaking down biopolymers, in order to examine the impact of bacterial interactions on the exometabolome.

We will molecularly characterize the exometabolome through a most comprehensive and holistic analytical approach via FT-ICR-MS. This approach will provide us with the molecular formulae of most compounds present in the exometabolome of our experiments. These molecular fingerprints can be compared to our extensive in-house data bank of the DOM geometabolome of >1000 seawater samples from around the globe. In collaboration within this CRC, a selected number of samples will be molecularly characterized by more conventional metabolic analyses. The analytical window of these techniques is more narrow compared to FT-ICR-MS, but quantitative and structural information can be obtained which will be highly complementary to FT-ICR-MS. Growth of the bacteria will be monitored by flow cytometry. Further, the physiological activity of the bacteria will be studied by hydrolytic enzyme activities (leucine aminopeptidase, a- and b-glucosidase, chitinase), transcriptomic and in selected experiments also proteomic profiling of the four selected growth stages.

Publications

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.

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.

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.

Ended

Principal investigator: Prof. Dr. Heribert Cypionka

PhD student: Christian Kirchhoff

Former PhD student: Maya Soora 

Objectives and Projects

Dinoroseobacter shibae is an aerobic anoxygenic phototroph (AAP), capable of using light as an additional energy source under oxic conditions. While light is known to increase growth yields in continuous cultures only marginally, we suspected that the cells benefit from light particularly under conditions of carbon and electron donor limitation. Using Dinoroseobacter shibae as model organism we tested the hypothesis that the role of light energy for the cellular metabolism is proportional to the degree of starvation. We showed that light can indeed enhanced survival during long term starvation (Soora et al. 2013).

In a subsequent study we  focused on cytotoxic reactive oxygen species which are produced as a direct result light exposure in D. shibae. We analyzed the role of the extrachromosomal elements  (ECRs) and found that the genes of the oxygen stress response on the 72-kb chromid were strongly activated under light/dark cycle, compared to cells which grew in complete darkness. A Δ72-kb curing mutant lost the ability to survive under starvation in a light/dark cycle demonstrating the essential role of this chromid for oxidative stress adapation (Soora et al. 2015)

Tt was documented that light supports proton translocation and therefore contributes to the ATP regeneration in D. shibae (Holert et al. 2011). The mechanisms behind the fast recovery of the energy charge after anoxia are not clear yet. We addressed the bioenergetics of short-term anoxia and the quick ATP recovery in D. shibae. We hypothesized that the proton-motive force is involved, assuming that it would be low in de-energized cells and increase during recovery. Therefore we analyzed ΔpH and ΔΨ during oxic-anoxic transitions. We found that ΔpH is not affected by short-term anoxia and does not contribute to the quick ATP regeneration in D. shibae. By contrast, ΔΨ was increased during anoxia, which was astonishing since none of the control organisms behaved that way. For the lifestyle of D. shibae as an epibiont of a dinoflagellate, the ability to stand phases of temporary oxygen depletion is beneficial. With a boosted ΔΨ, the cells are able to give their ATP regeneration a flying start, once oxygen is available again. (Kirchhoff and Cypionka, submitted 2016).

Methods

Cultivation

• Two continuous cultures (3-l fermentors) in order to produce cells under defined conditions.
• Batch cultivation

Analysis of biomass-related parameters

• Dry weight (ammonium acetate method)
• Total protein concentration (Lowry´s method)
• Total cell and Viable counts (SybrGreen and plate count)
• Bacteriochlorophyll a, carotenoids (Acetone/methanol extraction)
• Polyhydroxyalkanoates (Nile Blue staining)
• Transmission Electron Microscopy

Determination of physiological activities (schematics)

• Substrate-stimulated and endogenous respiration (Clarke electrode)
• Electron-transport driven proton translocation, oxic and anoxic respiration (pH meter)
• Measurement of cytoplasmic ATP concentration (luciferin-luciferase method, luminometer)    
• Intracellular pH and buffer capacity (butanol method )
• Life/Dead staining (Sybr Green and propidium iodide)
• Membrane potential visualization (DiOC/JC-10 staining)

Publications:

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.

Kirchhoff C, Cypionka H (2017) Propidium ion enters viable cells with high membrane potential during live-dead staining. J Microbiol Methods 142:79-82, https://doi.org/10.1016/j.mimet.2017.09.011.

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.

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, https://doi.org/10.3389/fmicb.2015.00233.

Soora M, Cypionka H (2013) Light enhances survival of Dinoroseobacter shibae during long-term starvation. PLoS ONE 8:e83960, https://doi.org/10.1371/journal.pone.0083960.

Holert J, Hahnke S, Cypionka H (2010) Influence of light and anoxia on chemiosmotic energy conservation in Dinoroseobacter shibae. Environm Microbiol Rep 3(1), 136-141, https://doi.org/10.1111/j.1758-2229.2010.00199.x.

Completed Master Thesis and Research Projects:

Christian Kirchhoff (Master Thesis) 2013. Key factors for the energy state of Dinoroseobacter shibae.

Robert Strodel (Reasearch Project) 2015. The sensitivity of Dinoroseobacter shibae for different membrane potential affecting agents.

Dang Nyguen (Research Project) 2015. Comparison of the membrane potential (Δψ)-indicating dyes JC-10 and DiOC2(3) by fluoresence microscopy

Conferences:

Kirchhoff C, Cypionka H; ISME 2016, Montreal. Membrane potential gives kick-off for quick ATP regeneration after short-term anoxia in Dinoroseobacter shibae

Kirchhoff C, Cypionka H; VAAM 2015, Marburg. Energetically depleted Dinoroseobacter shibae maintains strong membrane potential. poster

Kirchhoff C, Cypionka H; VAAM 2014, Dresden. Energetic state of Dinoroseobacter shibae during short-term anoxia. poster

Soora M, Cypionka H; VAAM 2013, Bremen. Light-enhanced survival of Dinoroseobacter shibae during long-term starvation. poster

Soora M, Cypionka H; VAAM 2011, Karlsruhe. Role of light in the survival of Dinoroseobacter shibae  during starvation. poster

Supervisors: apl. Prof. Dr. Thorsten Brinkhoff and Prof. Dr. Meinhard Simon

Research associates: Dr. Marco Dogs, Dr. Martine Berger, Laura Wolter (PhD student), Sven Breider (PhD student), Sujatha Srinivas (master student), Agnes Picard (master student).

Former research associates (topics see below): Paul Beyersmann (dissertation finished 2016), Sebastian Thole (dissertation finished 2012), Daniela Kalhoefer (dissertation finished 2011), Sarah Hahnke (dissertation finished 2011), Regina Gohl (master thesis finished 2012), Susann Zilkenat (master thesis finished 2011), Sven Breider (master thesis finished 2011), Ines Preuth (diploma thesis finished 2010).

Aims

Bacteria of the Roseobacter clade appear worldwide in marine habitats, often in high abundances. Overall, these organisms show a high phylogenetic and metabolic diversity. The aim of this project is to identify and study members of the Roseobacter clade producing secondary metabolites and finally to elucidate the ecological significance of the compounds for these organisms. Besides the investigation of established model organisms, new strains are tested under various conditions to determine if and when secondary metabolites are produced. By screening a variety of isolates, clusters or groups with increased potential for secondary metabolite production will be identified. Genetic experiments with selected model organisms elucidate which genes and biochemical pathways are involved and how the production is controlled. Further experiments unravel interactions of roseobacters with other pro- and eukaryotic microorganisms.

Methods

To assess the diversity (mainly richness, but also abundance of the most relevant organisms) of the Roseobacter clade with respect to secondary metabolite producing species, we use culture-dependent and -independent approaches (DGGE based Roseobacter clade specific primers as well as 454 sequencing in collaboration with project A3). Isolates were obtained from various marine habitats, i.e. from surfaces, which provide environments ruled by strong competition (e.g. surfaces of macroalgae, see Figure 1), and for comparison also from pelagic systems (in collaboration with project A1). Identification of new strains is performed by analysis of their 16S rRNA genes. Subsequently, the strains are screened for production of secondary metabolites. Therefor, biological and chemical methods are applied, e.g. inhibtion tests against a broad range of microorganisms on agar plates, but also chemical methods in collaboration with colleagues from other projects of the TRR 51 (B3 and C2).

For deeper knowledge the genomes of some model organisms were sequenced and analysed (i.e. Phaeobacter and Roseobacter spp.). They provide now an excellent basis for genetic experiments, to elucidate which genes and biochemical pathways are involved in the production of the secondary metabolites and how the production is controlled. The latter is also studied by microarray-experiments in collaboration with project B4. These experiments are currently focussed on organisms of the genus Phaeobacter, for which production of various secondary metabolites has been demonstrated.

Further experiments unravel interactions of roseobacters with other pro- and eukaryotic microorganisms. Here we perform colonization experiments of green fluorescent protein (gfp)-labeled Phaeobacter gallaeciensis DSM 17395 cells, which showed settlement of the Phaeobacter cells on various organisms and surfaces (see Figure 2).

For Phaeobacter gallaeciensis DSM 17395 we established several genetic methods. Presumably most genes involved in the production of the antibiotic tropodithietic acid and several regulatory parameters were determined (see publications of project B2). It is planned to deepen the studies on this organism, but also to investigate other secondary metabolite producing roseobacters, recently isolated from macroalgae. One promising example is a strain obtained from Fucus spp., showing inhibiting properties only when Fucus material is present in the growth medium. Another secondary metabolite producing bacterium, isolated from the marine alga Ulva australis, was recently characterized and described as a new species of a new genus, Epibacterium ulvae (in collaboration with colleagues from the University of New South Wales, Sydney, Australia). The secondary metabolite production of this organism and the interaction with its host will also be further studied.

Publications

List of Publications (Project B2)

2017

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.

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.

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].

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.

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.

2016

Giebel, H.-A., F. Klotz, S. Voget, A. Poehlein, K. Grosser, A. Teske, T. Brinkhoff. 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: DOI: 10.1186/s40793-016-0201-7.

Billerbeck, S., B. Wemheuer, S. Voget, A. Poehlein, H.-A. Giebel, T. Brinkhoff, L. Gram, W. H. Jeffrey, R. Daniel, M. Simon. 2016. Biogeography and environmental genomics of CHAB-I-5, a pelagic lineage of the marine Roseobacter clade. Nature Microbiol. 1: Article Number: 16063.

Wichmann, H., T. Brinkhoff, M. Simon, C. Richter-Landsberg. 2016. Dimethyl-sulfoniopropionate promotes process outgrowth in neural cells and exerts protective effects against tropodithietic acid. Marine Drugs. 14: Article Number: UNSP 89.

2015

Wichmann, H., F. Vocke, T. Brinkhoff, M. Simon, C. Richter-Landsberg. 2015. Cytotoxic effects of tropodithietic acid on mammalian clonal cell lines of neuronal and glial origin. Marine Drugs. 13: 7113–7123.

Ziesche, L., H. Bruns, M. Dogs, L. Wolter, F. Mann, I. Wagner-Döbler, T. Brinkhoff,. S. Schulz. 2015. Homoserine lactones, methyl oligohydroxybutyrates and other extracellular metabolites of macroalgae associated bacteria of the Roseobacter clade: Identification and function. ChemBioChem. 16: 2094-2107.

Gram, L., B. Barker Rasmussen, B. Wemheuer, N. Bernbom, Y. Yin Ng, C. H. Porsby, S. Breider, T. Brinkhoff. 2015. Phaeobacter inhibens from the Roseobacter-clade has an environmental niche as surface colonizer in harbours. Syst. Appl. Microbiol. 7: 483-493.

Billerbeck, S., J. Orchard, B.J. Tindall, H.-A. Giebel, T. Brinkhoff, M. Simon. 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. Int. J. Syst. Evol. Microbiol. 65: 1967-1974.

Klingner, A., A. Bartsch, M. Dogs, I. Wagner-Döbler, D. Jahn, M. Simon, T. Brinkhoff, J. Becker, C. Wittmann. 2015. Large-scale 13C-flux profiling reveals conservation of the Entner-Doudoroff pathway as glycolytic strategy among glucose-using marine bacteria. Appl. Environ. Microbiol. 81: 2408-2422.

Voget, S., B. Wemheuer, T. Brinkhoff, J. Vollmers, S. Dietrich, H.A. Giebel, C. Beardsley, C. Sardemann, I. Bakenhus, S. Billerbeck, R. Daniel, M. Simon. 2015. Adaptation of an abundant Roseobacter RCA organism to pelagic systems revealed by genomic and transcriptomic analyses. ISME J. 9: 371–384.

2014

Breider, S., C. Scheuner, P. Schumann, A. Fiebig, J. Petersen, S. Pradella, M. Simon, H.-P. Klenk, T. Brinkhoff, M. Göker. 2014. Genome-scale data suggest reclassifications in the Leisingera-Phaeobacter cluster including proposals for Sedimentitalea gen. nov. and Pseudophaeobacter gen. nov. Front. Microbiol. doi: 10.3389/fmicb.2014.00416.

Breider, S., H. Teshima, J. Petersen, O. Chertkov, H. Dalingault, A. Chen, A. Pati, N. Ivanova, A. Lapidus, L.A. Goodwin, P. Chain, J.C. Detter, M. Rohde, B.J. Tindall, N.C. Kyrpides, T. Woyke, M. Simon, M. Göker, H.-P. Klenk, T. Brinkhoff. 2014. Genome sequence of Leisingera nanhaiensis strain DSM 24252^T isolated from marine sediment. Stand. Genomic Sci. 9: 687-703.

2013

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 24564^T), 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 24252^T 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.

Buddruhs N, O. Chertkov, J. Petersen, A. Fiebig, A. Chen, A. Pati, N. Ivanova, A. Lapidus, L. Goodwin, P. Chain, J. Detter, S. Gronow, N. Kyrpides, T. Woyke, M. Göker, T. Brinkhoff, H.P. Klenk. 2013. Complete genome sequence of the marine methyl-halide oxidizing Leisingera methylohalidivorans type strain (DSM 14336^T), a member of the Roseobacter clade. Stand. Genomic Sci. 9: 128-141 (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) Molecular and phenotypic analyses reveal the non-identity of the Phaeobacter gallaeciensis type strain deposits CIP 105210^T and DSM 17395. Int. J. Syst. Evol. Microbiol. 63: 4340–4349.

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 (T5^T), 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).

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 23529^T), a facultatively anaerobic bacterium isolated from marine sediment, and emendation of Phaeobacter daeponensis. Stand Genomic Sci 9: 142-159.

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 23566^T. Stand Genomic Sci 8(3): 450–464.

Giebel, H.-A., D. Kalhoefer, R. Gahl-Janssen, Y.-J. Choo, K. Lee, J.-C. Cho, B.J. Tindall, E. Rhiel, C. Beardsley, Ö.O. Aydogmus, S. Voget, R. Daniel, M. Simon, T. Brinkhoff. 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. Syst. Evol. Microbiol. 63: 4207–4217.

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., M. Sperling, T. Langer, A. Wichels, G. Gerdts, C. Beardsley, T. Brinkhoff, M. Simon. 2013. Distinct seasonal growth patterns of the bacterium Planktotalea frisia in the North Sea and specific interaction with phytoplankton algae. FEMS Microbiol. Ecol. 86: 185-199.

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.

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.

Riedel, T., H. Teshima, J. Petersen, A. Fiebig, K. Davenport, H. Daligault, T. Erkkila, W. Gu, C. Munk, Y. Xu, A. Chen, A. Pati, N. Ivanova, L.A. Goodwin, P. Chain, J.C. Detter, M. Rohde, S. Gronow, N.C. Kyrpides, T. Woyke, M. Göker, T. Brinkhoff, H.-P. Klenk. 2013. Genome sequence of the Leisingera aquimarina type strain (DSM 24565^T), a member of the marine Roseobacter clade rich in extrachromosomal elements. Stand. Genomic Sci. 8: 389-402.

Thole S, Kalhoefer D, Voget S, Berger M, Engelhardt T, Liesegang H, Wollher 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 J 6: 2229–2244.

Vollmers, J., S. Voget, S. Dietrich, K. Gollnow, M. Smits, K. Meyer, T. Brinkhoff, M. Simon, R. Daniel. 2013. Poles apart: Arctic and Antarctic Octadecabacter strains share high genome plasticity and a new type of xanthorhodopsin. PloS one. 8: e63422.

2012

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.

Thole, S, Kalhoefer D, Voget S, Berger M, Engelhardt T, Liesegang H, Wollherr A, Kjelleberg S, Daniel R, Simon M et al..  2012.  Phaeobacter gallaeciensis genomes from globally opposite locations reveal high similarity of adaptation to surface life.. The ISME journal. 6(12):2229-44.

Penesyan, A, Breider S, Schumann P, Tindall BJ, Egan S, Brinkhoff T.  2012.  Epibacterium ulvae gen. nov., sp. nov., epibiotic bacteria isolated from the surface of a marine alga.. International journal of systematic and evolutionary microbiology.

2011

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.

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. 12:324.

List of Publications (Further publications concerning the Roseobacter clade)

2013

Hahnke, S, Tindall BJ, Schumann P, Simon M, Brinkhoff T.  2013.  Pelagimonas varians gen. nov., sp. nov., isolated from the southern North Sea.. International journal of systematic and evolutionary microbiology. 63(Pt 3):835-43.

2012

Hahnke, S, Tindall BJ, Schumann P, Sperling M, Brinkhoff T, Simon M.  2012.  Planktotalea frisia gen. nov., sp. nov., isolated from the southern North Sea.. International journal of systematic and evolutionary microbiology. 62(Pt 7):1619-24.

Lenk, S, Moraru C, Hahnke S, Arnds J, Richter M, Kube M, Reinhardt R, Brinkhoff T, Harder J, Amann R et al..  2012.  Roseobacter clade bacteria are abundant in coastal sediments and encode a novel combination of sulfur oxidation genes.. The ISME journal. 6(12):2178-87.

2011

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.. Molecular biology and evolution. 28(3):1229-40.

Giebel, H-A, Kalhoefer D, Lemke A, Thole S, Gahl-Janssen R, Simon M, Brinkhoff T.  2011.  Distribution of Roseobacter RCA and SAR11 lineages in the North Sea and characteristics of an abundant RCA isolate.. The ISME journal. 5(1):8-19.

2010

Zhao, C, Burchardt M, Brinkhoff T, Beardsley C, Simon M, Wittstock G.  2010.  Microfabrication of patterns of adherent marine bacterium Phaeobacter inhibens using soft lithography and scanning probe lithography.. Langmuir : the ACS journal of surfaces and colloids. 26(11):8641-7.

Thiel, V, Brinkhoff T, Dickschat JS, Wickel S, Grunenberg J, Wagner-Döbler I, Simon M, Schulz S.  2010.  Identification and biosynthesis of tropone derivatives and sulfur volatiles produced by bacteria of the marine Roseobacter clade.. Organic & biomolecular chemistry. 8(1):234-46.

Wagner-Döbler, I, Ballhausen B, Berger M, Brinkhoff T, Buchholz I, Bunk B, Cypionka H, Daniel R, Drepper T, Gerdts G et al..  2010.  The complete genome sequence of the algal symbiont Dinoroseobacter shibae: a hitchhiker's guide to life in the sea.. The ISME journal. 4(1):61-77.

2009

Zech, H, Thole S, Schreiber K, Kalhöfer D, Voget S, Brinkhoff T, Simon M, Schomburg D, Rabus R.  2009.  Growth phase-dependent global protein and metabolite profiles of Phaeobacter gallaeciensis strain DSM 17395, a member of the marine Roseobacter-clade.. Proteomics. 9(14):3677-97.

Giebel, H-A, Brinkhoff T, Zwisler W, Selje N, Simon M.  2009.  Distribution of Roseobacter RCA and SAR11 lineages and distinct bacterial communities from the subtropics to the Southern Ocean.. Environmental microbiology. 11(8):2164-78.

2008

Brinkhoff, T, Giebel H-A, Simon M.  2008.  Diversity, ecology, and genomics of the Roseobacter clade: a short overview.. Archives of microbiology. 189(6):531-9.

2007

Martens, T, Gram L, Grossart H-P, Kessler D, Müller R, Simon M, Wenzel SC, Brinkhoff T.  2007.  Bacteria of the Roseobacter clade show potential for secondary metabolite production.. Microbial ecology. 54(1):31-42.

2006

Martens, T, Heidorn T, Pukall R, Simon M, Tindall BJ, Brinkhoff T.  2006.  Reclassification of Roseobacter gallaeciensis Ruiz-Ponte et al. 1998 as Phaeobacter gallaeciensis gen. nov., comb. nov., description of Phaeobacter inhibens sp. nov., reclassification of Ruegeria algicola (Lafay et al. 1995) .... International journal of systematic and evolutionary microbiology. 56(Pt 6):1293-304.

2004

Selje, N, Simon M, Brinkhoff T.  2004.  A newly discovered Roseobacter cluster in temperate and polar oceans.. Nature. 427(6973):445-8.

Brinkhoff, T, Bach G, Heidorn T, Liang L, Schlingloff A, Simon M.  2004.  Antibiotic production by a Roseobacter clade-affiliated species from the German Wadden Sea and its antagonistic effects on indigenous isolates.. Applied and environmental microbiology. 70(4):2560-5.

Completed Master- and PhD-thesis within project B2

Martine Berger (PhD thesis). 2012. Genome-based investigations of the secondary metabolism of representatives of the Roseobacter clade and genetic analyses of the biosynthesis and regulation of tropodithietic acid production.

Sebastian Thole (PhD thesis). 2012. Comparative and functional genome analysis of two closely related Phaeobacter gallaeciensis strains and other host-associated Roseobacter clade members.

Daniela Kalhoefer (PhD thesis). 2011. Genome analysis and comparative genomics of host-associated bacteria of the marine Roseobacter clade.

Sarah Hahnke (PhD thesis). 2011. Physiological characterization and molecular ecological investigation of diverse organisms of the Roseobacter clade isolated from the North Sea.

Regina Gohl (Master thesis). 2012. Analysis of the diversity of algae associated organisms of the Roseobacter clade.

Susann Zilkenat (Master thesis). 2011. Characterization of the putative siderophore synthesis genes RRGA03155 and RRGA03157 of Phaeobacter gallaeciensis DSM 17395.

Sven Breider (Master thesis). 2011. Characterization of two epibiotic bacterial strains of the new genus Epibacterium isolated from the marine seaweed Ulva australis.

Ines Preuth (Diploma). 2010. Regulation der Tropodithietsäure-Produktion bei Phaeobacter gallaeciensis DSM 17395 in Abhängigkeit vom Substrat.

Contributions to conferences

Beyersmann, P., M. Berger, J. Tomasch, I. Wagner-Döbler, M. Simon, T. Brinkhoff. 2013. The antibiotic tropodithietic acid can replace acylated homoserine lactone as global gene regulator in Phaeobacter sp. DSM 17395. VAAM, Bremen, Germany. Oral presentation.

Wolter, L.A., R. Gohl, M. Dogs, M. Simon, T. Brinkhoff. 2013. Specific epibacterial communities on marine macroalgae: distribution patterns of the Roseobacter clade. VAAM, Bremen, Germany. Poster presentation.

Dogs, M., P. Beyersmann , T. Brinkhoff. 2012. Progress Report and Future Perspectives. 7th Status Seminar of the Transregio 51, Hanse Wissenschaftskolleg, Delmenhorst, Germany. Oral presentation.

Beyersmann, P., M. Simon, T. Brinkhoff. 2012. Investigation of biosynthesis and regulation of secondary metabolite production in Phaeobacter gallaeciensis (DSM 17395). 7th Status Seminar of the Transregio 51, Hanse Wissenschaftskolleg, Delmenhorst, Germany. Oral presentation.

Dogs, M., V. Lünsmann, R. Gohl, B. Wemheuer, S. Voget, R. Daniel, M. Simon, T. Brinkhoff. 2012. Specific epibacterial community on marine macroalgae: distribution pattern of the Roseobacter clade. ASM, San Francisco, USA. Poster presentation.

Beyersmann, P., M. Berger, J. Tomasch, I. Wagner-Döbler, M. Simon, T. Brinkhoff. 2012. AHL mediated quorum sensing in Phaeobacter gallaeciensis. ASM, San Francisco, USA. Poster presentation.

Dogs, M., V. Lünsmann, R. Gohl, B. Wemheuer, S. Voget, R. Daniel, M. Simon, T. Brinkhoff. 2012. Specific epibacterial community on marine macroalgae: secondary metabolite production of the Roseobacter clade. VAAM International Workshop, Braunschweig, Germany. Oral presentation.

Beyersmann, P., M. Berger, J. Tomasch, I. Wagner-Döbler, M. Simon, T. Brinkhoff. 2012. Microarray analysis: quorum sensing regulates expression of a large part of the Phaeobacter gallaeciensis genome. VAAM International Workshop, Braunschweig, Germany. Oral presentation.

Dogs, M., T. Brinkhoff. 2012. Specific epibacterial communities of the Roseobacter clade on marine macroalgae. 6th Status Seminar of the Transregio 51, HZI Braunschweig, Germany. Oral presentation.

Beyersmann, P., M. Simon, T. Brinkhoff. 2012. Investigation of biosynthesis and regulation of secondary metabolite production in Phaeobacter gallaeciensis (DSM 17395). 6th Status Seminar of the Transregio 51, HZI Braunschweig, Germany. Oral presentation.

Dogs, M., T. Brinkhoff. 2011. Ecological significance of secondary metabolite production by members of the Roseobacter clade. 5th Status Seminar of the Transregio 51, Oldenburg, Germany. Oral presentation.

Beyersmann, P., M. Simon, T. Brinkhoff. 2011. Investigation of biosynthesis and regulation of secondary metabolite production in Phaeobacter gallaeciensis (DSM 17395). 5th Status Seminar of the Transregio 51, Oldenburg, Germany. Oral presentation.

Dogs, M., M. Simon, T. Brinkhoff. 2011. Detection of specific epibacterial communities affiliated to the marine Roseobacter group reflects adaptation to various macroalgae. VAAM, Karlsruhe, Germany. Poster presentation.

Beyersmann, P., M. Berger, S. Thole, M. Simon, T. Brinkhoff. 2011. Investigation of biosynthesis, function and significance of siderophores in Phaeobacter gallaeciensis. VAAM, Karlsruhe, Germany. Poster presentation.

Berger, M., A. Neumann, M. Dogs1, I. Preuth, S. Schulz, M. Simon, T. Brinkhoff. 2011. Quorum‐sensing control of tropodithietic acid biosynthesis in Phaeobacter gallaeciensis. VAAM, Karlsruhe, Germany. Poster presentation.

Simon, M., S. Hahnke, H.-A. Giebel, H. Osterholz, H. Simon, M. Sperling, T. Brinkhoff. 2011. Physiology and interactions of phytoplankton-associated roseobacters. SAME; Rostock/Warnemünde, Germany. Oral presentation.

Berger, M., H. Liesegang, M. Simon, T. Brinkhoff. 2010. Enzyme with homology to archaeal indolepyruvate oxidoreductase (IOR) is involved in tropodithietic acid (TDA) production and phenylalanine metabolism of Phaeobacter gallaeciensis. Kick Off Symposium of the Transregional Collaborative Research Center (TRR 51). Hansewissenschaftskolleg, Delmenhorst, Germany. Oral presentation.

Hahnke, S., H.-A. Giebel, M.Sperling, M. Simon, T. Brinkhoff. 2010. Physiology and biogeography of phytoplankton-associated roseobacters. Kick-off Symposium of the Transregional Collaborative Research Center; Delmenhorst, Germany. Oral presentation.

Simon, M., S. Hahnke, H.-A. Giebel, H. Osterholz, M. Sperling, T. Brinkhoff. 2010. Physiology and biogeography of phytoplankton-associated roseobacters. Workshop: The microbial view of marine biogeochemical cycles; Banyuls, France. Oral presentation.

this project has been transferred to B7

Supervisor: J. S. Dickschat, University Bonn (https://www.chemie.uni-bonn.de/oc/forschung/arbeitsgruppen/ak_dickschat/prof.-dr.-jeroen-s.-dickschat)
Scientists: N. L. Brock, P. Rabe, R. Riclea

Objectives

Bacteria of the Roseobacter clade constitute one of the most important groups of marine bacteria. Genetic information reveals the importance of two pathways, i.e. sulfur metabolism—especially the degradation of dimethylsulfoniopropionate (DMSP) —and phenylacetate degradation. Both will be investigated in the two model organisms using a gene knockout approach in combination with feeding experiments. Both pathways cumulate in the biosynthesis of the antibiotic tropodithietic acid (TDA) that will be investigated in detail, flanked by studies towards the total synthesis of TDA and biosynthetic intermediates. Genetic information suggest that further secondary metabolites are produced, that will be identified.

Methods

The closed-loop stripping apparatus (CLSA) is a powerful tool for the investigation of volatiles from microorganisms. Bacterial cultures can be embedded in a glass vessel together with a charcoal filter. A continuous airstream is circulated through the apparatus. Volatiles that are emitted by the bacteria are trapped and enriched on the charcoal filter over 24 hours and can subsequently be eluted with an organic solvent. Analysis of these headspace extracts via GC-MS gives access to easy and high throughput compound identification by comparison of mass spectra to data bases. For unknown constituents of the headspace extract, structural proposals can be deduced from these mass spectra that need to be verified by total synthesis of a reference compound. Furthermore, isotopically labeled metabolites can be chemically synthesized and used in feeding experiments with the bacteria. Incorporation of label into volatile secondary metabolites can be monitored by the CLSA/GC-MS method as isotopic shifts will be observed in the mass-spectra. This allows in many cases for valuable conclusions about the underlying biosynthetic machinery. Moreover, gene knockouts of genes from a cluster that is crucial for the production of a certain metabolite can result in the accumulation of pathway intermediates which will allow for the reconstruction of the pathway and the identification of all its intermediates

Publications

2017

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.

2016

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.

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.

2015

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.

2014

Brock NL, Nikolay A, Dickschat JS (2014) Biosynthesis of the Antibiotic Tropodithietic Acid by the Marine Bacterium Phaeobacter inhibens. ChemComm 50:5487-5489.

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.

2013

Berger M, Brock NL, Liesegang H, Dogs M, 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.

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.

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.

Kielkowsky P, Brock NL, Dickschat JS, Hocek M (2013) Nucleobase Protection Strategy for Gene Cloning and Expression. ChemBioChem, 14:801-804.

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.

2012

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.. Applied and environmental microbiology. 78(10):3539-51.

Riclea, R, Gleitzmann J, Bruns H, Junker C, Schulz B, Dickschat JS.  2012.  Algicidal lactones from the marine Roseobacter clade bacterium Ruegeria pomeroyi.. Beilstein journal of organic chemistry. 8:941-50.

2010

Thiel, V, Brinkhoff T, Dickschat JS, Wickel S, Grunenberg J, Wagner-Döbler I, Simon M, Schulz S.  2010.  Identification and biosynthesis of tropone derivatives and sulfur volatiles produced by bacteria of the marine Roseobacter clade.. Organic & biomolecular chemistry. 8(1):234-46.

Dickschat, JS, Zell C, Brock NL.  2010.  Pathways and substrate specificity of DMSP catabolism in marine bacteria of the Roseobacter clade.. Chembiochem : a European journal of chemical biology. 11(3):417-25.

Schulz, S, Dickschat JS, Kunze B, Wagner-Dobler I, Diestel R, Sasse F.  2010.  Biological activity of volatiles from marine and terrestrial bacteria.. Marine drugs. 8(12):2976-87.

2005

Dickschat, JS, Wagner-Döbler I, Schulz S.  2005.  The chafer pheromone buibuilactone and ant pyrazines are also produced by marine bacteria.. Journal of chemical ecology. 31(4):925-47.

Supervisor: Prof. Dr. Wagner-Döbler
Scientists and students: Mathias Milici (PhD); Diana Patzelt (PhD); Hui Wang (PhD); Ina Buchholz (PhD); Dr. Jürgen Tomasch (Postdoc)

Aim

Cell-cell communication transforms clonal populations of bacteria into highly complex, well adapted communities. Here we unravel the quorum sensing (QS) regulon of the model organism Dinoroseobacter shibae and study interactions between Roseobacter bacteria and their eukaryotic host organisms.

Methods

D. shibae has a complex QS regulon comprised of three LuxI-type synthases and 5 LuxR-type transcriptional regulators. We are constructing knock-out mutants for these key genes and study their phenotype (growth, cell division, morphology, flagellae) and gene expression (microarrays and RNAseq). Population heterogeneity is analysed using time-lapse microscopy of strains that have been tagged with gfp or mcherry proteins for the promoter of interest, as well as FACS (fluorescence activated cell sorting). Using chemically synthesized autoinducers, we study the response of D. shibae to self-produced signals and to signals produced by other bacteria.
The interactions between algae and bacteria are studied in cultures of the dinoflagellate Prorocentrum minimum which is free of bacteria (axenic). This culture is inoculated with D. shibae and grows in a defined mineral medium (L1) without carbon source and without vitamin B12. Thus, algae and bacteria are critically dependent on each other: The heterotrophic bacteria require the products of algal photosynthesis, and the algae need the essential vitamin B12 which is synthesized by the bacteria.

Sampling with FS Polarstern in the Southern Ocean

Hui Wang and Irene Wagner-Döbler participated in cruise ANT28 into the Southern ocean as part of the Roseobacter group, joining cruise leg ANT28-4 (13th March – 9th April 2012, Punta Arenas – Punta Arenas) and cruise leg ANT28-5 (11th April – 16th May 2012, Punta Arenas – Bremerhaven). Water samples were obtained along a geographical gradient from defined depths. The water was filtered through membrane filters of 8 µm, 3 µm and 0,22 µm pore width. The filters were stored at -80°C. About 900 filters have been obtained. It is planned to investigate the microbiome and metatranscriptome with a focus on the interactions between algae and bacteria.

Common regulatory networks for the adaptation to low iron and oxygen tension

Principal investigators: Prof. Dr. Dieter Jahn, Dr. Elisabeth Härtig

PhD student: Maren Behringer, Miriam Becker

Objective

Dinoroseobacter shibae belongs to the abundant and ecological important marine Roseobacter clade. The bacterium is able to generate energy by anaerobic respiration via denitrification. Moreover, it performs arginine and pyruvate fermentation to sustain anaerobic long-time survival. The adaptation to changing oxygen concentrations is controlled via a fine-tuned regulatory network involving the oxygen-sensing regulator Fnr and several Dnrs organized in regulatory cascades. The anaerobic regulation is closely connected to iron acquisition, though the anaerobic regulators depend on Fe-containing [FeS]-cluster or heme as cofactors. Three potential iron-dependent regulators were found in the D. shibae genome: Fur, Irr and RirA. Using genetic techniques and transcriptome analyses we aim to identify the stimuli of the involved regulators and target regulons and to understand the interplay with the networks for the response to oxygen depletion, nitrate, carbon sources and different stresses.

Projects

Regulation of respiratory pathways for the energy generation in Dinoroseobacter shibae

Objectives

We analyzed the role of the four regulators FnrL, DnrD, DnrF and DnrE of D. shibae in regulating genes encoding nitrate respiration and denitrification pathways. Moreover, we studied low oxygen tension and NO as signals for anaerobic gene expression.

Material & Methods

Knockout mutant strains for fnrL, dnrD, dnrF and dnrE of D. shibae were generated. We defined the regulons by comparing transcript levels of the regulatory mutant strains with the D. shibae wild type strain after shift from aerobic to anaerobic growth conditions. After regulon definition, we deduced specific binding sites for FnrL, DnrD, DnrF and DnrE by comparing the promoter regions of the target genes. Furthermore, we created promoter-lacZ reporter gene fusions of target genes to analyse the anaerobic expression in more detail. FnrL was produced in E. coli and after purification we performed spectroscopic analysis.

Results

Global sequence alignments were performed and grouped FnrL of D. shibae DFL12^T to a Roseobacter specific phylum of FnrN type regulators of Crp/ Fnr transcriptional regulators. UV/ Vis spectroscopy of the purified FnrL protein revealed binding of an oxygen sensitive Fe-S cluster which enables Fnr to measure oxygen tension and regulate anaerobic gene expression. DnrD, DnrF and DnrE were classified within the Dnr phylum of Crp/ Fnr regulators. In D. shibae DFL12^T the denitrification genes were found clustered and transcribed in large transcriptional units. The napFDAGHBC operon, encoding the nitrate reduction step, is regulated in a close interplay of all four Crp/ Fnr regulators of D. shibae. The nirSECFDGHJN encoding the nitrite reductase and the norCBQDEF operon encoding nitric oxide reductase were transcribed divergently sharing an overlapping promoter region. Both operons were activated by FnrL in an oxygen dependent manner and by DnrD in response to nitric oxide. Using promoter-lacZ reporter gene fusions the regulation by FnrL and DnrD was analysed in detail. Based on the defined regulons of the analysed transcriptional regulators a hierarchical network for anaerobic regulation of gene expression in D. shibae was established.

Regulatory network for the adaptation of Dinoroseobacter shibae to iron limitation

Objectives

The rhizobial iron regulator RirA from D. shibaebelongs to the Rrf2- family of transcription factors and is supposed to coordinate a Fe-S cluster and thereby measure iron availability [1].

Materials & Methods

A ∆rirA knockout mutant strain was created to analyze the role of the regulator in adaptation to iron limitation. To complement the ∆rirA mutant strain, a construct with a N-terminal StrepII-tag and a constitutive promoter was used. RirA protein fused with a StrepII-tag was recombinantly produced and purified under anaerobic conditions. UV/Vis and electron paramagnetic resonance (EPR) spectroscopy as well as whole cell Mössbauer analyses were used to determine the nature of the Fe-S cluster. The Fe content of the protein was determined with the atom absorbance spectroscopy (AAS). Four cysteine residues of RirA were changed to alanine via site directed mutagenesis of the corresponding gene. DNA binding of the anaerobically purified RirA wildtype was analyzed using electro mobility shift assays (EMSA).

Results

The ∆rirA mutant strain showed a reduced growth under iron limitation compared to the wild type strain indicating a role in iron-dependent gene regulation. Complementation of the ∆rirA mutant strain was successful since the complemented strain grew like the wild type strain. Analyses of anaerobically purified wildtype RirA using UV/Vis spectroscopy revealed an absorption shoulder at 420 nm, typical of Fe‑S cluster containing proteins. Using EPR and Mössbauer spectroscopy a [3Fe‑4S]¹⁺ cluster was identified. AAS measurements of iron, resulting in a 3:1 ratio of iron per molecule RirA, supported [3Fe‑4S]¹⁺ as cofactor. Since three of the four cysteine mutants of RirA showed a drastically reduced absorption in UV/Vis spectroscopy these cysteines may serve as ligands for [3Fe‑4S]¹⁺ cluster. Using EMSA analyses, binding of RirA to hemB2 promoter sequences was shown.

Light-dependend regulation of photosynthesis-genes in Dinoroseobacter shibae

Objectives

Analyses of the role of Dshi_1135 in light-dependent regulation of Bchla biosynthesis in D. shibae.

Materials & Methods

We used in vivo UV/Vis spectroscopy to identify mutants with altered absorption spectra compared to the wild type strain. We defined the Dshi_1135 regulon by comparing transcript levels of the regulatory mutant strain with the D. shibae wild type strain grown in the dark. Furthermore, we created a bchF-lacZ reporter gene fusion to analyse the gene expression in more detail. The LOV-HisKA protein Dshi_1135 was recombinantly produced in E. coli and purified for biochemical analyses.

Results

Dshi_1135 encodes a protein consisting of a potential light-oxygen-voltage (LOV) domain fused to a histidine kinase domain. It shows 42 % identity to a blue light-activated HK from Erythrobacter litoralis from which structural data are available [3]. Inactivation of Dshi_1135 resulted in a complete loss of Bchla as shown by extraction and UV/Vis absorption measurement. Transcriptome analysis of the Dshi_1135 mutant strain compared to the wild type strain revealed loss of expression of the photosynthetic gene cluster. Additionally, in the D. shibae wild type strain DFL12^T we found an increase of the bchF-lacZreporter gene fusion.

Methods/Activities

• Transcriptome studies by RNA-microarrays and RNA-sequencing
• Construction and investigation of deletion mutants of enzyme and regulator genes involved in anaerobic metabolism
• Construction of a transposon library of D. shibae
• Isolation and characterization of regulator proteins
• Protein characterization by GPC, EMSA, EPR, Mössbauer

Publications

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

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

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 (DOI: 10.3389/fmicb.2016.00742).

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.

Laass S, Kleist S, Bill N, Drueppell K, Kossmehl S, Woehlbrand 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 DFL12^T during oxygen depletion, J  Biol Chem., 289:13219-13231

Ebert M, Laaß S, Burghartz M, Petersen J, Koßmehl S, Wöhlbrand L, Rabus R, Wittmann C, Tielen P, Jahn D (2013) Transposon mutagenesis identified chromosomal and plasmid genes essential for adaptation of the marine bacterium Dinoroseobacter shibae to anaerobic conditions, J Bac 195: 4769-4777 (DOI: 10.1128/JB.00860-13).

Piekarski T, Jahn D & Tielen P (2011) Marine Mikrobiologie: Etablierung genetischer Werkzeuge für Bakterien der Roseobacter-Gruppe, BIOspektrum 04/11

Wagner-Döbler I, Ballhausen B, Berger M, Brinkhoff T, Buchholz I, Bunk B, Cypionka H, Daniel R, Drepper T, Gerdts G, Hahnke S, Han C, Jahn D, Kalhoefer D, Kiss H, Klenk HP, Kyrpides N, Liebl W, Liesegang H, Meincke L, Pati A, Petersen J, Piekarski T, Pommerenke C, Pradella S, Pukall R, Rabus R, Stackebrandt E, Thole S, Thompson L, Tielen P, Tomasch J, von Jan M, Wanphrut N, Wichels A, Zech H, Simon M (2010) The complete genome sequence of the algal symbiont Dinoroseobacter shibae: a hitchhiker's guide to life in the sea. ISME J 4: 61-77 (DOI: 10.1038/ismej.2009.94).

Piekarski T, Buchholz I, Drepper T, Schobert M, Wagner-Doebler I, Tielen P & Jahn D (2009) Genetic tools for the investigation of Roseobacter clade bacteria, BMC Microbiology, 9: 265

Contribution to conferences

Ebert, M., Laaß, S., Eckweiler, D., Thürmer, A., Daniel, R., Härtig, E. and Jahn, D. 2017. FnrL and three Dnr regulators control the anaerobic adaptation in Dinoroseobacter shibae DFL12^T. Jahrestagung der Vereinigung für Allgemeine und Angewandte Mikrobiologie (VAAM), Würzburg, Deutschland. Oral presentation

Becker, M., Heyber, S., Härtig, E.,  Jahn,D. 2017. The role of thelight-oxygen-voltage (LOV)-histidine kinase Dshi_1135 for regulationof the bacteriochlorophyllabiosynthesis in Dinoroseobacter shibae. Jahrestagung der Vereinigung für Allgemeine und Angewandte Mikrobiologie (VAAM), Würzburg, Deutschland. Poster.

Behringer, M., Härtig, E.,  Jahn,D. 2017. Identification of a [3Fe-4S]¹⁺ cofactor and functional analysis of the iron responsive regulator RirA from Dinoroseobacter shibae. Jahrestagung der Vereinigung für Allgemeine und Angewandte Mikrobiologie (VAAM), Würzburg, Deutschland. Poster.

Ebert, M., Schweyen, P., Bröring, M., Härtig, E. and Jahn, D. 2016. Regulatory network for the adaptation to low oxygen tension of Dinoroseobacter shibae DFL12^T. Tetrapyrolles, Chemistry & Biology of Gordon research conference (GRC): Biology of Heme, Chlorophyll, Porphyrins, Chlorins and Billins- The Pigments of Life, Newport, RI, USA. Poster.

Ebert, M., Härtig, E. and Jahn, D. 2016. Regulatory network of Dinoroseobacter shibae DFL12^T for the adaptation to low oxygen tension. Jahrestagung der Vereinigung für Allgemeine und Angewandte Mikrobiologie (VAAM), Jena, Deutschland. Oral presentation.

Heyber, S., Härtig, E.,  Jahn,D. 2016. The regulation of the bacteriochlorophyll biosynthesis in Dinoroseobacter shibae. Jahrestagung der Vereinigung für Allgemeine und Angewandte Mikrobiologie (VAAM), Jena, Deutschland. Poster.

Behringer, M., Härtig, E.,  Jahn,D. 2016. Biochemical characterization and functional analysis of the iron responsive regulator RirA from Dinoroseobacter shibae. Jahrestagung der Vereinigung für Allgemeine und Angewandte Mikrobiologie (VAAM), Jena, Deutschland. Poster.

Ebert, M., Härtig, E. and Jahn, D. 2015. Regulation of anaerobic respiratory pathways in Dinoroseobacter shibae. Jahrestagung der Vereinigung für Allgemeine und Angewandte Mikrobiologie (VAAM), Marburg, Deutschland. Poster.

Jacobs, J., Laaß, S., Heyber, S., Engelmann, S., Härtig, E.,  Jahn,D. 2015. Iron regulation in the marine microorganism Dinoroseobacter shibae,  Jahrestagung der Vereinigung für Allgemeine und Angewandte Mikrobiologie (VAAM), Marburg, Deutschland. Poster.

Laaß, S., Klein, J., Heisig, M., Rohde, M., Tielen, P., Jahn, D. 2013. Regulation of anaerobic respiratory pathways in Dinoroseobacter shibae. VAAM, Bremen, Germany. Oral presentation.

Jacobs, J., Laaß, S., Tielen, P., Jahn, D. 2012. B5 Progress report and future perspectives. 7th Status Seminar of the Transregio 51, Hanse Wissenschaftskolleg, Delmenhorst, Germany. Oral presentation.

Laaß, S., Klein, J., Jahn, D., Tielen, P. 2012 Regulation of anaerobic respiratory pathways in Dinoroseobacter shibae. VAAM, Tübingen, Germany. Oral presentation.

Laaß, S., Klein, J., Heisig, M., Rohde, M., Tielen, P., Jahn, D. 2012. Regulation of anaerobic respiratory pathways in Dinoroseobacter shibae. Gordon Research Conference “Marine Microbes”. Lucca (Barga), Italy. Poster.

Laaß, S., Jacobs, J., Ebert, M., Heisig, M., Rhode, M., Tielen, P., Jahn, D. 2012. Regulation of anaerobic respiratory pathways in Dinoroseobacter shibae. 6th Status Seminar of the Transregio 51, HZI Braunschweig, Germany. Oral presentation.

Laaß, S., Klein, J., Jahn, D., Tielen, P., 2012. Anaerobic respiratory pathways in Dinoroseobacter shibae.  Mibi Retreat, Burg Warberg, Helmstedt, Germany. Oral presentation.

Laaß, S., Ebert, M., Tüpker, R., Tielen, P., Jahn, D. 2011.Regulatory networks of the Dinoroseobacter shibae energy metabolism. 2th Status Seminar of the Transregio 51, HZI Braunschweig, Germany. Oral presentation.

Principal investigator: Dr. Cristina Moraru

PhD student:

to be edited

Principal investigator: Prof. Dr. Ralf Rabus
PhD Students: K. Drüppel, S. Koßmehl

Project

The main goal of this project is to elucidate the metabolic strategies and molecular mechanisms enabling the habitat success of roseobacters from a systems biology perspective. To this end, Phaeobacter inhibens DSM 17395 was selected as representative of nutritional versatile Roseobacter clade members. During the first funding period, we mainly focus on elucidating the catabolic network of amino acids and carbohydrates and on advancing proteomics approaches for investigations with P. inhibens DSM 17395. Moreover, we perform extensive proteomic analysis of D. shibae DFL12^T studied in Braunschweig with respect to light/dark and oxic/anoxic shifts.

Amino acid catabolism of P. inhibens DSM 17395: Roseobacters, as abundant members of the marine bakterioplankton, contribute substantially to organic matter (OM) turnover in ocean waters. Since OM consists to a large part of proteins and since P. inhibens DSM 17395 grows best with amino acids, their utilization was investigated in close collaboration with AG Schomburg on 3 different levels. (i) To study the adaptive strategies to availability of complex and excess nutrients, as typically encountered in the course of collapsing algal blooms, Marine Broth (MB) and process-controlled fermenters were used to mimic such a nutritional scenario (Zech et al. 2013a). (ii) To resolve preferential utilization of certain amino acids from a complex while analytically traceable mixture of amino acids, casamino acids were used (Zech et al. 2013b). (iii) Despite the growing number of genome sequences from the Roseobacter clade, amino acid degradation remains in parts unclear or ambiguous. This was studied for nine selected individual amino acids. In all three topics, physiology was combined with enzymatic, proteomic and metabolomic analysis.

Proteomics approaches: At the beginning of the first funding period we assessed the influence of biological versus technical variation in 2D DIGE experiments of P. inhibens DSM 17395 on the basis of raw data. This led to the decision to only use biological replicates and to apply a conservative threshold of significance of -1.5 and 1.5 (Zech et al. 2011). Subcellular fractionation of P. inhibens DSM 17395, followed by gel- or nanoLC-based separation of proteins and peptides yielded MS-based identification of 1,187 proteins. From these, the functionalities of the cell envelope compartments were reconstructed, e.g. protein secretion/sorting and direct effector molecule transit. Notably, the functional prediction of 74 genes (including 17 coding for proteins of hitherto unknown function) could be refined (Koßmehl et al. 2013).

Methods

Physiology:

• cultivation ranging from Erlenmeyer flasks to process-controlled fermenters (1,5 to 50L; batch and continuous)
• complete stoichiometric balancing based on measurements of soluble (HPLC, IC) and gaseous compounds (MS)

Proteomics:

• Subcellular fractionation
• SDS-PAGE, 2D DIGE, image analysis (incl. DeCyder), nanoLC (incl. MALDI-coupling)
• ESI-MS/MS, MALDI-TOF-MS/MS
• Bioinformatics
• Metaproteomics

Publikationen

2017

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

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

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

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

2016

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.

2014

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.

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.

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

2013

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.

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.

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.

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, 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.

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.

2011

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.

2010

Wagner-Döbler, I, Ballhausen B, Berger M, Brinkhoff T, Buchholz I, Bunk B, Cypionka H, Daniel R, Drepper T, Gerdts G et al..  2010.  The complete genome sequence of the algal symbiont Dinoroseobacter shibae: a hitchhiker's guide to life in the sea.. The ISME journal. 4(1):61-77.

2009

Zech, H, Thole S, Schreiber K, Kalhöfer D, Voget S, Brinkhoff T, Simon M, Schomburg D, Rabus R.  2009.  Growth phase-dependent global protein and metabolite profiles of Phaeobacter gallaeciensis strain DSM 17395, a member of the marine Roseobacter-clade.. Proteomics. 9(14):3677-97.

Fürch, T, Preusse M, Tomasch J, Zech H, Wagner-Döbler I, Rabus R, Wittmann C.  2009.  Metabolic fluxes in the central carbon metabolism of Dinoroseobacter shibae and Phaeobacter gallaeciensis, two members of the marine Roseobacter clade.. BMC microbiology. 9:209.

Bachelor and Master theses

TRINKLER, Mirjam (Bachelor thesis, 2011) „Analysis of nitrogen and phosphate requirement by Phaeobacter gallaeciensis”

JONGMANS, Elanor (Bachelor thesis, 2011) „Growth condition-dependent morphotypes of Phaeobacter gallaeciensis”

BERGEN, Nils (Bachelor thesis, 2010) „Enzymaktivitäten im Zentralstoffwechsel von Phaeobacter gallaeciensis bei Wachstum im Minimalmedium“

VOCKE, Farina (Bachelor thesis, 2010) „Enzymaktivitäten im Zentralstoffwechsel von Phaeobacter gallaeciensis bei Wachstum im Vollmedium“

LEISKE, Maike Nicole (Bachelor thesis, 2012) „Enzymatik des Abbaus verzweigtkettiger Aminosäuren in Phaeobacter gallaeciensis”

RUPPERSBERG, Hanna Sibyll (Bachelor thesis, 2012) „Metaproteomic analysis of marine environmental samples”

NIEHAUS, Nils (Bachelor thesis, 2012) „Quantitative image analysis in proteomic research”

STOLTENBERG, Philip (Bachelor thesis, 2012) „Stoichiometry of amino acids (L-threonine, L-valine, L-leucine, L-isoleucine) utilization by Phaeobacter gallaeciensis DSM 17395 during growth in process-controlled fermenters”

LEHMANN, Jochen (Bachelor thesis, 2012) „Stoichiometry of amino acids (lysine, methionine, phenylalanine, tryptophane) utilization by Phaeobacter gallaeciensis DSM 17395 during growth in process-controlled fermenters”

BOOSMANN, Inka (Master thesis, 2011) „Cultivation and membrane proteome analysis of Phaeobacter gallaeciensis DSM 17395”

SCHWAB, Julia (Master thesis, 2011) „Cultivation and membrane proteome analysis of Phaeobacter gallaeciensis DSM 17395”

STRIJKSTRA, Annemieke (Master thesis, 2012) „Phaeobacter gallaeciensis DSM 17395 growth control by nitrogen and phosphorous: a physiological and proteomic perspective”

Principal investigator: Prof. Dr. Stefan Schulz
PhD Students: H. Bruns, L. Ziesche, T. Harig, M. Maczka

Objective

The secondary metabolites of different Roseobacter strains will be analyzed, including the model strains Dinoroseobacter shibae and Phaeobacter gallaeciensis but also other strains of potential interest. The identification of their function and their contribution to the success of the Roseobacter clade will be the main focus. Aiming at identifying as many secondary metabolites as possible, extracellular metabolite profiles will be established including compounds of a wide polarity spectrum. The compositional change of these profiles depending on different conditions, metabolites and micro- and macroorganisms will be explored in close cooperation with partners of the C‑ and B-area.

Methods

To elucidate the structure of volatile organic compounds (VOCs) emitted by bacteria the "Closed loop stripping apparatus" (CLSA) is used.[1,2] A cell culture of the bacterium grown in liquid media or on agar plates is placed into a closed air circuit. Volatiles emitted by the bacteria are collected on an activated charcoal filter which is extracted with an organic solvent after 24 hrs and analyzed by means of GC/MS. Identification of the compounds is carried out by comparison of the mass spectra with mass spectral data of libraries. If this doesn´t lead to identification of the compound a mass spectrum based structural proposal is made which is verified by synthesis of the compound in our workgroup.

For the investigation of extracellular metabolites of higher polarity porous, hydrophobe polymers like XAD are used. The polymer is directly added to the liquid cell culture. After some time the XAD is filtered off and extracted with an organic solvent. The extract is investigated by means of HPLC/MS, which is especially suited for the examination of polar substances. The structural elucidation is based upon various data like molecular weight, MSn fragmentation pattern and the chemical formular derived from high resolution mass spectrometry. If these data are not sufficient for resolving the structure the compound is isolated by preparative HPLC and examined with nuclear magnetic resonance (NMR) spectroscopy. This is followed by synthesis of the compound and data comparison with the natural product.

Other methods used in our workgroup as needed comprise OASIS, liquid-liquid extraction, solid phase micro extraction (SPME) and analysis of gases with gas sampling tubes.

[1] W. Boland, P. Ney, L. Jaenicke, G. Gassmann in Analysis of Volatiles, (Ed.: P. Schreier), de Gruyter, Berlin, 1984, pp. 371-380.
[2] S. Schulz, J. Fuhlendorff, H. Reichenbach, Identification and synthesis of volatiles released by the myxobacterium Chondromyces crocatus, Tetrahedron 2004, 60, 3863-3872.

Publications

2017

Bruns H, Crüsemann M, Letzel AC, Alanjary M, McInerney JO, Jensen PR, Schulz S, Moore BS, Ziemert N(2017) Function-related Pathway Replacement of Bacterial Siderophores. ISME J., in press (2017).

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.

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.

2015

Schulz S, Hötling S (2015) The use of the lactone motif in chemical communication. Nat Prod Rep 32:1042–1066.

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.

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.

2014

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.

2013

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.

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.

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.

Patzelt D, Wang, H, Buchholz, I, Rohde, M, Gröbe, L, Pradella, S, Neumann A, Schulz S, Heyber S, Muench K, Muench 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 7/12: 2274-2286.

2011

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.

2010

Thiel V, Brinkhoff T, Dickschat JS, Wickel S, Grunenberg J, Wagner-Döbler I, Simon M, Schulz S (2010) Identification and biosynthesis of tropone derivatives and sulfur volatiles produced by bacteria of the marine Roseobacter clade.. Organic & biomolecular chemistry. 8(1):234-46. Abstract

Schulz S, Dickschat JS, Kunze B, Wagner-Dobler I, Diestel R, Sasse F (2010) Biological activity of volatiles from marine and terrestrial bacteria.. Marine drugs. 8(12):2976-87.

2009

Thiel V, Kunze B, Verma P, Wagner-Döbler I, Schulz S (2009) New structural variants of homoserine lactones in bacteria.. Chembiochem : a European journal of chemical biology. 10(11):1861-8.

Thiel V, Vilchez R, Sztajer H, Wagner-Döbler I, Schulz S (2009) Identification, quantification, and determination of the absolute configuration of the bacterial quorum-sensing signal autoinducer-2 by gas chromatography-mass spectrometry.. Chembiochem : a European journal of chemical biology. 10(3):479-85.

2008

Bodor A, Elxnat B, Thiel V, Schulz S, Wagner-Döbler I (2008) Potential for luxS related signalling in marine bacteria and production of autoinducer-2 in the genus Shewanella.. BMC microbiology. 8:13.

2007

Vilchez R, Lemme A, Thiel V, Schulz S, Sztajer H, Wagner-Döbler I (2007) Analysing traces of autoinducer-2 requires standardization of the Vibrio harveyi bioassay.. Analytical and bioanalytical chemistry. 387(2):489-96.

2005

Bruhn J B, Nielsen K F, Hjelm M, Hansen M, Bresciani J, Schulz S, Gram L (2005) Ecology, inhibitory activity, and morphogenesis of a marine antagonistic bacterium belonging to the Roseobacter clade.. Applied and environmental microbiology. 71(11):7263-70.

Wagner-Döbler I, Thiel V, Eberl L, Allgaier M, Bodor A, Meyer S, Ebner S, Hennig A, Pukall R, Schulz S (2005) Discovery of complex mixtures of novel long-chain quorum sensing signals in free-living and host-associated marine alphaproteobacteria.. Chembiochem : a European journal of chemical biology. 6(12):2195-206.

Dickschat JS, Wagner-Döbler I, Schulz S (2005) The chafer pheromone buibuilactone and ant pyrazines are also produced by marine bacteria.. Journal of chemical ecology. 31(4):925-47.

Contributions to conferences

S. Schulz, Chemical Diversity of Microbial Volatiles, 32. ISCE meeting Foz de Iguazu, Juli 2016.

S. Schulz, Volatiles from Marine Bacteria , Gordon conference on Marine Natural Products, Ventura, March 2016

L. Ziesche, H. Bruns, M. Dogs, L. Wolter, T. Brinkhoff, S. Schulz, 07.04.2016, N-Acylhomoserine lactones of macroalgae associated Roseobacter bacteria, 7th Braunschweiger Jungchemiker Tagung, Haus der Wissenchaft, Braunschweig, Germany. Poster presentation.

L. Ziesche, H. Bruns, M. Dogs, L. Wolter, T. Brinkhoff, S. Schulz, 29.06-03.07.2015, N-Acylhomoserine lactones of macroalgae associated Roseobacter bacteria, International Society of Chemical Ecology Conference, Stockholm University, Stockholm, Sweden. Poster presentation.

S. Schulz, Bacterial volatiles - New compounds and functions , 2. European Conference on Natural Products and Bioflavour 2015, Frankfurt, September 2015

S. Schulz, Bacterial volatiles - Structures, biosynthesis and function 17. Challenges in Chemical Biology ISACS 16, Zürich, Juni 2015

L. Ziesche, H. Bruns, M. Maczka, N. Kahkin Taniwal, S. Schulz, 09.11.2015, C2 secondary metabolites of Roseobacter and their biological activity, 11th Status Seminar of the Transregio 51, Helmholtz-Center for Infection Research, Braunschweig, Germany. Poster presentation.

H. Bruns, S. Schulz, 05.03.2015, N Acylated Alanine Methyl Esters (NAMEs) from Roseovarius tolerans, Seminar Prof. Bradley Moore, Scripps Institute of Oceanography, University of California San Diego (UCSD), La Jolla, USA. Oral presentation.

L. Ziesche, H. Bruns, M. Maczka, 07.-08.05.2015, C2 secondary metabolites of Roseobacter and their biological activity, 10th Status Seminar of the Transregio 51, Alter Landtag zu Oldenburg, Oldenburg, Germany. Oral presentation.

S. Schulz, Analysis of Microbial Volatiles by Orthogonal Methods, 30. ISCE meeting Urbana, Juli 2014

S. Schulz, The Chemical Structure Space of Microbial Volatiles, 30. ISCE meeting Urbana, Juli 2014

H. Bruns, L. Ziesche, N. Khakin Taniwal, S. Schulz, 20.11.2014, Progress report and future perspectives (Algicidal activities and new N acylated amino acids), 9th Status Seminar the Transregio 51, Helmholtz Zentrum für Infektionsforschung, Braunschweig, Germany. Oral presentation.

L. Ziesche, M. Dogs, T. Brinkhoff, S. Schulz, 15.04.2014, N-Acylhomoserine lactones: signal molecules produced by macroalgae associated Roseobacter bacteria, 5th Braunschweiger Jungchemiker Tagung, Haus der Wissenchaft, Braunschweig, Germany. Poster presentation.

L. Ziesche, S. Schulz, 08.-09.05.2014, C2 Chemistry of secondary metabolite mediated interactions between bacteria of the Roseobacter clade an other organisms, 8th Status Seminar of the Transregio 51, Alter Landtag zu Oldenburg, Oldenburg, Germany. Oral presentation.

H. Bruns, S. Schulz, 21.01.2014, Progress report (N Acylated Alanine Methyl Esters (NAMEs) from Roseovarius tolerans), 2nd Meeting of the graduate school Microbial Natural Products (MINAS), Leibnizhaus, Hannover, Germany. Oral presentation.

S. Schulz, Chemical communication by volatiles in animals and bacteria - Are there common themes? , Flavor and Fragrances, Leipzig, September 2013

H. Bruns, A. Neumann, S. Schulz, 24.-26. 6. 2013, major outcome of 1st phase (Acylhomoserine lactones and other compounds from Roseobacter clade organisms), International Symposium of the Transregio 51, Hanse Wissenschaftskolleg, Delmenhorst, Germany. Oral presentation.

H. Bruns, S. Schulz, 15-16.10.2012, Progress report and future perspectives, 7th Status Seminar of the Transregio 51, Hanse Wissenschaftskolleg, Delmenhorst, Germany. Oral presentation.

H. Bruns, V. Thiel, S. Schulz, 27-29.09.2012, Acylated Alanine Methyl Esters from Roseovarius, VAAM, Braunschweig, Germany. Poster presentation.

A. Neumann, S. Schulz, 05.06.2012, Detection of signalling molecules and other metabolites, 6th Status Seminar of the Transregio 51, Helmholtz Centre for Infection Research, Braunschweig, Germany. Oral presentation.

A. Neumann, S. Schulz, 16-17.05.2011, Metabolic profiling and extracellular signaling compounds of Dinoroseobacter shibae and other members of the Roseobacter clade, 3rd Status Seminar of the Transregio 51, Hanse Wissenschaftskolleg, Delmenhorst, Germany. Oral presentation.

A. Neumann, S. Schulz, 23-25.02.2011, Metabolites of marine bacteria of the Roseobacter clade, 23rd Irseer Naturstofftage der Gesellschaft für Chemische Technik und Biotechnologie e.V. (DECHEMA), Irsee. Poster presentation.

H. Bruns, N. Brock, J. Dickschat, S. Schulz, 10.02.2011, Biosynthetic pathways to secondary metabolites of the Roseobacter clade, 2nd Status Seminar of the Transregio 51, University of Oldenburg, Oldenburg, Germany. Oral presentation.

Metabolome analysis and modelling of the metabolisms of Dinoroseobacter shibae and Phaeobacter inhibens DSM 17395

Principal investigators: D. Schomburg, K. Schmidt-Hohagen (née Schreiber)
PhD students: S. Will, E. Majer

Objective:
The overall goal of this project is to analyse and model the metabolome of Dinoroseobacter shibae and Phaeobacter inhibens DSM 17395 (formerly deposited as Phaeobacter gallaeciensis DSM 17395, Buddruhs et al. unpublished), serving as model organisms of the Roseobacter clade. This will be done using a closely integrated theoretical/experimental approach. Based on experimental data obtained from metabolome analyses and from the collaborating partners under various growth conditions, a model of the metabolic network will be constructed to deduce hypotheses. They will be tested experimentally to optimise the model.

Methods: 

• Cultivation of bacteria in fermenters

nvited talks / Contributions to conferences:
Schomburg D (2013) Metabolic networks and models – creation, application and experiment. 6^th June 2013, Uni Luxemburg (Talk)

Hensler M, Zech H, Koßmehl S, Drüppel K, Wöhlbrand L, Trautwein K, Schmidt-Hohagen K, Rabus R, Schomburg D (2013) Dynamics of amino acid utilization by Phaeobacter inhibens DSM 17395. VAAM 10^th - 13^th March 2013, Bremen (Poster)

Schreiber K, Schomburg D (2012) C3: Progress report and future perspectives. 7^th Status Seminar of the Transregio 51, 12^th - 13^th October 2012, Hanse Wissenschaftskolleg, Delmenhorst (Talk)

Rex R, Schomburg D (2012) Predicting concentration, enzyme capacity and flux distribution changes from integrated systems biology data using Boolean algebra. German Conference on Bioinformatics (Workshop Computational Proteomics and Metabolomics) 19^th - 22^nd September 2012, Jena (Talk)

Schomburg D (2011) Von Bioinformatik und Metabolom zur Systembiologie. 10^th November 2011, Uni Freiberg/Sachsen (Talk)

Schomburg D (2011) Theoretical and experimental aspects of genome-sized models. 5th International Beilstein Symposium on Experimental Standard Conditions of Enzyme Characterizations (ESCEC), 12^th - 16^th September 2011, Rüdesheim (Talk)

Schomburg D (2011) The creation and application of genome-scale metabolic models - theoretical and experimental steps. Dechema (Trends in Metabolomics – Analytics and Applications), 19^th - 20^th May 2011, Frankfurt (Talk)

Hensler, Bill N, Rex R, Schreiber K, Schomburg D (2011) Metabolome analysis and modelling of the metabolism of Dinoroseobacter shibae and Phaeobacter gallaeciensis. 3^rd Status Seminar of the Transregio 51, 16^th - 17^th May 2011, Hanse Wissenschaftskolleg, Delmenhorst (Talk)

Schomburg D (2011) From genome to genome-scale metabolic models – theoretical and experimental steps. Dechema (System Biology: Between Science and Application), 18^th - 19^th January 2011, Frankfurt (Talk)

Rex R, Schomburg D (2010) Automated creation of simulation-ready metabolic models. German Conference on Bioinformatics, 20^th - 22^nd September 2010, Braunschweig (Poster)

Schreiber K, Rex R, Schomburg D (2010) Metabolome analysis and modelling of the metabolism of Dinoroseobacter shibae and Phaeobacter gallaeciensis. Kick-off Symposium of the Transregio 51, 13^th - 15^th June 2010, Hanse Wissenschaftskolleg, Delmenhorst (Talk)

Schomburg D (2010) From Metabolism to Systems Biology. EMBO (Catalytic Mechanisms by Biological Systems: at the interface between Chemistry and Biology), 5^th - 7^th May 2010, EMBL Hamburg (Talk)

Publications:

2017

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.

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.

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.

2016

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.

Kleist S, Ulbrich M, Bill N, Schmidt-Hohagen K, Geffers R and Schomburg D (2016) Dealing with salinity extremes and nitrogen limitation - an unexpected strategy of the marine bacterium Dinoroseobacter shibae. Environ. Microbiol.

2014

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.

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.

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.

2013

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.

Riemer SA, Rex R, Schomburg D (2013) A metabolite-centric view on flux distributions in genome-scale metabolic models. BMC Syst Biol 7: 33.

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 by Phaeobacter inhibens DSM 17395. Proteomics, in press (doi: 10.1002/pmic.201200560).

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) Adaption of Phaeobacter inhibens DSM 17395 to growth with complex nutrients. Proteomics, in press (doi: 10.1002/pmic.201200513).

2009

Zech H, Thole S, Schreiber K, Kalhöfer D, Voget S, Brinkhoff T, Simon S, Schomburg D, Rabus R (2009) Growth phase-dependent global protein and metabolite profiles of Phaeobacter gallaeciensis strain DSM 17395, a member of the marine Roseobacter-clade. Proteomics 9: 3677–3697.

PhD dissertations:
René Rex (2012) Towards a new view on metabolic networks: automated reconstruction and large-scale computational analysis applied to Dinoroseobacter shibae. 19.12.2012.

Sarah Alessandra Kleist (2016) Metabolic adaptation processes of the marine bacterium Dinoroseobacter shibae DFL12T to changing environmental conditions

Principal investigators: Prof. Dr. C. Wittmann, Dr. Judith Becker
PhD students: A. Bartsch und A. Klingner

Aims

The goal of this project is the investigation of the metabolic flexibility, adaptation and robustness of the two model strains Dinoroseobacter shibae and Phaeobacter inhibens (former P. gallaeciensis) by quantitative ¹³C metabolic flux analysis. Despite the obvious ecological success of the Roseobacter clade, only little is known about their metabolic pathways. Most interestingly, the planned analysis will provide detailed insights into the metabolic response of the model strains to nutritional supply and other environmental parameters that are relevant for a marine life style. The study will be complemented with model-independent flux-profiling of novel isolates to unravel eco-specific flux signatures. This will be an initial step towards metafluxome studies, i.e. investigations of microbial communities, which will be carried out in close cooperation with subproject A.

Objectives/Methods

• Labelling experiments with ¹³C und ¹⁵N to investigate the carbon and nitrogen metabolism
• Metabolic modelling with OpenFlux
• Investigation of central metabolic pathways and systems-wide ¹³C-metabolic flux analysis for determining the in vivo activity
• Large-Scale ¹³C-Fluxom-Profiling of novel isolates of the Roseobacter clade
• Establishing of metafluxom-studies in mesocosm-experiments

Publications

2015

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.

2014

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.

2013

Ebert, M, Laaß S, Burghartz M, Petersen J, Koßmehl S, Wöhlbrand L, Rabus R, Wittmann C, Tielen P, Jahn D.  2013.  Transposon mutagenesis identified chromosomal and plasmid encoded genes essential for the adaptation of the marine bacterium Dinoroseobacter shibae to anaerobic conditions.. Journal of bacteriology.

2011

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.

2009

Fürch, T, Preusse M, Tomasch J, Zech H, Wagner-Döbler I, Rabus R, Wittmann C.  2009.  Metabolic fluxes in the central carbon metabolism of Dinoroseobacter shibae and Phaeobacter gallaeciensis, two members of the marine Roseobacter clade.. BMC microbiology. 9:209.

Contribution to conferences

Bartsch AK, Klingner A, Becker J, Wittmann C (2013) Functional contribution of central metabolic pathway to carbon dioxide assimilation in the marine bacterium Dinoroseobacter shibae. PhD Seminar of the Transregio 51, 8 May, TU Braunschweig (Talk)

Klingner A, Bartsch AK, Becker J, Wittmann C (2012) Fluxomics of selected marine bacteria and first results of a mesocosm experiment on metafluxomics. 5th Status Seminar of the Transregio 51, 6 February, HZI, Braunschweig (Talk).

Klingner A, Bartsch AK, Becker J, Wittmann C (2012) Large-scale 13C flux profiling of the Roseobacter clade. 7th Status Seminar of the Transregio 51, 15-16 October, Hanse Wissenschaftskolleg, Delmenhorst (Talk).

Bartsch AK, Klingner A Becker J, Wittmann C (2012) Functional contribution of central metabolic pathway to carbon dioxide assimilation in the marine bacterium Dinoroseobacter shibae. 7th Status Seminar of the Transregio 51, 15-16 October, Hanse Wissenschaftskolleg, Delmenhorst (Talk).

Bartsch AK, Klingner A, Becker J, Wittmann C (2012) Systems-wide metabolic flux analysis of Dinoroseobacter shibae. PhD Seminar of the Transregio 51, 2 July, TU Braunschweig (Talk)

Klingner A, Bartsch AK, Becker J, Wittmann C (2012) 13C metabolic flux profiling of P. gallaeciensis and novel isolates of the Roseobacter clade. PhD Seminar of the Transregio 51, 5 December, TU Braunschweig (Talk)

Bartsch AK, Klingner A, Becker J, Wittmann C (2012) Metabolic flux response of Dinoroseobacter shibae to genetic and environmental burdens. PhD Seminar of the Transregio 51, 5 December, TU Braunschweig (Talk)

Bartsch A, Klingner A, Becker J, Wittmann C (2012) Metabolic pathway fluxes of the marine model bacterium Dinoroseobacter shibae under changing environmental conditions. VAAM Annual Conference, 18-21 March, Tübingen (Vortrag).

Klingner A, Bartsch A, Becker J, Wittmann C (2012) Systems biology of the marine antibiotic producer Phaeobacter gallaeciensis. VAAM Annual Conference, March 18-21, Tübingen (Talk).

Wittmann C (2012) Systems biology and systems metabolic engineering, International Course on Microbial Physiology, 20 Januar, Delft, Holland (Talk).

Klingner A, Bartsch AK, Becker J, Wittmann C (2011) Metabolic network analysis of the Roseobacter clade: Pathways and pathway fluxes in Dinoroseobacter shibae, Phaeobacter gallaeciensis and other members. 3rd Status Seminar of the Transregio 51, 16-17 May, (Talk).

Becker J, Wittmann C (2011) Systems metabolic engineering of tailor-made cell factories,International Union of Microbiological Societies Congress, 6.September, Sapporo, Japan (Talk).

Wittmann C (2011) Systems biology and synthetic metabolic engineering, Research Colloquium, INSA Toulouse, 22. July, Toulouse, Frankreich (Talk).

Wittmann C (2011) From knowledge to improvement – analysis and engineering of microbial metabolism, Nestle Research Colloquium, 15 March, Lausanne, Schweiz (Talk).

Wittmann C (2010) Systembiologie. Deutsch-Japanisches Life Science Symposium. 31 August, Technische Universität Braunschweig (Talk).

Bolten C, Fürch T, Preusse M, Wittmann C (2010) Metabolic network analysis of the Roseobacter clade: Pathways and pathway fluxes in Dinoroseobacter shibae and Phaeobacter gallaeciensis. Kick-off Symposium of the Transregio 51, 13-15 June, Hanse Wissenschaftskolleg, Delmenhorst (Talk)

Bachelor- and Mastertheses

Samuel Hauf (2012) Marine Systembiologie: Untersuchung von Wachstum und Zentralstoffwechsel des Modellorganismus Dinoroseobacter shibae und verschiedener Mutanten

Supervisors: Prof. Dr. Wagner-Döbler, Prof. Dr. R. Rabus
Scientists: Dr. Jürgen Tomasch (Phd/Postdoc), Dr. Thomas Riedel (Phd/Postdoc)
PhD Students: Steffi Heyber
Bachelor- and master students: Meike Rohlfs, Regina Gohl

Aim

Two special types of generating energy through light play an important role In the world´s oceans : Aerobic anoxygenic photosynthesis and the light powered proton pump proteorhodopsin. We study the first one using Dinoroseobacter shibae, a symbiont of algae which is a model organism for the Roseobacter group, and the second one in Dokdonia donghaensis PRO95, one of the few published bacteria which carries a proteorhodopsin.

Methods

The adaptation of aerobic anoxygenic photosynthesis to the daily day-night rhythm is modelled using a systems biology approach. Data from all cellular levels are being integrated. Hypotheses derived from theoretical models are tested experimentally and optimized in an iterative process. The role of proteorhodopsin is investigated using physiological experiments, comparative genome analyses and studies of gene expression.

Publications

List of publications (AG Wagner Döbler):

2017

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.

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.

2016

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].

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].

2015

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.

2013

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 analogues to study sulfur metabolism in marine bacteria.. Beilstein journal of organic chemistry. 9:942-50.

Bruns, H, Thiel V, Voget S, Patzelt D, Daniel R, Wagner-Döbler I, Schulz S.  2013.  N-acylated alanine methyl esters (NAMEs) from Roseovarius tolerans, structural analogs of quorum-sensing autoinducers, N-acylhomoserine lactones.. Chemistry & biodiversity. 10(9):1559-73.

Neumann, A, Patzelt D, Wagner-Döbler I, Schulz S.  2013.  Identification of new N-acylhomoserine lactone signalling compounds of Dinoroseobacter shibae DFL-12(T) by overexpression of luxI genes.. Chembiochem : a European journal of chemical biology. 14(17):2355-61.

Riedel, T, Rohlfs M, Buchholz I, Wagner-Döbler I, Reck M.  2013.  Complete sequence of the suicide vector pJP5603.. Plasmid. 69(1):104-7.

Patzelt D, Wang, H, Buchholz, I, Rohde, M, Gröbe, L, Pradella, S, Neumann A, Schulz S, Heyber S, Muench K, Muench 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 7/12: 2274-2286.

Fiebig, A, Pradella S, Petersen J, Michael V, Päuker O, Rohde M, Göker M, Klenk H-P, Wagner-Döbler I.  2013.  Genome of the marine alphaproteobacterium Hoeflea phototrophica type strain (DFL-43(T)).. Standards in genomic sciences. 7(3):440-8.

Fiebig, A, Pradella S, Petersen J, Päuker O, Michael V, Lünsdorf H, Göker M, Klenk H-P, Wagner-Döbler I.  2013.  Genome of the R-body producing marine alphaproteobacterium Labrenzia alexandrii type strain (DFL-11(T)).. Standards in genomic sciences. 7(3):413-26.

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.

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. 24;13:117. doi: 10.1186/1471-2180-13-117.

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. 24;13:118. doi: 10.1186/1471-2180-13-118.

2012

Brinkhoff, T, Fischer D, Vollmers J, Voget S, Beardsley C, Thole S, Mussmann M, Kunze B, Wagner-Döbler I, Daniel R et al..  2012.  Biogeography and phylogenetic diversity of a cluster of exclusively marine myxobacteria.. The ISME journal. 6(6):1260-72.

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.

2011

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 5:1957-1968.

2010

Riedel T, Tomasch J, Buchholz I, Jacobs J, Kollenberg M, Gerdts G, Wichels A, Brinkhoff T, Cypionka H, Wagner-Döbler I. 2010. Constitutive expression of the proteorhodopsin gene by a flavobacterium strain representative of the proteorhodopsin-producing microbial community in the North Sea. Appl Environ Microbiol 76:3187-3197.

Riedel T, Tomasch J, Buchholz I, Jacobs J, Kollenberg M, Gerdts G, Wichels A, Brinkhoff T, Cypionka H, Wagner-Döbler I.  2010.  Constitutive expression of the proteorhodopsin gene by a flavobacterium strain representative of the proteorhodopsin-producing microbial community in the North Sea.. Applied and environmental microbiology. 76(10):3187-97.

Thiel, V, Brinkhoff T, Dickschat JS, Wickel S, Grunenberg J, Wagner-Döbler I, Simon M, Schulz S.  2010.  Identification and biosynthesis of tropone derivatives and sulfur volatiles produced by bacteria of the marine Roseobacter clade.. Organic & biomolecular chemistry. 8(1):234-46.

Wagner-Döbler I, Ballhausen B, Berger M, Brinkhoff T, Buchholz I, Bunk B, Cypionka H, Daniel R, Drepper T, Gerdts G et al..  2010.  The complete genome sequence of the algal symbiont Dinoroseobacter shibae: a hitchhiker's guide to life in the sea.. The ISME journal. 4(1):61-77.

2009

Thiel V, Kunze B, Verma P, Wagner-Döbler I, Schulz S.  2009.  New structural variants of homoserine lactones in bacteria.. Chembiochem : a European journal of chemical biology. 10(11):1861-8.

Thiel V, Vilchez R, Sztajer H, Wagner-Döbler I, Schulz S.  2009.  Identification, quantification, and determination of the absolute configuration of the bacterial quorum-sensing signal autoinducer-2 by gas chromatography-mass spectrometry.. Chembiochem : a European journal of chemical biology. 10(3):479-85.

Fürch T, Preusse M, Tomasch J, Zech H, Wagner-Döbler I, Rabus R, Wittmann C.  2009.  Metabolic fluxes in the central carbon metabolism of Dinoroseobacter shibae and Phaeobacter gallaeciensis, two members of the marine Roseobacter clade.. BMC microbiology. 9:209.

2008

Bodor A, Elxnat B, Thiel V, Schulz S, Wagner-Döbler I.  2008.  Potential for luxS related signalling in marine bacteria and production of autoinducer-2 in the genus Shewanella.. BMC microbiology. 8:13. Abstract

Pommerenke, C, Gabriel I, Bunk B, Münch R, Haddad I, Tielen P, Wagner-Döbler I, Jahn D.  2008.  ROSY--a flexible and universal database and bioinformatics tool platform for Roseobacter related species.. In silico biology. 8(2):177-86.

2007

Vilchez R, Lemme A, Thiel V, Schulz S, Sztajer H, Wagner-Döbler I.  2007.  Analysing traces of autoinducer-2 requires standardization of the Vibrio harveyi bioassay.. Analytical and bioanalytical chemistry. 387(2):489-96.

2006

Wagner-Döbler I, Biebl H.  2006.  Environmental biology of the marine Roseobacter lineage.. Annual review of microbiology. 60:255-80.

2005

Biebl H, Allgaier M, Lünsdorf H, Pukall R, Tindall BJ, Wagner-Döbler I.  2005.  Roseovarius mucosus sp. nov., a member of the Roseobacter clade with trace amounts of bacteriochlorophyll a.. International journal of systematic and evolutionary microbiology. 55(Pt 6):2377-83.

Biebl H, Allgaier M, Tindall BJ, Koblizek M, Lünsdorf H, Pukall R, Wagner-Döbler I.  2005.  Dinoroseobacter shibae gen. nov., sp. nov., a new aerobic phototrophic bacterium isolated from dinoflagellates.. International journal of systematic and evolutionary microbiology. 55(Pt 3):1089-96.

List of publications (AG Jahn / Münch):

2017

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.

2014

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.

2013

Patzelt D, Wang, H, Buchholz, I, Rohde, M, Gröbe, L, Pradella, S, Neumann A, Schulz S, Heyber S, Muench K, Muench 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 7/12: 2274-2286.

Ebert M, Laaß S, Burghartz M, Petersen J, Koßmehl S, Wöhlbrand L, Rabus R, Wittmann C, Tielen P, Jahn D (2013) Transposon mutagenesis identified chromosomal and plasmid encoded genes essential for the adaptation of the marine bacterium Dinoroseobacter shibae to anaerobic conditions.. Journal of bacteriology.

2012

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.

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.

2010

Wagner-Döbler I, Ballhausen B, Berger M, Brinkhoff T, Buchholz I, Bunk B, Cypionka H, Daniel R, Drepper T, Gerdts G et al. (2010) The complete genome sequence of the algal symbiont Dinoroseobacter shibae: a hitchhiker's guide to life in the sea.. The ISME journal. 4(1):61-77.

2009

Piekarski T, Buchholz I, Drepper T, Schobert M, Wagner-Doebler I, Tielen P, Jahn D (2009) Genetic tools for the investigation of Roseobacter clade bacteria.. BMC microbiology. 9:265.

2008

Pommerenke C, Gabriel I, Bunk B, Münch R, Haddad I, Tielen P, Wagner-Döbler I, Jahn D (2008) ROSY--a flexible and universal database and bioinformatics tool platform for Roseobacter related species.. In silico biology. 8(2):177-86.

Contributions to conferences

Wagner-Döbler I (2012) C5: Progress report and future perspectives. 7th Status Seminar of the Transregio 51, 12-13. October 2012, Hanse Wissenschaftskolleg, Delmenhorst (Talk)

Riedel T, Gómez-Consarnau L, Tomasch J, Jarek M, Martin M, Brinkhoff T, Cypionka H, Fuhrman J and Wagner-Döbler I (2012) A xanthorhodopsin-like second bacterial rhodopsin is expressed in the flavobacterium Dokdonia donghaensis PRO95. ISME 14, 19th – 24th August 2012, Copenhagen (Poster)

Riedel T, Gómez-Consarnau L, Tomasch J, Jarek M, Fuhrman J and Wagner-Döbler I Understanding the role of genomic context onn proteorhodopsin function through analysis of the Dokdonia donghaensis PRO95 genome. SAME 12, 28th August – 2nd September 2011, Rostock, Germany (Poster)

Tomasch J, Gohl R, Bunk B, Diez M-S, Wagner-Döbler I (2011) Transcriptional response of the photoheterotrophic marine bacterium Dinoroseobacter shibae to changing light regimes (2011) BAGECO 11, 29th May – 6th June, Corfu (Talk)

Tomasch J, Gohl R, Bunk B, Diez M-S, Wagner-Döbler I (2011) Transcriptional response of the photoheterotrophic marine bacterium Dinoroseobacter shibae to changing light regimes (2011) Gordon Research Conference „Applied and Environmental Microbiology“, 10th – 15th July, 2011, Mount Holyoke College (Poster)

Tomasch J, Gohl R, Bunk B, Suarez-Diez M, Wagner-Döbler I (2011) Transcriptional response of the photoheterotrophic marine bacterium Dinoroseobacter shibae to changing light regimes. VAAM 3rd – 6th April, Karlsruhe, 2011 (Poster)

Tomasch J, Wang H, Buchholz I and Wagner-Döbler I (2011) Statistische Analyse der morphologischen Heterogenität bakterieller Kulturen. Biostats – Biologie und Statistik in der Praxis, 22-24. März 2011, Deutsche Sammlung für Mikroorganismen und Zellkulturen, Brauschweig (Talk)

Tomasch J, Gohl R, Bunk B, Suarez-Diez M, Wagner-Döbler I (2010) Transcriptional response of the photoheterotrophic marine bacterium Dinoroseobacter shibae to light exposure. Workshop on Aerobic Anoxygenic Phototrophs; 22th – 24th September 2010, Institut for Microbiology, Academy of Sciences, Czech Republic, Trebon (Talk)

Wagner-Döbler I (2010) Transcriptional response of the photoheterotrophic marine bacterium Dinoroseobacter shibae to changing light regimes. Gordon Rearch Conference „Marine Microbes“, 4th to 9th July, 2010, Tilton School, NH, USA (Poster)

Tomasch J, Gohl R, Bunk B, Münch R and Wagner-Döbler I (2010) Transcriptional response of the photoheterotrophic marine bacterium Dinoroseobacter shibae to light exposure. Kick-off Symposium of the Transregio 51, 13th -15th June 2010, Hanse Wissenschaftskolleg, Delmenhorst (Talk)

Tomasch J, Bunk B, Münch R, Wagner-Döbler I (2010) Transcriptional Response of the Photoheterotrophic Marine Bacterium Dinoroseobacter shibae to Light. VAAM 29th – 31st March 2010, Göttingen (Poster)

Invited talks

Riedel T. (2012) Rhodopsin phototrophy in the oceans. Microbiological Colloquium, 18th April 2012, ICBM, University of Oldenburg, Germany. Wagner-Döbler I. Transcriptional response of the photoheterotrophic bacterium Dinoroseobacter shibae to changing light regimes – sustainable use of energy on a global scale. Invitation by Prof. Jed Fuhrman, University of Southern California, Los Angeles, U.S., 19th July, 2011, Prof. Feng Chen, Institute of Marine and Environmental Technology, Baltimore, U.S., 27th July, 2011, Prof. Farooq Azam, Woods Hole Oceanographic Institute, San Diego, U.S., 21th June, 2012.

Wagner-Döbler I (2011) Global transcriptome analysis of the response to light and quorum sensing signals in a marine Roseobacter strain – sustainable use of energy on a global scale. Mikrobiologisches Kolloquium, Universität Jena, 13th April, 2011, Jena.

Wagner-Döbler I (2010) Global transcriptome analysis of the response to light and quorum sensing signals in a marine Roseobacter strain. Mikrobiologisches Kolloquium, Universität Mainz, 6th December, 2010 (invitation by Prof. Dr. G. Unden)

Phd dissertations

Jürgen Tomasch (2011). Experimentelle und bioinformatische Analyse der aeroben anoxygenen Photosynthese in dem photoheterotrophen Meeresbakterium Dinoroseobacter shibae DFL12. TU Braunschweig, 27.06.2011.

Thomas Riedel (2012). Dokdonia sp. PRO95: A marine flavobacterium with two phylogenetically different rhodopsin genes in its genome. TU Braunschweig, 20.12.2012

Bachelor- und Master theses

Meike Rohlfs (2012) Untersuchung von Knockout-Strategien für Dokdonia donghaensis PRO95. Bachelorarbeit, FH Emden.
Regina Gohl (2009)

Ended

Principal investigators: Prof. Dr. Susanne Engelmann
PhD students:

Project outline:

Scientific questions

Dinoroseobacter shibae is a photoheterotophic bacterium and performs aerobic anoxygenic photosynthesis. As a marine bacterium living in the photic zone environment of marine eco-systems D. shibae is frequently exposed to oxygen and, hence, oxidative stress is one of the challenges the bacterium has to cope with. The aim of the present study is to provide detailed insights into the response of D. shibae to different kinds of oxidative stress. Hydrogen peroxide and paraquat will be used as agents that induce oxidative stress and changes in the protein pattern will be analysed in response to these substances in order to describe the respective stimulons. The proteomic data will be compared with transcriptomic data. One major effect of oxygen radicals in the cell is the oxidation of thiols in proteins also called disulfide stress resulting in reversible and irreversible modifications. Disulfide stress can be specifically induced by diamide which will be used to define the disulfide stress stimulon by proteomics and transcriptomics. The obtained OMICs data will be deposited in a database that can be used to extensively compare expression profiles and to identify marker proteins for the respective stimulus and to decipher regulatory networks involved in the adaptation to these stimuli. In collaboration with projects B5 and C5 the expression profiles will be compared with those generated under iron and oxygen limitation and in response to light. In future the marker proteins/genes will be used to characterize the physiology of the bacterium under more complex in vivo conditions. The genome of D. shibae codes for three OxyR like proteins. In Gram-negative bacteria, the LysR-type regulator OxyR is a major regular for genes involved in oxidative stress response. Consequently, we are interested in the function of the OxyR like proteins of D. shibae in the oxidative stress response.

Aims, work program and methods

Work package 1

To define the peroxide, the superoxide and the diamide stress stimulon in D. shibae we want to employ 2-D PAGE combined with MALDI-TOF MS for spot identification and gel free MS approaches. Moreover, DNA arrays will be used to analyse the transcriptome under these conditions. Marker genes and proteins will be identified whose expression significantly changed in response to the respective stimuli by cross comparisons of expression profiles ob-tained under different growth conditions. Postranslational modifications of thiol groups in cysteine residues in response to oxidative stress will be visualized by a fluorescence based proteomic approach.

Work package 2

To analyse the role of the three OxyR like proteins in oxidative stress response, the impact of these proteins on global gene expression in D. shibae will be analysed using a transcriptomic and proteomic approach. Northern blot experiments will be performed to study the transcrip-tion of the respective genes in response to different stimuli. Gel shifts and foot print analyses with the purified regulator proteins and PCR products will be applied to verify the direct in-teraction of these proteins with regulatory regions of selected genes, probably leading to the identification of possible DNA-binding motifs. A genome wide search using the genome se-quence of D. shibae and the possible binding motive can be used to identify possible targets of the OxyR like proteins. Additional regulatory proteins for oxidative stress induced genes will be identified by aligning upstream regions if these genes to search for conserved binding motifs and by using biotinylated PCR products of the respective regulatory regions, immobi-lized to strepatividin coated magnetic beads. These beads will be incubated with protein ex-tracts of D. shibae. Proteins that have bound can be identified by mass spectrometry.

Principal investigator: Prof. Dr. Bernd Blasius

PhD Students: