TRR 51:  Ecology, Physiology and Molecular Biology of the Roseobacter Clade: Towards a Systems Biology Understanding of a Globally Important Clade of Marine Bacteria

• Subject Area: Medicine ; Biology ; Chemistry
• Term: from 2010 to 2021
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 34509606

• Final Report Year: 2023

No abstract available

Publications

• 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.
  Wagner-Döbler, Irene; Ballhausen, Britta; Berger, Martine; Brinkhoff, Thorsten; Buchholz, Ina; Bunk, Boyke; Cypionka, Heribert; Daniel, Rolf; Drepper, Thomas; Gerdts, Gunnar; Hahnke, Sarah; Han, Cliff; Jahn, Dieter; Kalhoefer, Daniela; Kiss, Hajnalka; Klenk, Hans-Peter; Kyrpides, Nikos; Liebl, Wolfgang; Liesegang, Heiko ... & Simon, Meinhard
  
• Origin and Evolution of a Novel DnaA-Like Plasmid Replication Type in Rhodobacterales. Molecular Biology and Evolution, 28(3), 1229-1240.
  Petersen, J.; Brinkmann, H.; Berger, M.; Brinkhoff, T.; Pauker, O. & Pradella, S.
  
• Tropodithietic Acid Production in Phaeobacter gallaeciensis Is Regulated by N-Acyl Homoserine Lactone-Mediated Quorum Sensing. Journal of Bacteriology, 193(23), 6576-6585.
  Berger, M.; Neumann, A.; Schulz, S.; Simon, M. & Brinkhoff, T.
  
• Phaeobacter gallaeciensisgenomes from globally opposite locations reveal high similarity of adaptation to surface life. The ISME Journal, 6(12), 2229-2244.
  Thole, Sebastian; Kalhoefer, Daniela; Voget, Sonja; Berger, Martine; Engelhardt, Tim; Liesegang, Heiko; Wollherr, Antje; Kjelleberg, Staffan; Daniel, Rolf; Simon, Meinhard; Thomas, Torsten & Brinkhoff, Thorsten
  
• Pathways and substrate‐specific regulation of amino acid degradation in Phaeobacter inhibens DSM 17395 (archetype of the marine Roseobacter clade). Environmental Microbiology, 16(1), 218-238.
  Drüppel, Katharina; Hensler, Michael; Trautwein, Kathleen; Koßmehl, Sebastian; Wöhlbrand, Lars; Schmidt‐Hohagen, Kerstin; Ulbrich, Marcus; Bergen, Nils; Meier‐Kolthoff, Jan P.; Göker, Markus; Klenk, Hans‐Peter; Schomburg, Dietmar & Rabus, Ralf
  
• Planktomarina temperata gen. nov., sp. nov., belonging to the globally distributed RCA cluster of the marine Roseobacter clade, isolated from the German Wadden Sea. International Journal of Systematic and Evolutionary Microbiology, 63(Pt_11), 4207-4217.
  Giebel, Helge-Ansgar; Kalhoefer, Daniela; Gahl-Janssen, Renate; Choo, Yoe-Jin; Lee, Kiyoung; Cho, Jang-Cheon; Tindall, Brian J.; Rhiel, Erhard; Beardsley, Christine; Aydogmus, Ömer O.; Voget, Sonja; Daniel, Rolf; Simon, Meinhard & Brinkhoff, Thorsten
  
• Poles Apart: Arctic and Antarctic Octadecabacter strains Share High Genome Plasticity and a New Type of Xanthorhodopsin. PLoS ONE, 8(5), e63422.
  Vollmers, John; Voget, Sonja; Dietrich, Sascha; Gollnow, Kathleen; Smits, Maike; Meyer, Katja; Brinkhoff, Thorsten; Simon, Meinhard & Daniel, Rolf
  
• You are what you talk: quorum sensing induces individual morphologies and cell division modes in Dinoroseobacter shibae. The ISME Journal, 7(12), 2274-2286.
  Patzelt, Diana; Wang, Hui; Buchholz, Ina; Rohde, Manfred; Gröbe, Lothar; Pradella, Silke; Neumann, Alexander; Schulz, Stefan; Heyber, Steffi; Münch, Karin; Münch, Richard; Jahn, Dieter; Wagner-Döbler, Irene & Tomasch, Jürgen
  
• Adaptation of an abundantRoseobacterRCA organism to pelagic systems revealed by genomic and transcriptomic analyses. The ISME Journal, 9(2), 371-384.
  Voget, Sonja; Wemheuer, Bernd; Brinkhoff, Thorsten; Vollmers, John; Dietrich, Sascha; Giebel, Helge-Ansgar; Beardsley, Christine; Sardemann, Carla; Bakenhus, Insa; Billerbeck, Sara; Daniel, Rolf & Simon, Meinhard
  
• Carbohydrate Catabolism in Phaeobacter inhibens DSM 17395, a Member of the Marine Roseobacter Clade. Applied and Environmental Microbiology, 80(15), 4725–4737.
  Wiegmann, Katharina; Hensler, Michael; Wöhlbrand, Lars; Ulbrich, Marcus; Schomburg, Dietmar & Rabus, Ralf
  
• Homoserine Lactones, Methyl Oligohydroxybutyrates, and Other Extracellular Metabolites of Macroalgae‐Associated Bacteria of the Roseobacter Clade: Identification and Functions. ChemBioChem, 16(14), 2094-2107.
  Ziesche, Lisa; Bruns, Hilke; Dogs, Marco; Wolter, Laura; Mann, Florian; Wagner‐Döbler, Irene; Brinkhoff, Thorsten & Schulz, Stefan
  
• Inefficient microbial production of refractory dissolved organic matter in the ocean. Nature Communications, 6(1).
  Osterholz, Helena; Niggemann, Jutta; Giebel, Helge-Ansgar; Simon, Meinhard & Dittmar, Thorsten
  
• Large-Scale 13 C Flux Profiling Reveals Conservation of the Entner-Doudoroff Pathway as a Glycolytic Strategy among Marine Bacteria That Use Glucose. Applied and Environmental Microbiology, 81(7), 2408-2422.
  Klingner, Arne; Bartsch, Annekathrin; Dogs, Marco; Wagner-Döbler, Irene; Jahn, Dieter; Simon, Meinhard; Brinkhoff, Thorsten; Becker, Judith & Wittmann, Christoph
  
• Bacterioplankton Biogeography of the Atlantic Ocean: A Case Study of the Distance-Decay Relationship. Frontiers in Microbiology, 7.
  Milici, Mathias; Tomasch, Jürgen; Wos-Oxley, Melissa L.; Decelle, Johan; Jáuregui, Ruy; Wang, Hui; Deng, Zhi-Luo; Plumeier, Iris; Giebel, Helge-Ansgar; Badewien, Thomas H.; Wurst, Mascha; Pieper, Dietmar H.; Simon, Meinhard & Wagner-Döbler, Irene
  
• Biofilm plasmids with a rhamnose operon are widely distributed determinants of the ‘swim-or-stick’ lifestyle in roseobacters. The ISME Journal, 10(10), 2498-2513.
  Michael, Victoria; Frank, Oliver; Bartling, Pascal; Scheuner, Carmen; Göker, Markus; Brinkmann, Henner & Petersen, Jörn
  
• Biogeography and environmental genomics of the Roseobacter-affiliated pelagic CHAB-I-5 lineage. Nature Microbiology, 1(7).
  Billerbeck, Sara; Wemheuer, Bernd; Voget, Sonja; Poehlein, Anja; Giebel, Helge-Ansgar; Brinkhoff, Thorsten; Gram, Lone; Jeffrey, Wade H.; Daniel, Rolf & Simon, Meinhard
  
• Deciphering associations between dissolved organic molecules and bacterial communities in a pelagic marine system. The ISME Journal, 10(7), 1717-1730.
  Osterholz, Helena; Singer, Gabriel; Wemheuer, Bernd; Daniel, Rolf; Simon, Meinhard; Niggemann, Jutta & Dittmar, Thorsten
  
• Dynamic metabolic exchange governs a marine algal-bacterial interaction. eLife, 5.
  Segev, Einat; Wyche, Thomas P.; Kim, Ki Hyun; Petersen, Jörn; Ellebrandt, Claire; Vlamakis, Hera; Barteneva, Natasha; Paulson, Joseph N.; Chai, Liraz; Clardy, Jon & Kolter, Roberto
  
• Dual function of tropodithietic acid as antibiotic and signaling molecule in global gene regulation of the probiotic bacterium Phaeobacter inhibens. Scientific Reports, 7(1).
  Beyersmann, Paul G.; Tomasch, Jürgen; Son, Kwangmin; Stocker, Roman; Göker, Markus; Wagner-Döbler, Irene; Simon, Meinhard & Brinkhoff, Thorsten
  
• Phylogenomics ofRhodobacteraceaereveals evolutionary adaptation to marine and non-marine habitats. The ISME Journal, 11(6), 1483-1499.
  Simon, Meinhard; Scheuner, Carmen; Meier-Kolthoff, Jan P.; Brinkhoff, Thorsten; Wagner-Döbler, Irene; Ulbrich, Marcus; Klenk, Hans-Peter; Schomburg, Dietmar; Petersen, Jörn & Göker, Markus
  
• Rhodobacteraceae on the marine brown alga Fucus spiralis are abundant and show physiological adaptation to an epiphytic lifestyle. Systematic and Applied Microbiology, 40(6), 370-382.
  Dogs, Marco; Wemheuer, Bernd; Wolter, Laura; Bergen, Nils; Daniel, Rolf; Simon, Meinhard & Brinkhoff, Thorsten
  
• The Exometabolome of Two Model Strains of the Roseobacter Group: A Marketplace of Microbial Metabolites. Frontiers in Microbiology, 8.
  Wienhausen, Gerrit; Noriega-Ortega, Beatriz E.; Niggemann, Jutta; Dittmar, Thorsten & Simon, Meinhard
  
• Trajectories and Drivers of Genome Evolution in Surface-Associated Marine Phaeobacter. Genome Biology and Evolution, 9(12), 3297-3311.
  Freese, Heike M.; Sikorski, Johannes; Bunk, Boyke; Scheuner, Carmen; Meier-Kolthoff, Jan P.; Spröer, Cathrin; Gram, Lone & Overmann, Jörg
  
• VICTOR: genome-based phylogeny and classification of prokaryotic viruses. Bioinformatics, 33(21), 3396-3404.
  Meier-Kolthoff, Jan P. & Göker, Markus
  
• An Unprecedented Medium-Chain Diunsaturated N-acylhomoserine Lactone from Marine Roseobacter Group Bacteria. Marine Drugs, 17(1), 20.
  Ziesche, Lisa; Wolter, Laura; Wang, Hui; Brinkhoff, Thorsten; Pohlner, Marion; Engelen, Bert; Wagner-Döbler, Irene & Schulz, Stefan
  
• Horizontal operon transfer, plasmids, and the evolution of photosynthesis in Rhodobacteraceae. The ISME Journal, 12(8), 1994-2010.
  Brinkmann, Henner; Göker, Markus; Koblížek, Michal; Wagner-Döbler, Irene & Petersen, Jörn
  
• Packaging of Dinoroseobacter shibae DNA into Gene Transfer Agent Particles Is Not Random. Genome Biology and Evolution, 10(1), 359-369.
  Tomasch, Jürgen; Wang, Hui; Hall, April T. K.; Patzelt, Diana; Preusse, Matthias; Petersen, Jörn; Brinkmann, Henner; Bunk, Boyke; Bhuju, Sabin; Jarek, Michael; Geffers, Robert; Lang, Andrew S. & Wagner-Döbler, Irene
  
• The marine bacterium Phaeobacter inhibens secures external ammonium by rapid buildup of intracellular nitrogen stocks. FEMS Microbiology Ecology, 94(10).
  Trautwein, Kathleen; Hensler, Michael; Wiegmann, Katharina; Skorubskaya, Ekaterina; Wöhlbrand, Lars; Wünsch, Daniel; Hinrichs, Christina; Feenders, Christoph; Müller, Constanze; Schell, Kristina; Ruppersberg, Hanna; Vagts, Jannes; Koßmehl, Sebastian; Steinbüchel, Alexander; Schmidt-Kopplin, Philippe; Wilkes, Heinz; Hillebrand, Helmut; Blasius, Bernd; Schomburg, Dietmar & Rabus, Ralf
  
• Transcriptional response of the photoheterotrophic marine bacterium Dinoroseobacter shibae to changing light regimes. The ISME Journal, 5(12), 1957–1968.
  Tomasch, Jürgen; Gohl, Regina; Bunk, Boyke; Diez, Maria Suarez & Wagner-Döbler, Irene
  
• A marine plasmid hitchhiking vast phylogenetic and geographic distances. Proceedings of the National Academy of Sciences, 116(41), 20568-20573.
  Petersen, Jörn; Vollmers, John; Ringel, Victoria; Brinkmann, Henner; Ellebrandt-Sperling, Claire; Spröer, Cathrin; Howat, Alexandra M.; Murrell, J. Colin & Kaster, Anne-Kristin
  
• Amino Acid and Sugar Catabolism in the Marine Bacterium Phaeobacter inhibens DSM 17395 from an Energetic Viewpoint. Applied and Environmental Microbiology, 85(24).
  Wünsch, Daniel; Trautwein, Kathleen; Scheve, Sabine; Hinrichs, Christina; Feenders, Christoph; Blasius, Bernd; Schomburg, Dietmar & Rabus, Ralf
  
• Cobaviruses – a new globally distributed phage group infecting Rhodobacteraceae in marine ecosystems. The ISME Journal, 13(6), 1404-1421.
  Bischoff, Vera; Bunk, Boyke; Meier-Kolthoff, Jan P.; Spröer, Cathrin; Poehlein, Anja; Dogs, Marco; Nguyen, Mary; Petersen, Jörn; Daniel, Rolf; Overmann, Jörg; Göker, Markus; Simon, Meinhard; Brinkhoff, Thorsten & Moraru, Cristina
  
• Complementary energy acquisition via aerobic anoxygenic photosynthesis and carbon monoxide oxidation by Planktomarina temperata of the Roseobacter group. FEMS Microbiology Ecology, 95(5).
  Giebel, Helge-Ansgar; Wolterink, Mathias; Brinkhoff, Thorsten & Simon, Meinhard
  
• Does the Chemodiversity of Bacterial Exometabolomes Sustain the Chemodiversity of Marine Dissolved Organic Matter?. Frontiers in Microbiology, 10.
  Noriega-Ortega, Beatriz E.; Wienhausen, Gerrit; Mentges, Andrea; Dittmar, Thorsten; Simon, Meinhard & Niggemann, Jutta
  
• The Majority of Active Rhodobacteraceae in Marine Sediments Belong to Uncultured Genera: A Molecular Approach to Link Their Distribution to Environmental Conditions. Frontiers in Microbiology, 10.
  Pohlner, Marion; Dlugosch, Leon; Wemheuer, Bernd; Mills, Heath; Engelen, Bert & Reese, Brandi Kiel
  
• TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nature Communications, 10(1).
  Meier-Kolthoff, Jan P. & Göker, Markus
  
• Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria. Frontiers in Microbiology, 11.
  Hördt, Anton; López, Marina García; Meier-Kolthoff, Jan P.; Schleuning, Marcel; Weinhold, Lisa-Maria; Tindall, Brian J.; Gronow, Sabine; Kyrpides, Nikos C.; Woyke, Tanja & Göker, Markus
  
• A novel class of sulfur-containing aminolipids widespread in marine roseobacters. The ISME Journal, 15(8), 2440-2453.
  Smith, Alastair F.; Silvano, Eleonora; Päuker, Orsola; Guillonneau, Richard; Quareshy, Mussa; Murphy, Andrew; Mausz, Michaela A.; Stirrup, Rachel; Rihtman, Branko; Aguilo-Ferretjans, Maria; Brandsma, Joost; Petersen, Jörn; Scanlan, David J. & Chen, Yin
  
• Dinoroseobacter shibae Outer Membrane Vesicles Are Enriched for the Chromosome Dimer Resolution Site dif. mSystems, 6(1).
  Wang, Hui; Beier, Nicole; Boedeker, Christian; Sztajer, Helena; Henke, Petra; Neumann-Schaal, Meina; Mansky, Johannes; Rohde, Manfred; Overmann, Jörg; Petersen, Jörn; Klawonn, Frank; Kucklick, Martin; Engelmann, Susanne; Tomasch, Jürgen & Wagner-Döbler, Irene
  
• Microbial Growth and Organic Matter Cycling in the Pacific Ocean Along a Latitudinal Transect Between Subarctic and Subantarctic Waters. Frontiers in Marine Science, 8.
  Giebel, Helge-Ansgar; Arnosti, Carol; Badewien, Thomas H.; Bakenhus, Insa; Balmonte, John Paul; Billerbeck, Sara; Dlugosch, Leon; Henkel, Rohan; Kuerzel, Birgit; Meyerjürgens, Jens; Milke, Felix; Voss, Daniela; Wienhausen, Gerrit; Wietz, Matthias; Winkler, Holger; Wolterink, Mathias & Simon, Meinhard
  
• TYGS and LPSN:a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Research, 50(D1), D801-D807.
  Meier-Kolthoff, Jan P.; Carbasse, Joaquim Sardà; Peinado-Olarte, Rosa L. & Göker, Markus
  
• Availability of vitamin B12 and its lower ligand intermediate α-ribazole impact prokaryotic and protist communities in oceanic systems. The ISME Journal, 16(8), 2002-2014.
  Wienhausen, Gerrit; Dlugosch, Leon; Jarling, René; Wilkes, Heinz; Giebel, Helge-A. & Simon, Meinhard
  
• New Microviridae isolated from Sulfitobacter reveals two cosmopolitan subfamilies of single-stranded DNA phages infecting marine and terrestrial Alphaproteobacteria. Virus Evolution, 8(2).
  Zucker, Falk; Bischoff, Vera; Olo, Ndela Eric; Heyerhoff, Benedikt; Poehlein, Anja; Freese, Heike M.; Roux, Simon; Simon, Meinhard; Enault, Francois & Moraru, Cristina
  
• Selection, drift and community interactions shape microbial biogeographic patterns in the Pacific Ocean. The ISME Journal, 16(12), 2653-2665.
  Milke, Felix; Wagner-Doebler, Irene; Wienhausen, Gerrit & Simon, Meinhard
  
• Significance of gene variants for the functional biogeography of the near-surface Atlantic Ocean microbiome. Nature Communications, 13(1).
  Dlugosch, Leon; Poehlein, Anja; Wemheuer, Bernd; Pfeiffer, Birgit; Badewien, Thomas H.; Daniel, Rolf & Simon, Meinhard
  
• The overlooked role of a biotin precursor for marine bacteria - desthiobiotin as an escape route for biotin auxotrophy. The ISME Journal, 16(11), 2599–2609.
  Wienhausen, Gerrit; Bruns, Stefan; Sultana, Sabiha; Dlugosch, Leon; Groon, Luna-Agrippina; Wilkes, Heinz & Simon, Meinhard
  
• Ecological mechanisms and current systems shape the modular structure of the global oceans’ prokaryotic seascape. Nature Communications, 14(1).
  Milke, Felix; Meyerjürgens, Jens & Simon, Meinhard
  
• Metagenome-assembled genomes reveal greatly expanded taxonomic and functional diversification of the abundant marine Roseobacter RCA cluster. Microbiome, 11(1).
  Liu, Yanting; Brinkhoff, Thorsten; Berger, Martine; Poehlein, Anja; Voget, Sonja; Paoli, Lucas; Sunagawa, Shinichi; Amann, Rudolf & Simon, Meinhard
  
• The enigmatic nucleus of the marine dinoflagellate Prorocentrum cordatum. mSphere, 8(4).
  Kalvelage, Jana; Wöhlbrand, Lars; Schoon, Robin-Alexander; Zink, Fiona-Marine; Correll, Christina; Senkler, Jennifer; Eubel, Holger; Hoppenrath, Mona; Rhiel, Erhard; Braun, Hans-Peter; Winklhofer, Michael; Klingl, Andreas & Rabus, Ralf
  
• Vitamin B12 is not shared by all marine prototrophic bacteria with their environment. The ISME Journal, 17(6), 836-845.
  Sultana, Sabiha; Bruns, Stefan; Wilkes, Heinz; Simon, Meinhard & Wienhausen, Gerrit