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Eckweiler D, Dudek D, Hartlich J, Broetje D, Jahn D (2018) PRODORIC2: the bacterial gene regulation database in 2018. Nucleic Acids Res 46/D1: D320-326. DOI: 10.1093/nar/gkx1091 [INF]
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 [B1, B5]
Klotz F, Brinkhoff T, Freese HM, Wietz M, Teske A, Simon M, Giebel HA (2018) Tritonibacter horizontis gen. nov., sp. nov., a member of the Rhodobacteraceae, isolated from the Deepwater Horizon oil spill. Int J Syst Evol Microbiol 68: 736-744. DOI 10.1099/ijsem.0.002573 [A1, A7, B2]
Kopejtka K, Tomasch J, Bunk B, Spröer C, Wagner-Döbler I, Koblížek M (2018) The complete genome sequence of Rhodobaca barguzinensis alga05 (DSM 19920) documents its adaptation for life in soda lakes. Extremophiles 22(6): 839-849. doi: 10.1007/s00792-018-1041-8. [B4, A7]
Schlawis C, Kern S, Kudo Y, Grunenberg J, Moore B, Schulz S (2018) Structural elucidation of trace components combining GC/MS, GC/IR, DFT-calculation and synthesis - Salinilactones, unprecedented bicyclic lactones from Salinispora bacteria. Angew Chem Int Ed 57: 14921-14925. doi: 10.1002/anie.201807923: Angew Chem 130: 15137-15141. doi: 10.1002/ange.201807923 [C2]
Tomasch J, Wang H, Hall ATK, Patzelt D, Preusse M, Petersen J, Brinkmann H, Bunk B, Bhuju S, Jarek M, Geffers R, Lang AS, Wagner-Döbler I (2018) Packaging of Dinoroseobacter shibae DNA into Gene Transfer Agent particles is not random. Genome Biol Evol 10(1): 359-369. doi: 10.1093/gbe/evy005. [B4, A5, A7, C5]
Trautwein K, Hensler M, Wiegmann K, Skorubskaya E, Wöhlbrand L, Wünsch D, Hinrichs C, Feenders C, Müller C, Schell, K, Ruppersberg HS, Vagts J, Koßmehl S, Steinbüchel A, Schmidt-Kopplin P, Wilkes H, Hillebrand H, Blasius B, Schomburg D and Rabus R (2018) The marine bacterium Phaeobacter inhibens secures external ammonium by rapid buildup of intracellular nitrogen stocks. FEMS Microbiol Ecol 94/10: fiy154. doi: 10.1093/femsec/fiy154 [C1, C3, C7]
Ziesche L, Rinkel J, Dickschat JS, Schulz S (2018) Acyl-group specificity of AHL synthases involved in quorum-sensing in Roseobacter group bacteria. Beilstein J Org Che. 14: 1309-1316. doi: 10.3762/bjoc.14.112 [C2, B7]
Ziesche Lisa, Laura Wolter, Hui Wang, Thorsten Brinkhoff, Marion Pohlner, Bert Engelen, Irene Wagner-Döbler, Stefan Schulz. An unprecedented medium-chain di-unsaturated N-acylhomoserine lactone from marine Roseobacter group bacteria. Mar Drugs. 2018 Dec 31;17(1):20. doi: 10.3390/md17010020. PMID: 30602652; PMCID: PMC6356624. [C2, A2, B2, B4]
Ebert, M., Laass, S., Thürmer, A., Roselius, L., Eckweiler, D., Daniel, R., Härtig, E., and Jahn, D. (2017a) FnrL and three Dnr regulators are used for the metabolic adaptation to low oxygen tension in Dinoroseobacter shibae. Frontiers in Microbiology 8, doi.org/10.3389/fmicb.2017.00642
Ebert, M., Schweyen, P., Bröring, M., Laass, S., Härtig, E. & Jahn, D. (2017b) Heme and nitric oxide binding by the transcriptional regulator DnrF from the marine bacterium Dinoroseobacter shibae increases napDpromoter affinity. J. Biol. Chem., 292: 15468-15480
Beyersmann PG, Tomasch J, Son K, Stocker R, Göker M, Wagner-Döbler I, Simon M, Brinkhoff T (2017) Dual function of tropodithietic acid as antibiotic and signaling molecule in global gene regulation of the probiotic bacterium Phaeobacter inhibens. Sci Rep 7: 730. 10.1038/s41598-017-00784-7 [doi];10.1038/s41598-017-00784-7 [pii].
Bill N, Tomasch J, Riemer A, Müller K, Kleist S, Schmidt-Hohagen K, Wagner-Döbler I, Schomburg D (2017) Fixation of CO2 using the ethylmalonyl-CoA pathway in the photoheterotrophic marine bacterium Dinoroseobacter shibae. Environ Microbiol doi:10.1111/1462-2920.13746.
Blasenovic I, Kind T, Torbasinovic H, Obrenovic S, Mehta SS, Tsugawa H, Wermuth T, Schauer N, Jahn M, Biedendieck R, Jahn D (2017) Comprehensive comparison of in silico MS/MS fragmentation tools of the CASMI contest: database boosting is needed to achieve 93% accuracy. J Cheminform) 9: 32.
Breider S, Freese HM, Spröer C, Simon M, Overmann J, Brinkhoff T (2017) Phaeobacter porticola sp. nov., an antibiotic producing bacterium isolated from a harbor in the southern North Sea. Int J Syst Evol Microbiol. In press.
Burkhardt I, Lauterbach L, Brock NL, Dickschat JS (2017) Chemical Differentiation of Three DMSP Lyases from the Marine Roseobacter group. Org Biomol Chem (published online, doi: 10.1039/C7OB00913E).
Celik E, Maczka M, Bergen N, Brinkhoff T, Schulz S, Dickschat JS (2017) Metabolism of 2,3-dihydroxypropane-1-sulfonate by marine bacteria. Org Biomol Chem 15: 2919-2922.
Dogs M, Wemheuer B, Wolter L, Bergen N, Daniel R, Simon M, Brinkhoff T (2017) Rhodobacteraceae on the marine brown alga Fucus spiralis are predominant and show physiological adaptation to an epiphytic lifestyle. Syst Appl Microbiol, in press.
Ebert M, Laass S, Thürmer A, Roselius L, Eckweiler D, Daniel R, Härtig E, Jahn D (2017) FnrL and three Dnr regulators are used for the metabolic adaptation to low oxygen tension in Dinoroseobacter shibae. Frontiers in Microbiology 8:642
Kirchhoff C, Cypionka H (2017) Boosted membrane potential as bioenergetic response to anoxia in Dinoroseobacter shibae. Front Microbiol, 8:695, https://doi.org/10.3389/fmicb.2017.00695
Kleist S, Ulbrich M, Bill N, Schmidt-Hohagen K, Geffers R, Schomburg D (2017) Dealing with salinity extremes and nitrogen limitation - an unexpected strategy of the marine bacterium Dinoroseobacter shibae. Environ Microbiol 19: 894–908. doi:10.1111/1462-2920.13266.
Meier-Kolthoff JP, Göker M. (2017) Genome-based phylogeny and classification of bacteriophages. Bioinformatics, accepted.
Milici M, Vital M, Tomasch J, Badewien TH, Giebel H-A, Plumeier I, Wang H, Pieper DH, Wagner-Döbler I, Simon M. (2017) Diversity and community composition of particle-associated and free-living bacteria in mesopelagic and bathypelagic Southern Ocean water masses: evidence of dispersal limitation in the Bransfield strait. Limnol Oceanogr 62: 1080-1095.
Petersen J, Wagner-Döbler I (2017) Plasmid transfer in the ocean - a case study from the Roseobacter group. Front Microbiol, accepted.
Pohlner M, Marshall I, Schreiber L, Cypionka H, Engelen B (2017) Draft genome sequence of Pseudoruegeria str. SK021, a representative of the marine Roseobacter group, isolated from North Sea sediment. Genome Anouncements (in press).
Ruppersberg HS, Goebel MR, Kleinert SI, Wünsch D, Trautwein K, Rabus R (2017) Photometric determination of ammonium and phosphate in seawater medium using a microplate reader. J Mol Microbiol Biotechnol 27:73-80
Schneider D, Wemheuer F, Pfeiffer B, Wemheuer B (2017) Extraction of total DNA and RNA from marine filter samples and generation of a universal cDNA as universal template for marker gene studies. Methods in Molecular Biology 1539:13-22.
Shang Y, Sikorski J, Bonkowski M, Fiore-Donno A-M, Kandeler E, Boeddinghaus R, Marhan S, Solly E, Schrumpf M, Schöning I, Tesfaye W, Buscot F, Overmann J (2017) Inferring interactions in complex microbial communities from nucleotide sequence data and environmental parameters. PLoS One 12: e0173765. https://doi.org/10.1371/journal.pone.0173765
Simon C, Daniel R (2017) Construction of small-insert and large-insert metagenomic libraries. Methods in Molecular Biology 1539:1-12
Simon M, Scheuner C, Meier-Kolthoff JP, Brinkhoff T, Wagner-Döbler I, Ulbrich M, Klenk HP, Schomburg D, Petersen J, Göker M. (2017) Phylogenomics of Rhodobacteraceae reveals evolutionary adaptation to marine and non-marine habitats. ISME 11: 1483-1499.
Trautwein K, Feenders C, Hulsch R, Ruppersberg HS, Strijkstra A, Kant M, Vagts J, Wünsch D, Michalke B, Maczka M, Schulz S, Hillebrand H, Blasius B, Rabus R (2017) Non-Redfield, nutrient synergy, and flexible internal elemental stoichiometry in a marine bacterium. FEMS Microbiol Ecol doi: 10.1093/femsec/fix059
Will SE, Neumann-Schaal M, Heydorn RL, Bartling P, Petersen J, Schomburg D (2017) The limits to growth – energetic burden of the endogenous tropodithietic acid in Phaeobacter inhibens DSM 17395. PLoS ONE 12(5): e0177295. https://doi.org/10.1371/journal.pone.0177295 .
Wöhlbrand L, Wemheuer B, Feenders C, Ruppersberg HS, Hinrichs C, Blasius B, Daniel R, Rabus R (2017a) Complementary metaproteomic approaches to assess the bacterioplankton response toward a phytoplankton spring bloom in the Southern North Sea. Front Microbiol 8:442
Wöhlbrand L, Rabus R, Blasius B, Feenders C (2017b) Influence of nanoLC column- and gradient-length as well as MS/MS frequency and sample complexity on shotgun protein identification of marine bacteria. J Mol Microbiol Biotechnol accepted
Billerbeck S, Wemheuer B, Voget S, Poehlein A, Giebel HA, Brinkhoff T, Gram L, Jeffrey WH, Daniel R, Simon M (2016) Biogeography and environmental genomics of the Roseobacter group affiliated pelagic CHAB-I-5 lineage. Nature Microbiol. 1: Article no. 16063 (DOI: 10.1038/NMICROBIOL.2016.63).
Crenn K, Serpin D, Lepleux C, Spröer C, Bunk B, Overmann J, Jeanthon C (2016) Silicimonas algicola gen. nov., sp. nov., a novel member of the Roseobacter clade isolated from the cell surface of the marine diatom Thalassiosira delicatula. Int. J. Syst. Evol. Microbiol. 66: 4580-4588
Giebel HA, Klotz F, Voget S, Poehlein A, Grosser K, Teske A, Brinkhoff T (2016) Draft genome sequence of the marine Rhodobacteraceae strain O3.65, cultivated from oil-polluted seawater of the Deepwater Horizon oil spill. Stand Genomic Sci 11:81-93.
Gomez-Consarnau L, Gonzalez JM, Riedel T, Jaenicke S, Wagner-Döbler I, Sanudo-Wilhelmy SA, Fuhrman JA (2016) Proteorhodopsin light-enhanced growth linked to vitamin-B1 acquisition in marine Flavobacteria. ISME J 10: 1102-1112. ismej2015196 [pii];10.1038/ismej.2015.196 [doi].
Kanukollu S, Voget S, Pohlner M, Vandieken V, Petersen J, Kyrpides NC, Woyke T, Shapiro N, Göker M, Klenk H-P, Cypionka H, Engelen B (2016) Genome sequence of Shimia sp. SK013, a representative of the Roseobacter group isolated from marine sediment. Standards in Genomic Sciences 11: 25 (doi:10.1186/s40793-016-0143-0).
Kanukollu S, Wemheuer B, Herber J, Billerbeck S, Lucas J, Daniel R, Simon M, Cypionka H, Engelen B (2016) Distinct compositions of free-living, particle-associated and benthic communities of the Roseobacter group in the North Sea. FEMS Microbiol Ecol. 92/1: fiv145, doi: 10.1093/femsec/fiv145.
Lucas J, Koester I, Wichels A, Niggemann J, Dittmar T, Callies U, Wiltshire KH, Gerdts G (2016) Short-term dynamics of North Sea bacterioplankton-dissolved organic matter coherence on molecular level. Front Microbiol 7: 321.
Michael V, Frank O, Bartling P, Scheuner C, Göker M, Brinkmann H, Petersen J. (2016) Biofilm plasmids with a rhamnose operon are widely distributed determinants of the “swim-or-stick” lifestyle in roseobacters. ISME J 10: 2498-2513.
Milici M, Deng ZL, Tomasch J, Decelle J, Wos-Oxley ML, Wang H, Jauregui R, Plumeier I, Giebel HA, Badewien TH, Wurst M, Pieper DH, Simon M, Wagner-Döbler I (2016) Co-occurrence Analysis of Microbial Taxa in the Atlantic Ocean Reveals High Connectivity in the Free-Living Bacterioplankton. Front Microbiol 7: 649. 10.3389/fmicb.2016.00649 [doi].
Milici M, Tomasch J, Wos-Oxley M, Decelle J, Jáuregui R, Wang H, Deng ZL, Plumeier I, Giebel HA, Badewien T, Wurst M, Pieper DH, Simon M, Wagner-Doebler I (2016) Bacterioplankton biogeography in the Atlantic Ocean: a case study of the distance-decay relationship. Frontiers Microbiol. 7: Article 570.
Milici M, Tomasch J, Wos-Oxley ML, Wang H, Jauregui R, Camarinha-Silva A, Deng ZL, Plumeier I, Giebel HA, Wurst M, Pieper DH, Simon M, Wagner-Döbler I (2016) Low diversity of planktonic bacteria in the tropical ocean. Sci Rep 6: 19054. srep19054 [pii];10.1038/srep19054 [doi].
Mitulla M, Dinasquet J, Guillemette R, Simon M, Azam F, Wietz M (2016) Response of bacterial communities from California coastal waters to alginate particles and an alginolytic Alteromonas macleodii strain. Environ Microbiol 18: 4369–4377 (doi:10.1111/1462-2920.13314).
Moran MA, Kujawinski EB, Stubbins A, Fatland R, Aluwihare LI, Buchan A, Crump BC, Dorrestein PC, Dyhrman ST, Hess NJ, Howe B, Longnecker K, Medeiros PM, Niggemann J, Obernosterer I, Repeta DJ, Waldbauer JR (2016) Deciphering ocean carbon in a changing world. PNAS 113: 3143-3151.
Osterholz H, Singer G, Wemheuer B, Daniel R, Simon M, Niggemann J, Dittmar T (2016) Deciphering associations between dissolved organic molecules and bacterial communities in a pelagic marine system. ISME J 7: 1717-1730.
Overmann J, Lepleux C (2016) Marine Bacteria and Archaea: Diversity, Adaptations, and Culturability. In: Stal LJ, and Cretoiu MS (eds.) The Marine Microbiome. Chapter 2. Springer International Publishing, Switzerland. p. 21- 55
Patzelt D, Michael V, Päuker O, Ebert M, Tielen P, Jahn D, Tomasch J, Petersen J, Wagner-Döbler I (2016) Gene flow across genus barriers - Conjugation of Dinoroseobacter shibae’s 191-kb killer plasmid into Phaeobacter inhibens and AHL-mediated expression of type IV secretion systems. Front Microbiol 7: 742.
Segev E, Wyche TP, Kim KH, Petersen J, Ellebrandt C, Vlamakis H, Barteneva N, Pauson JN, Chai L, Clardy J, Kolter R (2016) Dynamic metabolic exchange governs a marine algal-bacterial interaction. eLife 5: e17473.
Trautwein K, Will SE, Hulsch R, Maschmann U, Wiegmann K, Hensler M, Michael V, Ruppersberg H, Wünsch D, Feenders C, Neumann-Schaal M, Kaltenhäuser S, Ulbrich M, Schmidt-Hohagen K, Blasius B, Petersen J, Schomburg D, Rabus R (2016) Native plasmids restrict growth of Phaeobacter inhibens DSM 17395. Energetic costs of plasmids assessed by quantitative physiological analyses. Environ Microbiol 18: 4817-4829.
Wagner-Döbler I (2016) Biofilm transplantation in the deep sea. Mol Ecol 25: 1905-1907. 10.1111/ mec.13612 [doi].
Wichmann H, Brinkhoff T, Simon M, Richter-Landsberg C (2016) Dimethylsulfoniopropionate promotes process outgrowth in neural cells and exerts protective effects against tropodithietic acid. Marine Drugs 14: 89 (doi:10.3390/md14050089).
Widderich N, Kobus S, Höppner A, Riclea R, Seubert A, Dickschat JS, Heider J, Smits SHJ, Bremer E (2016b) Biochemistry and Crystal Structure of Ectoin Synthase: a Metal-Containing Member of the Cupin Superfamily. PLoS ONE 11:e0151285.
Widderich N, Czech L, Elling FJ, Könneke M, Stöveken N, Pittelkow M, Riclea R, Dickschat JS, Heider J, Bremer E (2016a) Strangers in the archaeal world: Osmostress-responsive biosynthesis of ectoine and hydroxyectoine by the marine thaumarchaeon Nitrosopumilus maritimus. Environ Microbiol 18:1227-1248.
Zhan Y, Huang S, Voget S, Simon M, Chen F (2016) A novel Roseobacter phage possesses features of podoviruses, siphoviruses, prophages and gene transfer agents. Scientific Reports 6: 30372 (DOI: 10.1038/srep30372).
Ashauer KP, Wemheuer B, Daniel R, Meinicke P (2015) Tax4Fun: predicting functional profiles from metagenomics 16S rRNA data. Bioinformatics 31:2882-2884
Billerbeck S, Orchard J, Tindall BJ, Giebel HA, Brinkhoff T, Simon M (2015) Description of Octadecabacter temperatus sp. nov., isolated from the southern North Sea, emended description of the genus Octadecabacter and reclassification of Octadecabacter jejudonensis Park & Yoon 2014 as Pseudooctadecabacter jejudonensis gen. nov., comb. nov. Internat J System Evol Microbiol 65: 1967–1974.
Broy S, Chen C, Hoffmann T, Brock NL, Nau-Wagner G, Jebbar M, Smits SHJ, Dickschat JS, Bremer E (2015) Abiotic Stress Protection by Ecologically Abundant DMSP and its Natural and Synthetic Derivatives: Insights from Bacillus subtilis. Environ Microbiol 17:2362-2378.
Dickschat JS, Rabe P, Citron C (2015) The chemical biology of dimethylsulfoniopropionate. Org Biomol Chem 13:1954-1968.
Frank O, Göker M, Pradella S, Petersen J (2015) Ocean's twelve: Flagellar and biofilm chromids in the multipartite genome of Marinovum algicola DG898 exemplify functional compartmentalization. Environmental Microbiology 17: 4019-4034 (doi:10.1111/1462-2920.12947).
Frank O, Michael V, Päuker O, Boedeker C, Jogler C, Rohde M, Petersen J (2015) Plasmid curing and the loss of grip - The 65-kb replicon of Phaeobacter inhibens DSM 17395 is required for biofilm formation, motility and the colonization of marine algae. Syst Appl Microbiol 38: 120–127.
Gram L, Rasmussen B, Wemheuer B, Bernbom N, Yin Ng Y, Porsby CH, Breider S, Brinkhoff T (2015) Phaeobacter inhibens from the Roseobacter-clade has an environmental niche as surface colonizer in harbours. Syst Appl Microbiol 7: 483-493.
Hofner B, Boccuto L, Göker M (2015) Controlling false discoveries in high-dimensional situations: Boosting with stability selection. BMC Bioinformatics 16: 144 (doi:10.1186/s12859-015-0575-3).
Klingner A, Bartsch A, Dogs M, Wagner-Döbler I, Jahn D, Simon M, Brinkhoff T, Becker J, Wittmann C (2015) Large-scale 13C flux profiling reveals conservation of the Entner-Doudoroff pathway as a glycolytic strategy among marine bacteria that use glucose. Appl Environ Microbiol 81/7: 2408-2422.
Lau SC, Riedel T, Fiebig A, Han J, Huntemann M, Petersen J, Ivanova NN, Markowitz V, Woyke T, Göker M, Kyrpides NC, Klenk H-P, Qian P-Y (2015) Genome sequence of the pink-pigmented marine bacterium Loktanella hongkongensis type strain (UST950701-009PT), a representative of the Roseobacter group. Stand Genomic Sci 10: 51.
Neumann AM, Balmonte JP, Berger M, Giebel HA, Arnosti C, Voget S, Simon M, Brinkhoff T, Wietz M (2015) Different utilization of alginate and other algal polysaccharides by marine Alteromonas macleodii ecotypes. Environ Microbiol 17/10: 3857-3868.
Osterholz H, Niggemann J, Giebel H-A, Simon M, Dittmar T (2015) Inefficient microbial production of refractory dissolved organic matter in the ocean. Nature Commun 6: 7422.
Riedel T, Spring S, Fiebig A, Scheuner C, Petersen J, Göker M (2015) Genome sequence of the Roseovarius mucosus type strain (DSM 17069T), a bacteriochlorophyll a -containing representative of the marine Roseobacter group isolated from the dinoflagellate Alexandrium ostenfeldii. Stand Genomic Sci 10: 17.
Schulz S, Hötling S (2015) The use of the lactone motif in chemical communication. Nat Prod Rep 32:1042–1066.
Soora M, Tomasch J, Wang H, Michael V, Petersen J, Engelen B, Wagner-Döbler I, Cypionka H (2015) Oxidative stress and starvation in Dinoroseobacter shibae: The role of extrachromosomal elements. Front Microbiol 6: 233.
Voget S, Billerbeck, Simon, M, Daniel R (2015). Closed genome sequence of Octadecabacter temperatus SB1, the first mesophilic species of the genus Octadecabacter. Genome Announc 3(5): e01051-15. doi:10.1128/genomeA.01051-15.
Voget S, Bruns H, Wagner-Döbler I, Schulz S, Daniel R (2015) Draft Genome Sequence of Roseovarius tolerans EL-164, a Producer of N-Acylated Alanine Methyl Esters and N-Acylhomoserine Lactones. Genome Announcement 3(5):15.
Voget S, Valerio SMD, von Hoyningen-Huene AJE, Nattramilarasu PK, Vollheyde K, Xiao S, Daniel R (2015) Genome sequence of Jannaschia aquimarina GSW-M26, a member of the Roseobacter clade. Genome Announcements 3:e00353-15
Voget S, Wemheuer B, Brinkhoff T, Vollmers J, Dietrich S, Giebel HA, Beardsley C, Sardemann C, Bakenhus I, Billerbeck S, Daniel R, Simon M (2015) Adaptation of an abundant Roseobacter RCA organism to pelagic systems revealed by genomic and transcriptomic analyses. ISME J 9: 371-384.
Wang H, Tomasch J, Michael V, Bhuju S, Jarek M, Petersen J, Wagner-Döbler I (2015) Identification of genetic modules mediating the Jekyll and Hyde interaction of Dinoroseobacter shibae with the dinoflagellate Prorocentrum minimum. Front Microbiol 6: 1262.
Wemheuer B, Wemheuer F, Hollensteiner J, Meyer F-D, Voget S, Daniel R (2015) The green impact: bacterioplankton response towards a phytoplankton spring bloom in the southern North Sea assessed by comparative metagenomic and metatranscriptomic approaches. Front. Microbiol. 6:805.
Wichmann H, Vocke F, Brinkhoff T, Simon M, Richter-Landsberg C (2015) Cytotoxic effects of tropodithietic acid on mammalian clonal cell lines of neuronal and glial origin. Marine Drugs 13: 7113–7123.
Wietz M, Wemheuer B, Simon H, Giebel HA, Seibt MA, Daniel R, Brinkhoff T, Simon M (2015) Polysaccharides initiate distinct responses of bacterial communities from the Southern and Atlantic Oceans. Environ Microbiol 17/10: 3822-3831.
Ziesche L, Bruns H, Dogs M, Wolter L, Mann F, Wagner-Döbler I, Brinkhoff T, Schulz S (2015) Homoserine lactones, methyl oligohydroxybutyrates and other extracellular metabolites of macroalgae associated bacteria of the Roseobacter clade: Identification and function. ChemBioChem. 16: 2094-2107.
Breider S, Scheuner C, Schumann P, Fiebig A, Petersen J, Pradella S, Klenk H-P, Brinkhoff T, Göker M (2014) Genome-scale data suggest reclassifications in the Leisingera-Phaeobacter cluster including proposals for Sedimentitalea gen. nov. and Pseudophaeobacter gen. nov. Front Microbiol 5: 416.
Breider S, Teshima H, Petersen J, Fiebig A, Chertkov O, Dalingault H, Chen A, Pati A, Goodwin LA, Chain P, Detter JC, Ivanova NN, Lapidus A, Rohde M, Tindall BJ, Kyrpides NC, Woyke T, Simon M, Göker M, Klenk HP, Brinkhoff T (2014) Complete genome sequence of Leisingera nanhaiensis strain DSM 24252T isolated from marine sediment. Standards in Genomic Sciences 9: 687-703 (doi:10.4056/sigs.3828824).
Brock NL, Nikolay A, Dickschat JS (2014) Biosynthesis of the Antibiotic Tropodithietic Acid by the Marine Bacterium Phaeobacter inhibens. ChemComm 50:5487-5489.
Brock NL, Menke M, Klapschinski TA, Dickschat H (2014) Marine bacteria from the Roseobacter clade produce sulfur volatiles via amino acid and dimethylsulfoniopropionate catabolism. Org Biomol Chem 12: 4318-4323.
Drüppel K, Hensler M, Trautwein K, Koßmehl S, Wöhlbrand L, Schmidt-Hohagen K, Ulbrich M, Bergen N, Meier-Kolthoff JP, Göker M, Klenk H-P, Schomburg D, Rabus R (2014) Pathways and substrate-specific regulation of amino acid degradation in Phaeobacter inhibens DSM 17395 (archetype of the marine Roseobacter clade). Environ Microbiol 16: 218–238. doi:10.1111/1462-2920.12276.
Frank O, Pradella S, Rohde M, Scheuner C, Klenk H-P, Göker M, Petersen J (2014) Complete genome sequence of the Phaeobacter gallaeciensis type strain CIP 105210T (= DSM 26640T = BS107T). Stand Genomic Sci 9: 914–932.
Laass S, Kleist S, Bill N, Drüppel K, Kossmehl S, Wöhlbrand L, Rabus R, Klein J, Rohde M, Bartsch A, Wittmann C, Schmidt-Hohagen K, Tielen P, Jahn D, Schomburg D (2014) Gene regulatory and metabolic adaptation processes of Dinoroseobacter shibae DFL12T during oxygen depletion. J Biol Chem 289: 13219–13231. doi:10.1074/jbc.M113.545004.
Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M (2014) Highly parallelized inference of large genome-based phylogenies. Concurrency and Computation: Practice and Experience 26: 1715-1729 (doi:10.1002/cpe.3112
Petersen J, Ludewig AK, Michael V, Bunk B, Jarek M, Baurain D, Brinkmann H (2014) Chromera velia, endosymbioses and the Rhodoplex hypothesis - Plastid evolution in cryptophytes, alveolates, stramenopiles, and haptophytes (CASH lineages). Genome Biol Evol 6: 666–684.
Rabe P, Klapschinski TA, Brock NL, Citron CA, D'Alvise P, Gram L, Dickschat JS (2014) Synthesis and Bioactivity of Analogs of the Marine Antibiotic Tropodithietic Acid. Beilstein J Org Chem 10: 1796-1801.
Riedel T, Fiebig A, Han J, Huntemann M, Spring S, Petersen J, Ivanova NN, Markowitz V, Woyke T, Göker M, Kyrpides NC, Klenk H-P (2014b) Genome sequence of the Wenxinia marina type strain (DSM 24838T), a representative of the Roseobacter group isolated from oilfield sediments. Stand Genomic Sci 9: 855–865.
Riedel T, Spring S, Fiebig A, Petersen J, Göker M, Klenk H-P. (2014a) Genome sequence of the pink to light reddish-pigmented Rubellimicrobium mesophilum type strain (DSM 19309T), a representative of the Roseobacter group isolated from soil, and emended description of the species. Stand Genomic Sci 9: 902–913.
Riedel T, Spring S, Fiebig A, Petersen J, Kyrpides NC, Göker M, Klenk H-P (2014c) Genome sequence of the exopolysaccharide-producing Salipiger mucosus type strain (DSM 16094T), a moderately halophilic member of the Roseobacter clade. Stand Genomic Sci 9: 1331–1343.
Roselius, L., Langemann, D., Müller, J., Hense, B., Filges, S., Jahn, D. & Münch, R. (2014) Modeling and analysis of a gene-regulatory feed-forward loop with basal expression of the second regulator. J Theoret Biol., 363:290–299
Wang H, Tomasch J, Jarek M, Wagner-Döbler I (2014) A dual-species co-cultivation system to study the interactions between Roseobacters and dinoflagellates. Front Microbiol 5: 311. 10.3389/ fmicb.2014.00311 [doi].
Wang H, Ziesche L, Frank O, Michael V, Martin M, Petersen J, Schulz S, Wagner-Döbler I, Tomasch J (2014) The CtrA phosphorelay integrates differentiation and communication in the marine alphaproteobacterium Dinoroseobacter shibae. BMC Genomics 15: 130.
Wemheuer B, Güllert S, Billerbeck S, Giebel H-A, Voget S, Simon M, Daniel R (2014) Impact of a phytoplankton bloom on the diversity of the active bacterial community in the southern North Sea as revealed by metatranscriptomic approaches. FEMS Microbiol Ecol 87: 378-389 (DOI: 10.1111/1574-6941.12230).
Wiegmann K, Hensler M, Wöhlbrand L, Ulbrich M, Schomburg D, Rabus R (2014) Carbohydrate catabolism in Phaeobacter inhibens DSM 17395, member of the marine Roseobacter clade. Appl Environ Microbiol 80:4725-4737
Beyersmann PG, Chertkov O, Petersen J, Fiebig A, 11 co-authors, Simon M, Göker M, Klenk HP, Brinkhoff T (2013) Genome sequence of Phaeobacter caeruleus type strain (DSM 24564T), a surface-associated member of the marine Roseobacter clade. Stand Genomic Sci 8: 403-419.
Breider S, Teshima H, Petersen J, Fiebig A, 12 co-authors, Simon M, Göker M, Klenk HP, Brinkhoff T (2013) Complete genome sequence of Leisingera nanhaiensis strain DSM 24252T isolated from marine sediment. Stand Genomic Sci, 9: 687-703.
Brock NL, Citron CA, Zell C, Berger M, Wagner-Döbler I, Petersen J, Brinkhoff T, Simon M, Dickschat JS (2013) Isotopically Labeled Sulfur Compounds and Synthetic Selenium and Tellurium Analogs to Study Sulfur Metabolism in Marine Bacteria. Beilstein J Org Chem 9:942-950.
Bruns H, Thiel V, Voget S, Patzelt H, Daniel R, Wagner-Döbler I, Schulz S (2013) N-Acylated Alanine Methyl Esters from Roseovarius tolerans, Structural Analogs of Quorum-Sensing Autoinducers, N-Acylhomoserine Lactones. Chem Biodiversity: 10/9: 1559-1573.
Buddruhs N, Chertkov O, Fiebig A, Petersen J, 10 co-authors, Göker M, Brinkhoff T, Klenk HP (2013) Complete genome sequence of the marine methyl-halide oxidizing Leisingera methylohalidivorans type strain (DSM 14336T), a member of the Roseobacter clade. Stand Genomic Sci, 9(1):128-41 (doi: 10.4056/sigs.4297965).
Buddruhs N, Pradella S, Göker M, Päuker O, Michael V, Pukall R, Spröer C, Schumann P, Petersen J, Brinkhoff T (2013) Biological non-identity of Phaeobacter gallaeciensis type-strain deposits revealed by sequence and phenotypic analysis. Int J Syst Evol Microbiol 63: 4340-4349.
Dogs M, Teshima H, Petersen J, Fiebig A, 13 co-authors, Simon M, Klenk HP, Göker M, Brinkhoff T (2013) Genome sequence of Phaeobacter daeponensis type strain (DSM 23529T), a facultatively anaerobic bacterium isolated from marine sediment, and emendation of Phaeobacter daeponensis. Stand Genomic Sci 9: 142-159.
Dogs M, Voget S, Teshima H, Petersen J, Fiebig A, 12 co-authors, Simon M, Klenk HP, Göker M, Brinkhoff T (2013) Genome sequence of Phaeobacter inhibens type strain (T5T), a secondary-metabolite producing member of the marine Roseobacter clade, and emendation of the species Phaeobacter inhibens. Stand Genomic Sci, 9: 334-350 DOI:10.4056/sigs.4448212).
Ebert M, Laaß S, Burghartz M, Petersen J, Rabus R, Wöhlbrand L, Tielen P, Jahn D. (2013) Chromosomal and plasmid encoded genes are essential for the anaerobic growth of the marine bacterium Dinoroseobacter shibae. J.Bacteriol, 195/20: 4769-4777.
Fiebig A, Pradella S, Petersen J, Michael V, Päuker O, Rohde M, Göker M, Klenk HP, Wagner-Döbler I (2013b) Genome of the marine alphaproteobacterium Hoeflea phototrophica type strain (DFL-43T). Stand Genomic Sci 7:440-444.
Fiebig A, Pradella S, Petersen J, Päuker O, Michael V, Lünsdorf H, Göker M, Klenk HP, Wagner-Döbler I (2013a). Genome of the R-body producing marine alphaproteobacterium Labrenzia alexandrii type strain (DFL-11T). Stand Genomic Sci 7: 413-426.
Freese H, Dalingault H, Petersen J, Pradella S, Fiebig A, 12 co-authors, Brinkhoff T, Göker M, Overmann J, Klenk HP (2013) Genome sequence of the phage-gene rich marine Phaeobacter arcticus type strain DSM 23566T. Stand Genomic Sci 8(3): 450–464.
Giebel HA, Kalhoefer D, Gahl-Janssen R, Choo YJ, Lee K, Cho JC, Tindall BJ, Rhiel E, Beardsley C, Aydogmus ÖO, Voget S, Daniel R, Simon M, Brinkhoff T (2013) Planktomarina temperata gen. nov., sp. nov., belonging to the globally distributed RCA cluster of the marine Roseobacter clade, isolated from the German Wadden Sea. Int J System Evol Microbiol, 63: 4207–4217.
Göker M, Klenk HP (2013) Phylogeny-driven target selection for genome-sequencing (and other) projects. Stand Genomic Sci, 8(2): 360–374.
Groenhagen U, Baumgartner R, Bailly A, Gardiner A, Eberl L, Schulz S, Weisskopf L (2013) Production of bioactive volatiles by various Burkholderia ambifaria strains. J. Chem. Ecol: 39/10: 1343-1345
Hahnke S, Brock NL, Zell C, Simon M, Dickschat JS, Brinkhoff T (2013) Physiological diversity of Roseobacter clade bacteria co-occurring during a phytoplankton bloom in the North Sea. Syst Appl Microbiol 36:39-48.
Hahnke S, Sperling M, Langer T, Wichels A, Gerdts G, Beardsley C, Brinkhoff T, Simon M (2013b) Distinct seasonal growth patterns of the bacterium Planktotalea frisia in the North Sea and specific interactions with phytoplankton algae. FEMS Microbiol Ecol, 86: 185-199.
Kielkowsky P, Brock NL, Dickschat JS, Hocek M (2013) Nucleobase Protection Strategy for Gene Cloning and Expression. ChemBioChem, 14:801-804.
Koßmehl S, Wöhlbrand L, Drüppel K, Feenders C, Blasius B, Rabus R (2013) Subcellular protein localization (cell envelope) in Phaeobacter inhibens DSM 17395. Proteomics 13/18-19 SI: 2743-2760
Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 14: 60.
Neumann A, Patzelt, D, Wagner-Döbler, I, Schulz, S. (2013). Identification of New N-Acylhomoserine Lactone Signalling Compounds of Dinoroseobacter Shibae DFL-12 by Overexpression of LuxI Genes. Chembiochem 14/17: 2355-2361.
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Penesyan A, Breider S, Schumann P, Tindall BJ, Egan S, Brinkhoff T (2013) Epibacterium ulvae gen. nov., sp. nov., epibiotic bacteria isolated from the surface of a marine alga. Int J Syst Evol Microbiol 63: 1589 - 1596.
Petersen J, Frank O, Göker M, Pradella S (2013) Extrachromosomal, extraordinary and essential--the plasmids of the Roseobacter clade. Appl Microbiol Biotechnol 97: 2805-2815.
Rabus R (2013) Environmental Microbial Proteomics: New avenues for a molecular understanding of the functional role of microorganisms in the natural environment. Proeomics 13/18-19 SI: 2697-2699.
Rex R, Bill N, Schmidt-Hohagen K, Schomburg D (2013) Swimming in light: A large-scale computational analysis of the metabolism of Dinoroseobacter shibae.PLOS Comp Biol, 9/10 Article e1003224.
Riedel T, Fiebig A, Petersen J, Gronow S, Göker M, Klenk HP (2013a) Genome sequence of the Litoreibacter arenae type strain (DSM 19593T), a member of the Roseobacter clade isolated from sea sand. Stand Genomic Sci, 9(1): 117–127..
Riedel T, Gomez-Consarnau L, Tomasch J, Martin M, Jarek M, Gonzalez JM, Spring S, Rohlfs M, Brinkhoff T, Cypionka H, Göker M, Fiebig A, Klein J, Goesmann A, Fuhrman JA, Wagner-Döbler I. 2013a. Genomics and physiology of a marine flavobacterium encoding a proteorhodopsin and a xanthorhodopsin-like protein. PLoS One 8:e57487.
Riedel T, Rohlfs M, Buchholz I, Wagner-Döbler I, Reck M. 2013b. Complete sequence of the suicide vector pJP5603. Plasmid 69:104-107.
Riedel T, Teshima H, Petersen J, Fiebig A, 16 co-authors, Göker M, Brinkhoff T, Klenk HP (2013c) Genome sequence of the Leisingera aquimarina type strain (DSM 24565T), a member of the marine Roseobacter clade rich in extrachromosomal elements. Stand Genomic Sci, 8: (3):389-402.
Riemer SA, Rex R, Schomburg D (2013) A metabolite-centric view on flux distributions in genome-scale metabolic models. BMC Syst Biol 7: 33.
Soora M, Cypionka H (2013) Light enhances survival of Dinoroseobacter shibae during long-term starvation. PLoS ONE 8:e83960. doi:10.1371/journal.pone.0083960
Spring S, Riedel T, Spröer K, Yan S, Harder J, Fuchs BM. 2013. Taxonomy and evolution of bacteriochlorophyll a-containing members of the OM60/NOR5 clade of marine gammaproteobacteria: Description of Luminiphilus syltensis gen. nov., sp. nov., reclassification of Haliea rubra as Pseudohaliea rubra gen. nov., comb. nov., and emendation of Chromatocurvus halotolerans. BMC Microbiol 13: Article Number: UNSP 118.
Spring S, Riedel T. 2013. Mixotrophic growth of bacteriochlorophyll a-containing members of the OM60/NOR5 clade of marine gammaproteobacteria is carbon-starvation independent and correlates with the type of carbon source and oxygen availability. BMC Microbiol 13: Article number 117.
Vaas LAI, Sikorski J, Hofner B, Buddruhs N, Fiebig A, Klenk HP, Göker M (2013) opm: An R package for analysing OmniLog® Phenotype MicroArray Data. Bioinformatics, 29(14):1823-4.
Vollmers J, Voget S, Dietrich S, Gollnow K, Smits M, Meyer K, Brinkhoff T, Simon M, Daniel R (2013) Poles apart: arctic and antarctic Octadecabacter strains share high genome plasticity and a new type of xanthorhodopsin. PLoS One 8:e63422.
Wöhlbrand L, Trautwein K, Rabus R (2013) Proteomic tools for environmental microbiology – a roadmap from sample preparation to protein identification and quantification. Proteomics 13/18-19 SI: 2700-2730
Zech H, Echtermeyer C, Wöhlbrand L, Blasius B, Rabus R (2011) Biological versus technical variability in 2D DIGE experiments with environmental bacteria. Proteomics 11: 3380-3399.
Zech H, Hensler M, Koßmehl S, Drüppel K, Wöhlbrand L, Trautwein K, Hulsch R, Maschmann U, Colby T, Schmidt J, Reinhardt R, Schmidt-Hohagen K, Schomburg D, Rabus R (2013a) Adaptation of Phaeobacter gallaeciensis DSM 17395 to growth with complex nutrients. Proteomics doi:10.1002/pmic.201200513
Zech H, Hensler M, Koßmehl S, Drüppel K, Wöhlbrand L, Trautwein K, Colby T, Schmidt J, Reinhardt R, Schmidt-Hohagen K, Schomburg D, Rabus R (2013b) Dynamics of amino acid utilization in Phaeobacter inhibens DSM 17395. Proteomics doi:10.1002/pmic.201200560.
Berger M, Brock NL, Liesegang H, Dogs M, Preuth I, Simon M, Dickschat JS, Brinkhoff T (2012) Genetic analysis of the upper phenylacetate catabolic pathway in the production of tropodithietic acid by Phaeobacter gallaeciensis. Appl Environ Microbiol 78: 3539-3551.
Klein, J., Leupold, S., Biegler, I., Biedendieck, R., Münch, R. & Jahn D. (2012) TLM-Tracker: software for cell segmentation, tracking and lineage analysis in time-lapse microscopy movies. Bioinformatics 28:2276-2277.
Petersen J, Brinkmann H, Bunk B, Michael V, Päuker O, Pradella S (2012) Think pink: photosynthesis, plasmids and the Roseobacter clade. Environ Microbiol 14: 2661-2672.
Riclea R, Gleitzmann J, Bruns H, Junker C, Schulz B, Dickschat JS (2012) Algicidal Lactones from the Marine Roseobacter Clade Bacterium Ruegeria pomeroyi. Beilstein J Org Chem 8:941-950.
Riedel T, … Rohde M, Tindall BJ, Göker M, Klenk HP, and 27 authors. 2012a. Genome sequence of the Antarctic rhodopsins-containing flavobacterium Gillisia limnaea type strain (R-8282T). Standards in Genomic Sciences 7:117-119.
Riedel T, … Rohde M, Tindall BJ, Göker M, Klenk HP, and 27 authors. 2012b. Genome sequence of the orange-pigmented sea-water bacterium Owenweeksia hongkongensis type strain (UST20020801 T ). Standards in Genomic Sciences 7:120-130.
Shevchuk, O., Roselius, L., Günther, G., Klein, J., Jahn, D., Steinert, M. & Münch R. (2012) InFiRe - a novel computational method for the identification of insertion sites in transposon mutagenized bacterial genomes. Bioinformatics 28:306-310.
Simon M, Billerbeck S, Kessler D, Selje N, Schlingloff A (2012) Bacterioplankton communities in the Southern Ocean:Composition and growth response to various substrate regimes. Aquat Microb Ecol 68:13–28.
Thole S, Kalhoefer D, Voget S, Berger M, Engelhardt T, Lliesegang H, Wollherr A, Kjelleberg S, Daniel R, Simon M, Thomas T, Brinkhoff T (2012) Phaeobacter gallaeciensis genomes from globally opposite locations reveal high similarity of adaptation to surface life. ISME Journal 6: 2229-2244.
Vaas LAI, Sikorski J, Michael V, Göker M, Klenk HP (2012) Visualization and curve-parameter estimation strategies for efficient exploration of Phenotype Microarray kinetics. PLoS ONE 7: e34846.
Wemheuer B, Wemheuer F, Daniel R (2012) RNA-based assessment of diversity and composition of active archaeal communities in the German Bight. Archaea 2012: 695826.
Bartsch, A., Bunk, B., Haddad, I., Klein, J., Münch, R., Johl, T., Kärst, U., Jänsch, L., Jahn, D., & Retter, I. (2011) GeneReporter-sequence-based document retrieval and annotation. Bioinformatics 27:1034-1035
Berger M, Neumann A, Schulz S, Simon M, Brinkhoff T (2011) Tropodithietic acid production in Phaeobacter gallaeciensis is regulated by N-acyl homoserine lactone-mediated quorum sensing. J. Bacteriol. 193: 6576–6585.
Jaramillo-Colorado B, Olivero-Verbel, J, Stashenko, EE, Wagner-Döbler, I, Kunze, B. (2011). Anti-Quorum Sensing Activity of Essential Oils From Colombian Plants. Nat Prod Res 26(12):1075-86.
Kalhoefer D, Thole S, Voget S, Lehmann R, Liesegang H, Wollher A, Daniel R, Simon M, Brinkhoff T (2011) Comparative genome analysis and genome-guided physiological analysis of Roseobacter litoralis. BMC Genomics. DOI: 10.1186/1471-2164-12-324.
Lemme A, Gröbe, L, Reck, M, Tomasch, J, Wagner-Döbler, I. (2011). Subpopulation-Specific Transcriptome Analysis of Competence-Stimulating-Peptide-Induced Streptococcus Mutans. J Bacteriol 193(8):1863-77.
Münch, R., Klein J. & Jahn D. (2011) Prediction and Analysis of Gene Regulatory Networks in Prokaryotic Genomes. (Yang N., Ed.).Systems and Computational Biology - Molecular and Cellular Experimental Systems. 149-162.
Petersen J (2011) Phylogeny and compatibility: plasmid classification in the genomics era. Arch Microbiol 193: 313-321.
Petersen J, Brinkmann H, Berger M, Brinkhoff T, Päuker O, Pradella S (2011) Origin and evolution of a novel DnaA-like plasmid replication type in Rhodobacterales. Mol Biol Evol 28: 1229-1240.
Simon C, Daniel R (2011) Metagenome analyses: past and future trends. Applied and Environmental Microbiology 77: 1153–1161.
Tomasch J, Gohl, R, Bunk, B, Diez, MS, Wagner-Döbler, I. (2011). Transcriptional Response of the Photoheterotrophic Marine Bacterium Dinoroseobacter Shibae to Changing Light Regimes. ISME J 5(12):1957-68.