Here you find a chronological list of all peer-reviewed publications of the working group Biology of Geological Processes.

Members of our working group are marked in bold:

Adenaya A, Berger M, Brinkhoff T, Ribas-Ribas M, Wurl O (2023) Usage of antibiotics in aquaculture and the impact on coastal waters. Mar Poll Bull 188: 114645 https://doi.org/10.1016/j.marpolbul.2023.114645

Bruns S, Wienhausen G, Scholz-Böttcher B, Heyen S, Wilkes H (2023) Method development and quantification of all B vitamins and selected biosynthetic precursors in winter and spring samples from the North Sea and de novo synthesized by Vibrio campbellii. Mar Chem 256: 104300 (https://doi.org/10.1016/j.marchem.2023.104300))

De Corte D, Louro MA, Bercovici SK, Niggemann J, Valencia J, Sintes E, Baltar F, Simon M, Dittmar T, Bode A, Varela MM (2023) Zooplankton-derived dissolved organic matter composition and its bioavailability to natural prokaryotic communities. Limnol. Oceanogr. 68: 336-347. https://doi.org/10.1002/lno.12272

Milke F, Meyerjürgens J, Simon M (2023) Ecological mechanisms and current systems shape the modular structure of the global oceans’ prokaryotic seascape. Nature Comm 14: 6141 (https://doi.org/10.1038/s41467-023-41909-z).

Rahlff J, Wietz M, Giebel HA, Bayfield O, Nilsson E, Bergström K, Kieft K, Anantharaman K, Ribas-Ribas M, Schweitzer H, Wurl O, Hoetzinger M, Antson A, Holmfeldt K (2023) Ecogenomics and cultivation reveal distinctive viral-bacterial communities in the surface microlayer of a Baltic Sea slick. ISME Comm 3: 97. https://doi.org/10.1038/s43705-023-00307-8

Rahlff J, Esser SP, Plewka J, Herinrichs ME, Soares A, Scarchilli C, Grigioni P. Wex H, Giebel HA, Probst A (2023) Marine viruses disperse bidirectionally along the natural water cycle. Nature Comm 14: 6354. https://doi.org/10.1038/s41467-023-42125-5

Tran QD, Milke F, Niggemann J, Simon M (2023) The diatom Thalassiosira rotula induces distinct growth responses and colonization patterns of Roseobacteraceae, Flavobacteria and Gammaproteobacteria. Environ Microbiol, online first (https://doi.org/10.1111/1462-2920.16506)..

Liu Y, Brinkhoff T, Berger M, Poehlein A, Voget S, Paoli L, Sunagawa S, Amann R, Simon M (2023) Metagenome assembled genomes reveal greatly expanded taxonomic and functional diversification of the abundant marine Roseobacter RCA cluster. Microbiome 11: Article number: 265. https://doi.org/10.1186/s40168-023-01644-5

Dlugosch L, Bunse C, Bunk B, Böttcher L, Tran QD, Dittmar T, Hartmann M, Heinrichs M, Hintz NH, Mori C, Niggemann J, Spröer C, Striebel M, Simon M (2023) Naturally-induced biphasic phytoplankton spring bloom reveals rapid and distinct substrate and bacterial community dynamics. FEMS Microbiol Ecol 99: 1-14.

Sultana S, Bruns S, Wilkes H, Simon M, Wienhausen G (2023) Vitamin B₁₂ is not shared by all marine prototrophic bacteria with their environment. ISME J 17: 836–845.

Tebbe DA, Gruender C, Dlugosch L, Löhmus K, Rolfes S, Könneke M, Chen Y, Engelen B, Schäfer H (2023) Microbial drivers of DMSO reduction and DMS-dependent methanogenesis in saltmarsh sediments. ISME J 17: 2340-2351 (https://doi.org/10.1038/s41396-023-01539-1).

Tran QD, Neu T, Sultana S, Giebel HA, Simon M, Billerbeck S (2023) Distinct glycoconjugate cell surface structures make the pelagic diatom Thalassiosira rotula an attractive habitat for bacteria. J Phycol 59: 309-322. https://DOI:10.1111/jpy.13308  

Aguilar-Cruz Y, Milke F, Leinberger J, Poehlein A, Zotz G, Brinkhoff T (2022) Diversity and putative metabolic function of prokaryotic communities in tank bromeliads along an elevation gradient in tropical Mexico. Front Microbiol 13: 945488. https://doi.org/10.3389/fmicb.2022.945488

Bartlau N, Wichels A, Krohne G, Adriaenssens EM, Heins A, Fuchs BM, Amann R, Moraru C (2022) Highly diverse flavobacterial phages isolated from North Sea spring blooms. ISME J 16, 555–568 (https://doi:10.1038/s41396-021-01097-4

Bergen N, Krämer P, Romberg J, Wichels A, Gerlach G, Brinkhoff T (2022) Shell disease syndrome is associated with reduced and shifted epibacterial diversity on the carapace of the crustacean cancer pagurus. Microbiology Spectrum 10: e03419-22. https://doi.org/10.1128/spectrum.03419-22

Bruns S, Wienhausen G, Scholz-Böttcher B, Wilkes H (2022) Simultaneous quantification of all B vitamins and selected biosynthetic precursors in seawater and bacteria by means of different mass spectrometric approaches. Anal Bioanal Chem 414: 7839-7854 (https://doi:10.3762/bjoc.14.276)

Kever L, Hardy A, Luthe T, Huennefeld M, Gaetgens C, Milke L, Wiechert J, Wittmann J, Moraru C, Marienhagen J, Frunzke J (2022) Aminoglycoside Antibiotics Inhibit Phage Infection by Blocking an Early Step of the Infection Cycle. mBio 3: https://DOI10.1128/mbio.00783-22.

Milke F, Wagner-Doebler I, Wienhausen G, Simon M (2022) Selection, drift and community interactions shape microbial biogeographic patterns in the Pacific Ocean. ISME J 16/12: 2653–2665. https://doi.org/10.1038/s41396-022-01318-4.

Sauer S, Dlugosch L, Milke F, Brinkhoff T, Kammerer DR, Stintzing FC, Simon M (2022) Succession of bacterial and fungal communities during fermentation of medicinal plants. Fermentation, 8: 383. https://doi.org/10.3390/fermentation808038. 

Srinivas, S., M. Berger, T. Brinkhoff, J. Niggemann. 2022. Impact of quorum sensing and tropodithietic acid production on the exometabolome of Phaeobacter inhibens. Frontiers Microbiol. 13: 917969. doi.org/10.3389/fmicb.2022.917969

Wienhausen, G., M.J. Bittner, R.W. Paerl (2022). Key Knowledge Gaps to Fill at the Cell-To-Ecosystem Level in Marine B-Vitamin Cycling. Front. Mar. Sci., 9:876726. doi.org/10.3389/fmars.2022.876726

Wienhausen G, Bruns S, Sultana S, Groon LA, Wilkes H, Simon M (2022) The overlooked role of a biotin precursor for marine bacteria - desthiobiotin as an escape route for biotin auxotrophy. ISME J . doi.org/10.1038/s41396-022-01304-w

Bartlau, N., Wichels, A., Krohne, G., Adriaenssens, E.M., Heins, A., Fuchs, B.M., Amann, R., and Moraru, C. (2022) Highly diverse flavobacterial phages isolated from North Sea spring blooms. ISMEJ 16, 555–568 (doi: 10.1038/s41396-021-01097-4.)

Degenhardt J., Khodami S., Milke F., Waska H., Engelen B., Arbizu P.M., 2021. The three domains of life within the discharge area of a shallow subterranean estuary at a high energy beach. Frontiers in Environmental Science 9, 642098.

Sutorius M, Mori C, Greskowiak, Boettcher L, Bunse C, Dittmar T, Dlugosch L, Hintz NH , Simon M, Striebel M, Pahnke K (2022) Rare earth element behaviour in seawater under the influence of organic matter cycling during a phytoplankton spring bloom- a mesocosm study. Front Mar Sci, accepted.

Bunse M, Daniels R, Gründemann C, Heilmann J, Kammerer DR, Keusgen M, Lindequist U, Melzig MF, Morlock G, Schulz H, Schweiggert R, Simon M, Stintzing FC, Wink M (2022) Essential oils as example for multicomponent mixtures – their potential for human health and well-being. Frontiers Pharmacology, in press.

Leinberger, J., F. Milke, M. Christodoulou, A. Poehlein, J. Caraveo-Patino, A. Teske, T. Brinkhoff. 2022. Microbial epibiotic community of the deep-sea galatheid squat lobster Munidopsis alvisca. Sci. Rep., 12, Article number: 2675.

Zucker F, Bischoff V, Heyerhoff B, Poehlein A, Freese HM, Ndela EO, Roux S, Enault F, Simon M, Moraru C (2022) New Microviridae isolated from Sulfitobacter reveals two cosmopolitan subfamilies of ssDNA phages infecting marine and terrestrial Alphaproteobacteria. Virus Evolution, accepted.

Milke F, Sanchez-Garcia S, Dlugosch L, McNichol J, Fuhrman JA, Simon M, Wagner-Döbler I (2022) Composition and biogeography of planktonic pro- and eukaryotic communities in the Atlantic Ocean: primer choice matters. Front Microbiol, online first. doi.org/10.3389/fmicb.2022.895875

Dlugosch, L., Poehlein, A., Wemheuer, B., Pfeifer, B., Badewien, T.H., Daniel, R., Simon, M. (2022). Significance of gene variants for the functional biogeography of the near-surface Atlantic Ocean microbiome. Nat Commun 13, 456. doi.org/10.1038/s41467-022-28128-8

Wienhausen G, L Dlugosch, R Jarling, H Wilkes, H-A Giebel and M Simon (2022). Availability of vitamin B12 and its lower ligand intermediate α-ribazole impact prokaryotic and protist communities in oceanic systems. ISME J 16, 2002–2014. doi.org/10.1038/s41396-022-01250-7

Barrero-Canosa, J., Moraru, C. (2021) Linking microbes to their genes at single cell level with direct-geneFISH. In Nuno F. Azevedo, Carina Almeida (Eds.): Fluorescence In-Situ Hybridization (FISH) for Microbial Cells. Methods and Concepts: Springer US (Methods in Molecular Biology), pp. 169-205.

Floeder, S., J. Yong, T. Klauschies, U. Gaedke, T. Poprick, T. Brinkhoff, S. Moorthi. 2021. Intraspecific trait variation alters the outcome of competition in freshwater ciliates. Ecol Evol.,11 (15) , pp.10225-10243 ; DOI: 10.1002/ece3.7828

Calabrese, F., Stryhanyuk, H., Moraru, C., Schlömann, M., Wick, L.Y., Richnow, H.H., Musat, F., and Musat, N. (2021) Metabolic history and metabolic fitness as drivers of anabolic heterogeneity in isogenic microbial populations. Environmental Microbiology, doi: 10.1111/1462-2920.15756.

Hagström Å, Zweifel UL, Sundh J, Osbeck CMG, Bunse C, Sjöstedt J, Müller-Karulis B and Pinhassi J (2021) Composition and Seasonality of Membrane Transporters in Marine Picoplankton. Frontiers in Microbiology: 12:714732. doi: 10.3389/fmicb.2021.714732

Krupovic, M., Turner, D., Morozova, V., Dyall-Smith, M., Oksanen, H.M., Edwards, R., Dutilh, B.E., Lehman, S.M., Reyes, A., Baquero, D.P., Sullivan, M.B., Uchiyama, J., Nakavuma, J., Barylski, J., Young, M.J., Du, S., Alfenas-Zerbini, P., Kushkina, A., Kropinski, A.M., Kurtböke, I., Brister, J.R., Lood, C., Sarkar, B.L., Yigang, T., Liu, Y., Huang, L., Wittmann, J., Chanishvili, N., van Zyl, L.J., Rumnieks, J., Mochizuki, T., Jalasvuori, M., Aziz, R.K., Lobocka, M., Stedman, K.M., Shkoporov, A.N., Gillis, A., Peng, X., Enault, F., Knezevic, P., Lavigne, R., Rhee, S.-K., Cvirkaite-Krupovic, V., Moraru, C., Moreno Switt, A.I., Poranen, M.M., Millard, A., Prangishvili, D., and Adriaenssens, E.M. (2021) Bacterial Viruses Subcommittee and Archaeal Viruses Subcommittee of the ICTV: update of taxonomy changes in 2021. Archives of Virology 166 (11), doi: 10.1007/s00705-021-05205-9.

Leinberger, J., J. Holste, B. Bunk, H.M. Freese, C., Sproeer, L. Dlugosch, A.C. Kueck, S. Schulz, T. Brinkhoff. 2021 High potential for secondary metabolite production of Paracoccus marcusii CP157, isolated from the crustacean Cancer pagurus. Frontiers Microbiol., 12: Article Number: 688754.

Pontiller B, Pèrez-Martínez C, Bunse C, Osbeck CMG, González CMG, Lundin D, Pinhassi J (2021) Taxon-specific shifts in bacterial and archaeal transcription of dissolved organic matter cycling genes in a stratified fjord. mSystems 6:6 e00575-21 DOI:10.1128/mSystems.00575-21

Rahlff, J., Turzynski, V., Esser, S.P., Monsees, I., Bornemann, T.L.V., Figueroa-Gonzalez, P.A., Schulz, F., Woyke, T., Klingl, A., Moraru, C., Probst, A. (2021) Lytic archaeal viruses infect abundant primary producers in Earth's crust. Nature Communications 12, pp 4642

Zayed, A.A., Lücking, D., Mohssen, M., Cronin, D., Bolduc, B., Gregory, A.C., Hargreaves, K.R., Piehowski, P.D, White III, R.A., Huang, E.L., Adkins, J.N., Roux, S., Moraru, C.* and Sullivan, M.B.* (2021). efam: an expanded, metaproteome-supported HMM profile database of viral protein families. Bioinformatics, doi: 10.1093/bioinformatics/btab451.

Mori C, Beck M, Hintz N, Merder J, Bunse C, Dittmar T, Dlugosch L, Böttcher L, Pahnke K, Striebel M, Schnetger B, Simon M, Brumsack HJ (2021) Biogeochemical thallium cycling during a mesocosm phytoplankton spring bloom: biotic versus abiotic drivers. Geochim Cosmochim Acta 313: 257-276. 

Sauer S, Dlugosch L, Kammerer DR, Stintzing FC, Simon M (2021) The microbiome of the medicinal plants Achillea millefolium L. and Hamamelis virginiana L. Front Microbiol 12: Article 696398.

Bunse C, Koch H, Breider S, Simon M, Wietz M (2021) Sweet spheres: Succession and CAZyme expression of marine bacterial communities colonising a mix of alginate and pectin particles. Environ Microbiol 23(6): 3130–3148.

Giebel H-A, Arnosti C, Badewien TH, Bakenhus I, Balmonte JP, Billerbeck S, Dlugosch L, Henkel R, Kuerzel B, Meyerjürgens J, Milke F, Voss D, Wienhausen G, Wietz M, Winkler H, Wolterink M and S Meinhard (2021) Microbial Growth and Organic Matter Cycling in the Pacific Ocean Along a Latitudinal Transect Between Subarctic and Subantarctic Waters. Front. Mar. Sci. 8:764383. doi.org/10.3389/fmars.2021.764383

Balmonte JP, M Simon, HA Giebel, C Arnosti (2021) A sea change in microbial enzymes: Heterogeneous latitudinal and depth-related gradients in bulk water and particle-associated enzymatic activities from 30°S to 59°N in the Pacific Ocean. Limnol. Oceanogr. 66 (9): 3489-3507. doi.org/10.1002/lno.11894

Giebel, H-A (2021). Educational cruise - Biological oceanography: Plankton dynamics in the German Bight, HE571, March 22 - March 28, 2021, Bremerhaven (Germany) - Bremerhaven (Germany). Heincke-Berichte, cruise report. doi.org/10.48433/cr_he571

Rahlff  J, C Stolle C, HA Giebel, NIH Mustaffa, O Wurl and DPR Herlemann (2021) Sea foams are ephemeral hotspots for distinctive bacterial communities contrasting sea-surface microlayer and underlying surface water. FEMS Microbiol Ecol, fiab035, doi.org/10.1093/femsec/fiab035

Moraru C (2021) Gene-PROBER - a tool to design polynucleotide probes for targeting microbial genes. System Appl Microbiol 44 1: Article 126173.

Wolter LA, Wietz M, Ziesche L, Breider S, Leinberger J, Poehlein A, Daniel R, Schulz S, Brinkhoff T (2021) Pseudooceanicola algae sp. nov., isolated from the marine macroalga Fucus spiralis, shows genomic and physiological adaptations for an algae-associated lifestyle. Syst Appl Microbiol 44(1): 126166. doi.org/10.1016/j.syapm.2020.126166

Alneberg J, Bennke C, Beier S, Bunse C, Quince C, Ininbergs, K, Riemann L, Ekman M, Jürgens K, Labrenz M, Pinhassi J, Andersson AF (2020) Ecosystem-wide metagenomic binning enables prediction of ecological niches from genomes. Communications Biology 3:119. doi:10.1038/s42003- 020-0856-x.

Bischoff V, Zucker F, Moraru C (2020): Marine Bacteriophages. In Encyclopedia of Virology 4th edition, Reference Module in Life Sciences, Elsevier. doi.org/10.1016/B978-0-12-809633-8.20988-6

Castillo,YM, Sebastián M, Forn I, Grimsley N, Yau S, Moraru C, Vaqué D. (2020) Visualization of viral infection dynamics in a unicellular eukaryote and quantification of viral production using virus fluorescence in situ hybridization. Frontiers in microbiology, 11, article 1559. doi.org/10.3389/fmicb.2020.01559

Koch H, Germscheid N, Freese H, Noriega-Ortega BE, Lücking D, Berger M, Qiu G, Marzinelli E, Campbell A, Steinberg PD, Overmann J, Dittmar T, Simon M, Wietz M (2020) Genomic, metabolic and phenotypic variability shapes ecological differentiation and intraspecies interactions of Alteromonas macleodii. Sci Reports, 10: 809 DOI: 10.1038/s41598-020-57526-5.

Miranda, ML, H Osterholz, HA Giebel, P. Bruhnke, T. Dittmar; O Zielinski (2020) Impact of UV radiation on DOM transformation on molecular level using FT-ICR-MS and PARAFAC. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 230, 118027. doi.org/10.1016/j.saa.2020.118027

Giebel, H-A (2020). Educational cruise - Biological oceanography: Plankton dynamics in the German Bight, HE549, March 19 - March 21, 2020, Bremerhaven (Germany) - Bremerhaven (Germany). Heincke-Berichte, cruise report. doi.org/10.2312/cr_he549

Moraru C, Varsani A, Kropinski AM. (2020) VIRIDIC – a novel tool to calculate the intergenomic similarities of prokaryote-infecting viruses. Viruses 12(11). doi.org/10.3390/v12111268

Pinto M, Zenner PP, Langer TM, Harrison J, Simon M, Varela MM, Herndl GJ (2020) Putative degraders of low-density polyethylene-derived compounds are ubiquitous members of plastic-associated bacterial communities in the marine environment. Environ Microbiol 22/11: 4779-4793.

Rahlff J, Giebel HA, Stolle C, Wurl O, Probst AJ, Herlemann DPR (2020) Overlooked diversity of ultramicrobacterial minorities at the air-sea interface. Atmosphere, 11(11), 1214; doi.org/10.3390/atmos11111214.

Silvano E, Yang M, Wolterink M, Giebel HA, Simon M, Scanlan DJ, Zhao Y, Cen Y (2020) Lipidomic analysis of roseobacters of the pelagic RCA cluster and their response to phosphorus limitation. Front Microbiol 11:552135. doi.org/10.3389/fmicb.2020.552135

Wolter LA, Wietz M, Ziesche L, Breider S, Leinberger J, Poehlein A, Daniel R, Schulz S, Brinkhoff T (2021) Pseudooceanicola algae sp. nov., isolated from the marine macroalga Fucus spiralis, shows genomic and physiological adaptations for an algae-associated lifestyle. Syst Appl Microbiol 44(1): 126166. doi: 10.1016/j.syapm.2020.12616

Bischoff V, Bunk B, Meier-Kolthoff J, Spröer C, Poehlein A, Dogs M, Nguyen M, Petersen J, Daniel R, Overmann J, Göker M, Simon M, Brinkhoff T, Moraru C (2019) Cobaviruses – a new globally distributed phage group infecting Rhodobacteraceae in marine ecosystems. ISME J: 13, 1404–1421.

Hansen CT, J Niggemann, HA Giebel, M Simon, W Bach, T Dittmar (2019). Biodegradability of hydrothermally altered deep-sea dissolved organic matter. Marine Chemistry 217, 103706. doi.org/10.1016/j.marchem.2019.103706

Giebel, HA (2019). Educational cruise - Biological oceanography: Plankton dynamics in the German Bight, HE526, March 12 - March 16, 2019, Bremerhaven (Germany) - Bremerhaven (Germany). Heincke-Berichte, cruise report. doi.org/10.2312/cr_he526

Robinson, T-B, H-A Giebel and O Wurl (2019). Riding the plumes: Characterizing bubble scavenging conditions for the enrichment of the sea-surface microlayer by transparent exopolymer particles. Atmosphere 10 (8), 454. doi.org/10.3390/atmos10080454

Bakenhus, I., B. Wemheuer, P. Akyolb, H.-A. Giebel, L. Dlugosch, R. Daniel, M. Simon (2019) Distinct relationships between fluorescence in situ hybridization and16S rRNA gene- and amplicon-based sequencing data of bacterioplankton lineages.. Syst Appl Microbiol. doi: 10.1016/j.syapm.2019.06.005

Giebel, H-A, M Wolterink, T Brinkhoff and M Simon (2019). Complementary energy acquisition via aerobic anoxygenic photosynthesis and carbon monoxide oxidation by Planktomarina temperata of the Roseobacter group. FEMS Microbiol Ecol 95,5: fiz050. doi.org/10.1093/femsec/fiz050

Koch H, Dürwald A, Schweder T, Noriega-Ortega B, Vidal-Melgosa S, Hehemann J-H, Dittmar T, Freese HM, Becher D, Simon M, Wietz M (2019) Biphasic cellular adaptations and ecological implications of Alteromonas macleodii degrading a mixture of algal polysaccharides. ISME 13/1: 92-103.

Koch H, Freese HM, Hahnke RL, Simon M, Wietz M (2019) Adaptations of Alteromonas sp. 76-1 to polysaccharide degradation: A CAZyme plasmid for ulvan degradation and two alginolytic systems. Front Microbiol 10: Article 504.

Majzoub M, Beyersmann P, Simon M, Thomas T, Brinkhoff T, Egan S (2019) Phaeobacter inhibens controls bacterial community assembly on a marine diatom. FEMS Microb Ecol 95/6: fiz060.

Barrero-Canosa J, Moraru C (2019) PhageFISH for monitoring phage infections at single cell level. In: Methods in molecular biology (Clifton, N.J.) Volume 1898: 1-26. DOI:10.1007/978-1-4939-8940-9_1.

Noriega-Ortega BE, Wienhausen G, Mentges A, Dittmar T, Simon M, Niggemann J (2019) Does the chemodiversity of bacterial exometabolomes sustain the chemodiversity of marine dissolved organic matter? Front Microbiol 10: Article 215.

Steinert G, Wemheuer B, Janussen D, Erpenbeck D, Daniel R, Simon M, Brinkhoff T, Schupp P (2019) Prokaryotic diversity and community patterns in Antarctic continental shelf sponges. Front Mar Sci 6: Article 297.

Ziesche L, Wolter L, Wang H, Brinkhoff T, Pohlner M, Engelen B, Wagner-Döbler I, Schulz S (2019) An unprecedented medium-chain diunsaturated N-acylhomoserine lactone from marine Roseobacter group bacteria, Mar Drugs 17: E20. doi: 10.3390/md17010020.

Rahlff J, Stolle C, Giebel H-A, Ribas-Ribas M, Damgaard LR and Wurl O (2019). Oxygen Profiles Across the Sea-Surface Microlayer - Effects of Diffusion and Biological Activity. Front. Mar. Sci. 6:11. doi: 10.3389/fmars.2019.00011

Bakenhus I, Dlugosch L, Giebel HA, Beardsley C, Simon M, Wietz M (2018) Distinct biogeographic patterns of bacterioplankton composition and single-cell activity between the subtropics and Antarctica. Environ Microbiol. Accepted. doi.org/10.1111/1462-2920.14383

Bakenhus I, Voget S, Poehlein A, Brinkhoff T, Daniel R, Simon M (2018) Genome sequence of Planktotalea frisia type strain (SH6-1T), a representative of the Roseobacter group isolated from the North Sea during a phytoplankton bloom. Stand Gen Sci 13: 7.

Klotz F, T Brinkhoff, HM Freese, M Wietz, A Teske, M Simon and HA Giebel 2018. Tritonibacter horizontis gen. nov., sp. nov., a member of the Rhodobacteraceae, isolated from the Deepwater Horizon oil spill. Int J Sys Evol Microbiol. First Published Online: doi: 10.1099/ijsem.0.002573

Daniel R, Simon M, Wemheuer B (2018) Editorial: Molecular Ecology and Genetic Diversity of the Roseobacter clade. Frontiers Microbiol 9: Article 1185.

Bruns H, Ziesche L, Taniwal NK, Wolter L, Brinkhoff T, Herrmann J, Müller R, Schulz S (2018) N-Acylated amino acid methyl esters from marine Roseobacter group bacteria. Beilstein J Org Chem 14: 2964-2973. doi: 10.3762/bjoc.14.276

Wienhausen G, Noriega-Ortega B E, Niggemann J, Dittmar T, Simon M (2017). The Exometabolome of Two Model Strains of the Roseobacter Group: A Marketplace of Microbial Metabolites. Front Microbiol. 8:1985. doi: 10.3389/fmicb.2017.01985

Bakenhus I, Dlugosch L, Billerbeck S, Giebel HA, Milke F and M Simon (2017) Composition of total and cell-proliferating bacterioplankton community in early summer in the North Sea – roseobacters are the most active component. Front Microbiol. 8:1771. doi.org/10.3389/fmicb.2017.01771

Breider S, Freese H, Spröer K, Simon M, Overmann J, Brinkhoff T (2017) Phaeobacter porticola sp. nov., an antibiotic producing bacterium isolated from a harbor in the southern North Sea. Internat J System Evol Microbiol 67: 2153-2159, doi: 10.1099/ijsem.0.001879

Rahlff J, Stolle C, Giebel HA, Brinkhoff T, Ribas-Ribas M, Hodapp D, Wurl O (2017) High wind speeds prevent formation of a distinct bacterioneuston community in the sea-surface microlayer. FEMS Microbiol Ecol. 93: Article Number: fix041. doi:  10.1093/femsec/fix041 

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.

Milici M, Vital M, Tomasch J, Badewien TH, Giebel HA, 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 DOI:10.1002/lno.10487.

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. Scientific Reports 7: 730. doi:10.1038/s41598-017-00784-7

Simon M (2017) RV SONNE SO254 PoriBacNewZ Cruise Report / Fahrtbericht Auckland, New Zealand, January 26^th, 2017, Auckland, New Zealand, February 27^th, 2017, PTJ (doi.org/10.2312/cr_so254)

Djurhuus A, Mikalsen S-O, Giebel HA, Rogers A (2017) Cutting through the smoke: diversity of free-living bacteria in deep-sea hydrothermal plumes. R. Soc. Open sci. 4: 160829. doi.org/10.1098/rsos.160829.

Fischer R, Giebel HA, Ptacnik R (2017) Identity of the limiting nutrient (N vs. P) affects the competitive success of mixotrophs. Mar Ecol Prog Ser 563:51-63. doi.org/10.3354/meps11968.

Simon M (2016) RV SONNE SO248 BacGeoPac Cruise Report / Fahrtbericht Auckland, New Zealand, May 1^st, 2016, Dutch Harbor, USA: June 3^rd, 2016, PTJ (doi.org/10.2312/cr_so248).

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. (DOI: 10.1186/s40793-016-0201-7).

Fischer R, Giebel HA, Hillebrand H, Ptacnik R. (2016) Importance of mixotrophic bacterivory can be predicted by light and loss rates. Oikos. DOI:10.1111/oik.03539.

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-affiliated pelagic CHAB-I-5 lineage. Nature Microbiol. Article no. 16063, DOI: 10.1038/NMICROBIOL.2016.63.

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.

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.

Milici M, Deng1 ZL, Tomasch J, Decelle J, Wos-Oxley M, Wang H, Jáuregui R, Plumeier I, Giebel HA, 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 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 590 (doi:10.3389/fmicb.2016.00590).

Milici M, Tomasch J, Wos-Oxley ML, Wang H, Jáuregui 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. Scientific Reports 6: 19054 (DOI: 10.1038/srep19054).

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(12): 4369-4377.

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.

Wichmann H, Brinkhoff T, Simon M, Richter-Landsberg C (2016) Dimethylsulfoniopropionate promotes process outgrowth in neural cells and exerts protective effects against tropodithietic acid. Mar. Drugs, 14: 89 (doi:10.3390/md14050089).

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. doi: 10.1099/ijs.0.000205.

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. System Appl Microbiol 38: 483-493.

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 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.
doi: 10.1111/1462-2920.12862

Osterholz H, Niggemann J, Giebel HA, Simon M, Dittmar T (2015) Inefficient microbial production of refractory dissolved organic matter in the ocean. Nature Comm 6: 7422. doi:10.1038/ncomms8422.

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).

Seidel M, Beck M, Greskowiak J, Riedel T, Waska H, Suryaputra IGNA, Schnetger B, Niggemann J, Simon M, Dittmar T (2015) Benthic-pelagic coupling of nutrients and dissolved organic matter composition in an intertidal sandy beach. Mar Chem 176: 150–163.

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.

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.

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. Mar 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-Doebler I, Brinkhoff T, Schulz S (2015) Homoserine lactones, methyl oligohydroxybutyrates, and other extracellular metabolites of macroalgae-associated bacteria of the Roseobacter clade: Identification and functions. ChemBioChem 16: 2094-2107 (ISSN: 1439-4227).

Simon H, Lipsewers YA, Giebel HA, Wiltshire KH, Simon M (2014) Temperature effects on aggregation during a spring diatom bloom. Limnol Oceanogr. Limnol Oceanogr. 59 (6): 2089-2100.

Seidel M, Beck M, Riedel T, Waska H, Suryaputra IGNA, Schnetger B, Niggemann, Simon M, Dittmar T (2014) Biogeochemistry of dissolved organis matter in an anoxic intertidfal creek bank. Geochim Cosmochim Acta 140: 418-434.

Breider S, Scheuner C, Schumann P, Fiebig A, Petersen J, Pradella S, Klenk H, Brinkhoff T and 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

Osterholz H, Simon H, Beck M, März J, Rackebrand S, Brumsack HJ, Feudel U, Simon M (2014) Impact of diatom growth on trace metal dynamics (Mn, Mo, V, U). J Sea Res 87: 35-45.

Wemheuer B, Güllert S, Billerbeck S, Giebel HA, 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 Micro Ecol 87 (2): 378-89.

Dogs M, Voget V, Teshima H, Petersen J, Fiebig A, 12 co-authors, Simon M, Klenk HP, Göker M, Brinkhoff T(2013b) Genome sequence of Phaeobacter inhibens type strain (T5T), a secondary metabolite producing representative of the marine Roseobacter clade, and emendation of the species description of Phaeobacter inhibens. Stand Genomic Sci 9 (2): 334-350.

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.

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: 128-141.

Dogs M, Teshima H, Petersen J, Fiebig A, 13 co-authors, Simon M, Klenk HP, Göker M, Brinkhoff T (2013a) 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: 450-464.

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: 398-403.

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.

Beyersmann PG, Chertkov O, Petersen J, Fiebig A, Chen A, Pati A, Ivanova N, Lapidus A, Goodwin LA, Chain P, Detter JC, Rohde M, Gronow S, Kyrpides NC, Woyke T, 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 Gen Sci 8: 403-419.

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.

Hahnke S, Sperling M, Langer T, Wichels A, Gerdts G, Beardsley C, Brinkhoff T, Simon M (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. 

Brock NL, Citron CA, Zell C, Berger M, Wagner-Döbler I, Petersen J, Brinkhoff T, Simon M, Dickschat J (2013) Isotopically labeled sulfur compounds and synthetic selenium and tellurium analogues to study sulfur metabolism in marine bacteria. Beilstein J Org Chem 9: 942-950.

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):e63422.

Hahnke S, Tindall BJ, Schumann P, Simon M, Brinkhoff T (2013) Pelagimonas elegans gen. nov., sp. nov., isolated from the southern North Sea. Internat J System Evol Microbiol 63: 835–843.

Kisand V, Gebhardt S, Rullkötter J, Simon M (2013) Significant bacterial transformation of riverine humic matter detected by pyrolysis GC-MS in serial chemostat experiments. Mar Chem 149: 23-31.

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. System Appl Microbiol 36: 39-48.

Rocker D, Kisand V, Scholz-Böttcher B, Kneib T, Lemke A, Rullkötter J, Simon M (2012) Differential decomposition of humic acids by marine and estuarine bacterial communities at varying salinities. Biogeochem 111: 331–346.

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, Liesegang H, Wollherr A, Kjelleberg S, Daniel R, Simon M, Thomas T, Brinkhoff T (2012) Genome analysis of two Phaeobacter gallaeciensis strains from globally almost opposite locations reveals high similarity of adaptation to a surface associated lifestyle. ISME J 6/12: 2229-2244.

Lenk S, Moraru C, Hahnke S, Arnds J, Richter M, Kube M, Reinhardt R, Brinkhoff T, Harder J, Amann R, Mußmann M (2012) Roseobacter clade bacteria are abundant in coastal sediments and encode a novel 2 combination of sulfur oxidation genes. ISME J 6: 2178-2187.

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(10): 3539-3551. (DOI: 10.1128/AEM.07657-11).

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 6/6: 1260-1272.

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. Internat J System Evol Microbiol 62: 1619-1624. (DOI 10.1099/ijs.0.033563-0).

Rocker D, Brinkhoff T, Grüner N, Dogs M, Simon M (2012) Composition of humic acid degrading estuarine and marine bacterial communities. FEMS Microbiol Ecol 80/1: 45-63.

Sperling M, Giebel HA, Rink B, Grayek S, Staneva J, Stanev E, Simon M (2012) Differential effect of hydrographic and biogeochemical properties on SAR11 and Roseobacter RCA populations in the southern North Sea. Aquat Microb Ecol 67: 25-34.

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 193/23: 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 enhanced physiological description of Roseobacter litoralis. BMC Genomics 12: 324.

Giebel HA, 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, ISME J 5: 8-19 (doi:10.1038/ismej.2010.87).

Kattner G, Simon M, Koch BP (2011) Molecular characterization of dissolved organic matter and constraints for prokaryotic utilization. In Microbial Carbon Pump in the Ocean, N. Jiao, F. Azam, S. Sanders, (Eds.) (Science/AAAS, Washington, DC), pp 60-61 (pdf).

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.

Rink B, Grüner N, Brinkhoff T, Ziegelmüller K, Simon M (2011) Regional patterns of bacterial community composition and biogeochemical properties in the southern North Sea. Aquat. Microb. Ecol. 63: 207-222.

Lemke A, Lunau M, Badewien TH, Simon M (2010) Short-term and seasonal dynamics of bacterial biomass production and amino acid turnover in the water column of an intertidal ecosystem, the Wadden Sea. Aquat. Microb. Ecol. 61: 205-218 (doi 10.3354/ame01453).

Zhao C, Burchardt M, Brinkhoff T, Simon M, Wittstock G (2010) Microfabrication of patterns of adherent marine bacterium Phaeobacter inhibens using soft lithography and scanning probe lithography. Langmuir: 26/11: 8641-8647.

Thiel V, Brinkhoff T, Dickschat J, 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. Org Biomol Chem 8: 234-246.

Wagner-Döbler I, Baumgart B, 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 S, 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.

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. Environ. Microbiol. 11/8:2164-2178 (doi:10.1111/j.1462-2920.2009.01942.x).

Grossart HP, Thorwest M, Plitzko I, Brinkhoff T, Simon M, Zeeck A (2009) Production of a blue pigment (Glaukothalin) by marine Rheinheimera spp. Int. J. Microbiol, Article ID 701735, 7 pages, doi:10.1155/2009/701735.

Lemke, A., Lunau, M., Stone, J., Dellwig, O., Simon, M. 2009. Spatio-temporal dynamics of suspended matter properties and bacterial communities in the back-barrier tidal flat system of Spiekeroog Island. Ocean Dyn. 59/2: 277-290.

Zhao, C., Brinkhoff, T., Burchardt, M., Simon M., Wittstock, G. 2009. Surface selection, adhesion and retention behaviour of marine bacteria on synthetic organic surfaces using self-assembled monolayers and atomic force microscopy. Ocean Dyn. 59/2: 305-315.

Stevens, H., Simon, M., Brinkhoff, T. 2009. Cultivable bacteria from bulk water, aggregates and surface sediments of a tidal flat ecosystem. Ocean Dyn. 59/2: 291-309.

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: 3677-3697 (DOI 10.1002/pmic.200900120).

Kisand, V., Rocker, D., Simon, M. 2008. Significant decomposition of riverine humic-rich DOC by marine but not estuarine bacteria assessed in sequential chemostat experiments. Aquat. Microb. Ecol. 53: 151-160.

Scherr, C., Simon, M., Spranger, J., Baumgartner, S. 2008. Test System Stability and Natural Variability of a Lemna Gibba L. Bioassay. PloS One 3(9): e3133. doi:10.1371/journal.

Rink, B., Martens, T., Fischer, D., Lemke, A., Grossart, H.P., Simon, M., Brinkhoff, T. 2008. Short-term dynamics of bacterial communities in a tidally affected coastal ecosystem. FEMS Microbiol. Ecol. 66: 306-319.

Gasol, J.M., Pinhassi, J., Alonso-Sáez, L., Ducklow, H., Herndl, G.J., Koblížek, M., Labrenz, M., Luo, Y., Morán, X.A.G., Reinthaler, T., Simon, M. 2008. Towards a better understanding of the microbial carbon flux in the sea. Aquat. Microb. Ecol. 53: 21-38.

Brinkhoff, T., Giebel, H.A., Simon, M. 2008. Diversity, ecology, and genomics of the Roseobacter clade: a short overview. Arch. Microbiol. 189: 531-539.

Dellwig, O., Beck, M., Lemke, A., Lunau, M. Schnetger, B., Brumsack, H.J. 2007. Non-conservative behaviour of molybdenum in coastal waters: Coupling geochemical, biological, and sedimentological processes. Geochim. Cosmochim. Acta 71 2745-2761

Sabdono, A., Kang., S., Hur., H-G, Grossart., H-P., Simon, M. , Radjasa, O.K. 2007. Organophosphate residues in coral tissues of Indonesian coastal waters. Pak. J. Biol. Sci. 7: 239-246.

Stevens, H., Brinkhoff, T., Rink, B, Vollmers, J., Simon, M. 2007. Diversity and abundance of gram-positive bacteria in a tidal flat ecosystem. Environ. Microb. 9(7): 1810-1822.

Rink, B., Seeberger, S., Martens, T., Duerselen, C., Simon, M., Brinkhoff, T. 2007. Effects of a phytoplankton bloom in a coastal ecosystem on the composition of bacterial communities. Aquat. Microb. Ecol. 48: 47-60.

Radjasa, O.K., Martens, T., Grossart, H.P., Brinkhoff, T., Sabdono, A., Simon, M. 2007. Antagonistic activity of a marine bacterium Pseudoalteromonas luteoviolacea TAB 4.2 associated with coral Acropora sp. J. Biol. Sci. 7: 239-246.

Grossart, H.P., Simon, M. 2007. Interactions of planktonic algae and bacteria: Effects on algal growth and organic matter dynamics. Aquat. Microb. Ecol. 47: 163-176.

Martens T, Gram L, Grossart HP, Kessler D, Müller, R, Simon M, Wenzel SC, Brinkhoff T. 2007. Bacteria of the Roseobacter clade show potential for secondary metabolite production. Microb Ecol. 54: 31-42.

Simon, M., Rosenstock, B. 2007. Different coupling of dissolved amino acid, protein, and carbohydrate turnover to heterotrophic picoplankton production in the Southern Ocean in austral summer and fall. Limnol. Oceanogr. 52: 85-95.

Winter, C., Becker, M., Ernstsen, V.B., Hebbeln, D, Port, A., Bartholomä, A., Flemming, B., Lunau, M. 2007. In-situ observation of aggregate dynamics in a tidal channel using acoustics, laser diffraction and optics. J. Coast. Res. SI 50: 1173-1177.

Wang, L., Große, T., Stevens, H., Brinkhoff, T., Simon, M., Liang, L., Bitzer, J., Bach, G., Zeeck, A., Tokuda, H., Lang, S. 2006. Bioactive hydroxyphenylpyrrole-dicarboxylic acids from a new marine Halomonas sp.: production and structure elucidation. Appl. Microbiol. Biotechnol. 72: 816-822.

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., antibiotic-producing members of the Roseobacter clade, reclassification of Ruegeria algicola (Lafay et al. 1995) Uchino et al. 1998 as Marinovum algicola gen. nov., comb. nov., and consequences for the circumscription of the genera Roseobacter, Ruegeria, and Leisingera. J. System. Evol. Microbiol. 56: 1293-1304.

Grossart, H.P., Czub, G., Simon, M. 2006. Algae-bacteria interactions and their effects on aggregation and organic matter flux in the sea. Environ. Microb. 8: 1074-1084.

Lunau, M., Lemke, A., Dellwig, O., Simon, M. 2006. Physical and biogeochemical controls of microaggregate dynamics in a tidally affected coastal ecosystem. Limnol. Oceanogr. 51: 847-859.

Bhaskar, P.V., Grossart, H.P., Bhosle, N.B., Simon, M. 2005. Production of macroaggregates from dissolved exopolymeric substances (EPS) of bacterial and diatom origin. FEMS Microbiol. Ecol. 53: 255-264.

Brinkhoff, T., Kuever, J., Muyzer, G., Jannasch, H.W. 2005. The genus Thiomicrospira. Bergey's Manual of Systematic Bacteriology, 2^nd edition, Vol. 2. Brenner DJ, Krieg NR, Staley JT (eds), 193-199, Springer, New York.

Dickschat, J. S., Martens, T., Brinkhoff, T., Simon, M., Schulz. S. 2005. Volatiles released by a Streptomyces species isolated from the North Sea. Chemistry and Biodiversity 2: 837-865.

Grossart, H.P., Levold, F., Allgaier, M., Simon, M., Brinkhoff T. 2005. Composition of bacterial communities associated with marine diatoms. Environ. Microbiol. 7: 860-873.

Knittel, K., J. Kuever, A. Meyerdierks, R. Meinke, R. Amann, and T. Brinkhoff. 2005. Thiomicrospira arctica sp. nov. and Thiomicrospira psychrophila sp. nov., psychrophilic obligately chemolithoautotrophic sulfur-oxidizing bacteria isolated from marine Arctic sediments. Int. J. Syst. Evol. Microbiol. 55: 781-786.

Lunau, M., Lemke, A., Walther, K., Martens-Habbena, W., Simon, M. 2005. An improved method for counting bacteria in samples with high proportions of particle-associated cells by epifluorescence microscopy: Environ. Microbiol. 7: 961-968.

Rosenstock, B., Zwisler, W., Simon, M. 2005. Bacterial consumption of humic and non-humic low and high molecular weight DOM and the effect of solar irradiation on the turnover of amino acids and carbohydrates in the Southern Ocean. Microb. Ecol. 50: 90-101.

Selje, N., Brinkhoff, T. Simon, M. 2005. Detection of abundant bacteria in the Weser estuary by culture-dependent and culture independent approaches. Aquat. Microb. Ecol. 39: 17-34.

Stevens, H., Brinkhoff, T., Simon, M. 2005. Composition and seasonal dynamics of free-living, aggregate- and sediment surface-associated bacterial communities in the German Wadden Sea. Aquat. Microb. Ecol. 38: 15-30.

Stevens, H., Stuebner, M., Simon, M., Brinkhoff, T. 2005. Phylogeny of Proteobacteria and Bacteroidetes from oxic habitats of a tidal flat ecosystem. FEMS Microbiol. Ecol. 54: 351-365.

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. Appl. Environ. Microbiol. 70: 2560-2565.

Grossart, H.P., Schlingloff, A., M. Bernhard, Simon, M., Brinkhoff, T. 2004. Antagonistic activity of bacteria isolated from organic aggregates of the German Wadden Sea. FEMS Microbiol. Ecol. 47: 387-396.

Grossart, H.P., Brinkhoff, T., Martens, T., Duerselen, C., Liebezeit, G., Simon, M. 2004. Tidal dynamics of dissolved and particulate matter and bacteria in the German Wadden Sea in spring and fall. Limnol. Oceanogr. 49: 2212-2222.

Lunau, M., A. Sommer, A., Grossart, H.P., Simon. M. 2004. A new sampling device for microaggregates in turbid aquatic systems. Limnol. Oceanogr. Methods 2: 387-397.

Selje, N., Simon, M., Brinkhoff, T. 2004. A newly discovered Roseobacter cluster in temperate and polar oceans. Nature 427: 445-448.

Simon, M. 2004. Die Roseobacter-Gruppe: Wichtiges Strukturelement mariner Bakteriengemeinschaften. Biospektrum 10/5: 633-635.

Simon, M., Rosenstock, B., Zwisler, W. 2004. Coupling of epipelagic and mesopelagic heterotrophic picoplankton production to phytoplankton biomass in the Antarctic polar frontal region. Limnol. Oceanogr: 49: 1035-1043.

Bruns, A., H. Philipp, H. Cypionka, and T. Brinkhoff. 2003. Aeromicrobium marinum sp. nov., an abundant pelagic bacterium isolated from the German Wadden Sea. Int. J. Syst. Evol. Microbiol. 53: 1917 - 1923.

Grossart, H.P., Hietanen^, S., Ploug, H. 2003. Microbial dynamics on diatom aggregates in Øresund, Denmark. Mar. Ecol. Progr. Ser. 249: 69-78.

Grossart, H.P., Kiørboe, T., Kam, T., Ploug, H. 2003. Bacterial colonization of marine particles: growth and inter-specific interactions. Appl. Environ. Microbiol. 69: 3500-3509.

Kiørboe, T., Grossart, H.P., Ploug, H., Kam, T. 2003. Microbial dynamics on particles: colonization, growth, detachment, and grazing mortality of attached bacteria. Appl. Environ. Microbiol. 69: 3036-3047.

Rosenstock, B., Simon, M. 2003. Consumption of dissolved amino acids and carbohydrates by limnetic bacterioplankton according to molecular weight fractions and proportions bound to humic matter. Microb. Ecol. 45: 433-443.

Zwisler, W. Selje, N, Simon, M. 2003. Seasonal patterns of the bacterioplankton community composition in a large mesotrophic lake. Aquat. Microb. Ecol. 31: 211-225.

Selje, N., Simon, M. 2003. Composition and dynamics of particle-associated and free-living bacterial communities in the Weser estuary, Germany. Aquat. Microb. Ecol. 30: 221-236.

Gram, L., Grossart, H.-P., Schlingloff, A., Kiørboe, T. 2002. Production of acylated homoserine lactones by Roseobacter strains isolated from marine snow. Appl. Eviron. Microbiol. 68:4111-4116.

Grossart, H.P., Simon, M. 2002. Bacterioplankton dynamics in the Golf of Aqaba and the northern Red Sea in early spring, Mar. Ecol. Prog. Ser. 239: 263-276.

Kiørboe, T., Grossart, H.P., Ploug, H., Kam, T. 2002. Bacterial colonization of sinking aggregates: mechanisms and rates. Appl. Environm. Microbiol. 68: 3996-4006.

Kuever J., S. M. Sievert, H. Stevens, T. Brinkhoff, and G. Muyzer. 2002. Microorganisms of the oxidative and reductive part of the sulphur cycle at a shallow-water hydrothermal vent in the Aegean Sea (Milos, Greece). Cah. Biol. Mar. 43: 413-416.

Simon, M., Grossart, H.P., Schweitzer, B. Ploug, H. 2002. Microbial ecology of organic aggregates in aquatic ecosystems. Aquat. Microb. Ecol. 28: 175-211.

Brachvogel, T., Schweitzer, B., Simon, M. 2001. Dynamics and bacterial colonization of microaggregates in a large mesotrophic lake. Aquat. Microb. Ecol. 26: 23-35.

Brinkhoff, T., and E. J. van Hannen. 2001. Use of silicone grease to avoid "smiling effect" in denaturing gradient gel electrophoresis. J. Rapid Meth. Aut. Mic. 9: 259-261.

Grossart, H.P., Ploug, H. 2001. Microbial degradation of organic carbon and nitrogen on diatom aggregates. Limnol. Oceanogr. 46: 267-277.

Grossart H.P., Riemann L., Azam F. 2001. Bacterial motility in the sea and its ecological implications. Aquat. Microb. Ecol. 25: 247-258.

Knoll, S., Zwisler, W., Simon, M. 2001. Bacterial colonization of early stages of limnetic diatom microaggregates. Aquat. Microb. Ecol. 25: 141-150.

Rosenstock, B., Simon, M. 2001. Sources and Sinks of dissolved amino acids and proteins in a large and deep mesotrophic lake. Limnol. Oceanogr. 46: 644-654.

Schweitzer B, Huber, I., Amann, R., Ludwig, W., Simon, M. 2001. Alpha- and beta-proteobacteria control the consumption and release of amino acids on lake snow aggregates. Appl. Environ. Microbiol. 67: 632-645.

Grossart, H.P., Ploug, H. 2000. Bacterial production and growth efficiencies: Direct measurements on riverine aggregates. Limnol. Oceanogr. 45: 436-445.

Grossart, H.P., Steward, G.F., Martinez, J., Azam, F. 2000. A simple, rapid method for demonstrating bacterial flagella. Appl. Environ. Microbiol. 66:3632-3636.

Ploug, H., Grossart, H.P. 2000. Bacterial growth and grazing on diatom aggregates: Respiratory carbon turnover as a function of aggregate size and sinking velocity. Limnol. Oceanogr. 45: 1467-1475.

Simon, M., Jontofsohn, M., Parparov, A., Berman, T. 2000. Turnover of combined amino acids and carbohydrates on organic aggregates and in the bulk water in Lake Kinneret and other pelagic ecosystems. Arch. Hydrobiol. Spec. Issues Adv. Limnol. 55: 365-377.

Teske, A., T. Brinkhoff, G. Muyzer, D. P. Moser, J. Rethmeier, and H. W. Jannasch. 2000. Diversity of thiosulfate-oxidizing bacteria from marine sediments and hydrothermal vents. Appl. Environ. Microbiol. 66:3125-3133.

Berman, T., Parparov, A., Simon, M. 1999. Carbon fluxes in limnetic seston: relative significance of respiration, solubilization control of bacterioplankton and non-photosynthetic formation. Arch. Hydrobiol. Spec. Ser. Adv. Limnol. 54: 77-90.

Brinkhoff, T., S. M. Sievert, J. Kuever, and G. Muyzer. 1999. Distribution and diversity of sulfur-oxidizing Thiomicrospira spp. at a shallow-water hydrothermal vent in the Aegean Sea (Milos, Greece). Appl. Environ. Microbiol. 65:3843-3849.

Brinkhoff, T., G. Muyzer, C. O. Wirsen, and J. Kuever. 1999. Characterization of Thiomicrospira kuenenii sp. nov. and Thiomicrospira frisia sp. nov., two mesophilic oligately chemolithoautotrophic sulfur-oxidizing bacteria isolated from an intertidal mud flat. Int. J. Syst. Bacteriol. 49:385-392.

Brinkhoff, T., G. Muyzer, C. O. Wirsen, and J. Kuever. 1999. Characterization of Thiomicrospira chilensis sp. nov., a mesophilic obligately chemolithoautotrophic sulfur-oxidizing bacterium isolated from a Thioploca mat. Int. J. Syst. Bacteriol. 49:875-879.

Bunte, C., Simon, M. 1999. Bacterioplankton turnover of dissolved free monosaccharides in a mesotrophic lake. Limnol. Oceanogr. 44: 1862-1870.

Ploug, H., Grossart, H.P. 1999. Bacterial production and respiration in suspended aggregates -a matter of the incubation method. Aquat. Microb. Ecol. 20: 21-29.

Schulz, H. N., T. Brinkhoff, T. G. Ferdelman, M. Hernández Mariné, A. Teske, and B. B. Jørgensen. 1999. Dense populations of a giant sulfur bacterium in Namibian shelf sediments. Science 284:493-495.

Simon, M., Glöckner, F.O., Amann, R. 1999. Differences in the community structure are reflected by a different temperature adaptation of bacterioplankton growth in the Southern Ocean. Aquat. Microb. Ecol. 18: 275-284.

Weiss, M., Simon, M. 1999. Consumption of labile dissolved organic matter by limnetic bacterioplankton: the relative significance of amino acids and carbohydrates. Aquat. Microb. Ecol. 17: 1-12.

Brinkhoff, T., C. M. Santegoeds, K. Sahm, J. Kuever, and G. Muyzer. 1998. A polyphasic approach to study the diversity and vertical distribution of sulfur-oxidizing Thiomicrospira species in coastal sediments of the German Wadden Sea. Appl. Environ. Microbiol. 64: 4650-4657.

Grossart, H.P., Berman, T., Simon, M., Pohlmann, K. 1998. Occurrence and microbial dynamics of macroscopic organic aggregates (lake snow) in Lake Kinneret in fall. Aquat. Microb. Ecol. 14: 59-67.

Grossart, H.P., Simon, M. 1998. Significance of limnetic organic aggregates (lake snow) for the sinking flux of particulate organic matter in a large lake. Aquat. Microb. Ecol. 15: 115-125.

Grossart, H.P., Simon, M. 1998. Bacterial colonization and microbial decomposition of limnetic organic aggregates (lake snow). Aquat. Microb. Ecol. 15: 127-140.

Muyzer, G., T. Brinkhoff, U. Nübel, C. Santegoeds, H. Schäfer, and C. Wawer. 1998. Denaturing gradient gel electrophoresis (DGGE) in microbial ecology, p. 3.4.4: 1-27. In A. D. L. Akkermans, J. D. van Elsas, and F. J. de Bruijn (ed.), Molecular microbial ecology manual, 3^rd ed. Kluwer Academic Publishers, Dordrecht, The Netherlands.

Parparov, A., Berman, T., Grossart, H.P., Simon, M. 1998. The metabolic activity of seston-associated microorganisms in Lake Kinneret. Aquat. Microb. Ecol. 15: 77-78.

Simon, M. 1998. Bacterioplankton dynamics in a large mesotrophic lake: II. concentrations and turnover of dissolved amino acids. Arch. Hydrobiol. 144: 1-23.

Simon, M., Bunte, C., Schulz, M., Weiss, M., Wünsch, C. 1998. Bacterioplankton dynamics in Lake Constance (Bodensee): Substrate utilization, growth control, and long-term trends. Arch. Hydrobiol. Spec. Issues Advanc. Limnol. 53: 195-221.

Simon, M., Wünsch, C. 1998. Temperature control of bacterioplankton growth in a large temperate lake. Aquat. Microb. Ecol. 16: 119-130.

Simon, M., Tilzer, M.M, Müller, H. 1998. Bacterioplankton dynamics in a large mesotrophic lake: I. abundance, growth and relationships to phytoplankton growth. Arch. Hydrobiol. 143: 385-407.

Sorokin, D. Y., G. Muyzer, T. Brinkhoff, J. G. Kuenen, and M. S. M. Jetten. 1998. Isolation and characterization of a novel facultatively alkaliphilic Nitrobacter species, N. alkalicus sp. nov. Arch. Microbiol. 170: 345-352.

Wichels, A., S. S. Biel, H. R. Gelderblom, T. Brinkhoff, G. Muyzer, and C. Schütt. 1998. Bacteriophage diversity in the North Sea. Appl. Environ. Microbiol. 64: 4128-4133.

Wirsen, C. O., T. Brinkhoff, J. Kuever, G. Muyzer, S. Molyneaux, and H. W. Jannasch. 1998. Comparison of a new Thiomicrospira strain from the Mid-Atlantic Ridge with known hydrothermal vent isolates. Appl. Environ. Microbiol. 64: 4057-4059.

Brinkhoff, T., and G. Muyzer. 1997. Increased species diversity and extended habitat range of sulfur-oxidizing Thiomicrospira spp. Appl. Environ. Microbiol. 63: 3789-3796.

Grossart, H.P., Simon, M., Logan, B. 1997. Formation of macroscopic organic aggregates (lake snow) in a large lake: The significance of transparent exopolymer particles (TEP), phyto- and zooplankton. Limnol. Oceanogr. 42: 1651-1659.

Hanisch, K., Schweitzer, B., Simon, M. 1996. Utilization of dissolved carbohydrates by planktonic bacteria in Lake Constance. Microb. Ecol. 31: 41-55.

Reichart, I., Simon, M. 1996. Horizontal variability of bacterioplankton growth dynamics in a large lake. Aquat. Microb. Ecol. 11: 31-41.

Weiss, P., Schweitzer, B., Amann, R., Simon, M. 1996. Identification in situ and dynamics of bacteria on limnetic organic aggregates (lake snow). Appl. Environ. Microbiol. 62: 1998-2005.

Hennes, K., Simon, M. 1995. Significance of bacteriophages for controlling bacterioplankton growth in a mesotrophic lake. Appl. Environ. Microbiol. 61: 333-340.

Logan, B.E., Passow, U., Alldredge, A.L., Grossart, H.P., Simon, M. 1995. Mass sedimentation of diatom blooms as large aggregates is driven by coagulation of transparent exopolymer particles (TEP). Deep Sea Res. 42: 203-214.

Schweitzer, B., Simon, M. 1995. Limiting nutrients for bacterioplankton growth in a mesotrophic temperate large lake, Microb. Ecol. 30: 89-104.

Logan, B.E., Grossart, H.P., Simon, M. 1994. Direct observation of phytoplankton and aggregates on polycarbonate filters using brightfield microscopy, J. Plankton Res. 16: 1811-1815.

Simon, M. 1994. Diel variability of bacterioplankton biomass production and cell multiplication in Lake Constance. Arch. Hydrobiol. 130: 283-302.

Simon, M., Lenhard, A., M.M. Tilzer. 1993. Bacterial production and the sinking flux of particulate organic carbon in a large and deep lake in comparison to oceanic environments. Mar. Microb. Food Webs 7: 161-176.

Grossart, H.P., Simon, M. 1993. Limnetic macroscopic organic aggregates (lake snow): abundance, characteristics, and bacterial dynamics in Lake Constance. Limnol. Oceanogr. 38: 532-546.

Kirchman, D.L., Keil, R.G., Simon, M., Welschmeyer, N.A. 1993. Biomass and production of heterotrophic bacterioplankton in the oceanic subarctic Pacific. Deep-Sea Res. 40: 967-988.

Rosenstock, B., Simon, M. 1993. Use of dissolved combined and free amino acids by planktonic bacteria in Lake Constance. Limnol. Oceanogr. 38: 1521-1531.

Simon, M., Cho, B.C., Azam, F. 1992. Significance of bacterial biomass in lakes and the ocean: comparison to phytoplankton biomass and biogeochemical implications. Mar. Ecol. Prog. Ser. 86: 103-110.

Simon, M., Welschmeyer, N.A., Kirchman, D.L. 1992. Bacterial production and the sinking flux of particulate organic matter in the subarctic Pacific. Deep-Sea Res. 39: 1997-2008.

Simon, M., Rosenstock, B. 1992. Carbon and nitrogen sources of planktonic bacteria in Lake Constance studied by the composition and isotope dilution of intracellular amino acids. Limnol. Oceanogr. 37: 1496-1511.

Smith, D.C., Simon, M., Alldredge, A.L., Azam, F. 1992. Intense hydrolytic enzyme activity on marine aggregates and implications for rapid particle dissolution. Nature 359: 139-142.