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Publications 2007
Publikationen 2007
Department of Biogeochemistry
| Aspetsberger, F., M. Zabel, T. Ferdelman, U. Struck, A. Mackensen, A. Ahke and U. Witte: Instantaneous benthic response to different organic matter quality: In situ experiments in the Benguela Upwelling System. Marine Biology Research 3(5):342 - 356 (2007). TFO |
| Dellwig, O., K. Bosselmann, S. Kölsch, M. Hentscher, J. Hinrichs, M. E. Böttcher, R. Reuter, and H.-J. Brumsack: Sources and fate of manganese in a tidal basin of the German Wadden Sea. Journal of Sea Research 57:1-18 (2007). ScienceDirect |
| D′Hondt, S., F. Inagaki, T. Ferdelman, B. B. Jørgensen, K. Kato, P. Kemp, P. Sobecky, M. Sogin, and K. Takai: Exploring subseafloor life with the Integrated Ocean Drilling Program. Scientific Drilling 5:26-37 (2007). IODP Full Text |
| Fenton, S., K. Grice, R. J. Twitchett, M. E. Böttcher, C. Looy, and B. Nabbefeld: Changes in biomarker abundances and sulfur isotopes of pyrite across the Permian-Triassic (P/Tr) Schuchert Dal section (East Greenland). Earth and Planetary Science Letters 262:230-239 (2007). ScienceDirect |
| Finke, N., V. Vandieken, and B. B. Jørgensen: Acetate, lactate, propionate, and isobutyrate as electron donors for iron and sulfate reduction in Arctic marine sediments, Svalbard. FEMS Microbiology Ecology 59:10-22 (2007). PubMed |
| Finke, N., T. M. Hoehler, and B. B. Jørgensen: Hydrogen ′leakage′ during methanogenesis from methanol and methylamine: implications for anaerobic carbon degradation pathways in aquatic sediments. Environmental Microbiology 9(4):1060-1071 (2007). PubMed |
| Glud, R. N., P. Berg, H. Fossing, and B. B. Jørgensen: Effect of the diffusive boundary layer on benthic mineralization and O2 distribution: A theoretical model analysis. Limnology and Oceanography 52(2):547-557 (2007). ASLO Full Text |
| Jørgensen, B. B. and A. Boetius: Feast and Famine – microbial life in the deep-sea bed. Nature Review Microbiology 5: 770-781 (2007). PubMed Full Text |
| Kano, A., T. G. Ferdelman, T. Williams, J. -P. Henriet, T. Ishikawa, N. Kawagoe, C. Takashima, Y. Kakizaki, K. Abe, S. Sakai, E. L. Browning, X. Li and the IODP Expedition 307 Scientists: Age constraints on the origin and growth history of a deep-water coral mound in the northeast Atlantic drilled during Integrated Ocean Drilling Program Expedition 307. Geology 35(11):1051-1054 (2007). Geology |
| Leloup, J., A. Loy, N. J. Knab, C. Borowski, M. Wagner, and B. B. Jørgensen: Diversity and abundance of sulfate-reducing microorganisms in the sulfate and methane zones of a marine sediment, Black Sea. Environmental Microbiology 9(1):131-142 (2007). PubMed |
| Niggemann, J., T. G. Ferdelman, B. A. Lomstein, J. Kallmeyer, and C. J. Schubert: How depositional conditions control input, composition, and degradation of organic matter in sediments from the Chilean coastal upwelling region. Geochimica et Cosmochimica Acta 71:1513-1527 (2007). ScienceDirect |
| Parkes, R. J., B. A. Cragg, N. Banning, F. Brock, G. Webster, J. C. Fry, E. Hornibrook, R. D. Pancost, S. Kelly, N. Knab, B. B. Jørgensen, J. Rinna, and A. J. Weightman: Biogeochemistry and biodiversity of methane cycling in subsurface marine sediments (Skagerak, Denmark). Environmental Microbiology 9(5):1146-1161 (2007). PubMed |
| Preisler, A., D. de Beer, A. Lichtschlag, G. Lavik, A. Boetius, and B. B. Jørgensen: Biological and chemical sulfide oxidation in a Beggiatoa inhabited marine sediment. The ISME Journal 1:341-353 (2007). PubMed Full Text |
| Schäfer, H., T. G. Ferdelman, H. Fossing and G. Muyzer: Microbial diversity in the deep sediments of the Benguela Upwelling System. Aquatic Microbial Ecology 50:1-9 (2007). AME |
| Schippers, A., D. Kock, M. Schwartz, M. E. Böttcher, H. Vogel, and M. Hagger: Geomicrobiological and geochemical investigation of a pyrrhotite-containing mine waste tailings dam near Selebi-Phikwe in Botswana. Journal of Geochemical Exploration 92:151-158 (2007). ScienceDirect |
| Stubbe, M., M. Holtappels and J. Gimsa: A new working principle for ac electro-hydrodynamic on-chip micro-pumps. J. Phys. D: Appl. Phys. 40:6850-6856 (2007). IOPscience |
| Wakeham, S. G., R. Amann, K. H. Freeman, E. C. Hopmans, B. B. Jørgensen, I. F. Putnam, S. Schouten, J. S. Sinninghe Damsté, H. M. Talbot, and D. Woebken: Microbial ecology of the stratified water column of the Black Sea as revealed by a comprehensive biomarker study. Organic Chemistry 38:2070-2097 (2007). ScienceDirect |
| Suraiya, Laloo: Using Nitrate-Reducing Sulphide-Oxidising Bacteria for the detection for alternate fractionation pathways in the sulphur cycle (2007). |
| Sawicka, Joanna E.: Freeze-thaw effects on sulfate reduction rates and microbial community dynamics in Arctic sediments. Master thesis, MarMic, University of Bremen, Bremen (2007), 38pp. |
| Ahke, Astrid: Composition of molecular organic matter pools, pigments and proteins, in Benguela Upwelling and Arctic sediments. Berichte aus dem Fachbereich Geowissenschaften der Universität Bremen No. 256, Dissertation Universität Bremen, Bremen (2007), 218pp. |
| Bosselmann, Katja: Sulfate reduction and iron-manganese cycling in intertidal surface sediments of the southern North Sea. Dissertation Carl von Ossietzky Universität, Oldenburg (2007), 228pp. |
| Knab, Nina: Controls of anaerobic oxidation of methane in ocean margin sediments. Dissertation Universität Bremen, Bremen (2007), 196pp. |
Habitat Group
| Berg, P., H. Røy, and P. Wiberg: Eddy correlation flux measurements: The sediment surface area that contributes to the flux. Limnol. Oceanogr. 52(4):1672–1684 (2007). ResearchGate |
| Billerbeck, M., H. Røy, K. Bosselmann, and M. Huettel: Benthic photosynthesis in submerged Wadden Sea intertidal flats. Estuarine Coastal and Shelf Sience 71:704-716 (2007). ScienceDirect |
| Boetius, A., I.G. Priede, C. Mevel: Infrastructure and critical technology. In: The Deep Sea Frontier – Science Challenges for a sustainable future. European Communities, ISBN 978-92-79-05266-8 (2007). |
| Cook, P. L. M., B. Veuger, S. Böer, and J. J. Middelburg: Effect of nutrient availability on carbon and nitrogen incorporation and flows through benthic algae and bacteria in near-shore sandy sediment. Aquatic Microbial Ecology 49:165-180 (2007). AME |
| Cook, P.L.M., F. Wenzhöfer, R. N. Glud, F. Janssen and M. Huettel: Benthic solute exchange and carbon mineralization in two shallow subtidal sandy sediments: Effect of advective pore-water exchange. Limnol. Oceanogr. 52(2):1943–1963 (2007). ASLO Full Text |
| Dupré, S., J. Woodside, J.-P. Foucher, G. de Lange, J. Mascle, A. Boetius, V. Mastalerz, A. Stadnitskaia, H. Ondréas, C. Huguen, H. Harmégnies, S. Gontharet, L. Loncke, E. Deville, H. Niemann, E. Omoregie, K. Olu-Le Roy, A. Fiala-Medioni, A. Dählmann, J. C. Caprais, A. Prinzhofer, M. Sibuet, C. Pierre, J. S. Damsté and the NAUTINIL Scientific Party: Seafloor geological studies above active gas chimneys off Egypt (Central Nile Deep Sea Fan). Deep-Sea Res. I 54:1146-1172 (2007). ScienceDirect |
| Edgcomb, V. P., S. J. Molyneaux, S. Böer, C. O. Wirsen, M. Saito, M. S. Atkins, K. Lloyd, and A. Teske: Survival and growth of two heterotrophic hydrothermal vent archaea, Pyrococcus strain GB-D and Thermococcus fumicolans under low pH and high sulfide concentrations in combination with high temperature and pressure regimes. Extremophiles 11:329-342 (2007). PubMed |
| Elvert, M. and H. Niemann: Occurrence of unusual steroid and hopanoids derived from aerobic methanotrophs at an actice marine mud volcano. Org. Geochem. 39:167-177 (2007). ScienceDirect |
| Hoffmann, F., Sauter, E., Sachs, O., Røy, H., Klages, M.: Oxygen distribution in Tentorium semisuberites and in its habitat in the Arctic deep sea. pp.379-382, In: Porifera Research: Biodiversity, Innovation and Sustainability. Custódio M, L′bo-Hajdu G, Hajdu E, Muricy G (eds.), Série Livros. Museu Nacional, Rio de Janeiro (2007). Full Text |
| Huettel, M., P. L. M. Cook, F. Janssen, G. Lavik, and J. J. Middelburg: Transport and degradation of a dinoflagellate bloom in permeable sublittoral sediment. Mar. Ecol. Prog. Ser. 340:139-153 (2007). MEPS |
| Jørgensen, B. B., and A. Boetius: Feast and famine – microbial life in the deep-sea bed. Nat. Rev. Microbiol. 5:770-781 (2007). PubMed Full Text |
| Meysman, F. J. R., O. S. Galaktionov, P. L. M. Cook, F. Janssen, M. Huettel, and J. J. Middelburg: Quantifying biologically and physically induced flow and tracer dynamics in permeable sediments. Biogeosciences 4:627-646 (2007). KNAW Full Text |
| Niemann, H., and M. Elvert: Diagnostic lipid biomarker and stable carbon isotope signatures of microbial communities mediating the anaerobic oxidation of methane with sulphate. Org. Geochem. doi 10.1016/j.orggeochem.2007.11.003 (2007). ScienceDirect |
| Ramette, A.: Multivariate analyses in microbial ecology. FEMS Microbiol. Ecol. 62:142-160 (2007). PubMed Full Text |
| Roberts, H., R. Carney, M. Kupchik, C. Fischer, K. Nelson, E. Becker, L. Goehring, S. Lessard-Pilon, G. Telesnicki, B. Bernard, J. Brooks, M. Bright, E. Cordes, S. Hourdez, J. Hunt Jr., W. Shedd, G. Boland, S. Joye, V. Samarkin, M. Bernier, M. Bowles, I. McDonald, H. Niemann, C. Petersen, C. Morrison, and J. Potter: Alvin explores the deep northern Gulf of Mexico slope. EOS 88(35):341-348 (2007). Wiley Full Text |
| Spetland, F., Rapp H.T., Hoffmann F., Tendal O.S.: Sexual reproduction of Geodia barretti Bowerbank, 1858 (Porifera, Astrophorida) in two Scandinavian fjords. pp.613-620 In: Porifera Research: Biodiversity, Innovation and Sustainability. Custódio MR, L′bo-Hajdu G, Hajdu E, Muricy G (edss), Série Livros 28. Museu Nacional, Rio de Janeiro (2007). Full Text |
| Treude, T., V. Orphan, K. Knittel, A. Gieseke, C. H. House and A. Boetius: Consumption of Methane and CO2 by Methanotrophic Microbial Mats from Gas Seeps of the Anoxic Black Sea. Appl. Environ. Microb. 73(7):2271-2283 (2007). PubMed Full Text |
| Braunshausen, A: Archaea im Arktischen Tiefseeschwamm Tentorium semisuberites. Diploma Thesis, Universität Bochum in cooperation with Max Planck Institute for Marine Microbiology, Bremen (2007). |
| Schöttner, S. I: Microbial Habitats in Cold-Water Coral Reef Ecoystems: Exploring Diversity, Structure and Dynamics of Associated Prokaryotic Communities. Master thesis/ PhD Thesis proposal, University of Bremen (2007), 48pp. |
| Omoregie, Osasuyi Enoma: Function and diversity of marine and hypersaline mat forming microbial communities. PhD thesis, MarMic, Jacobs University Bremen (2007), 239pp. |
| Sweetman, A. K: Macrofaunal and foraminiferal community structure and their response to simulated phytodetrital food pulses. Dissertation Universität Bremen, Bremen (2007), 132pp. |
Mathematic Modeling Group
| Bera, P. and A. Khalili: Stability of buoyancy opposed mixed convection in a vertical channel and its dependence on permeability. Adv. Water Res. 30: 2296-2308 (2007). ScienceDirect |
Microsensor Group
| Abed, R. M. M., B. Zein, A. Al-Thukair, and D. de Beer: Phylogenetic diversity and activity of aerobic heterotrophic bacteria from a hypersaline oil-polluted microbial mat. Syst. Appl. Microbiol. 30:319-330 (2007). PubMed |
| Abed, R.M.M., K. Kohls, and D. de Beer: Effect of salinity changes on the bacterial diversity, photosynthesis and oxygen consumption of cyanobacterial mats from an intertidal flat of the Arabian Gulf. Environm. Microbiol. 9(6):1384-1392 (2007). PubMed |
| Bachar, A., E. Omoregie, R. de Wit, and H. M. Jonkers: Diversity and Function of Chloroflexus-Like Bacteria in a Hypersaline Microbial Mat: Phylogenetic Characterization and Impact on Aerobic Respiration. Applied and Environmental Microbiology 73(12):3975-3983 (2007). PubMed Full Text |
| Collins G, T. Mahony,A.M. Enright, A. Gieseke, D. deBeer & V.O. Flaherty: Determination and Localisation of In Situ Substrate Uptake by Anaerobic Wastewater Treatment Granular Biofilms. Water Science & Technologies 55 (8,9): 369-376 (2007). PubMed |
| de Beer, D., A. Lichtschlag, G. Lavik and B.B. Jørgensen: Biological versus chemical sulfide oxidation in Beggiatoa inhabited sediment. Goldschmidt Conference Abstracts A209 (2007). PubMed Full Text |
| Filthuth, H., G. Eickert, P. Faerber, H. M. Jonkers, L. Polerecky, and D. de Beer: A novel radioactivity microsensor for high spatial resolution measurements of β-radiation. Limnol. Oceanogr. Methods 5:309-316 (2007). ASLO Full Text |
| Filthuth, H., G. Eickert, P. Faerber, H. Jonkers, L. Polerecky, and D. de Beer: Microsensor for radioactivity. Journal of Labelled Compounds and Radiopharmaceuticals 50:492-493 (2007). ResearchGate |
| Hinck, S., Neu, T.R., Lavik, G., Mussmann, M., deBeer, D., Jonkers, H.M: Physiological Adaptation of a Nitrate-Storing Beggiatoa sp. to Diel Cycling in a Phototrophic Hypersaline Mat. Applied and Environmental Microbiology 73(21):7013-7022 (2007). PubMed Full Text |
| Lavermann, A.M., C. Meile, P. van Cappellen, and E.B.A. Wieringa: Vertical Distribution of Dentrification in an Estuarine Sediment: Integrating Sediment Flowthrough Reactor Experiments and Microprofiling via Reactive Transport Modeling. Applied and Environmental Microbiology 73(1):40-47 (2007). ASM Full Text |
| Ploug, H., U. Passow: Direct measurement of diffusivity within diatom aggregates containing transparent exopolymer particles. Limnology and Oceanography 52(1):1-6 (2007). ASLO Full Text |
| Polerecky, L., A. Bachar, R. Schoon, M. Grinstein, B. B. Jørgensen, D. de Beer, and H.M. Jonkers: Contribution of Chloroflexus respiration to oxygen cycling in a hypersaline microbial mat from Lake Chiprana, Spain. Environmental Microbiology 9:2007–2024 (2007). PubMed |
| Preisler, A., D. de Beer, A. Lichtschlag, G. Lavik, A. Boetius, and B. B. Jørgensen: Biological and chemical sulfide oxidation in a Beggiatoa inhabited marine sediment. ISME-Journal 1:341-353 (2007). PubMed Full Text |
| Schläppy, M.-L., F. Hoffmann, H. Røy, R. H. Wijffels, D. Mendola, M. Sidri, and D. de Beer: Oxygen dynamics and flow patterns of Dysidea avara (Porifera: Demospongiae). Journal of the Marine Biological Association of the United Kingdom. Spec. Issue 87(6):1677-1682 (2007). ResearchGate |
| Schroeder, C. R., L. Polerecky, and I. Klimant: Time-Resolved pH/pO2 Mapping with Luminescent Hybrid Sensors. Analytical Chemistry 79:60-70 (2007). PubMed |
| Sievert, S.M., E.B.A. Wieringa, C.O. Wirsen, and C.D. Taylor: Growth and mechanism of filamentous-sulfur formation by Candidatus Arcobacter sulfidicus in opposing oxygen-sulfide gradients. Environmental Microbiology 9(1):271-276 (2007). PubMed |
| Stief, P.: Enhanced exoenzyme activities in sediments in the presence of deposit-feeding Chironomus riparius larvae. Freshwater Biology 52:1807-1819 (2007). Wiley |
| Volkenborn, N., L. Polerecky, S. I. C. Hedtkamp, J. E. E. van Beusekom, and D. de Beer: Bioturbation and bioirrigation extend the open exchange regions in permeable sediments. Limnology and Oceanography 52(5):1898–1909 (2007). ASLO Full Text |
| Weber, M., P. Faerber, V. Meyer, C. Lott, G. Eickert, K. E. Fabricius, and D. De Beer: In situ applications of a new diver-operated motorized microsensor Profiler. Environmental Science & Technology 41:6210-6215 (2007). PubMed |
| Weber, M., C. Lott, K. E. Fabricius: Corrigendum to "Sedimentation stress in a scleractinian coral exposed to terrestrial and marine sediments with contrasting physical, organic and geochemical properties" [JEMBE 336 (2006) 18-32]. JEMBE 341:151 (2007). ResearchGate Full Text |
| Al-Najjar, M.: An approach to measure flow of energy in benthic photosynthetic mats, tested on an artificial film of Diatoms. Master theis, MarMic, University of Bremen, Bremen (2007), 48pp. |
| Löffler, Birte: Nitrifizierende Biofilme als Inspiration für energetische Innovationen. Bachelorarbeit Hochschule Bremen im FB Bionik, Bremen (2007). |
Department of Microbiology
| Büttner, M., P. Weber, F. Schmidl, A. Steppke, V. Grosse, T. Müller, M. Röder, P. Görnert, C. Lang, D. Schüler, and P. Seidel: Temperature-dependent Néel relaxation (TMRX) measurements on magnetosomes. J. Magnetism and Magnetic Materials (2007). |
| Coker, V. S., C. I. Pearce, C. Lang, G. van der Laan, R.A.D. Pattrick, N. D. Telling, D. Schüler, E. Arenholz and J. R. Lloyd: Cation site occupancy of biogenic magnetite compared to polygenic ferrite spinels determined by X-ray magnetic circular dichroism. European Journal of Mineralogy 19:707-716 (2007). Schweizerbart |
| Faivre D.: Biomimetic Formation of Magnetite Nanoparticles. pp.159-172, In: Handbook of Biomineralization (Vol. 2):Biomimetic and Bio-inspired Materials Chemistry. E. Bäuerlein and P. Behrens (eds.), Wiley-VCH, Weinheim (2007). Wiley |
| Hartung, A., M.R. Lisy, K.-H. Herrmann, I. Hilger, D. Schüler, C. Lang, M. E. Bellemann, W. A. Kaiser, and J. R. Reichenbach: Labeling macrophages using bacterial magnetosomes and their characterization by magnetic resonance imaging. J. Magnetism and Magnetic Materials 311: 454-459 (2007). ScienceDirect |
| Heider, J., and Rabus R.: Genomic insights in the anaerobic biodegradation of organic pollutants. pp.24-54, In: Microbial biodegradation: genomics and molecular biology, E. Diaz (ed), Horizon Scientific Press (2007). PubMed |
| Knaust, F., M. Kube, R. Reinhardt, R. Rabus: Analyses of the vrl gene cluster in Desulfococcus multivorans: homologous to the virulence associated locus of the ovine footrot pathogen Dichelobacter nodosus strain A198. J. Mol. Microbiol. Biotechnol. 13:156-164 (2007). PubMed |
| Kniemeyer, O., F. Musat, S.M. Sievert, K. Knittel, H. Wilkes, M. Blumenberg, W. Michaelis, A. Classen, C. Bolm, S.B. Joye, and F. Widdel: Anaerobic oxidation of short-chain hydrocarbons by marine sulphate-reducing bacteria. Nature 449:898-901 (2007). PubMed |
| Lang, C., Schüler D. and Faivre D.: Synthesis of Magnetite Nanoparticles for Bio- and Nanotechnology: Genetic Engineering and Biomimetics of Bacterial Magnetosomes. Macromolecular Bioscience 7:144-151 (2007). PubMed |
| Lisy, M. R., A. Hartung, C. Lang, D. Schüler, W. Richter, J. R. Reichenbach, W. A. Kaiser, and I. Hilger: Fluoresecent bacterial magnetic nanoparticles as bimodal contrast agents. Investigative Radiology 42(4):235-241 (2007). PubMed |
| Meyer, B., and J. Kuever: Phylogeny of the alpha and beta subunits of the dissimilatory adenosine-5′-phosphosulfate (APS) reductase from sulfate-reducing prokaryotes – origin and evolution of the dissimilatory sulfate-reduction pathway. Microbiology 153:2026-2044 (2007). PubMed Full Text |
| Meyer, B., and J. Kuever: Molecular analysis of the distribution and phylogeny of dissimilatory adenosine-5′-phosphosulfate reductase-encoding genes (aprBA) among sulfur-oxidizing prokaryotes. Microbiology 153: 3478-3498 (2007). PubMed Full Text |
| Meyer, B., Imhoff, J.F., and J. Kuever: Molecular analysis of the distribution and phylogeny of the soxB gene among sulfur-oxidizing bacteria-evolution of the sulfur-oxidation (Sox)-sulfur-oxidation enzyme system. Environ. Microbiol. 9(12):2957-2978 (2007). PubMed |
| Meyer, B., and J. Kuever: Molecular analysis of the diversity of sulfate-reducing and sulfur-oxidizing prokaryotes in the environment, using aprA as functional marker gene. Appl. Environ. Microbiol. 73(23):7664-7679 (2007). PubMed Full Text |
| Meyer, B., and J. Kuever: Phylogenetic diversity and spatial distribution of the microbial community associated with the Caribbean deep-water sponge Polymastia cf. corticata by 16S rRNA, aprA and amoA gene analysis. Microbial Ecology doi 10.1007/s00248-007-9348-5 (2007). PubMed Full Text |
| Nauhaus, K., M. Albrecht, M. Elvert, A. Boetius, and F. Widdel: In vitro cell growth of marine archaeal-bacterial consortia during anaerobic oxidation of methane with sulfate. Environ. Microbiol. 9(1):187-196 (2007). PubMed |
| Rabus, R, and A. Strittmatter: Chapter 3. Functional genomics of sulfate-reducing prokaryotes, pp.117-140. In: Sulphate-reducing bacteria - environmental and engineered systems. L.L. Barton and W.A. Hamilton (ed.), Cambridge University Press, Cambridge (2007). CUP |
| Richter, M., M. Kube, D. A. Bazylinski, T. Lombardot, F. O. Glöckner, R. Reinhardt, and D. Schüler: Comparative genome analysis of four magnetotactic bacteria reveals a complex set of group-specific genes implicated in magnetosome biomineralization and function. J. Bacteriol. 189(13): 4899-4910 (2007). PubMed Full Text |
| Scheffel, A., and D. Schüler: The acidic repetitive domain of the Magnetospirillum gryphiswaldense MamJ protein displays hypervariability but is not required for magnetosome chain assembly. J. Bacteriol. 189(17):6437-6446 (2007). PubMed Full Text |
| Wacker, R., B. Ceyhan, P. Alhorn, D. Schüler, C. Lang, and C.M. Niemeyer: Magneto immuno-PCR: A novel Immunoassay based on biogenic magnetosome nanoparticles. Biochem. Biophys. Res. Commun. 357:391-396 (2007). PubMed |
| Widdel, F., F. Musat, K. Knittel, and A. Galushko: Chapter 9. Anaerobic degradation of hydrocarbons with sulphate as electron acceptor. pp. 265-303, In: Sulphate-reducing bacteria - environmental and engineered systems. L.L. Barton and W.A. Hamilton (ed.), Cambridge University Press, Cambridge (2007). CUP |
| Wöhlbrand L, B. Kallerhoff, D. Lange, P. Hufnagel, J. Thiermann, R. Reinhardt, and R. Rabus: Functional proteomic view of metabolic regulation in Aromatoleum aromaticum strain EbN1. Proteomics 7 2222-2239 (2007). PubMed |
| Hahnke, Richard: T-RFLP Fragmentgrößenbestimmung. B.Sc. thesis, University of Applied Sciences Gelsenkirchen (2007), 53pp. |
| Katzmann, Emanuel: Genetische und ultrastrukturelle Untersuchungen zur Zellbiologie und Assemblierung der Magnetosomenkette in Magnetospirillum gryphiswaldense. Diplomarbeit Universität Bremen, Bremen (2007), 81pp. |
| Langhammer, Philipp Andreas: Physiology of Rhodopirellula baltica in chemostats. Diploma thesis, Fachhochschule Flensburg (2007). |
| Navratil, Jeanette: T-RFLP analyses of the bacterial community in abyssal sediments. B.Sc. thesis, University of Applied Sciences Bonn-Rhein-Sieg (2007). |
| Puschell, Ann: Enumeration and cultivation of microorganisms from oligotrophic marine sediments of the South Pacific gyre. Master thesis, MarMic, University of Bremen, Bremen (2007), 48pp. |
| Zedelius, Johannes: Untersuchungen zum anaeroben Abbau von Cycloalkanen mit Anreicherungskulturen Diplomarbeit , Universität Freiburg (2007), 77pp. |
| Jacob, Jacob H: Regulation of anaerobic catabolism of aromatic compounds and sulfate reduction in Desulfobacula toluolica Tol2. PhD thesis, MarMic, Universität Bremen, Bremen (2007), 116pp. |
| Scheffel, André: Molekulare und strukturelle Untersuchungen zur Bildung von magnetosomen und zur Assemblierung von Magnetospirillum gryphiswaldense. Dissertation Universität Bremen, Bremen (2007), 200pp. |
Department of Molecular Ecology
| Allers, E., L. Goméz-Consarnau, J. Pinhassi, J. M. Gasol, K. Å imek, and J. Pernthaler: Response of Alteromonadaceae and Rhodobacteriaceae to glucose and phosphorus manipulation in marine mesocosms. Environ. Microbiol. 9(10):2417-2429 (2007). PubMed |
| Alonso, C., F. Warnecke, R. Amann, and J. Pernthaler: High local and global diversity of Flavobacteria in marine plankton. Environ. Microbiol. 9(5):1253-1266 (2007). PubMed |
| Dupperon, S., A. Fiala-Médioni, J.-C. Caprais, K. Olu and M. Sibuet: Evidence for chemoautotrophic symbiosis in a Mediterranean cold seep clam (Bivalvia: Lucinidae): comparative sequence analysis of bacterial 16S rRNA, APS reductase and RubisCO genes. FEMS Microbiol Ecol 59:64-70 (2007). PubMed |
| Foti, M., D. Y. Sorokin, B. Lomans, M. Mussman, E. E. Zacharova, N. V. Pimenov, J. G. Kuenen and G. Muyzer: Diversity, activity and abundance of sulfate-reducing bacteria in saline and hypersaline soda lakes. Appl. Environ. Microbiol. 73(7):2093-2100 (2007). PubMed Full Text |
| Fuchs, B. M., S. Spring, H. Teeling, C. Quast, J. Wulf, M. Schattenhofer, S. Yan, S. Ferriera, J. Johnson, F. O. Glöckner, and R. Amann: Characterization of a marine gammaproteobacterium capable of aerobic anoxygenic photosynthesis. PNAS 104(8):2891-2896 (2007). PubMed Full Text |
| Fuchs, B. M., J. Pernthaler, and R. Amann: Chapter 39. Single cell identification by fluorescence in situ hybridization. pp. 886-896, In: Methods for General and Molecular Microbiology, 3rd Edition. C.A. Reddy, T. J. Beveridge, J.A. Breznak, G. Marzluf, T. M. Schmidt, and L. R. Snyder (eds.), ASM Press, Washington D.C. (2007). |
| Lösekann, T., K. Knittel, T. Nadalig, B. Fuchs, H. Niemann, A. Boetius, and R. Amann: Diversity and abundance of aerobic and anaerobic methane oxidizers at the Haakon Mosby mud volcano, Barents Sea. Appl. Environ. Microbiol. 73(10):3348-3362 (2007). PubMed Full Text |
| Mußmann, M., F. Z. Hu, M. Richter, D. de Beer, A. Preisler, B. B. Jørgensen, M. Huntemann, F. O. Glöckner, R. Amann, W. J. H. Koopman, R. S. Lasken, B. Janto, J. Hogg, P. Stoodley, R. Boissy, and G. D. Ehrlich: Insights into the genome of large sulfur bacteria revealed by analysis of single filaments. PLoS Biology 5:1923-1937 (e230) (2007). PubMed Full Text |
| Prast, M., A. Bischoff, U. Waller, R. Amann, and U.-G. Berninger: Impact of ciliates on nitrification and nitrifying bacteria in Baltic Sea sediments. Marine Ecol. Progress Ser. 350:55-61 (2007). MEPS |
| Santos, F., A. Meyerdierks, A. Peña, R. Rosselló-Mora, R. Amann, and P. Antón: Metagenomic approach to the study of halophages: the environmental halophage 1. Environ. Microbiol. 9(7):1711-1723 (2007). PubMed |
| Soria-Carrasco, V., M. Valens-Vadell, A. Peña, J. Antón, R. Amann, J. Castresana, and R. Rosselló-Mora: Phylogenetic position of Salinibacter ruber based on concatenated protein alignments. Syst. Appl. Microbiol. 30:171-179 (2007). PubMed |
| Vila-Costa, M., J. Pinhassi, C. Alonso, J. Pernthaler and R. Simó: An annual cycle of dimethylsulfoniopropionate-sulfur and leucine assimilating bacterioplankton in the coastal NW Mediterranean. Environmental Microbiology 9(10):2451-2463 (2007). PubMed |
| Wakeham, S. G., R. Amann, K. H. Freeman, E. C. Hopmans, B. B. Jørgensen, I. F. Putnam, S. Schouten, J. S. S. Damsté, H. M. Talbot, and D. Woebken: Microbial ecology of the stratified water column of the Black Sea as revealed by a comprehensive biomarker study. Organic Geochemistry 38:2070-2097 (2007). ScienceDirect |
| Woebken, D., B. M. Fuchs, M. M. M. Kuypers, and R. Amann: Potential interactions of particle-associated anammox bacteria with bacterial and archaeal partners in the Namibian upwelling system. Appl. Environ. Microbiol. 73(14):4648-4657 (2007). PubMed Full Text |
| Woebken, D., H. Teeling, P. Wecker, A. Dumitriu, I. Kostadinov, E. F. DeLong, R. Amann, and F. O. Glöckner: Fosmids of novel marine planctomycetes from the Namibian and Oregon coast upwelling systems and their cross-comparison with Planctomycete genomes. ISME J. 1:419-435 (2007). PubMed Full Text |
| Yutin, N., M. T. Suzuki, H. Teeling, M. Weber, J. C. Venter, D. B. Rusch and O. Béjà : Assessing diversity and biogeography of aerobic anoxygenic phototrophic bacteria in surface waters of the Atlantic and Pacific Oceans using the Global Ocean Sampling expedition metagenomes. Environmental Microbiology 9(6):1646-1475 (2007). PubMed |
| Zubkov, M. V., I. Mary, E. M. S. Woodward, P. E. Warwick, B. M. Fuchs, D. J. Scanlan, and P. H. Burkill: Microbial control of phosphate in the nutrient-depleted North Atlantic subtropical gyre. Env. Microbiol. 9(8):2079-2089 (2007). PubMed |
| Gomez, Paola: Diversity and ecological role of marine planktonic Cytophaga/Flavobacteria-like bacteria. Master thesis/ PhD Thesis proposal, MarMic, Universität Bremen, Bremen (2007), 59pp. |
| Meziti, Alexandra: Diversity and detection of Archaea in deep-sea sediments. Master thesis/ PhD Thesis proposal, MarMic, Universität Bremen, Bremen (2007), 59pp. |
| Wietz, Matthias: Microbial communities of larval rearing systems and wild phyllosoma of the ornate rock lobster, Panulirus ornatus, and options for microbial management in aquaculture. Diplomarbeit Universität Bremen, Bremen (2007). |
| Schreiber, Lars: Development of a novel screening method for screening large metagenomic libraries for low-abundance genes. Master thesis, MarMic, Universität Bremen, Bremen (2007), 83pp. |
| Allers, Elke: Response of marine bacterioplankton to experimental manipulation of growth conditions. Dissertation, Universität Bremen, Bremen (2007), 135pp. |
| Prast, Mario: Studies of the impact of food web effects on nitrification in aquatic sediments. Dissertation, Universität Bremen, Bremen (2007), 140pp. |
| Wöbken, Dagmar: Diversity and ecology of marine planctomycetes. PhD thesis, MarMic, Universität Bremen, Bremen (2007), 195pp. |
Genomics Group
| Borriss, M., T. Lombardot, F. O. Glöckner, D. Becher, D. Albrecht, and T. Schweder: Genome and proteome characterization of the psychrophilic Flavobacterium bacteriophage 11b. Extremophiles 11:95-104 (2007). PubMed |
| Field, D., G. Garrity, T. Gray, J. Selengut, P. Sterk, N. Thomson, T. Tatusova, G. Cochrane, F. O. Glöckner, R. Kottmann, A. L. Lister, Y. Tateno, and R. Vaughan: eGenomics: Cataloguing our complete genome collection III. Comparative and Functional Genomics, doi 10.1155/2007/47304 (2007). PMC Full Text |
| Fuchs, B. M., S. Spring, H. Teeling, C. Quast, J. Wulf, M. Schattenhofer, S. Yan, S. Ferriera, J. Johnson, F. O. Glöckner, and R. Amann: Characterization of a marine gammaproteobacterium capable of aerobic anoxygenic photosynthesis. PNAS 104(8):2891-2896 (2007). PubMed Full Text |
| Lombardot, T., R. Kottmann, G. Giuliani, A. de Bono, N. Addor and F. O. Glöckner: MetaLook: a 3D visualisation software for marine ecological genomics. BMC Bioinformatics 8:406/8pp. (2007). PubMed Full Text |
| Mußmann, M., F. Z. Hu, M. Richter, D. de Beer, A. Preisler, B. B. Jorgensen, M. Huntemann, F. O. Glöckner, R. Amann, W. J. H. Koopman, R. S. Lasken, B. Janto, J. Hogg, P. Stoodley, R. Boissy, and G. D. Ehrlich: Insights into the genome of large sulfur bacteria revealed by analysis of single filaments. PLoS. Biol. 5(9): e230 (2007). PubMed Full Text |
| Pruesse, E., C. Quast, K. Knittel, B. Fuchs, W. Ludwig, J. Peplies, and F. O. Glöckner: SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 35(21):7188-7196 (2007). PubMed Full Text |
| Richter, M., M. Kube, D. A. Bazylinski, T. Lombardot, F. O. Glöckner, R. Reinhardt, and D. Schüler: Comparative genome analysis of four magnetotactic bacteria reveals a complex set of group-specific genes implicated in magnetosome biomineralization and function. J. Bacteriol. 189(13): 4899-4910 (2007). PubMed Full Text |
| Vrijenhoek, R. C., M. Duhaime, and W. J. Jones: Subtype Variation Among Bacterial Endosymbionts of Tubeworms (Annelida: Siboglinidae) from the Gulf of California. Biol. Bull. 212:180-184 (2007). PubMed Full Text |
| Woebken, D., H. Teeling, P. Wecker, A. Dumitriu, I. Kostadinov, E. F. DeLong, R. Amann, and F. O. Glöckner: Fosmids of novel marine Planctomycetes from Namibian and Oregon coast upwelling systems and their cross-comparison with planctomycete genomes. ISME Journal 1:419-435 (2007) PubMed Full Text |
| Prüsse, Elmar: Incremental Approach to Multiple Sequence Alignment using Directed Acyclic Graphs (2007). |
| Duhaime, Melissa: Marine Virus Population Dynamics and Genomics: Lessons from the North Atlantic and North Sea. Master thesis, MarMic, University of Bremen, Bremen (2007), 81pp. |
| Kostadinov, Ivaylo: Detection of group specific genes in the phyla Planctomycetes and Bacteroidetes – from comparative genomics to metagenomics. Master thesis, MarMic, University of Bremen, Bremen (2007), 57pp. |
| Wohlrab, Sylke: Analyse differentieller Genexpression bei Rhodopirellula baltica unter Einfluss verschiedener Umweltfaktoren. Diplomarbeit Universität Bremen, Bremen (2007), 93pp. |
Symbiosis Group
| Duperron, S., M. Sibuet, B. J. MacGregor, M.M.M Kuypers, C. R. Fisher, and N. Dubilier: Diversity, relative abundance, and metabolic potential of bacterial endosymbionts in three Bathymodiolus mussel species from cold seeps in the Gulf of Mexico. Environ. Microbiol. 9(6):1423-1438 (2007). PubMed |
| Haase., K. M., S. Petersen, A. Koschinsky, R. Seifert, C. W. Devey, R. Keir, K. S. Lackschewitz, B. Melchert, M. Perner, O. Schmale, J. Süling, N. Dubilier, F. Zielinski, S. Fretzdorff, D. Garbe-Schönberg, U. Westernströer, C. R. German, T. M. Shank, D. Yoerger, O. Giere, J. Kuever, H. Marbler, J. Mawick, C. Mertens, U. Stöber and M. Walter: Young volcanism and related hydrothermal activity at 5°S on the slow-spreading southern Mid-Atlantic Ridge. Geochemistry Geophysics Geosystems 8(11):doi 10.1029/2006GC001509 (2007). Wiley Full Text |
| Musat, N., O. Giere, A. Gieseke, F. Thiermann, R. Amann, and N. Dubilier: Molecular and morphological characterization of the association between bacterial endosymbionts and the marine nematode Astomonema sp. from the Bahamas. Environ. Microbiol. 9(5):1345-1353 (2007). PubMed |
| Pernice, M., S. Wetzel, O. Gros, R. Boucher-Rodoni, and N. Dubilier: Enigmatic dual symbiosis in the excretory organ of Nautilus macromphalus (Cephalopoda: Nautiloidea). Proc. R. Soc. B. 274:1143-1152 (2007). PubMed Full Text |
| Pradillon, F., A. Schmidt, J. Peplies, and N. Dubilier: Species identification of marine invertebrate early stages by whole – larvae in situ hybridisation of 18S ribosomal RNA. Mar. Ecol. Prog. Ser. 333:103-116 (2007). Full Text |
| Raggi, Luciana: Molecular studies of two different bacterial symbioses in invertebrates: diversity and biogeography. Master thesis/ PhD Thesis Proposal, MarMic, University of Bremen, Bremen (2007),38pp. |
Nutrient Group
| Carrigg, C., O. Rice, S. Kavanagh, G. Collins, V. O′Flaherty: DNA extraction method affects microbial community profiles from soils and sediment. Appl. Microbiol. Biotechnol. 77:955-964 (2007). PubMed |
| Coolen, M.J.L., B. Abbas, J. van Blejswijk, E.C. Hopmans, M.M M. Kuypers, S.G. Wakeham and J. S. Sinninghe Damsté: Putative ammonia-oxidizing Crenarchaeota in suboxic waters of the Black Sea: A basinwide ecological study using 16S ribosomal and functional genes and membrane lipids. Environmental Microbiology 9(4):1001–1016 (2007). PubMed |
| Duperron, S., M. Sibuet, B.J. MacGregor, M.M.M. Kuypers, C.R. Fisher, and N. Dubilier: Diversity, relative abundance and metabolic potential of bacterial endosymbionts in three Bathymodiolus mussel species from cold seeps in the Gulf of Mexico. Environmental Microbiology 9(6):1423–1438 (2007). PubMed |
| Francis, C.A., J.M. Beman and M.M.M. Kuypers: New processes and players in the nitrogen cycle: the microbial ecology of anaerobic and archaeal ammonia oxidation. The ISME Journal 1:19–27 (2007). PubMed Full Text |
| Hamersley, M.R., G. Lavik, D. Woebken, J.E. Rattray, P. Lam, E.C. Hopmans, J.S. Sinninghe Damsté, S. Krüger, M. Graco, D. Gutiérrez, and M.M.M. Kuypers: Anaerobic ammonium oxidation in the Peruvian oxygen minimum zone. Limnol. Oceanogr. 52:923–933 (2007). ASLO Full Text |
| Hannig, M., G. Lavik, M.M.M. Kuypers, D. Woebken, W. Martens-Habbena, K. Jürgens: Shift from denitrification to anammox after inflow events in the central Baltic Sea. Limnol. Oceanogr. 52:1336–1345 (2007). Full Text |
| Hinck, S., T.R. Neu, G. Lavik, M. Mussmann, D. de Beer, H.M. Jonkers: Physiological adaptation of a nitrate-storing Beggiatoa sp. to diel cycling in a phototrophic hypersaline mat. Appl. Environ. Microbiol. 73(1):7013-7022 (2007). PubMed Full Text |
| Huettel, M., P. Cook, F. Janssen, G. Lavik, and J.J. Middelburg: Transport and degradation of a dinoflagellate bloom in permeable sublittoral sediment. Marine Ecology Progress Series 340:139-153 (2007). MEPS |
| Kartal, B., M.M.M. Kuypers, G. Lavik, J. Schalk, H.J.M. Op den Camp, M.S.M. Jetten and M. Strous: Anammox bacteria disguised as denitrifiers: Nitrate reduction to dinitrogen gas via nitrite and ammonium. Environmental Microbiology 9(3):635–642 (2007). PubMed |
| Kuypers, M.M.M: Sizing up the uncultivated majority. Science 317:1510-1511 (2007). PubMed |
| Kuypers, M.M.M. and B. Barker Jørgensen: The future of single-cell environmental microbiology (in Crystal ball 2007). Environmental Microbiology 9(1):6-7 (2007). PubMed |
| Lam, P., M.M. Jensen, G. Lavik, D.F. McGinnis, B. Müller, C.J. Schubert, R. Amann, B. Thamdrup, and M.M.M. Kuypers: Linking crenarchaeal and bacterial nitrification to anammox in the Black Sea. PNAS, doi: 10.1073/pnas.061081104 (2007). PubMed Full Text |
| Neretin, L.N., R.M.M. Abed, A. Schippers, C.J. Schubert, K. Kohls, and M.M.M. Kuypers: Inorganic carbon fixation by sulfate-reducing bacteria in the Black Sea water column. Environmental Microbiology, doi: 10.1111/j.1462-2920.2007.01413.x (2007). PubMed |
| Preisler A., D. de Beer, A. Lichtschlag, G. Lavik, A. Boetius, B.B. Jørgensen: Biological and chemical sulfide oxidation in a Beggiatoa inhabited marine sediment. The ISME Journal 1:341-353 (2007). PubMed Full Text |
| Schmid, M.C., Risgaard-Petersen N., van de Vossenberg J., M.M.M. Kuypers, G. Lavik, J. Petersen, S. Hulth, B. Thamdrup, D. Canfield, T. Dalsgaard, S. Rysgaard, M. K. Sejr, M. Strous, H.J. M. Op den Camp and M. S. M. Jetten: Anaerobic ammonium-oxidizing bacteria in marine environments: widespread occurrence but low diversity. Environmental Microbiology 9(6):1476–1484 (2007). PubMed |
| Siegel, H., T. Ohde, M. Gerth, G. Lavik and T. Leipe: Identification of coccolithophore blooms in the SE Atlantic Ocean off Namibia by satellites and in-situ methods. Continental Shelf Research 27:258-274(2007). ScienceDirect |
| Woebken, D., B.M. Fuchs, M.M.M. Kuypers, and Rudolf Amann: Potential Interactions of Particle-Associated Anammox Bacteria with Bacterial and Archaeal Partners in the Namibian Upwelling System. Appl. Envir. Microbiol. 73(14):4648-4657 (2007). PubMed Full Text |