Publications 2005

Publications 2005

Department of Biogeochemistry

Arnosti, C., N. Finke, O. Larsen and S. Ghobria: Anoxic carbon degradation in Arctic sediments: Microbial transformations of complex substrates. Geochimica et Cosmochimica Acta 69(9):2309-2320 (2005). ScienceDirect

Böttcher, M. E. and Jørgensen B. B.: Leben an der Grenze: Die alltägliche Sinnflut. Einblicke (Carl von Ossietzky Universität Oldenburg) 41:19-21 (2005). Full Text

Böttcher, M. E., B. Thamdrup, M. Gehre and A. Theune: 34S/32S and 18O/16O fractionation during sulfur disproportionation by Desulfobulbus propionicus. Geomicrobiology Journal 22:219-226 (2005). TFO

Grice, K., C. Cao, G. D. Love, M. E. Böttcher, R. J. Twitchett, E. Grosjean, R. E. Summons, S. C. Turgeon, W. Dunning and Y. Jin: Photic zone euxinia during the Permian-Triassic superanoxic event. Science 307:706-709 (2005). PubMed Full Text

Grice, K., R. E. Summons, E. Grosjean, R. J. Twitchett, S. X. Wang, W. Dunning and M. E. Böttcher: Depositional conditions of the northern onshore Perth basin (Basal Triassic). Australian Petroleum Product Exploration Association Journal 2005:263-273 (2005).

Jørgensen, B. B., R. N. Glud and O. Holby: Oxygen distribution and bioirrigation in Arctic fjord sediments (Svalbard, Barents Sea). Marine Ecology Progress Series 292:85-95 (2005). MEPS

Jørgensen, B. B., A. Teske and A. Ahmad: Genus VII. Thioploca Lauterborn 1907, 242 ^AL. pp. 171-178, In: Bergey's Manual of Determinative Bacteriology. 2^nd ed., Vol. II, Part B, D.J. Brenner, N.R. Krieg, J.T. Staley, G.M. Garrity (eds.), Springer, NY, USA (2005).

Kolonic, S., Wagner T., Forster A., Damsté J. S. S., Walsworth-Bell B., Erba E., Turgeon S., Brumsack H. J., Chellai E. I., Tsikos H., Kuhnt W., and Kuypers M. M. M.: Black shale deposition on the northwest African Shelf during the Cenomanian/Turonian oceanic anoxic event: Climate coupling and global organic carbon burial. Paleoceanography 20(1): PA1006, doi:10.1029/2003PA000950 (2005) igitur

Nägler, T. F., C. Siebert, H. Lüschen and M. E. Böttcher: Sedimentary Mo isotope record across the Holocene fresh-brackish water transition of the Black Sea. Chemical Geology 219:283-2959 (2005). ScienceDirect

Neumann, T., N. Rausch, T. Leipe, O. Dellwig, Z. Berner and M. E. Böttcher: Intense pyrite formation under low-sulfate conditions in the Achterwasser lagoon, SW Baltic Sea. Geochimica et Cosmochimica Acta 69(14):3619-3630 (2005). ScienceDirect

Parkes, R. J., G. Webster, B. A. Cragg, A. J. Weightman, C. J. Newberry, T. G. Ferdelman, J. Kallmeyer, B. B. Jørgensen, I. W. Aiello and J. C. Fry: Deep sub-seafloor prokaryotes stimulated at interfaces over geological time. Nature 436:390-394 (2005). PubMed

Schippers, A., L. N. Neretin, J. Kallmeyer, T. G. Ferdelman, B. A. Cragg, R. J. Parkes and B. B. Jørgensen: Prokaryotic cells of the deep sub-seafloor biophsere identified as living bacteria. Nature 433:861-864 (2005). PubMed

Schippers, A., L. N. Neretin, G. Lavik, T. Leipe and F. Pollehne: Manganese(II) oxidation driven by lateral oxygen intrusions in the western Black Sea. Geochimica et Cosmochimica Acta 69(9):2241-2252 (2005). ScienceDirect

Schubert, C. J., J. Niggemann, G. Klockgether and T. G. Ferdelman: Chlorin Index: a new parameter for organic matter freshness in sediments. Geochemistry Geophysics Geosystems 6(3), doi: 10.1029/2004GC000837 (2005). Wiley

Schulz, H. N. and B. B. Jørgensen: Genus VI. Thiomargarita Schulz, Brinkhoff, Ferdelman, Hernández Mariné, Teske and Jørgensen 1999b, 1325^VP . pp. 169-171, In: Bergey's Manual of Determinative Bacteriology. 2^nd ed., Vol. II, Part B, D.J. Brenner, N.R. Krieg, J.T. Staley, G.M. Garrity (eds.), Springer, NY, USA (2005).

Master thesis

Robador, Alberto: Responses in activity and community composition of sulfate-reducing bacteria to moderate temperature changes in Svalbard sediments (Arctic Ocean). Master Thesis, MarMic, University of Bremen, Bremen (2005), 39pp.

Ph. D. theses

Niggemann, Jutta: Composition and degradation of organic matter in sediments from the Peru-Chile upwelling region. Dissertaion Universität Bremen, Bremen (2005), 206pp.

Nüster, Jochen: New Methods in Biogeochemistry: The development of electrochemical tools for the measurement of dissolved and solid state compounds in natural system. Dissertaion Universität Bremen, Bremen (2005), 199pp.

Preisler, André: Beggiatoa – the ecophysiological significance of large, white, filamentous sulfur oxidizers within the nitrogen and the sulfur cycle. Dissertation Universität Bremen, Bremen (2005), 93pp.

Vandieken, Verona: Microbiological and biogeochemical studies of microbial Mn(IV) and Fe(III) reduction in Arctic sediments (Svalbard). Dissertaion Universität Bremen, Bremen (2005), 163pp.

Microbial Habitat Group

Boetius, A.: Microfauna - macrofauna interaction in the seafloor: lessons from the tubeworm. PLOS Biology 3(3):0375-0378 (2005). PubMed Full Text

Boetius, A.: Lost City Life. Science 307:1420-1422 (2005). Sciencemag

Bühring, S. I., M. Elvert and U. Witte: The microbial community structure of different permeable sandy sediments characterized by the investigation of bacterial fatty acids and fluorescence in situ hybridization. Environmental Microbiology 7(2):281-293 (2005). PubMed

Elvert, M., E. C. Hopmans, T. Treude, A. Boetius, E. Suess: Spatial variations of methanotrophic consortia at cold methane seeps: implications from a high-resolution molecular and isotopic approach. Geobiology 3(3):195-209 (2005). Wiley

Glud, R. N., F. Wenzhöfer, A. Tengberg, M. Middelboe, K. Oguri and H. Kitazato: Distribution of oxygen in surface sediments from central Sagami Bay, Japan: In situ measurements by microelectrodes and planar optodes. Deep-Sea Research I 52:1974-1987 (2005). ScienceDirect

Hoffmann, F., O. Larsen, H. T. Rapp and R. Osinga: Oxygen dynamics in choanosomal sponge explants. Marine Biology Research 1:160-163 (2005). WageningenUR

Hoffmann, F., O. Larsen, V. Thiel, H. T. Rapp, T. Pape, W. Michaelis and J. Reitner: An anaerobic world in sponges. Geomicrobiology Journal 22:1-10 (2005). ResearchGate

Janssen, F., P. Faerber, M. Huettel, V. Meyer and U. Witte: Pore-water advection and solute fluxes in permeable marine sediments (I): calibration and performance of the novel benthic chamber system Sandy. Limnology and Oceanography 50(3):768-778 (2005). ASLO Full Text

Janssen, F., M. Huettel and U. Witte: Pore-water advection and solute fluxes in permeable marine sediments (II): Benthic respiration at three sandy sites with different permeabilities (German Bight, North Sea). Limnology and Oceanography 50(3):779-792 (2005). ASLO Full Text

Niemann, H., M. Elvert, M. Hovland, B. Orcutt, A. Judd, I. Suck, J. Gutt, S. Joye, E. Damm, K. Finster and A. Boetius: Methane emission and consumption at a North Sea gas seep (Tommeliten area). Biogeosciences 2:335-351 (2005). Biogeosciences Full Text

Orcutt, B., A. Boetius, M. Elvert, V. Samarkin and S. B. Joye: Molecular biogeochemistry of sulfate reduction, methanogenesis and the anaerobic oxidation of methane at Gulf of Mexico cold seeps. Geochimica et Cosmochimica Acta 69(17):4267-4281 (2005). ScienceDirect

Røy, H., M. Huettel and B. B. Jørgensen: The influence of topography on the functional exchange surface of marine soft sediments, assessed from sediment topography measured in situ. Limnology and Oceanography 50(1):106–112 (2005). ASLO Full Text

Tarpgaard, I.H., A. Boetius and K. Finster: Desulfobacter psychrotolerans sp. nov., a new psychrotolerant sulfate-reducing bacterium and descriptions of its physiological response to temperature changes. Antonie van Leeuwenhoek (doi 10.1007/s10482-005-9014-1) (2005). PubMed

Treude, T., K. Knittel, M. Blumenberg, R. Seifert and A. Boetius: Subsurface microbial methanotrophic mats in the Black Sea. Applied and Environmental Microbiology 71(10):6375-6378 (2005). PubMed Full Text

Treude, T., M. Krüger, A. Boetius and B. B. Jørgensen: Environmental control on anaerobic oxidation of methane in the gassy sediments of Eckernförde Bay (German Baltic). Limnology and Oceanography 50(6):1771-1786 (2005). ASLO Full Text

Treude, T., J. Niggemann, J. Kallmeyer, P. Wintersteller, C. J. Schubert, A. Boetius and B. B. Jørgensen: Anaerobic oxidation of methane and sulfate reduction along the Chilean continental margin. Geochimica et Cosmochimica Acta 69(11):2767-2779 (2005). ScienceDirect

Vopel, K., D. Thistle, J. Ott, M. Bright and H. Røy: Wave-induced H₂S flux sustains a chemoautotrophic symbiosis. Limnology and Oceanography 50(1):128-133 (2005). AUT Full Text

Wild, C., M. Rasheed, C. Jantzen, P. Cook, U. Struck, M. Huettel and A. Boetius: Benthic metabolism and degradation of natural particulate organic matter in carbonate and silicate reef sands of the northern Red Sea. Marine Ecology Progress Series 298:69-78 (2005). MEPS

Wild, C., H. Røy and M. Huettel: Role of pelletization in mineralization of fine grained coastal sediments. Marine Ecology Progress Series 291:23–33 (2005). MEPS

Wild, C., H. Woyt and M. Huettel: Influence of coral mucus on nutrient fluxes in carbonate sands. Marine Ecology Progress Series 287:87–98 (2005). MEPS

Diploma and M.Sc theses

Duarte, Joana: Processes related to geo-biosphere interactions in marine sediments of the Gulf of Cadiz (2005).

Dunker, Rita: Microsensor studies on a Beggiatoa mat under changing oxygen concentrations. Master Thesis, MarMic, University of Bremen, Bremen (2005), 51pp.

Felden, Janine: Tracing changes in the community structure in sediments of the Haakon Mosby Mud Volcano (HMMV) by molecular and biogeochemical methods. Master Thesis University of Bremen, Bremen (2005), 63pp.

Naumann, Malik: The role of coral mucus in scavenging picoplankton as a food source for benthic passive suspension feeders (2005). Shovitri, Maya: Biogeochemistry and molecular ecology of sandy sediment from a North Sea gas seep. Master Thesis, MarMic, University of Bremen, Bremen (2005), 42pp.

Ph.D. theses

Billerbeck, Markus: Pore Water Transport and Microbial Activity in Intertidal Wadden Sea Sediments. Dissertation Universität Bremen, Bremen (2005), 203pp.

Niemann, Helge: Rates and signatures of methane turnover in sediments of continental margins. PhD thesis, MarMic, Universität Bremen, Bremen (2005), 305pp .

Mathematical Modeling Group

Goharzadeh, A., A. Khalili and B. B. Jørgensen: Transition layer thickness at a fluid-porous interface. Physics of Fluids 17:057102 (2005). AIP

Stöhr, M. and K. Roth: Gradient-Based Estimation of Local Parameters for Flow and Transport in Heterogeneous Porous Media. Water Resources Research 41:W08401 (2005). Wiley Full Text

Microsensor Group

Abed, R. M. M. and S. Grötzschel: Applications of denaturing gradient gel electrophoresis and microsensor techniques in oil biodegradation studies. pp. 75-91, In: Oil Pollution and its Environmental Impact in the Arabian Gulf Region. Al Azab, M., W. El-Shorbagy and S. Al-Ghais (eds.), Elsevier (2005). ScienceDirect

Abed, R. M. M. and J. Köster: The direct role of aerobic heterotrophic bacteria associated with cyanobacteria in the degradation of oil compounds. International Biodeterioration and Biodegradation 55:29-37 (2005). ScienceDirect

Al-Horani, F.A., T. Ferdelman, S. M. Al-Moghrabi and D. de Beer: Spatial distribution of calcification and photosynthesis in the scleractinian coral Galaxea fascicularis. Coral Reefs 24:173-180 (2005). Springer

Blue, R., N. Kent, L. Polerecky, H. McEvoy, D. Gray and B. D. MacCraith: Platform for enhanced detection efficiency in luminescence-based sensors. Electronics Letters 41(12):682-684 (2005). IEEexplore

Collins, G., L. O'Connor, T. Mahony, A. Gieseke, D. de Beer and V. O'Flaherty: Distribution, localization and phylogeny of abundant populations of Crenarchaeoty in anaerobic granular sludge. Applied and Environmental Microbiology 71(11):7523-7527 (2005). PubMed Full Text

Cytryn, E., D. Minz, I. Gelfand, A. Neori, A. Gieseke, D. de Beer and J. van Rijn: Sulfide oxidizing activity and bacterial community structure in a fluidized bed reactor from a zero-discharge mariculture system. Environmental Science and Technology 39:1802-1810 (2005). PubMed Full Text

Cytryn, E., J. van Rijn, A. Schramm, A. Gieseke, D. de Beer and D. Minz: Identification of bacteria potentially responsible for oxic and anoxic sulfide oxidation in biofilters of a recirculating mariculture system. Applied and Environmental Microbiology 71:6134-6141 (2005). PubMed Full Text

Gieseke, A., J. Nielsen, R. Amann, P.H. Nielsen and D. de Beer: In situ substrate conversion and assimilation by nitrifying bacteria in a model biofilm. Environmental Microbiology 7(9):1392–1404 (2005). PubMed

Hölker F. and Stief, P.: Adaptive behaviour of chironomid larvae (Chironomus riparius) in response to chemical stimuli from predators and resource density. Behavioral Ecology and Sociobiology 58:256-263 (2005). Springer

Köhler-Rink, S. and M. Kühl: The chemical microenvironment of the symbiotic planktonic foraminifer Orbulina universa. Mar. Biol. Res. 1:68-78 (2005). UTSePress

Ludwig, R., F. A. Al-Horani, D. de Beer and H. M. Jonkers: Photosynthesis controlled calcification in a hypersaline microbial mat. Limnology and Oceanography 50(6):1836-1843 (2005). ASLO Full Text

McEvoy H. M. , R. Blue, N. Kent, L. Polerecky, C. Mc Donagh, B.D. Mc Craith: Novel polymer platform for enhanced biochip performance. Proc. SPIE 5826(512):512-519 (2005). SPIE

Polerecky, L., U. Franke, U. Werner, B. Grunwald and D. de Beer: High spatial resolution measurement of oxygen consumption rates in permeable sediments. Limnology and Oceanography Methods 3:75-85 (2005). ASLO Full Text

Stief, P. and G. Becker: Structuring of epilithic biofilms by the caddisfly Tinodes rostocki: photosynthetic activity and photopigment distribution in and beside larval retreats. Aquatic Microbial Ecology 38:71-79 (2005). AME

Stief, P., L. Nazarova and D. de Beer: Chimney construction by Chironomus riparius larvae in response to hypoxia:Microbial implications for freshwater sediments. JNABS 24(4):858-871 (2005). BioOne

Stoodley, P., I. Dodds, D. de Beer, H. Lappin Scott and J. D. Boyle: Flowing biofilms as a transport mechanism for biomass through porous media under laminar and turbulent conditions in a laboratory reactor system. Biofouling 21(3/4):161–168 (2005). PubMed

Diploma and M.Sc theses

Kohls, Katharina: Molecular characterization of bacterial communities in microbial mats from an extreme environment (2005). da Purificação, Rodrigo C.: Diatoms and green algae in an intertidal area: seasonal and areal distribution and response to sulfide (2005).

Ph.D. theses

Franke, Ulrich: Applications of planar oxygen optodes in biological aquatic systems. Dissertation Universität Bremen, Bremen (2005), 183pp.

Werner, Ursula: Microbial activity and transport processes in near-shore, permeable sediments. Dissertation Universität Bremen, Bremen (2005), 233pp.

Department of Microbiology

Albrecht, M., V. Janke, S. Sievers, U. Siegner, D. Schüler, and U. Heyen: Scanning Force Microscopy Study of Biogenic Nanoparticles for Medical Applications. J. Magnetism Magnetic Materials 290-291:269-271 (2005). ScienceDirect

Arató, B., Z. Szányi, C. Flies, D. Schüler, R. B. Frankel, P. R. Buseck, and M. Pósfai: Crystal-size and shape distributions of magnetite from uncultured magnetotactic bacteria as a potential biomarker. American Mineralogist 90:1233-1241 (2005). AM

Brinkhoff, T., Kuever J., Muyzer G. and H.W. Jannasch: Genus VI. Thiomicrospira Kuenen and Veldkamp 1927, 253^AL . pp. 193-199, In: Bergey's Manual of Determinative Bacteriology. 2^nd ed., Vol. II, Part B, D.J. Brenner, N.R. Krieg, J.T. Staley, G.M. Garrity (eds.), Springer, NY, USA (2005).

Eller, G., P. Deines, J. Grey, H.-H. Richnow and M. Krüger: Methane cycling in lake sediments and its influence on chironomid larvae δ¹³C. FEMS Microbiology Ecology 54:339-350 (2005). PubMed

Eberbeck, D., V. Janke, S. Hartwig, U. Heyen, D. Schüler, M. Albrecht, and L. Trahms: Blocking of Magnetic Moments of Magnetosomes Measured by Magnetorelaxometry and Direct Observation by Magnetic Force Microscopy. J. Magnetism Magnetic Materials 289:70-73 (2005). ScienceDirect

Flies, C.B., J. Peplies and D. Schüler: Combined approach for characterization of uncultivated magnetotactic bacteria from various aquatic environments. Applied and Environmental Microbiology 71(5):2723-2731 (2005). PubMed Full Text

Flies, C., H.M. Jonkers, D. deBeer, K. Bosselmann, M.E. Böttcher, and D. Schüler: Diversity and vertical distribution of magnetotactic bacteria along chemical gradients in freshwater microcosms. FEMS Microbiol. Ecol. 52:185-195 (2005). PubMed

Gade, D., J. Gobom and R. Rabus: Proteomic analysis of carbohydrate catabolism and regulation in the marine bacterium Rhodopirellula baltica. Proteomics 5:3672-3683 (2005) . PubMed

Gade, D., Stührmann, T., Reinhardt, R. and R. Rabus: Growth phase dependent regulation of protein composition in Rhodopirellula baltica. Envionmental Microbiology 7(8):1074-1084 (2005) . PubMed

Gade, D., D. Theiss, D. Lange, E. Mirgorodskaya, T. Lombardot, F.O. Glöckner, M. Kube, R. Reinhardt, R. Amann, H. Lehrach, R. Rabus and J. Gobom: Towards the proteome of the marine bacterium Rhodopirellula baltica: mapping the soluble proteins. Proteomics 5:3654-3671 (2005) . style="color: black;" PubMed

Hergt, R., R. Hiergeist, M. Zeisberger, D. Schüler, U. Heyen, I. Hilger, and W. A. Kaiser: Magnetic properties of bacterial magnetosomes as potential diagnostic and therapeutic tools. J. Magnetism Magnetic Materials 293:80-86 (2005). ScienceDirect

Koch, B.P., J. Harder, R. J. Lara and G.Kattner: The effect of selective microbial degradation on the composition of mangrove derived pentacyclic triterpenols in surface sediments. Organic Geochemistry 36:273-285 (2005) . ScienceDirect

Krüger, M. and T. Treude: New insights into the physiology and regulation of the anaerobic oxidation of methane. pp. 303-320, In: Microorganisms and earth systems - Advances in Geomicrobiology. Gadd, G. M., Semple, K. T. and Lappin-Scott, H. M. (eds.), SGM Microbiology 65, G. M. Gadd, K. T. Temple and H. M. Lappin-Scott (eds.), Cambridge University Press (2005).

Krüger, M., T. Treude, H. Wolters, K. Nauhaus and A. Boetius: Microbial methane turnover in different marine habitats. Palaeogeography, Palaeoclimatology, Palaeoecology 227:6-17 (2005). ScienceDirect

Kube, M., A. Beck, A. Meyerdierks, R. Amann, R. Reinhardt and R. Rabus: A catabolic gene cluster for anaerobic benzoate degradation in methanotrophic microbial Black Sea mats. Systematic and Applied Microbiology 28:287-294 (2005) . PubMed

Kuehner, S., L. Wöhlbrand, I. Fritz, W. Wruck, C. Hultschig, P. Hufnagel, M. Kube, R. Reinhardt and R. Rabus: Substrate-dependent regulation of anaerobic degradation pathways for toluene and ethylbenzene in a denitrifying bacterium, strain EbN1. Journal of Bacteriology 187(4):1493-1503 (2005) . PubMed Full Text

Nauhaus, K., T. Treude, A. Boetius and M. Krüger: Environmental regulation of the anaerobic oxidation of methane: A comparison of ANME-I or -II communities. Environmental Microbiology 7(1):98-106 (2005).

Rabus, R.: Biodegradation of hydrocarbons under anoxic conditions. pp. 277-299, In: Petroleum Microbiology, Ollivier, B. and M. Magot (eds.), ASM Press, Washington, D.C. (2005). ScienceDirect

Rabus, R.: Functional genomics of an anaerobic aromatic-degrading denitrifying bacterium, strain EbN1. Applied Microbiology and Biotechnology 68:580-587 (2005). PubMed

Rabus, R., M. Kube, J. Heider, A. Beck, K. Heitmann, F. Widdel and R. Reinhardt: The genome sequence of an anaerobic aromatic-degrading denitrifying bacterium, strain EbN1. Archives of Microbiology 183:27-36 (2005). PubMed Full Text

Schüler, D.: Nanokristalle für die Magnetfeldorientierung: Biomineralisation von Magnetosomen in Bakterien. Biospektrum 3/11:291-294 (2005). Full Text

Schübbe, S., C. Würdemann, J. Peplies, U. Heyen, C. Wawer, F. O. Glöckner, and D. Schüler: Transcriptional organization and regulation of magnetosome operons in Magnetospirillum gryphiswaldense. AEM 72(9):5757-5765 (2005). PubMed Full Text

Schultheiss, D., R. Handrick, D. Jendrossek, M. Hanzlik and D. Schüler: The presumptive magnetosome protein Mms16 is a poly(3-hydroxybutyrate) granule-bound protein (phasin) in Magnetospirillum gryphiswaldense. Journal of Bacteriology 187(7):2416-2425 (2005). PubMed Full Text

Schultheiss, D., R. Handrick, D. Jendrossek, M. Hanzlik and D. Schüler: The presumptive magnetosome protein Mms 16 is a poly(3-hydroxybutyrate) granule-bound protein (phasin) in Magnetospirillum gryphiswaldense. Journal of Bacteriology 187:2416-2425 (2005). PubMed Full Text

Ullrich, S., M. Kube, S. Schübbe, R. Reinhardt and D. Schüler: A hypervariable 130-kilobase genomic region of Magnetospirillum gryphiswaldense comprises a magnetosome island which undergoes frequent rearrangements during stationary growth. Journal of Bacteriology 187(21):7176-7184 (2005). PubMed Full Text

Contribution in collected edition

Kuever, J., Rainey, F.A., Widdel, F.: Class IV. Deltaproteobacteria. , pp. 922; Order I. Desulfurellales. pp. 922; Family I. Desulfurellaceae. pp. 923-924; Order II. Desulfovibrionales. pp. 925-926; Family I.. Desulfovibrionaceae. pp. 926; Genus I. Desulfovibrio. pp. 926-938; Family II.. Desulfomicrobiaceae. pp. 944; Family III. Desulfohalobiaceae. pp. 948-949; Genus III. Desulfothermus. pp. 955-956; Family IV. Desulfonatronumaceae. pp. 956; Order III Desulfobacterales. pp. 959; Family I. Desulfobacteraceae. pp. 959-960; Genus I. Desulfobacter. pp. 961-964; Genus II. Desulfobacterium. pp. 965-967; Genus III. Desulfobacula. pp. 968-969; Genus IV. Desulfobotulus. pp. 970-971; Genus VI. Desulfococcus. pp. 972-974; Genus VII. Desulfofaba. pp. 975-976; Genus VIII. Desulfofrigus. pp. 976-977; Genus IX. Desulfonema. pp. 977-981Genus X. Desulfosarcina. pp. 981-984; Genus XII. Desulfotignum. pp. 987-988; Family II. Desulfobulbaceae. pp. 988; Genus I. Desulfobulbus. pp. 988-992; Genus II. Desulfocapsa. pp. 992-994; Genus IV. Desulforhopalus. pp. 995-997; Genus V. Desulfotalea. pp. 997-999; Order IV. Desulfarcales. pp. 1003; Family I. Desulfarculaceae. pp. 1003; Genus I. Desulfarculus. pp. 1004-1005; Order V. Desulfuromonales. pp. 1005-1006; Family I. Desulfuromonaceae. pp. 1006; Genus I. Desulfuromonas. pp. 1007-1010; Order VI. Syntrophobacterales. pp. 1021; Family I. Syntrophobacteraceae. pp. 1021; Genus III. Desulforhabdus. pp. 1029-1030; Genus IV. Desulfovirga. pp. 1030-1031; Family II. Syntrophaceae. pp. 1033; Genus I. Syntrophus. pp. 1033-1035; In: D.J. Brenner, N.R. Krieg, J.T. Staley and G. M. Garrity (eds), Bergey’s Manual of Systematic Bacteriology, second edition, Vol. 2 (The Proteobacteria), part C (The Alpha-, Beta-, Delta-, and Epsilonproteobacteria), Springer, New York, (2005). Full Text

Kuever, J. and B. Schink: Genus III. Malonomonas. pp. 1012-1013, In: D.J. Brenner, N.R. Krieg, J.T. Staley and G. M. Garrity (eds), Bergey’s Manual of Systematic Bacteriology, second edition, Vol. 2 (The Proteobacteria), part C (The Alpha-, Beta-, Delta-, and Epsilonproteobacteria), Springer, New York, (2005). Full Text

Schüler, D., and K.H. Schleifer: Genus IV. The genus Magnetospirillum Schleifer, Schüler and Ludwig 1992, 291^VP. pp. 28-31, In: D.J. Brenner, N.R. Krieg, J.T. Staley and G. M. Garrity (eds.), Bergey’s Manual of Systematic Bacteriology, second edition, Vol. 2 (The Proteobacteria), part C (The Alpha-, Beta-, Delta-, and Epsilonproteobacteria), Springer, New York, (2005). Full Text

Diploma and M.Sc theses

Bakr, Alaa Eldin Ali Nour Ali: Bacterial communities in coastal surface waters along the Egyptian Mediterranean coast (2005).

Basen, Mirko: Archaeal and bacterial populations in the Skagerrak seep (2005).

Gärdes, Astrid: Deletionsmutagenese eines Magnetosomenproteins in Magnetospirillum gryphiswaldense unter Etablierung des Cre-loxP-Systems. Diplomarbeit. Fachhochschule Emden (2005).

Hube, Annina E.: Untersuchungen zur Zusammensetzung der Bakteriengemeinschaft auf der antarktischen Eisdiatomee Amphiprora kufferathiiMANGUIN (2005).

Käne, Layla l: Characterization and isolation of key enzymes from anaerobically methane-oxidizing mats (2005).

Liebner, Susanne: Dynamic, Adaptation and Phylogenetic Characterisation of Methanotrophic Communities in Siberian Permafrost Soils. MarMic, MSc and PhD proposal, University of Bremen (2005), 45pp.

Neogi, Sucharit Basu: Occurrence, survival and diversity of vibrios along a gradient of brackish to freshwater in Karnaphuli river estuary, Bangladesh (2005).

Schauer, Regina: Molekulare Charakterisierung der Sedimentmikroorganismen der drei abyssalen Becken, Kapbecken, Angolabecken und Guineabecken, des Südatlantiks (2005).

Ph.D. theses

Grünberg, Karen: Biochemische und molekularbiologische Untersuchung der Magnetosomenmembran von Magnetospirillum gryphiswaldense. Dissertation Universität Bremen, Bremen (2005), 101pp.

Kühner, Simon : Untersuchungen zur Regulation der anaeroben Verwertung von Alkylbenzolen im denitrifizierenden Stamm EbN1. Dissertation Universität Bremen, Bremen (2005), 230pp.

Musat, Florin: Physiological investigations of aerobic petroleum degradation in marine sediment microcosms. Dissertation Universität Bremen, Bremen (2005), 134pp.

Schübbe, Sabrina: Untersuchungen zur molekularen Organisation und Regulation der mam-Gene in Magnetospirillum gryphiswaldense MSR-1. Dissertation Universität Bremen, Bremen (2005), 167pp.

Department of Molecular Ecology

Amann, R. and K. H. Schleifer: Nucleic acid probes and their application in Environmental Microbiology. pp.67-82, In: Bergey’s Manual for Systematic Bacteriology. Vol. 1, 2^nd edition, D.R. Boone, R.W. Castenholz (eds.), Springer, New York, Berlin, Heidelberg (2005). Springer

Alonso, C. and J. Pernthaler: Incorporation of Glucose under Anoxic Conditions by Bacterioplankton from Coastal North Sea Surface Waters. Applied and Environmental Microbiology 71(4):1709-1716 (2005). PubMed Full Text

Beardsley, C., K. Knittel, R. Amann and J. Pernthaler: Quantification and distinction of aplastidic and plastidic marine nanoplankton by fluorescence in situ hybridization. Aquatic Microbial Ecology 41:163-169 (2005). AME

Blazejak, A., C. Erséus, R. Amann and N. Dubilier: Coexistence of bacterial sulfide oxidizers, sulfate reducers, and spirochetes in a gutless worm (Oligochaeta) from the Peru Margin. Applied and Environmental Microbiology 71(3):1553-1561 (2005). PubMed Full Text

Duperron, S., T. Nadalig, J.-C. Caprais, M. Sibuet, A. Fiala-Médioni, R. Amann and N. Dubilier: Dual symbiosis in a Bathymodiolus mussel from a methane seep on the Gabon continental margin (Southeast Atlantic): 16S rRNA phylogeny and distribution of the symbionts in gills. Applied and Environmental Microbiology 71(4):1694-1700 (2005). PubMed Full Text

Fuchs, B. M., D. Woebken, M. V. Zubkov, P. Burkill and R. Amann: Molecular identification of picoplankton populations in contrasting waters of the Arabian Sea. Aquatic Microbial Ecology 39:145-157 (2005). AME

Herndl, G. J., T. Reinthaler, E. Teira, H. van Aken, C. Veth, A. Pernthaler and J. Pernthaler: Contribution of Archaea to Total Prokaryotic Production in the Deep Atlantic Ocean. Applied and Environmental Microbiology 71(5):2303-2309 (2005). PubMed Full Text

Kämpfer, P., R. Schulze, U. Jäckel, K. A. Malik, R. Amann and S. Spring: Hydrogenophaga defluvii sp. nov. and Hydrogenophaga atypica sp. nov., isolated from activated sludge. International Journal of Systematic and Evolutionary Microbiology 55:341-344 (2005). PubMed Full Text

Knittel, K., J. Kuever, A. Meyerdierks, R. Meinke, R. Amann and T. Brinkhoff: Thiomicrospira arctica sp. nov. and Thiomicrospira psychrophila sp. nov., psychrophilic, obligately chemolithoautotrophic, sulfur-oxidizing bacteria isolated from marine Arctic sediments. International Journal of Systematic and Evolutionary Microbiology 55:781-786 (2005). PubMed Full Text

Knittel, K., T. Lösekann, A. Boetius, R. Kort and R. Amann: Diversity and distribution of methanotrophic archaea at cold seeps. Applied and Environmental Microbiology 71(1):467-479 (2005). PubMed Full Text

Kumar, Y., R. Westram, S. Behrens, B. Fuchs, F. O. Glöckner, R. Amann, H. Meier and W. Ludwig: Graphical representation of ribosomal RNA probe accessibility data using ARB software package. BMC Bioinformatics 6: 61 (doi:10.1186/1471-2105-6-61) (2005). PubMed Full Text

Meyerdierks, A., M. Kube, T. Lombardot, K. Knittel, M. Bauer, F. O. Glöckner, R. Reinhardt and R. Amann: Insights into the genomes of archaea mediating the anaerobic oxidation of methane. Environmental Microbiology 7(12):1937-1951 (2005). PubMed

Mindl, B., B. Sonntag, J. Pernthaler, J. Vrba, R. Psenner and T. Posch: Effects of phosphorus loading on interactions of algae and bacteria: reinvestigation of the ‘phytoplankton–bacteria paradox’ in a continuous cultivation system. Aquatic Microbial Ecology 38:203-213 (2005). AME

Mußmann, M., K. Ishii, R. Rabus, and R. Amann: Diversity and vertical distribution of cultured and uncultured Deltaproteobacteria in an intertidal mud flat of the Wadden Sea. Environmental Microbiology 7(3):405-418 (2005). PubMed

Mußmann, M., M. Richter, T. Lombardot, A. Meyerdierks, J. Kuever, M. Kube, F. O. Glöckner and R. Amann: Clustered genes related to sulfate respiration in uncultured prokaryotes support the theory of their concomitant horizontal transfer. Journal of Bacteriology 187(20):7126–7137 (2005). PubMed Full Text

Peña, A., M. Valens, F. Santos, S. Buczolits, J. Antón, P. Kämpfer, H.-J. Busse, R. Amann and R. Rosselló-Mora: Intraspecific comparative analysis of the species Salinibacter ruber. Extremophiles 9:151-161 (2005). PubMed

Pernthaler, J.: Predation on prokaryotes in the water column and its ecological implications. Nat. Rev. Micro. 3:537-546 (2005). PubMed

Pernthaler, J. and R. Amann: Fate of heterotrophic microbes in pelagic habitats: focus on populations. Microbiol. Mol. Biol. Rev. 69(3):440-461 (2005). PubMed Full Text

Pernthaler, A. and J. Pernthaler: Diurnal variation of cell proliferation in three bacterial taxa from coastal North Sea waters. Applied and Environmental Microbiology 71(8):4638-4644 (2005). PubMed Full Text

Salcher, M. M., J. Pernthaler, R. Psenner and T. Posch: Succession of bacterial grazing defense mechanisms against protistan predators in an experimental microbial community. Aquatic Microbial Ecology 38:215–229 (2005). AME

Urakawa, H., N. Dubilier, Y. Fujiwara, D. E. Cunningham, S. Kojima and D. A. Stahl: Hydrothermal vent gastropods from the same family (Provannidae) harbour ε- and γ-proteobacterial endosymbionts. Environmental Microbiology 7: 750-754 (2005). PubMed

Warnecke, F., R. Sommaruga, R. Sekar, J. S. Hofer and J. Pernthaler: Abundances, Identity, and Growth State of Actinobacteria in Mountain Lakes of Different UV Transparency. Applied and Environmental Microbiology 71(1):5551-5559 (2005). PubMed Full Text

Diploma and M.Sc theses

Rotaru , Amelia: Genomic analysis of the endosymbiotic communities of a gutless marine worm (Olavius algarvensis). Master thesis, MarMic, Universität Bremen, Bremen (2005), 59pp.

Serrano , Wilbert: Characterization of a purple sulfur bacterium, strain SW26 isolated from Sylt (Wadden Sea). Master thesis, MarMic, Universität Bremen, Bremen (2005). Shovitri, Maya: Biogeochemistery and molecular ecology of sandy sediment from a North Sea gas seep. Master thesis, MarMic, Universität Bremen, Bremen (2005), 42pp.

Ph.D. theses

Alonso, Cecilia: Identity and activity of marine microbial populations as revealed by single cell techniques. PhD thesis, MarMic, Universität Bremen, Bremen (2005), 151pp.

Blazejak, Anna: Phylogenetic and functional characterization of symbiotic bacteria in gutless marine worms (Annelida, Oligochaeta). Dissertation Universität Bremen, Bremen (2005), 167pp.

Burkert, Ulrike: Mikrobielle Aktivität in dem huminstoffreichen Moorsee Große Fuchskuhle. Dissertation Universität Bremen, Bremen (2005), erschienen 2006, 119pp.

Duperron, Sebastien: Symbioses bactériennes de bivalves mytilidés associés aux sources de fluides en domaine océanique profond : diversité, rôle nutritionnel et influence de l’environnement. (Bacterial symbioses in mytilid bivalves associated with cold seeps and hydrothermal vents: diversity, nutritional role, and influence of the environment.) PhD thesis, MarMic, Universität Bremen (2005), 226pp.

Microbial Genomics Group

Babenzien, H.-D., F. O. Glöckner and I. M. Head:Genus II. Genus Achromatium Schewiakoff 1893, 1^AL. pp. 142-147, In: Bergey's Manual of Determinative Bacteriology. 2^nd ed., Vol. II, Part B, D.J. Brenner, N.R. Krieg, J.T. Staley, G.M. Garrity (eds.), Springer, NY, USA (2005). Gade, D., D. Theiss, D. Lange, E. Mirgorodskaya, T. Lombardot, F. O. Glöckner, M. Kube, R. Reinhardt, R. Amann, H. Lehrach, R. Rabus and J. Gobom: Towards the proteome of the marine bacterium Rhodopirellula baltica: Mapping the soluble proteins. Proteomics 5:3654-3671 (2005). PubMed

Gernert, C., F. O. Glöckner, G. Krohne and U. Hentschel: Microbial diversity of the freshwater sponge Spongilla lacustris. Microbiology Ecology 50:206-212 (2005). PubMed

Lombardot, T., M. Bauer, H. Teeling, R. Amann and F. O. Glöckner: The transcriptional regulator pool of the marine bacterium Rhodopirellula baltica SH1^T as revealed by whole genome comparisons. FEMS Microbiology Letters 242:137-145 (2005). PubMed

Wallner, S. R., M. Bauer, C. Würdemann, P. Wecker, F. O. Glöckner and K. Faber: Highly enantioselective sec-Alkyl Sulfatase activity of the marine Planctomycete Rhodopirellula baltica shows retention of configuration. Angewandte Chemie,. International Edition 44:6381-6384 (2005). PubMed

M.Sc theses

Kottmann, Renzo: Data Acquisition, Design and Implementation of an Integrative Database for Metagenomics. Master thesis, MarMic, University of Bremen, Bremen (2005), 47pp.

Nutrient Group

Hamersley, M. R. and B. L. Howes: Coupled nitrification-denitrification measured in situ in a Spartina alterniflora marsh with a ¹⁵NH₄⁺tracer. Marine Ecology Progress Series 299:123-135 (2005). MEPS

Hamersley, M. R. and B. L. Howes: An Evaluation of the N₂ flux approach for measuring sediment denitrification. Estuarine, Coastal, and Shelf Science 62:711-723 (2005). ScienceDirect

Kolonic S., T. Wagner, A. Forster, J. S. S. Damsté, B. Walsworth- Bell, E. Erba, S. Turgeon, H. J. Brumsack, E. H. Chellai, H. Tsikos, W. Kuhnt and M. M. M. Kuypers: Black shale deposition on the northwest African Shelf during the Cenomanian/Turonian oceanic anoxic event: Climate coupling and global organic carbon burial. Paleoceanography 20(1) PA1006 10.1029/2003PA000950 (2005). UU Full Text

Kuypers, M. M. M., G. Lavik, D. Woebken, M. Schmid, B. M. Fuchs, R. Amann, B. Barker Jørgensen and M. S. M. Jetten: Massive nitrogen loss from the Benguela upwelling system through anaerobic ammonium oxidation. PNAS 102(18):6478-6483 (2005). PubMed Full Text

Manske, A. K., J. Glaeser, M. M. M. Kuypers and J. Overmann: Physiology and phylogeny of green sulfur bacteria forming a monospecific phototrophic assemblage at a depth of 100 meters in the Black Sea. Applied and Environmental Microbiology 71(12):8049-8060 (2005). PubMed Full Text

Schippers, A., L. N. Neretin, G. Lavik, T. Leipe and F. Pollehne: Manganese(II) oxidation driven by lateral oxygen intrusions in the western Black Sea. Geochimica Et Cosmochimica Acta 69(9):2241-2252 (2005). ScienceDirect

Schmid M.C., B. Maas, A. Dapena, K. van de Pas-Schoonen, J. van de Vossenberg, B. Kartal, L. van Niftrik, I. Schmidt, I. Cirpus, J. G. Kuenen, M. Wagner, J. S. S. Damsté, M. Kuypers, N. P. Revsbech, R. Mendez, M. S. M. Jetten and M. Strous: Biomarkers for in situ detection of anaerobic ammonium-oxidizing (anammox) bacteria. Applied and Environmental Microbiology 71(4):1677-1684 (2005). PubMed Full Text

Stuut, J.-B. W., M. Zabel, V. Ratmeyer, E. Schefuß, G. Lavik, P. Helmke and R. Schneider: Provenance of present-day eolian dust collected off NW Africa. JGR – Atmospheres 110:D04202 (2005). Wiley Full Text

Tengberg, A., P.O.J. Hall, U. Andersson, B. Lindén, O. Styrenius, G. Boland, F. de Bovee, B. Carlsson, S. Ceradini, A. Devol, G. Duineveld, J.-U. Friemann, R.N. Glud, A. Khripounoff, J. Leather, P. Linke, L. Lund-Hansen, G. Rowe, P. Santschi, P. de Wilde and U. Witte: Intercalibration of benthic flux chambers II. Hydrodynamic characterization and flux comparisons of 14 different designs. Marine Chemistry 94: 147-173 (2005). ScienceDirect