Publications 2006

Department of Biogeochemistry

Arnosti, C. and B. B. Jørgensen: Organic carbon degradation in Arctic marine sediments, Svalbard: A comparison of initial and terminal steps. Geomicrobiology Journal 23:551-563 (2006). TFO

Blake, R.E., Surkov A.V., Böttcher M.E., Ferdelman T.G. and Jorgensen B.B.: Chapter 7. Oxygen isotope composition of dissolved sulfate in deep-sea sediments: Eastern Equatorial Pacific Ocean. pp. 1-23 , In: Proc. ODP, Sci. Res. Vol. 201(116), Jørgensen B.B., D`Hondt S.L. and Miller D.J. (eds.) (2006) ODP Full Text

Böttcher, M.E., Hetzel A., Brumsack H.-J. and Schipper A.: Sulfur-iron-carbon geochemistry in sediments of the Demerara Rise. pp.1–23, In: Proc. ODP, Sci. Results 207, College Station, TX (Ocean Drilling Program), Mosher, D.C., Erbacher, J., and Malone, M.J. (eds.), doi:10.2973/odp.proc.sr.207.108.2006 (2006). ODP Full Text

Böttcher, M. E., T. G. Ferdelman, B. B. Jørgensen, R. E. Blake, A. V. Surkov and G. E. Claypool: Sulfur isotope fractionation by the deep biosphere within sediments of the Eastern Equatorial Pacific and Peru Margin. pp. 1-21. In: Proc. ODP, Sci. Res. 201. Ocean Drilling Program, Texas A and M University, College Station TX 77845-9547, USA (2006). ODP

Bouillon, S. and Böttcher, M.E.: Preface Stable Isotopes in Biogeosciences. Org. Geochem. 37, 1197-1199 (2006). Full Text

Brüchert, V., B. Currie, K. R. Peard, U. Lass, R. Endler, A. Dübecke, E. Julies, T. Leipe and S. Zitzmann: Biogeochemical and Physical Control on shelf Anoxia and Water column Hydrogen Sulphide in the Benguel a coastal upwelling System off Namibia. pp. 161-193, In: Past and Present Water Column Anoxia. L. N. Neretin (ed.), Springer, Netherlands (2006). Springer

Ferdelman, T.G., Kano A., Williams T., Cragg B.A., Frank T.D., Gharib J.J., Léonide P., Mangelsdorf K., Sakai S., Samrikin V.A., Spivack A.J., The IODP Expedition 307 Scientific Party: Scientific drilling of a cold-water carbonate mound: Shipboard biogeochemical results from IODP Expedition 307, Goldschmidt Conference Abstracts 2006:A170, doi: 10.1016/j.gca.2006.06.341 (2006). Full Text

Hetzel, A., Brumsack H.-J., Schnetger B. and Böttcher M.E.: Inorganic geochemical characterization of lithologic units recovered during ODP Leg 207 (Demerara Rise). pp. 1–37, In: Proc. ODP, Sci. Results, 207: College Station, TX (Ocean Drilling Program), Mosher, D.C., Erbacher, J., and Malone, M.J. (eds.), doi:10.2973/odp.proc.sr. 207.107.2006 (2006). ODP

Hübscher, C. and Borowski, C.: Seismic evidence for fluid escape from Mesozoic cuesta type topography in the Skagerrak. Marine and Petroleum Geology 23:17-28 (2006). ScienceDirect

Inagaki, F., T. Nunoura, S. Nakagawa, A. Teske, M. Lever, A. Lauer, M. Suzuki, K. Takai, M. Delwiche, F. S. Colwell, K. H. Nealson, K. Horikoshi, S. D'Hondt and B. B. Jørgensen: Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments on the Pacific Ocean Margin. Proceedings of the National Academy of Science, USA 103(8):2815-2820 (2006). PubMed Full Text

Inagaki, F., M.M.M. Kuypers, U. Tsunogai, J. Ishibashi, K. Nakamura, T. Treude, S. Ohkubo, M. Nakaseama, K. Gena, H. Chiba, H. Hirayama, T. Nunoura, K. Takai, B. B. Jørgensen, K. Horikoshi and A. Boetius: Microbial community in a sediment-hosted CO₂ lake of the southern Okinawa Trough hydrothermal system. PNAS 103(38):14164-14169 (2006). PubMed Full Text

Inagaki, Fumio and Nealson Kenneth H.: Molecular Signals from Ancient Materials: Challenges to Deep-Biosphere and Paleoenvironmental Research - A Response to the Comments of Sinninghe Damsté and Coolen, Astrobiology 6(2):303-307 (2006). deepdyve

Jørgensen, B. B. and S. D′Hondt: A starving majority dep beneath the seafloor. Science 314:932-934 (2006). PubMed

Jørgensen, B.B., S.L. D′Hondt and D.J. Miller: Chapter 1. Leg 201 Synthesis: Controls on microbial communities in deeply buried sediments.pp. 1-45, In: Proc. ODP, Sci. Res. 201. Ocean Drilling Program, Texas < A&M University, College Station TX 77845-9547, Jørgensen, B.B., S.L. D′Hondt and D.J. Miller (eds.), USA (2006). ODP Full Text

Jørgensen, B. B. and S. Kasten: Chapter 8. Sulfur cycling and methane oxidation. pp. 271-309, In: Marine Geochemistry, 2nd ed., H. D. Schulz and M. Zabel (eds.), Springer, Berlin (2006). Springer

Jørgensen, B. B.: Chapter 5. Bacteria and marine biogeochemistry, pp. 169-206. In: Marine Geochemistry, 2nd ed., H. D. Schulz and M. Zabel (eds.), Springer, Berlin (2006). Springer

Lomstein, B. A., B. B. Jørgensen, C. J. Schubert and J. Niggemann: Amino acid biogeo- and stereochemistry in coastal Chilean sediments. Geochimica et Cosmochimica Acta 70:2970-2989 (2006). ScienceDirect

Niggemann, J., Schubert C.J.: Sources and fate of amino sugars in coastal Peruvian sediments, Geohimica et Cosmochimica Acta 70:2229-2237 (2006). ScienceDirect

Niggemann, J., Schubert C.J.: Fatty acid biogeochemistry of sediments from the Chilean coastal upwelling region: Sources and diagenetic changes, Organic Geochemistry 37:626-647 (2006). ScienceDirect

Schippers, A. and L.N. Neretin: Quantification of microbial communities in near-surface and deeply buried marine sediments on the Peru continental margin using real-time PCR, Environmental Microbiology 8(7):1251-1260 (2006). PubMed

Vandieken, V., N. Finke and B. B. Jørgensen: Pathways of carbon oxidation in an Arctic fjord sediment (Svalbard) and isolation of psychrophilic and psychrotolerant Fe(III)-reducing bacteria. Marine Ecology Progress Series 322:29-41 (2006). MEPS

Vandieken, V., M. Nickel and B. B. Jørgensen: Carbon mineralization in Arctic sediments northeast of Svalbard: Mn(IV) and Fe(III) reduction as principal anaerobic respiratory pathways. Marine Ecology Progress Series 322:15-27 (2006). PubMed

Vandieken, V., C. Knoblauch and B.B. Jørgensen: Desulfotomaculum arcticum sp. nov., a novel spore-forming, moderately thermophilic, sulfate-reducing bacterium isolated from a permanently cold fjord sediment of Svalbard. Journal of Systematic and Evolutionary Microbiology 56:687-690 (2006). PubMed Full Text

Vandieken, V., C. Knoblauch and B.B. Jørgensen: Desulfovibrio frigidus sp. nov. and Desulfovibrio ferrireducens sp. nov., two psychrotolerant bacteria isolated from Arctic fjord sediments (Svalbard) with the ability to reduce Fe(III). International Journal of Systematic and Evolutionary Microbiology 56:681-685 (2006). PubMed Full Text

Vandieken, V., M. Mußmann, H. Niemann and B.B. Jørgensen: Desulfuromonas svalbardensis sp. nov. and Desulfuromusa ferrireducens sp. nov. psychrophilic Fe(III)-reducing bacteria isolated from Arctic sediments, Svalbard. International Journal of Systematic and Evolutionary Microbiology 56:1133-1139 (2006). PubMed Full Text

Ph.D. theses

Maren Nickel: Mineralization pathways and thermophilic sulfate reduction in Arctic sediments, Svalbard. PhD thesis, MarMic, Universität Bremen, Bremen (2006), 99pp.

Microsensor Group

Abed, R. M. M., A. Al-Thukair, and D. de Beer: Bacterial diversity of a cyanobacterial mat degrading petroleum compounds at elevated salinities and temperatures. FEMS Microb. Ecol. 57:290-301 (2006). PubMed

Abed, R. M. M., L. Polerecky, M. Al Najjar, and D. de Beer: Effect of temperature on photosynthesis, oxygen consumption and sulfide production in an extremely hypersaline cyanobacterial mat. Aq. Microb. Ecol. 44:21-30 (2006). AME

Abed, R.M.M., Palinska K. A., Camoin G.and Golubic S.: Common ecolutinary origin of planktonic and benthic nitrogenfixing oscillatoriacean cyanobacteria from tropical oceans. FEMS Microbiol. Letters 260:171-177 (2006). PubMed

Alvarez, M., Gieseke A., Godoy R., Härtel S.: Surface – bound phosphatase activity in ectomycorrhizal fungi: a comparative study between a colorimetric and a microscope-based method. Biol. Fertil Soils 42: 561-568 (2006). Springer

Bissett, A., J. Bowman, and C. Burke: Bacterial diversity in organically-enriched fish farm sediments. FEMS Microbiology Ecology 55:48-56 (2006). PubMed

Bissett, A., C. Burke, P. L. M. Cook and J. P. Bowman: Bacterial community shifts in organically perturbed sediments. Environm. Microbiol. 9(1):46-60 (2006). PubMed

Cytryn, E., Minz D., Gieseke A. and van Rijn J.: Transient development of filamentous Thiothrix species in a marine sulfide oxidizing, denitrifying fluidized bed reactor. FEMS Microbiol. Lett. 256:22-29 (2006). PubMed

de Beer, D., E. Sauter, H. Niemann, N. Kaul, J. P. Foucher, U. Witte, M. Schlüter, and A. Boetius: In situ fluxes and zonation of microbial activity in surface sediments of the Håkon Mosby Mud Volcano. Limnol. Oceanogr. 51(3):1315-1331 (2006). PubMed Full Text

Franke, U., L. Polerecky, E. Precht, and M. Huettel: Wave tank study of particulate organic matter degradation in permeable sediments. Limnol. Oceanogr. 51(2):1084-1096 (2006). ASLO Full Text

Gieseke, A., S. Tarre, M. Green, and D. de Beer: Nitrification in a biofilm at low pH: The role of in situ microenvironments and acid tolerance. Appl Environ Microbiol 72(6):4283-4292 (2006). PubMed Full Text

Green, M., M. Beliavski, N. Denekamp, A. Gieseke, D. de Beer, and S. Tarre: High nitrification rate at low pH in a fluidized bed reactor with either chalk or sintered glass as the biofilm carrier. Israel Journal of Chemistry 46:53-58 (2006). PubMed

Grossart H.P., Kiørboe T., Tang K.W., Allgaier M., Yam E.M., Ploug H.: Interactions between marine snow and heterotrophic bacteria: aggregate formation and microbial dynamics. Aquatic Microbial Ecology Vol. 42:19-26 (2006). AME

Hall-Stoodley, L., H. F. Ze, Gieseke A., Nistico L., Nguyen D., Hayes J., Forbes M., Greenberg D.P., Dice B., Burrows A., Wackym P.A., Stoodley P., Post J.C., Ehrlich G.D., Kerschner J.E.: Direct Detection of Bacterial Biofilms on the Middle-Ear Mucosa of Children With Chronic Otitis Media. Jama-Journal of the American medical Association296(2):202-211 (2006). PubMed Full Text

Kamp, A.., Stief P. and Schulz-Vogt H.N.: Anaerobic Sulfide Oxidation with Nitrate by a Freshwater Beggiatoa Enrichment Culture. Applied and Environmental Microbiology 72(7):4755-4760 (2006). PubMed Full Text

Ludwig, R., O. Pringault, R. DeWit, D. de Beer, and H. M. Jonkers: Limitation of oxygenic photosynthesis and oxygen consumption by phosphate and organic nitrogen in a hypersaline microbial mat: A microsensor study. FEMS Microbiology Ecology 57:9-17 (2006). PubMed

Musat, N., U. Werner, K. Knittel, S. Kolb, T. Dodenhof, J. E. E. van Beusekom, D. de Beer, N. Dubilier, and R. Amann: Microbial community structure of sandy intertidal sediments in the North Sea, Sylt-Rømø Basin, Wadden Sea. Syst. Appl. Microbiol. 29:333-348 (2006). PubMed

Polerecky, L., N. Volkenborn, and P. Stief: High temporal resolution oxygen imaging in bioirrigated sediments. Envir.Sci.Technol. 40:5763-5769 (2006). PubMed

Stief, P. and de Beer D.: Probing the microenvironment of freshwater sediment macrofauna: Implications of deposit-feeding and bioirrigation for nitrogen cycling. Limnol Oceanogr. 51(6):2538-2548 (2006). Full Text

Stief, P. and Hölker F.: Trait-Mediated indirect effects of predatory fish on microbial mineralization in Aquatic sediments. Ecology 87(12):3152-3159 (2006). PubMed

Stief, P. and Eller G.: The gut microenvironment of sediment – dwelling Chironomus plumosus larvae as haracterized with O, pH, and redox microsensors. J Comp Physiol B 176:673-683 (2006). PubMed

Van Gaever, S., Moodley L., de Beer D., Vanreusel A.: Meiobenthos at the Artic Håkon Mosby Mud Volcano, with a parental-caring nematode thriving in sulphide-rich sediments. Marine Ecology Progress Series 321:143-155 (2006). PubMed

Kamp, A.., Stief P. and Schulz-Vogt H.N.: Anaerobic Sulfide Oxidation with Nitrate by a Freshwater Beggiatoa Enrichment Culture. Applied and Environmental Microbiology 72(7):4755-4760 (2006). PubMed Full Text

Polerecky, L., N. Volkenborn, and P. Stief: High temporal resolution oxygen imaging in bioirrigated sediments. Envir.Sci.Technol. 40:5763-5769 (2006). PubMed

Stief, P. and Hölker F.: Trait-Mediated indirect effects of predatory fish on microbial mineralization in Aquatic sediments. Ecology 87(12):3152-3159 (2006). PubMed

Weber, M., C. Lott, and K. E. Fabricius: Sedimentation stress in a scleractinian coral exposed to terrestrial and marine sediments with contrasting physical, organic and geochemical properties. J. Exp. Mar. Biol. Ecol. 336:18-32 (2006). ScienceDirect

Werner, U., M. Billerbeck, L. Polerecky, U. Franke, M. Huettel, J. E. E. van Beusekom, and D. de Beer: Spatial and temporal patterns of mineralization rates and oxygen distribution in a permeable intertidal sand flat (Sylt, Germany). Limnol Oceanogr 51(6):2549-2563 (2006). UQeSpace Full Text

Werner, U., P. Bird, C. Wild, T. Ferdelman, L. Polerecky, G. Eickert, R. Jonstone, O. Hoegh-Guldberg, and D. de Beer: Spatial patterns of aerobic and anaerobic mineralization rates and oxygen penetration dynamics in coral reef sediments. Mar. Ecol. Prog. Series 309:93-105 (2006). UQeSpace

Microbial Habitat Group

Alain, K., T. Holler, F. Musat, M. Elvert, T. Treude, and M. Krüger: Microbiological investigation of methane- and hydrocarbon-discharging mud volcanoes in the Carpathian mountains, Romania. Environ. Microbiol. 8(4):574-590 (2006). PubMed

Billerbeck, M., U. Werner, K. Bosselmann, E. Walpersdorf, and M. Huettel: Nutrient release from an exposed intertidal sand flat. Mar. Ecol. Prog. Ser. 316:35-51 (2006). MEPS

Billerbeck, M., U. Werner, L. Polerecky, E. Walpersdorf, D. de Beer, and M. Huettel: Surficial and deep pore water circulation governs spatial and temporal scales of nutrient recycling in intertidal sand flat sediment. Mar. Ecol. Prog. Ser. 326:61-76 (2006). MEPS

Boetius, A.: Mikroorganismen des Tiefseebodens: Vielfalt, Verteilung und Funktion. pp. 279-287, In: Faszination Meeresforschung. Ein Lesebuch.G. and I. Hempel and S. Schiel (eds.), Hauschild Verlag, Bremen (2006).

Bühring, S. I., N. Lampadariou, L. Moodley, A. Tselepides, and U. Witte: Benthic microbial and whole-community responses to different amounts of ¹³C-enriched algae: In situ experiments in the deep Cretan Sea (Eastern Mediterranean). Limnol. Oceanogr. 51(1):157-165 (2006). CiteSeerX Full Text

Bühring, S. I., Ehrenhauss S., Kamp A., Moodley L., and Witte U.: Enhanced benthic activity in sandy sublittoral sediments: Evidence from ¹³C-tracer experiments. Marine Biology Research 2:120-129 (2006). ResearchGate Full Text

Chain, P.S.G., Denef V.J., Konstantinidis K.T., Vergez L.M., Agulló L., Reyes V. Latorre, Hauser L., Córdova M., Gómez L., Gonzáles M., Land M., Lao V., Larimer F., LiPuma J.J., Mahenthiralingam E., Malfatti S.A., Marx C.J., Parnell J.J., Ramette A., Richardson P., Seeger M., Smith D., Spilker T., Sul W.J., Tsoi T.V., Ulrich L.E., Zhulin I.B., and Tiedje J.M.: Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility. PNAS 103(42):15280-15287 (2006). PubMed Full Text

Cook, P. L. M., and H. Røy: Advective relief of CO₂ limitation in microphytobenthos in highly productive sandy sediments. Limnol. Oceanogr. 51(4):1594-1601 (2006). Refdoc

Cook, P. L. M., F. Wenzhöfer, S. Rysgaard, O. S. Galaktionov, F. J. R. Meysman, B. D. Eyre, J. Cornwell, M. Huettel, and R. N. Glud: Quantification of denitrification in permeable sediments: Insights from a two dimensional simulation analysis and experimental data. Limnol. Oceanogr.: Meth. 4:294-307 (2006). KNAW

de Beer, D., E. Sauter, H. Niemann, N. Kaul, J.-P- Foucher, U. Witte, M. Schlüter, and A. Boetius: In situ fluxes and zonation of microbial activity in surface sediments of the Håkon Mosby Mud Volcano. Limnol. Oceanogr. 51(3):1315-1331 (2006). ASLO Full Text

Hoffmann, F., H. T. Rapp, and J. Reitner: Monitoring microbial community composition by fluorescence in situ hybridization during cultivation of the marine cold-water sponge Geodia barretti. Mar. Biotechnol. 8:373-379 (2006). PubMed

Huettel, M., C. Wild, and S. Gonelli: Mucus trap in coral reefs: formation and temporal evolution of particle aggregates caused by coral mucus. Mar. Ecol. Prog. Ser. 307:69-84 (2006). MEPS

Ianora, A., M. Boersma, R. Casotti, A. Fontana, J. Harder, F. Hoffmann, H. Pavia, P. Potin, S. A. Poulet, and G. Toth: New trends in marine chemical ecology. Estuaries Coasts. 29:531-551 (2006). Springer Full Text

Inagaki, F., M. M. M. Kuypers, U. Tsunogai, J. Ishibashi, K. Nakamura, T. Treude, S. Ohkubo, M. Nakaseama, K. Gena, H. Chiba, H. Hirayama, T. Nunoura, K. Takai, B. B. Jørgensen, K. Horikoshi, and A. Boetius: Microbial community in a sediment-hosted CO₂ lake of the southern Okinawa Trough hydrothermal system. PNAS 103(38):14164-14169 (2006). PubMed Full Text

Jonsson, P.R., van Duren L.A., Amielh M., Asmus R., Aspden R.J., Daunys D., Friedrichs M., Friend P.L., Olivier F., Pope N., Precht E., Sauriau P.-G., Schaaff E.: Making water flow: a comparison of the hydrodynamic characteristics of 12 different benthic biological flumes. Aquat Ecol 40:409-438, DOI 10.1007/s10452-006-9049-z (2006). Springer

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 Discuss. 3:1809-1858 (2006). Full Text

Middelboe, M., R.N. Glud, F. Wenzhöfer, K. Oguri, and H. Kitazato: Spatial distribution and activity of viruses in the deep-sea sediments of Sagami Bay, Japan. Deep-Sea Res. I 53:1-13 (2006). ScienceDirect

Niemann, H., J. Duarte, C. Hensen, E. Omoregie, V. H. Magalhães, M. Elvert, L. M. Pinheiro, A. Kopf, and A. Boetius: Microbial methane turnover at mud volcanoes of the Gulf of Cadiz. Geochim. Cosmochim. Ac. 70:5336-5355 (2006). ScienceDirect

Niemann, H., T. Lösekann, D. de Beer, M. Elvert, T. Nadalig, K. Knittel, R. Amann, E. J. Sauter, M. Schlüter, M. Klages, J. P. Foucher, and A. Boetius: Novel microbial communities of the Haakon Mosby mud volcano and their role as a methane sink. Nature 443:854-858 (2006). PubMed

Pape, T., F. Hoffmann, N. V. Quéric, K. von Juterzenka, J. Reitner, and W. Michaelis: Dense populations of Archaea associated with the demosponge Tentorium semisuberites Schmidt, from Arctic deep-waters. Polar Biol. 29:662-667 (2006). Springer

Precht, E., F. Janssen, and M. Huettel: Near-bottom performance of the Acoustic Doppler Velocimeter (ADV) - a comparative study. Aquat. Ecol.40:481-492 (2006). Springer

Rasheed, M., C. Wild, C. Jantzen, and M. Badran: Mineralization of particulate organic matter derived from coral-reef organisms in reef sediments of the Gulf of Aqaba. Chem. Ecol. 22(1):13-20 (2006).

Rusch, A., M. Huettel, C. Wild, and C. E. Reimers: Benthic oxygen consumption and organic matter turnover in organic-poor, permeable shelf sands. Aquat. Geochem. 12:1-19 (2006). Springer

Sauter, E.J., S. I. Muyakshin, J.-L. Charlou, M. Schlüter, A. Boetius, K. Jerosch, E. Damm, J.-P. Foucher, and M. Klages: Methane discharge from a deep-sea submarine mud volcano into the upper water column by gas hydrate-coated methane bubbles. Earth. Planet. Sc. Lett. 243:354-365 (2006). ScienceDirect

Vandieken, V., M. Mußmann, H. Niemann, and B. B. Jørgensen: Desulfuromonas svalbardensis sp. nov. and Desulfuromusa ferrireducens sp. nov., psychrophilic, Fe(III)-reducing bacteria isolated from Arctic sediments, Svalbard. Int. J. Syst. Evol. Microbiol. 56:1133-1139 (2006). PubMed Full Text

Werner, U., M. Billerbeck, L. Polerecky, U. Franke, M. Huettel, J. E. E. van Beusekom, and D. de Beer: Spatial and temporal patterns of mineralization rates and oxygen distribution in a permeable intertidal sand flat (Sylt, Germany). Limnol. Oceanogr. 51:2549-2563 (2006). UQeSpace Full Text

Wild, C., C. Laforsch, and M. Huettel: Detection and enumeration of microbial cells within highly porous calcareous reef sands. Mar. Freshwater Res. 57:415-420 (2006). MFR

Diploma theses

Kirf, M. K.: Investigating small scale advective processes at a sandy sediment water interface from a diffusive approach. Diploma thesis, Universität Oldenburg in cooperation with Max Planck Institute for Marine Microbiology, Bremen (2006).

Mathematical Modeling Group

Bera, P., Khalili A.: Influence of Prandtl number on stability of mixed convective flow in a vertical channel filled with a porous medium. Physics of Fluids 18:124103, DOI 10.1063/1.2405321 (2006). AIP

Goharzadeh A., A. Saidi, D. Wang, W. Merzkirc and A. Khalili: An experimental investigation of the Brinkman layer thickness at a fluid-porous interface. pp.445-454, In: IUTAM Symposium on One Hundred Years of Boundary Layer Research. Part 7. G.E.A. Meier and K.R. Sreenivasan (eds.) , Solid Mechanics and Its Applications Book Series, Springer, Netherlands (2006). Springer

Bhattacharyya, S., Maiti D. K. and Dhinakaran, S.: Influence of buoyancy on vortex shedding and heat transfer from a square cylinder in proximity to a Wall. Numerical Heat Transfer, Part A 50:585-606 (2006). TFO

Stöhr, M. and Khalili, A.: Dynamic regimes of buoyancy-affected two-phase flow in unconsolidated porous media. Phys. Rev. E. 73:036301, DOI 10.1103/PhysRevE.73.036301 (2006). PubMed

Department of Microbiology

Amann, R., J. Peplies, D. Schüler: Diversity and Taxonomy of Magnetotactic Bacteria. pp.25-36, In: Magnetoreception and Magnetosomes in Bacteria. D. Schüler(ed.), Springer Verlag Berlin Heidelberg (2006). Springer

Blumenberg, M., Krüger M., Nauhaus K., Talbott H. M., Oppermann B. I., Seifert R., Pape T. and Michaelis W.: Biosynthesis of hopanoids by sulfate-reducing bacteria (genus Desulfovibrio), Environmental Microbiology (doi 10.1111/j.1462-2920.2006.01014.x) (2006). PubMed

Ceyhan, B., Alhorn P., Lang C., Schüler D., Niemeyer C.M.: Semisynthetic biogenic magnetosome nanoparticles for the detection of proteins and nucleic acids. Small 2(11): 1251-1255 (2006). PubMed

Dalisay, D.S., Webb J.S., Scheffel A. Svenson C., James S., Holmström C., Egan S. and Kjelleberg S.: A mannose-sensitive haemagglutinin (MSHA)-like pilus promotes attachment of Pseudoalteromonas tunicata cells to the surface of the green alga Ulva australis. Microbiology 152:2875-2883 (2006). PubMed Full Text

Faivre, D. and Zuddas P.: Mineralogical and isotopic properties of biogenic nanocrystalline magnetites. pp.175-196, In: Microbiology Monographs (Vol. 3), Magnetoreception and Magnetosomes in Bacteria, D. Schüler (ed.), Springer, Berlin, Heidelberg (2006). PubMed

Grabovich, M., Gavrish E., Kuever J., Lysenko A.M., Podkopaeva D.and Dubinina G.: Proposal of Giesbergeria voronezhensis gen. nov., sp. nov. and G. kuznetsovii sp. nov. and reclassification of (Aquaspirillum) anulus, (A.) sinuosum and (A.) giesbergeri as Giesbergeria anulus comb.nov., G., sinuosa comb. nov. and G. giesbergeri com. nov., and (Aquaspirillum) metamorphum and (A.) psychrophilum as Simplicispira metamorpha gen. nov., nov. and S. psychrophila comb. nov.. International Journal of Systematic and Evolutionary Microbiology 56:569-576 (2006). PubMed Full Text

Hirt, A.M., Brem F., Hanzlik M., and Faivre D.: Anomalous magnetic properties of brain tissue at low temperature: The 50 K anomaly. Journal of Geophyical Research 111:B12S06 (doi 10.1029/2006JB004570) (2006). Wiley Full Text

Höffken, H.W., Duong M., Friedrich T., Breuer M., Hauer B., Reinhardt R., Rabus R., Heider J.: Crystal structure and enzyme kinetics of the (S)-specific 1-phenylethanol dehydrogenase of the denitrifying bacterium strain EbN1. Biochemistry 45: 82-93 (2006). PubMed

Hufnagel, P., Rabus R.: Mass spectrometric identification of proteins in complex post-genomic projects. Soluble proteins of the metabolically versatile, denitrifying 'Aromatoleum' sp. strain EbN1. Journal of Molecular Microbiology and Biotechnology 11:53-81 (2006). PubMed

Ianora, A., Boersma M., Casotti R., Fontana A., Harder J., Hoffman F., Pavia H., Potin P., Poulet S.A., Toth G.: New trends in marine chemical ecology. Estuaries and Coasts 29:531-551 (2006). Springer Full Text

Jogler, C., D. Schüler: Genetic Analysis of Magnetosome Biomineralization. pp.133-161, In: Magnetoreception and Magnetosomes in Bacteria. D. Schüler: (ed.), Springer Verlag Berlin, Heidelberg (2006). PubMed

Lang, C., and D. Schüler: Biogenic nanoparticles: production, characterization, and application of bacterial magnetosomes. Journal of Physics: Condensed Matter 18:S2815-S2828 (2006). IOPscience

Lang, C., Schüler, D.: Chapter 5. Biomineralization of magnetosomes in bacteria: Nanoparticles with potential applications. pp. 107-124, In: Microbial bionanotechnology: Biological self-assembly systems and biopolymer-based nanostructures. Rehm B (ed.), Horizon biosciences, Wymondham (2006).

Musat, F., Harder J., Widdel F.: Study of nitrogen fixation in microbial communities of oil-contaminated marine sediment microcosms. Environmental Microbiology 8(10):1834-1843 (2006). PubMed

Pósfai, M., Moskowitz, B.M., Arató, B., Schüler, D., Flies, C., Bazylinski, D.A., Frankel, R.B.: Properties of instracellular magnetite crystals produced by Desulfovibrio magneticus strain RS-1. Earth and Planetary Science Letters 249:444-455 (2006). Full Text

Rabus, R. T. Hansen and F. Widdel: Dissimilatory sulfate- and sulfur-reducing prokaryotes. In: The prokaryotes, electronic edition. pp. 659-768, M. Dworkin, S. Falkow, E. Rosenberg, K.-H. Schleifer, E. Stackebrandt (eds.), Springer, New York (2006). Springer

Scheffel, A., Gruska M., Faivre D., Linaroudis A., Plitzko J.M., Schüler D.: An acidic protein aligns magnetosomes along a filamentous structure in magnetotactic bacteria. Nature 440:110-114 (2006). PubMed

Scheffel, A. and D. Schüler: Magnetosomes of magnetotactic bacteria. pp.167-191. In: Complex Intrecellular Structures in Prokaryotes. Vol. 1, J. M. Shively (ed.), Springer, Heidelberg (2006). Springer

Schübbe, S., Würdemann C., Peplies J., Heyen U., Wawer C., Glöckner F.O., Schüler D.: Transcriptional organization and regulation of magnetosome operons in Magnetospirillum gryphiswaldense. Applied and Environmental Microbiology 72(9):5757-5765 (2006). PubMed Full Text

Seifert, R., Nauhaus K., Blumenberg M., Krüger M., Michaelis W.: Methane dynamics in a microbial community of the Black Sea traced by stable carbon isotopes in vitro. Organic Geochemistry 37:1411-1419 (2006). ScienceDirect

Würdemann, C., Peplies J., Schübbe S., Ellrott A., Schüler D., Glöckner F.O.: Evaluation of gene expression analysis using RNA-targeted partial genome arrays. Systematic and Applied Microbiology 29:349-357 (2006). PubMed

Diploma, M.Sc and B.Sc theses

Bienhold, Christina: Vergleichende Charakterisierung der mikrobiellen Sedimentgemeinschaften der drei abyssalen Becken, Kapbecken, Angolabecken und Guineabecken, des Südatlantiks mittels Terminalem Restriktions Fragment Längen-Polymorphismus (T-RFLP). Diploma thesis, Universität Bremen, Bremen (2006),122pp.

Germer, Frauke: Charakterisierung eines DNA-Abschnitts des anaeroben Myrcenabbaus und Versuche zur Isolierung der Linalool-Dehydratase aus Castellaniella (ex Alcaligenes) defragrans 65Phen. Diploma thesis, Universität Bremen, Bremen (2006), 110pp.

Jaekel, Ulrike: Modified isolation methods and MLSA design for the Planctomycetes species Rhodopirellula baltica. Bachelor thesis, FH Bonn-Rhein-Sieg (2006), 66pp.

Klatt, Judith Marlene: T-RFLP analysis of Planctomycetes in marine sediment. Bachelor thesis, Universität Hannover (2006), 52pp.

Trautwein, Kathleen: Stress response of the denitrifying, aromatic-degrading bacterium strain EbN1 to sublethal concentrations of aromatic solvents. Diploma thesis, Friedrich-Schiller-Universität Jena (2006), 132pp.

Department of Molecular Ecology

Alonso, C. and Pernthaler J.: Concentration-Dependent Patterns of Leucine Incorporation by Coastal Picoplankton. Applied and Environmental Microbiology 72(3):2141-2147 (2006). PubMed Full Text

Bauer, M., M. Kube, H. Teeling, M. Richter, T. Lombardot, E. Allers, C.A. Würdemann, C. Quast, H. Kuhl, F. Knaust, D. Woebken, K. Bischof, M. Mussmann, J.V. Choudhuri, F. Meyer, R. Reinhardt, R.I. Amann, and F.O. Glöckner: Whole genome analysis of the marine Bacteroidetes Gramella forsetii reveals adaptations to degradation of polymeric organic matter. Environ. Microbiol. 8:2201-2213 (2006). PubMed

Blazejak, A., J. Kuever, C. Erseus, R. Amann, and N. Dubilier: Phylogeny of 16S rRNA, Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase, and Adenosine 5′-Phosphosulfate Reductase genes from gamma- and alphaproteobacterial symbionts in gutless marine worms (Oligochaeta) from Bermuda and the Bahamas. Appl. Environ. Microbiol. 72(8):5527-5536 (2006). PubMed Full Text

Cypionka, H., H.-D. Babenzien, F. O. Glöckner, and R. Amann: Chapter 3.3.46. The genus Nevskia. pp. 1152-1155, In: The Prokaryotes. Third Edition. Volume 6: Proteobacteria: Gamma Subclass,M. Dworkin, S. Falkow, E. Rosenberg, K. H. Schleifer and E. Stackebrandt (eds.), Springer Sciences+Business Media, LLC (2006). Full Text

Da Silva S.G., Gillan D.C., Dubilier N., De Ridder, C.: Characterization by 16S rRNA gene analysis and in situ hybridization of bacteria living in the hindgut of a deposit-feeding echinoid (Echinodermata). J. Mar. Biol. Assoc. 86:1209-1213 (2006). CUP

Dubilier, N., A. Blazejak, C. Rühland: Symbioses between bacteria and gutless marine oligochaetes. pp. 251-275, In: Molecular Basis of Symbiosis. Progress in Molecular and Subcellular Biology Book Series. J. Overmann (ed.), Springer-Verlag, Berlin, Heidelberg (2006). PubMed

Duperron, S., C. Bergin, F. Zielinski, A. Blazejak, A. Pernthaler, Z.P. McKiness, E. DeChaine, C.M. Cavanaugh, and N. Dubilier: A dual symbiosis shared by two mussel species, Bathymodiolus azoricus and B. puteoserpentis (Bivalvia: Mytilidae), from hydrothermal vents along the northern Mid-Atlantic Ridge. Environ. Microbiol. 8(8):1441-1447 (2006). Full Text

Heywood, J.L., M.V. Zubkov, G.A. Tarran, B.M. Fuchs, and P.M. Holligan: Prokaryoplankton standing stocks in oligotrophic gyre and equatorial provinces of the Atlantic Ocean: Evaluation of inter-annual variability. Deep Sea Research Part II: Topical Studies in Oceanography 53:1530-1547 (2006). ScienceDirect

MacGregor, B. J. and R. Amann: Single-stranded conformational polymorphism for separation of mixed rRNAs (rRNA-SSCP), a new method for profiling microbial communities. Syst. Appl. Microbiol. 29:661-670 (2006). PubMed

MacGregor, B. J., H.T.S. Boschker, and R. Amann: Comparison of rRNA and polar-lipid-derived fatty acid biomarkers for assessment of ¹³C-substrate incorporation by microorganisms in marine sediments. Appl. Environ. Microbiol. 72(8):5246-5253 (2006). PubMed Full Text

Mary, I., J. L. Heywood, B. M. Fuchs, R. Amann, G. A. Tarran, P. H. Burkill, and M. V. Zubkov: SAR11 dominance among metabolically active low nucleic acid bacterioplankton in surface waters along an Atlantic meridional transect. Aquat. Microb. Ecol. 45:107-113 ( 2006). PubMed

Niemann, H., T. Lösekann, D. de Beer, M. Elvert, T. Nadalig, K. Knittel, R. Amann, E.J. Sauter, M. Schlüter, M. Klages, J.P. Foucher, and A. Boetius: Novel microbial communities of the Haakon Mosby mud vulcano and their role as a methane sink. Nature (London) 443:854-858 (2006). PubMed

Rühland, C., C. Bergin, C. Lott, and N. Dubilier: Darmlose marine Würmer. Symbiosen mit mikrobiellen Konsortien. BIOSpektrum 6:600-602 (2006). Full Text

Tujula, N.A., Holmström C., Mussmann M., Amann R., Kjelleberg S., Crocetti G.R.: A CARD-FISH protocol for the identification and enumeration of epiphytic bacteria on marine algae, Journal of Microbiological Methods 65:604-607 (2006). PubMed

Woyke, T., H. Teeling, N.N. Ivanova, M. Huntemann, M. Richter, F.O. Glöckner, D. Boffelli, I.J. Anderson, K.W. Barry, H.J. Shapiro, E. Szeto, N.C. Kyrpides, M. Mussmann, R. Amann, C. Bergin, C. Ruehland, E.M. Rubin, and N. Dubilier: Symbiosis insights through metagenomic analysis of a microbial consortium. Nature 443:950-955 (2006). PubMed

M.Sc theses

Lenk, Sabine: Diversity and Abundance of Sulfur-Oxidizing Bacteria in Wadden Sea Sediments Revealed by DsrAB Phylogeny and dsrAB-Targeted Real-Time PCR. MarMic, MSc, University of Bremen (2006), 72pp.

Yan, Shi: Biogeography of NOR5 clade, a wide-spread group of Gammaproteobacteria. MarMic, MSc, University of Bremen (2006), 61pp.

Ph.D. theses

Lösekann, Tina: Molecular characterization of methanotrophic and chemoautotrophic communities at cold seeps. PhD thesis, MarMic, Universität Bremen, Bremen (2006), 201pp.

Musat, Niculina: Molecular characterization of symbiotic associations between chemoautotrophic sulfur-oxidizing microorganisms and nematodes in shallow marine sediments. PhD thesis, MarMic, Universität Bremen, Bremen (2006), 132pp.

Microbial Genomics Group

Bauer, M., M. Kube, H. Teeling, M. Richter, T. Lombardot, E. Allers, C. A. Würdemann, C. Quast, H. Kuhl, F. Knaust, D. Woebken, K. Bischof, M. Mussmann, J. V. Choudhuri, F. Meyer, R. Reinhardt, R. I. Amann, and F. O. Glöckner: Whole genome analysis of the marine Bacteroidetes 'Gramella forsetii' reveals adaptations to degradation of polymeric organic matter. Environ. Microbiol. 8(12):2201-2213 (2006). PubMed

Glöckner, F. O.: Metagenome Analysis. In: Molecular Identification, Systematics, and Population Structure of Prokaryotes. E. Stackebrandt (ed.), Springer-Verlag, Heidelberg (2006).

Glöckner, F. O.: Umweltgenomik: Schlüssel zum Verständnis mariner mikrobieller Diversität und Funktion. Jahrbuch der Max Planck Gesellschaft (2006), 6pp. Full Text

Lombardot, T., R. Kottmann, H. Pfeffer, M. Richter, H. Teeling, C. Quast, and F. O. Glöckner: Megx.net-database resources for marine ecological genomics. Nucleic Acids Res. 34:D390-D393 (2006). PubMed Full Text

Peplies, J., C. Lachmund, F. O. Glöckner, and W. Manz: A DNA microarray platform based on direct detection of rRNA for characterization of freshwater sediment-related prokaryotic communities. Appl. Environ. Microbiol. 72(7):4829-4838 (2006). PubMed 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. Appl. Environ. Microbiol. 72(9):5757-5765 (2006). PubMed Full Text

Teeling, H., and F. O. Gloeckner: RibAlign: a software tool and database for eubacterial phylogeny based on concatenated ribosomal protein subunits. BMC Bioinformatics 7:66 (2006). PubMed Full Text

Woyke, T., H. Teeling, N. N. Ivanova, M. Huntemann, M. Richter, F. O. Glöckner, D. Boffelli, I. J. Anderson, K. W. Barry, H. J. Shapiro, E. Szeto, N. C. Kyrpides, M. Mussmann, R. Amann, C. Bergin, C. Ruehland, E. M. Rubin, and N. Dubilier: Symbiosis insights through metagenomic analysis of a microbial consortium. Nature 443:950-955 (2006). PubMed

Würdemann, C., J. Peplies, S. Schübbe, A. Ellrott, D. Schüler, and F. O. Glöckner: Evaluation of gene expression analysis using RNA-targeted partial genome arrays. Syst. Appl. Microbiol. 29:349-357 (2006). PubMed

Zaunmüller, T., D. J. Kelly, F. O. Glöckner, and G. Unden: Succinate dehydrogenase functioning by a reverse redox loop mechanism and fumarate reductase in sulphate-reducing bacteria. Microbiology 152:2443-2453 (2006). PubMed Full Text

Nutrient Group

Inagaki, F., Kuypers, M.M.M., Tsunogai, U., Ishibashi, J., Nakamura, K., Treude, T., Ohkubo, S., Nakaseama, M., Gena, K., Chiba, H., Hirayama, H., Nunoura, T., Takai, K., Jørgensen, B.B., Horikoshi, K., and Boetius, A.: Microbial community in a sediment-hosted CO₂ lake of the southern Okinawa Trough hydrothermal system. PNAS 103(38):14164-14169 (2006). PubMed Full Text

Kuypers, M.M.M., G. Lavik and B. Thamdrup: Anaerobic ammonium oxidation in the marine environment. pp.311-335, In: Past and Present Marine Water Column Anoxia, L. N. Neretin (ed.), Springer (2006). Springer

Op den Camp, H.J.M., B. Kartal, D. Guven, L.A.M.P. van Niftrik, S.C.M. Haaijer, W.R.L. van der Star,K.T. van de Pas-Schoonen, A. Cabezas, Z. Ying, M.C. Schmid, M.M.M. Kuypers, J. van de Vossenberg, H.R. Harhangi, C. Picioreanu, M.C.M. van Loosdrecht, J.G. Kuenen, M. Strous and M.S.M. Jetten: Global impact and application of the anaerobic ammonium-oxidizing (anammox) bacteria, Biochemical Society Transactions 34(1):174-178 (2006). PubMed Full Text

Schubert, C.J., Coolen, M.J.L., Neretin, L.N., Schippers, A., Abbas, B., Durisch-Kaiser, E., Wehrli, B., Hopmans, E.C., Damste, J.S.S., Wakeham, S., and Kuypers, M.M.M.: Aerobic and anaerobic methanotrophs in the Black Sea water column, Environmental Microbiology 8(19):1844-1856 (2006). PubMed

Schubert, C.J., Durisch-Kaiser, E., Wehrli, B., Thamdrup, B., Lam, P., and Kuypers, M.M.M.: Anaerobic ammonium oxidation in a tropical freshwater system (Lake Tanganyika), Environmental Microbiology 8(10):1857-1863 (2006). PubMed

Schubert, C.J., E. Durisch-Kaiser, L. Klauser, F. Vazquez, B. Wehrli, C.P. Holzner, R. Kipfer, O. Schmale, J. Greinert and M.M.M. Kuypers: Recent studies on sources and sinks of methane in the Black Sea. pp.419-441, In: Past and Present Marine Water Column Anoxia, L. N. Neretin (ed.), Springer (2006). Springer