Publikationen 2004

Department of Biogeochemistry

Böning, H.P., Brumsack H.-J., Böttcher M.E., Schnetger B., Kriete C., Kallmeyer J. & Borchers S.L.: Geochemistry of Peruvian near-surface sediments. Geochim. Cosmochim. Acta 68(21):4429-4451 (2004). ScienceDirect

Böttcher , M.E., Hespenheide B., Brumsack H.-J. & Bosselmann K.: Stable isotope biogeochemistry of the sulfur cycle in modern marine sediments: I. Seasonal dynamics in a temperate intertidal sandy surface sediment. Isotopes Environ. Health Stud. 40(4):267-283 (2004). PubMed

Böttcher, M.E. & Schnetger B.: Chapter 27. Direct measurement of the content and isotopic composition of sulfur in black shales by means of combustion-isotope-ratio-monitoring mass spectrometry (C-irmMS). Handbook of Stable Isotope Analytical Techniques, Vol. I (P. de Groot, ed.), Elsevier, pp.597-603 + 2pp. References (2004).

Böttcher, M.E., Khim B.-K., Suzuki A., Gehre M., Wortmann U.G. & Brumsack H.-J.: Microbial sulfate reduction in deep sediments of the southwest Pacific (ODP Leg 181, Sites 1119 to 1125): Evidence from stable sulfur isotopes fractionation and pore water modeling. Mar. Geol. 205:249-260 (2004). ScienceDirect

Butler, I.B., Böttcher M.E., Rickard D. & Olroyd A.: Sulfur isotope partitioning during experimental formation of pyrite via the polysulfide and hydrogen sulfide pathways: Implications for the interpretation of sedimentary and hydrothermal pyrite isotope records. Earth Planet. Sci. Lett. 228:495-509 (2004). ScienceDirect

D′Hondt, S.D., Jørgensen, B.B., Miller, D.J., Batzke, A., Blake, R., Cragg, B.A., Cypionka, H., Dickens, G.R., Ferdelman, T., Hinrichs, K.-H., Holm, N.G., Mitterer, R., Spivack, A., Wang, G., Bekins, B., Engelen, B., Ford, K., Gettemy, G., Rutherford, S.D., Sass, H., Skilbeck, C.G., Aiello, I.W., Guèrin, G., House, C.H., Inagaki, F., Meister, P., Naehr, T., Niitsuma, S., Parkes, R.J., Schippers, A., Smith, D.C., Teske, A., Wiegel, J., Naranjo Padilla, C., Solis Acosta, J.L.: Distributions of microbial activities in deep subseafloor sediments. Science 306:2216-2221 (2004). PubMed Full Text

Emeis, K-C., Brüchert, V., Currie, B., Endler, R., Ferdelman, T., Kiessling, A., Leipe, T., Noli-Peard, K., Struck, U. and Vogt, T.: Shallow gas in shelf sediments of the Namibian Coastal Upwelling Ecosystem. Cont. Shelf Res., 24:627-642 (2004). ScienceDirect

Jørgensen, B. B., Böttcher, M. E., Lüschen, H., Neretin, L. N. and Volkov, I.I.: Anaerobic methane oxidation and a deep H₂S sink generate isotopically heavy sulfides in Black Sea sediments. Geochimica et Cosmochimica Acta, 68(9):2095-2118 (2004). ScienceDirect

Jørgensen, B. B. & D. C. Nelson: Sulfide oxidation in marine sediments: Geochemistry meets microbiology, pp. 63-81. In Sulfur Biogeochemistry – Past and Present., J. P. Amend, K. J. Edwards, and T. W. Lyons (eds.), Geological Society of America, Special Paper 379 (2004). GSA

Kallmeyer, J., Ferdelman, T. G., Weber, A., H. Fossing & B. B. Jørgensen: A cold chromium distillation procedure for radiolabeled sulfide applied to sulfate reduction measurements. Limnology and Oceanography: Methods, 2: 171-180 (2004). Full Text

Kallmeyer, J. and Boetius, A.: Effects of temperature and pressure on sulfate reduction and anaerobic oxidation of methane in hydrothermal sediments of Guaymas Basin. Applied and Environmental Microbiology, 70(2):1231-1233 (2004). PubMed Full Text

Kolb, J., Hellmann A., Rogers A., Sindern S., Vennemann T.W., Böttcher M.E. & Meyer F.M.: The role of a transcrustal shear zone in orogenic gold mineralization at the Ajjanahalli mine, Dharwar Craton, South India. Econ. Geol. 99:743-759 (2004). GeoSci

Kuypers, M.M.M., Van Breugel, Y., Schouten, S., Erba, E., Sinninghe Damsté, J. S.: N₂-fixing cyanobacteria supplied nutrient N for Cretaceous oceanic anoxic events. Geology, 32(10):853-856 (2004). Geology

Kuypers, M. M. M., Lourens L. J., Rijpstra W. F. C., Pancost R. D., Nijenhuis I. A., and Damsté J. S. S.: Orbital forcing of organic carbon burial in the proto-North Atlantic during oceanic anoxic event 2. Earth and Planetary Science Letters 228(3-4):465-482 (2004). ScienceDirect

Mienert, J., P. P. E. Weaver, S. Berné, W. C. Dullo, D. Evans, A. Freiwald, J.-P. Henriet, B. B. Jørgensen, G. Lericolais, V. Lykousis, J. Parkes, F. Trincardi and G. Westbrook: Overview of recent, ongoing, and future investigations on the dynamics and evolution of European margins. Oceanography, 17(4):16-33 (2004). Oceanography Full Text

Neretin, L. N., M. E. Böttcher, B. B. Jørgensen, I. I. Volkov, H. Lüschen & K. Hilgenfeldt: Pyritization processes and greigite formation in the advancing sulfidization front in the upper Pleistocene sediments of the Black Sea. Geochimica et Cosmochimica Acta, 68(9):081-2093 (2004). ScienceDirect

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

Schouten, S., Strous M., Kuypers M. M. M., Rijpstra W. I. C., Baas M., Schubert C. J., Jetten M. S. M., and Damste J. S. S.: Stable carbon isotopic Fractionations associated with inorganic carbon fixation by anaerobic ammonium-oxidizing bacteria. Applied and Environmental Microbiology 70(6):3785-3788 (2004). PubMed Full Text

Zopfi, J, T. Ferdelman and H. Fossing: Distribution and fate of sulfur intermediates – sulfite, tetrathionate, thiosulfate, and elemental sulfur – in marine sediments. GSA Special Papers 379:97-116 (2004). GSA

Diploma theses

Peters, Lydia: Zur Biogeochemistry eines Sedimentkernes aus dem Mischwatt der südlichen Nordsee (2004).

Theune, Alexandra: Biogeochemische Prozesse im Kohlenstoff-, Eisen-, Mangan- und Schwefelkreislauf intertidaler Sedimente der südlichen Nordsee (2004).

Department of Microbiology

Detmers, J., Strauss, H., Schulte, U., Bergmann, A., Knittel, K., Kuever, J.: FISH shows that Desulfotomaculum spp. are the dominating sulfate-reducing bacteria in a pristine aquifer. Microbial Ecology, 47:236-242 (2004). PubMed

Dinh, H.T., Kuever, J., Mußmann, M., Hassel, A. W., Stratmann, M., Widdel, F.: Iron corrosion by novel anaerobic microorganisms. Nature 427:829-832 (2004). PubMed

Gade, D., H. Schlesner, F. O. Glöckner, R. Amann, S. Pfeiffer, and M. Thomm: Identification of planctomycetes with order-, genus- and strain-specific 16S rRNA-targeted probes. Microbiology Ecology 47:243-251 (2004). PubMed

Grünberg, K., E. C. Müller, A. Otto, R. Reszka, D. Linder, M. Kube, R. Reinhardt, and D. Schüler: Biochemical and proteomic analysis of the magnetosome membrane in Magnetospirillum gryphiswaldense. Appl. Eviron. Microbiol. 70(2):1040-1050 (2004). PubMed Full Text

Hai, T., Lange D., Rabus R., Steinbüchel A.: Polyhydroxyalkanoate (PHA) accumulation in sulfate-reducing bacteria and identification of a class-III PHA synthase (PhaEC) in Desulfococcus multivorans. Appl Environ Microbiol 70(8):4440-4448 (2004). PubMed Full Text

Handrick, R., S. Reinhardt, D. Schultheiss, T. Reichart, D. Schüler, V. Jendrossek, and D. Jendrossek: Unraveling the function of the Rhodospirillum rubrum activator of polyhydroxybutyrate (PHB) degradation: the activator is a PHB-granule-bound protein (phasin). J. Bacteriol. 186(8):2466-75 (2004). PubMed Full Text

Hoell, A., A. Wiedenmann, U. Heyen, and D. Schüler: Nanostructure and field-induced arrangement of magnetosomes studied by SANSPOL. Physica B: Condensed Matter 350:e309-e313 (2004). ScienceDirect

Hufnagel, P., Schweiger-Hufnagel U., Behrens M., Macht M., Baessmann C., Suckau D., Schürenberg M., Rabus R.: Bakterium mit vorhergesagten ORFs – eine Herausforderung für die Proteomanalytik. Laborwelt 5(4):31-34 (2004).

Kube, M., Heider J., Amann J., Hufnagel P., Kühner S., Beck A., Reinhardt R., Rabus R.: Genes involved in the anaerobic degradation of toluene in a denitrifying bacterium, strain EbN1. Arch Microbiol 181:182-194 (2004). PubMed

Musat, F., Wieland, A., Widdel, F.: Marine sediment with surface contamination by oil in microcosms for microbiological studies. Ophelia 58 (3):217-222 (2004). TFO

Rabus, R., Ruepp A., Frickey T., Rattei T., Fartmann B., Stark M., Bauer M., Zibat A., Lombardot T., Becker I., Amann J., Gellner K., Reeling H., Leuschner W.D., Glöckner F.-O., Lupas A.N., Amann R., Klenk H.-P.: The genome of Desulfotalea psychrophila, a sulphate-reducing bacterium from permanently cold Arctic sediments. Envionmental Microbiology, 6(9):887-902 (2004). PubMed

Rehm, B., and D. Schüler: Klein–Kleiner–Am Kleinsten: Nanobiotechnologie, eine Schlüsseltechnologie des 21. Jahrhunderts, pp.56-61, In: Biotechnologie 2020. DECHEMA, Frankfurt (2004). UO

Schlesner, H, Rensmann C, Tindall B J, Gade D, Rabus R, Pfeiffer S, Hirsch P: Taxonomic heterogeneity within the Planctomycetales as derived by DNA-DNA hybridization, description of Rhodopirellula baltica gen. nov., sp. nov. and transfer of Pirellula marina to the genus Blastopirellula gen. nov. as Blastopirellula marina comb. nov. and emended description of the genus Pirellula. Int. J. Syst. Evol. Microbiol. 54:1567-1580 (2004). PubMed Full Text

Schüler, D.: Chapter 4. Biochemical and genetic analysis of the magnetosome membrane in Magnetospirillum gryphiswaldense. pp.61-73, In Biomineralization. 2nd ed., E. Bäuerlein (ed.), Wiley-VCH, Weinheim, Germany (2004). PubMed Full Text

Schüler, D.: Molecular analysis of a subcellular compartment: The magnetosome membrane in Magnetospirillum gryphiswaldense. Arch. Microbiol. 181:1-7 (2004). PubMed

Schweiger-Hufnagel, U., Behrens M., Jürgens M., Baessmann C., Suckau D., Rabus R.: Neues Werkzeug für die de-novo Sequenzierung von Proteinen. Biospektrum Sonderausgabe 10. Jahrgang, 566-567 (2004). Full Text

Widdel, F., Boetius, A., Rabus, R.: Anaerobic biodegradation of hydrocarbons including methane. In The Prokaryotes, electronic edition. Dworkin, M., Falkow, S., Rosenberg, E., Schleifer, K.-H., Stackebrandt, E. (eds), Springer, New York (2004). Springer

Zhilina, T.N., Appel, R., Probian, C., Llobet Brossa, E., Harder, J., Widdel, F., Zavarzin, G.A.: Alkaliflexus imshenetskii gen. nov. sp. nov., a new alkaliphilic gliding carbohydrate-fermenting bacterium with propionate formation from a soda lake. Arch. Microbiol. 182: 244-253 (2004). PubMed

Diploma theses

Gärdes, Astrid: Deletionsmutagenese eines Magnetosomenproteins in Magnetospirillum gryphiswaldense unter Etablierung des Cre-loxP-Systems. Diplomarbeit. Fachhochschule Emden (2004).

Ullrich, Susanne: Untersuchungen zur Genetik und Mutabilität der Magnetosomeninsel von Magnetospirillum gryphiswaldense MSR-1. Diplomarbeit. Universität Bremen (2004)

Ph.D. theses

Amann, Judith: Metabolische Regulation und Rekonstruktion bei Desulfobacterium autotrophicum. Dissertation Universität Bremen, Bremen (2004), 161pp.

Flies, Christine: Isolierung und kulivierungsunabhängige Untersuchungen von magnetotaktischen Bakterien aus marinen und limnischen Sedimenten. Dissertation Universität Bremen, Bremen (2004) 176pp.

Gade, Dörte: Physiologische und proteomische Untersuchungen am marinen Planktomyceten Rhodopirellula baltica. Dissertation Universität Bremen, Bremen (2004), 223pp.

Schultheiss, Daniel: Entwicklung eines genetischen Systems für die Untersuchung der Magnetitbiomineralisation bei dem magnetischen Bakterium Magnetospirillum gryphiswaldense MSR-1. Dissertation Universität Bremen, Bremen (2004), 186pp.

Habilitation

Dirk Schüler: Habilitation, Universität Bremen, Bremen (2004).

Molecular Ecology Group

Amann, R., R. Rosselló-Mora, C. Flies, and D. Schüler: Chapter 3. Phylogeny and in situ identification of magnetotactic bacteria. p. 45-60, In: Biomineralization (2nd Edition), E. Bäuerlein (Ed.), Wiley-VCH, Weinheim, Germany (2004).Wiley

Behrens, S., Fuchs B. M. , and R. Amann: The effect of nucleobase-specific fluorescence quenching on in situ hybridization with rRNA-targeted oligonucleotide probes. System. Appl. Microbiol. 27:565-572 (2004). PubMed

Brinkmeyer, R., F.-O. Glöckner, E. Helmke, and R. Amann: Predominance of Î²-proteobacteria in summer melt pools on Arctic pack ice. Limnol. Oceanogr. 49(4):1013-1021 (2004). ASLO Full Text

Dubilier, N.: Multiple bacterial endosymbionts in gutless marine worms: competitors or partners? Nova Acta Leopoldina N.F. 88:107-112 (2004).

Gillan, D.C. and N. Dubilier.: Novel epibiotic Thiothrix bacterium on a marine amphipod. Appl. Environ. Microbiol. 70(6):3772-3775 (2004). PubMed Full Text

Ishii, K., M. Mußmann, B. J. MacGregor, and R. Amann: An improved fluorescence in situ hybridization protocol for the identification of bacteria and archaea in marine sediments. FEMS Microbiol. Ecol. 50:203-212 (2004). PubMed

Oren, A., F. Rodriguez-Valera, J. Anton, S. Benlloch, R. Rosselló-Mora, R. Amann, J. Coleman, and N. J. Russell: Chapter 3. Red, extremely halophilic, but not archaeal: the physiology and ecology of Salinibacter ruber, a bacterium isolated from saltern crystallizer ponds. pp. 63-76, In: Halophilic microorganisms, A. Ventosa. (ed.). Springer-Verlag, Berlin Heidelberg (2004). Springer

Peplies, J., S. C. K. Lau, J. Pernthaler, R. Amann, and F. O. Glöckner: Application and validation of DNA microarrays for the 16S rRNA-based analysis of marine bacterioplankton. Environ. Microbiol. 6(6):638-645 (2004). PubMed

Pernthaler, A. and R. Amann: Simultaneous fluorescence in situ hybridization of mRNA and rRNA in environmental bacteria. Appl. Environ. Microbiol. 70(9):5426-5433 (2004). PubMed Full Text

Pernthaler, A., J. Pernthaler, and R. Amann: Sensitive multi-color fluorescence in situ hybridization for the identification of environmental microorganisms. In: Molecular Microbial Ecology Manual, Second Edition, 3.11. pp. 711-726, Kowalchuk, G. et al. (Eds.), Kluwer Academic Publishers, Dordrecht, The Netherlands (2004). Springer

Pernthaler, J., E. Zöllner, F. Warnecke, and K. Jürgens: Bloom of filamentous bacteria in a mesotrophic lake: Identity and potential controlling mechanism. Appl. Environ. Microbiol. 70(10):6272-6281 (2004). PubMed Full Text

Sekar, R., B. M. Fuchs, R. Amann, and J. Pernthaler: Flow sorting of marine bacterioplankton after fluorescence in situ hybridization. Appl. Environ. Microbiol. 70(10):6210-6219 (2004). PubMed Full Text

Teira, E., T. Reinthaler, A. Pernthaler, J. Pernthaler, and G. J. Herndl: Combining catalyzed reporter deposition-fluorescence in situ hybridization and microautoradiography to detect substrate utilization by Bacteria and Archaea in the deep ocean. Appl. & Environ. Microbiol. 70(7):4411-4414 (2004). PubMed Full Text

Warnecke, F., R. Amann, and J. Pernthaler: Actinobacterial 16S rRNA genes from freshwater habitats cluster in four distinct linages. Environ. Microbiol. 6(3):242-253 (2004). PubMed

Zubkov M., L. J. Linn, R. Amann, and R. P. Kiene: Temporal patterns of biological dimethylsulfide (DMS) consumption during laboratory-induced phytoplankton bloom cycles. Mar. Ecol. Prog. Ser. 271:77-86 (2004). NERC

Zubkov, M. V., G. A. Tarran, and B. M. Fuchs: Depth related amino acid uptake by Prochlorococcus cyanobacteria in the Southern Atlantic tropical gyre. FEMS Microbiol. Ecol. 50:153-161 (2004). PubMed

Ph.D. thesis

Warnecke, Falk: Diversität und Ökologie von limnischen Actinobakterien. Dissertation Universität Bremen, Bremen (2004), 139pp.

Flux Group

Boetius, A., Suess, E.: Hydrate Ridge: A natural laboratory for the study of microbial life fueled by methane from near-surface gas hydrates. Chemical Geology 205:291-310 (2004). ScienceDirect

Ehrenhauss, S., Witte, U., Janssen, F., Huettel, M.: Decomposition of diatoms and nutrient dynamics in permeable North Sea sediments. Continental Shelf Research 24:721-737 (2004). ScienceDirect

Ehrenhauss, S., Witte, U., Bühring, S., Hüttel, M.: Effect of advective pore water transport on distribution and degradation of diatoms in permeable North Sea sediments. Marine Ecology Progress Series 271:99-111 (2004). MEPS

Ehrenhauss, S. and Huettel, M.: Advective transport and decomposition of chain-forming planktonic diatoms in permeable sediments. Journal of Sea Research 52:179-197 (2004). ScienceDirect

Hensen, C., Pfeifer K., Wenzhöfer F., Volbers A., Schulz S., Holstein J., Romero O., Seiter K.: Fluxes at the benthic boundary layer - A global view from the South Atlantic. pp. 401-430, In: The South Atlantic in the late Quaternary. G. Wefer, S. Mulitza, V. Ratmeyer (eds.), Springer Vlg. Berlin (2004).

Joye, S. B., Boetius, A., Orcutt, B.N., Montoya, J. P., Schulz, H. N., Erickson, M. J., Lugo, S. K.: The anaerobic oxidation of methane and sulfate reduction in sediments from Gulf of Mexico cold seeps. Chemical Geology 205:219-238 (2004). ScienceDirect

Orcutt, B.N., Boetius, A., Lugo, S. K., MacDonald, I. R., Samarkin, V. A., Joye, S. B.: Life at the edge of methane ice: microbial cycling of carbon and sulfur in Golf of Mexico gas hydrates. Chemical Geology 205:239-251 (2004). ScienceDirect

Precht, E. and M. Huettel: Rapid wave-driven advective pore water exchange in a permeable coastal sediment. Journal of Sea Research 51:93-107. ScienceDirect

Precht, E., U. Franke, L. Polerecky, and M. Huettel: Oxygen dynamics in permeable sediments with wave-driven pore water exchange. Limnol. Oceanogr. 49(3):693-705. ASLO Full Text

Rasheed, M., Wild, C., Franke, U. and Huettel, M.: Benthic photosynthesis and oxygen consumption in permeable carbonate sediments at Heron Island, Great Barrier Reef, Australia. Estuarine Coastal and Shelf Science 59:139-150 (2004). ScienceDirect

Reimers, C. E., Stecher, H. A., Taghon, G. L., Fuller, C. M., Huettel, M., Rusch, A., Ryckelynck, N. and Wild, C.: In situ measurements of advective solute transport in permeable shelf sands. Continental Shelf Research 24:183-201 (2004). Ingenta

Røy, H., Huettel, M., Jørgensen, B B.: Transmission of oxygen concentration fluctuations through the diffusive boundary layer overlying aquatic sediments. Limnology and Oceanography 49(3):686-692 (2004). RefDoc

Saidi, A. and Kim, J.: Heat Flux Sensor with Minimal Impact on Boundary Conditions. Exp. Thermal and Fluid Science 28:903-908 (2004). ScienceDirect

Stöhr, M. Goharzadeh, A. and Khalili, A.: Investigation of flow and transport in the vicinity of uprising bubbles near the interface of permeable sediments using 3D PLIF and PIV. pp. 1-11, In: Proceeding of 12th InternationalSymposium on Applications of Laser Techniques to Fluid Mechanics, Lisbon (2004). ResearchGate Full Text

Wild, C., Tollrian, R. and Huettel, M.: Rapid recycling of coral mass spawning products in permeable reef sediments. Marine Ecology Progress Series 271:159-166 (2004).

Wild, C., M. Huettel, A. Klueter, S. G. Kremb, M.Y.M. Rasheed and B. B. Jørgensen: Coral mucus functions as energy carrier and particle trap in the reef ecosystem. Nature 428:66-70 (2004). PubMed

Wild, C., Rasheed, M., Werner, U., Franke, U., Johnstone, R. and Huettel, M.: Degradation and mineralization of coral mucus in reef environments. Marine Ecology Progress Series 267, 159-171 (2004). MEPS

Ph.D. theses

Bühring, Solveig: Microbial carbon processing in marine sediments: Case studies in North Sea sands and oligotrophic deep-sea sediments.Dissertation Universität Bremen, Bremen (2004), 185pp.

Janssen, Felix: Pore-water advection and organic matter mineralization in North Sea shelf sands. Dissertation Universität Bremen, Bremen (2004), 189pp.

Treude, Tina: Anaerobic oxidation of methane in marine sediments. Dissertation Universität Bremen, Bremen (2004), 272pp.

Microbial Genomics Group

Bauer, M., Lombardot, T., Teeling, H., Naomi, W., Amann, R.I., Glöckner, F.O.: Archaea-like Genes for C₁-Transfer Enzymes in Planctomycetes: Phylogenetic Implications of Their Unexpected Presence in This Phylum. Journal of Molecular Evolution 59:571-586 (2004). PubMed

Glöckner, F. O.: Umweltgenomik mit Pirellula. Biospektrum 3:262-263 (2004). Full Text

Heuchert, A., F. O. Glöckner, R. Amann, and U. Fischer: Psychrobacter nivimaris sp. nov.*, a heterotrophic bacterium attached to organic particles isolated from the South Atlantic (Antarctica). Syst. Appl. Microbiol. 27:399-406 (2004). PubMed

Peplies, J., F. O. Glöckner, R. Amann, and W. Ludwig: Comparative sequence analysis and oligonucleotide probe design based on the 23S rRNA genes of Alphaproteobacteria from North Sea bacterioplankton. System. Appl. Microbiol. 27:573-580 (2004). PubMed

Teeling, H., T. Lombardot, M. Bauer, W. Ludwig, and F. O. Glöckner: Evaluation of the phylogenetic position of the planctomycete "Rhodopirellula baltica SH 1" by means of concatenated ribosomal protein sequences, DNA-directed RNA polymerase subunit sequences and whole genome trees. Int. J. Syst. Evol. Microbiol. 54:791-801 (2004). PubMed Full Text

Teeling, H., A. Meyerdierks, M. Bauer, R. Amann, and F. O. Glöckner: Application of Tetranucleotide Frequencies for the Assignment of Genomic Fragments. Environ. Microbiol. 6(9):938-947 (2004). PubMed

Teeling, H., J. Waldmann, T. Lombardot, M. Bauer, and F. O. Glöckner: TETRA: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences. BMC Bioinformatics 5:163 (2004). PubMed Full Text

Diploma theses

Richter, Michael: Bioinformatischer Genomvergleich der sulfatreduzierenden Bakterien Desulfotalea psychrophila und Desulfovibrio vulgaris (2004).

Wecker, Patricia: Versuche zur Entwicklung eines genetischen Systems für Rhodopirellula baltica SH1^T (2004).

Ph.D. theses

Lombardot, Thierry: The genome of the free-living, marine Planctomycete Pirellula sp. strain 1 ("Rhodopirellula baltica"): Bioinformatics and Biology. Dissertation Universität Bremen, Bremen (2004), 155pp.

Teeling, Hanno: Aspekte der bioinformatischen Analyse und Annotation des Genoms von Rhodopirellula baltica ^T. Dissertation Universität Bremen, Bremen (2004), 136pp.

Microsensor Group

Altmann, D., Stief, P., Amann, R., De Beer,D.: Nitrification in freshwater sediments as influenced by insect larvae: Quantification by microsensors and fluorescence in situ hybridization. Microbial Ecology 48:145-153 (2004). PubMed

Altmann, D., Stief, P., Amann, R., de Beer, D.: Distribution and activity of nitrifying bacteria in natural stream sediment versus laboratory sediment microcosms. Aquatic Microbial Ecology 36(1):73-81 (2004). Full Text

De Beer, D., Wenzhöfer, F., Ferdelman, T.G., Boehme, S., Huettel, M., van Beusekom, J.E.E., Boettcher, M.E., Musat, N., Dubilier, N.: Transport and mineralization rates in North Sea sandy intertidal sediments (Sylt-Rømø Basin, Wadden Sea). Limnology and Oceanography 50(1):113-127 (2005). ePIC

Garcia-Pichel, F., Al-Horani, F.A., Farmer, J.D., Ludwig, R., Wade, B.D.: Balance between microbial calcification and metazoan bioerosion in modern stromatolitic oncolites. Geobiology 2:49-57 (2004). Wiley

Gieseke, A. and De Beer, D.:Use of microelectrodes to measure in situ microbial activities in biofilms, sediments, and microbial mats. In: Molecular Microbial Ecology Manual (2nd edition). Kowalchuk G.G., de Bruijn F.J., Head I.M., Akkermans A.D., van Elsas J.D. (eds.), Heidelberg. Springer (2004), 30pp. Springer

Grötzschel, S., Koester, J., De Beer, D.: Degradation of 2,4-dichlorophenoxyacetic acid (2,4-D) by a hypersaline microbial mat and related functional changes in the mat community. Microbial Ecology 48:254-262 (2004). PubMed

Grunwald, B., G. Holst: Fibre optic refractive index microsensor based on white-light SPR excitation. Sensors and Actuators A 113:174-180 (2004). ScienceDirect

Grunwald, B. and Kühl, M.: A system for imaging variable chlorophyll fluorescence of aquatic phototrophs. Ophelia 58(2):79-89 (2004). TFO

Henning, D., G.-P. Zauke, P. Stief and E. Vareschi: Integrated effects of marine benthic photosynthetically active microorganisms and a bioturbating polychaete, Hediste diversicolor (O.W. Müller), on oxygen distribution at the sediment-water interface: A geostatistical analysis. pp. 271-287. In T. Nishida et al. (eds.), Proc. 2nd Int. Symp. GIS, Vol. 2, Fishery Aquatic reserach Group, Kawagoe-City, Japan (2004). ResearchGate Full Text

Kiørboe, T., Grossart, H.-P., Ploug, H., Tang, K., Auer, B.: Particle-associated flagellates: swimming patterns, colonization rates, and grazing on attached bacteria. Aquatic Microbial Ecology 35:141-152 (2004). AME

Smith, S. M., Abed, R. M. M., Garcia-Pichel, F.: Biological soil crusts of sand dunes in Cape Cod National Seashore, Massachusetts, USA. Microbial Ecology 48:200-208 (2004). PubMed

Stehning, C. and G.A. Holst: Addressing Multiple Indicators on a Single Optical Fiber - Digital Signal Processing Approaches for Temperature Compensated Oxygen Sensing. IEEE Sensors Journal 4(1):153-159 (2004). IEEexplore

Stief, P., Altmann, D., de Beer, D., Bieg, R., Kureck, A.: Microbial activities in the burrow environment of the potamal mayfly Ephoron virgo. Freshwater Biology 49:1152-1163 (2004). Wiley

Tarre, S., Beliavski, M., Denekamp, N., Gieseke, A., de Beer, D., Green, M.: High nitrification rate at low pH in a fluidized bed reactor with chalk as the biofilm carrier. Water Science Technology 49(11):95-105 (2004). PubMed

Diploma theses

Schoon, Raphaela: Comparison of Different Techniques for Measuring Photosynthesis in Foraminifera (2004).

Ph. D. theses

Ludwig, Rebecca: Carbon cycling and calcification in hypersaline microbial mats. Dissertation Universität Bremen, Bremen (2004), 163pp.