Publications 2000

Department of biogeochemistry

Direktor: Prof. Dr. Bo Barker Jørgensen

Arnosti, C.: Substrate specificity in polysaccaride hydrolysis: Contrasts between bottom water and sediments. Limnology and Oceanography 45, 1112-1119 (2000).

Boetius, A. and K. Lochte: Regional variation of total microbial biomass in sediments of the deep Arabian Sea. Deep-Sea Research II 47, 149-168 (2000).

Boetius, A., T. Ferdelmann and K. Lochte: Bacterial activity in sediments of the deep Arabian Sea in relation to vertical flux. Deep Sea Research II 47, 2835-2875 (2000).

Boetius, A., B. Springer and C. Petry: Microbial activity and particulate matter in the benthic nepheloid layer (BNL) of the deep Arabian Sea. Deep Sea Research II 47, 2687-2706 (2000).

Boetius, A., K. Ravenschlag, C. J. Schubert, D. Rickert, F. Widdel, A. Gieseke, R. Amann, B. B. Jorgensen, U. Witte and O. Pfannkuche: A marine microbial consortium apparently mediating anaerobic oxidation of methane. Nature 407, 623-626 (2000).

Böttcher, M. E.: Stable isotope fractionation furing experimental formation of norsethite (BaMg[CO₃]₂): A mineral analogue of dolomite. Aquatic Geochemistry 6, 201-213 (2000).

Böttcher, M. E. and A. Lepland: Biogeochemistry of sulfur in a sediment core from the west-central Baltic Sea: Evidence from stable isotopes and pyrite textures. Journal of Marine Systems 25, 299-312 (2000).

Böttcher, M. E., H. Schale, B. Schnetger, K. Wallmann and H.-J. Brumsack: Stable sulfur isotopes indicate net sulfate reduction in near-surface sediments of the deep Arabian Sea. Deep-Sea Research 47, 2769-2783 (2000).

Böttcher, M. E., B. Hespenheide, E. Llobet Brossa, C. Beardsley, O. Larsen, A. Schramm, A. Wieland, G. Böttcher, U.-G. Berninger and R. Amann: The biogeochemistry, stable isotope geochemistry and microbial community structure of a temperate intertidal mudflat: An integrated study. Continental Shelf Research 20, 1749-1769 (2000).

Boudreau, B. P. and B. B. Jørgensen: (Eds.) The Benthic Boundary Layer: Transport Processes and Biogeochemistry. Oxford University Press 2000, 404.

Boudreau, B. P. and B. B. Jørgensen: Diagenesis and the benthic boundary layer, Chapter 9. In: The Benthic Boundary Layer: Transport Processes and Biogeochemistry. (Eds.) B. P. Boudreau, B. B. Jørgensen. Oxford University Press 2000, 211-244.

Brüchert, V., M. Elena Pérez and C. B. Lange: Coupled primary production, benthic foraminiferal assemblage, and sulfur diagenesis in organic-rich sediments of the Benguela upwelling system. Marine Geology. 163, 27-40 (2000).

Christiansen, B. and A. Boetius: Mass sedimentation of the swimming crab Charybdis smithii (Crustacea: Decapoda) in the deep Arabian Sea. Deep Sea Research II 47, 2673-2685 (2000).

Elberling, B., A. Schippers and W. Sand: Bacterial and chemical oxidation of pyritic mine tailings at low temperatures. Journal of Contaminant Hydrology 41, 225-238 (2000).

Fossing, H., T. G. Ferdelman and P. Berg: Sulfate reduction and methane oxidation in continental margin sediments influenced by irrigation. Geochimica et Cosmochimica Acta 64, 897-910 (2000).

Hansen, J. W., B. Thamdrup and B. B. Jørgensen: Anoxic incubation of sediment in gas-tight plastic bags: A method for biogeochemical process studies. Marine Ecology Progress Series 208, 273-282 (2000).

Jørgensen, B. B.: Bacteria and marine biogeochemistry. In: Marine Geochemistry. (Eds.) H. D. Schulz, M. Zabel. Springer, Berlin 2000, 173-207.

Jørgensen, B. B.: Microbial life in the diffusive boundary layer, Chapter 14. In: The Benthic Boundary Layer: Transport Processes and Biogeochemistry. (Eds.) B. P. Boudreau, B. B. Jørgensen. Oxford University Press 2000, 348-373.

Kasten, S. and B. B. Jørgensen: Sulfate reduction in marine sediments. In: Marine Geochemistry. (Eds.) H. D. Schulz, M. Zabel. Springer, Berlin 2000, 263-281.

Larsen, O. and C. B. Koch: Application of ⁵⁷Fe-enriched synthetic ferrihydrite to speciate the product of bacterial reduction. Hyperfine Interactions 126, 225-234 (2000).

Lochte, K., A. Boetius and C. Petry: Microbial food webs under severe nutrient limitations: life in the deep sea. In: Microbial Biosystems: New Frontiers. Proceedings of the 8th International Symposium on Microbial Ecology. Atlantic Canada Society for Microbial Ecology. (Eds.) C. R. Bell, M. Brylinsky, P. Johnson-Green. Halifax/Canada 2000, 95-102.

Oldenburg, T. B. P., J. Rullkötter, M. E. Böttcher and A. Nissenbaum: Molecular and isotopic characterization of organic matter in recent and sub-recent sediments from the Dead Sea. Organic Geochemistry 31, 251-265 (2000).

Oldenburg, T. B. P., J. Rullkötter, M. E. Böttcher and A. Nissenbaum: Addendum to molecular and isotopic characterization of organic matter in recent and sub-recent sediments from the Dead Sea. Organic Geochemistry 31, 773-774 (2000).

Schippers, A., P.-G. Jozsa and W. Sand: Microbiological pyrite oxidation in a mine tailings heap and its relevance to the death of vegetation. Geomicrobiology Journal 17, 151-162 (2000).

Schubert, C. J. and S. E. Calvert: Nitrogen and carbon isotopic composition of marine and terrestrial organic matter in Arctic Ocean sediments: implications for nutrient utilization and organic matter composition. Deep Sea Research 48, 789-810 (2000).

Schubert, C. J. and B. Nielsen: Effects of decarbonation treatments on d13C values in marine sediments. Marine Chemistry 72, 55-59 (2000).

Schubert, C. J., T. Ferdelman and B. Strotmann: Organic matter composition and sulfate reduction rates in sediments off Chile. Organic Geochemistry 31, 351-361 (2000).

Schulz, H. N. and D. Riechmann: Thiomargarita namibiensis: Ein Gigant mit langem Atem. BioSpektrum 6, 116-118 (2000).

Schulz, H. N., B. Strotmann, V. A. Gallardo and B. B. Jørgensen: Population study of the filamentous sulfur bacteria Thiploca spp. off the Bay of Concepcion, Chile. Marine Ecology Progress Series 200, 117-126 (2000).

Thamdrup, B., R. Rossello-Mora and R. Amann: 2000. Microbial manganese and sulfate reduction in Black Sea shelf sediments. Applied and Environmental Microbiology 66, 2888-2897.

Diplomarbeiten

Riechmann, D.: Nitratspeichernde Schwefelbakterien und ihre Bedeutung in den Auftriebsgebieten vor der Küste Chiles und Namibias. Göttingen 2000.

Scheuner, M.: Erfassung des qualitativen und quantitativen Abbaus von organischen Substanzen unter verschiedenen Redoxbedingungen. Bremen 2000.

Dissertation

Zopfi, J.: Sulfide oxidation and speciation of sulfur intermediates in selected marine environments. Bremen 2000.

Leiter: Dr. Markus Hüttel

Chakraborty, B. B., D. Khattar and A. Khalili: Effect of rotation on stability of suspended sediments. Physics of Fluids 12, 3074-3077 (2000).

Dando, P. R., S. Aliani, H. Arab, C. N. Bianchi, M. Brehmer, S. Cocito, S. W. Fowler, J. Gundersen, L. E. Hooper, R. Kolbl, J. Kuever, P. Linke, K. C. Makropoulos, R. Meloni, J. C. Miquel, C. Morri, S. Muller, C. Robinson, H. Schlesner, S. Sievert, R. Stohr, D. Stuben, M. Thomm, S. P. Varnavas and W. Ziebis: Hydrothermal studies in the Aegean Sea. Physics & Chemistry of the Earth Part B-Hydrology Oceans & Atmosphere 25, 1-8 (2000).

Huettel, M. and A. Rusch: Transport and degradation of phytoplankton in permeable sediment. Limnology and Oceanography 45, 534-549 (2000).

Huettel, M. and I. T. Webster: Porewater flow in permeable sediment. In: The Benthic Boundary Layer: Transport Processes and Biogeochemistry. (Eds.) B. P. Boudreau, B. B. Jørgensen. Oxford University Press 2000, 144-179.

Janßen, F., T. Treude and U. Witte: Scavenger communities of the deep Arabian Sea. Deep-Sea Research II 47, 2999-3026 (2000).

Khalili, A., A. J. Basu and J. Mathew: A new implicit method for calculation of time-dependent incompressible flows. GWDG-Bericht Nr. 54, Göttingen 2000, 71-80.

Khalili, A., M. Huettel and W. Merzkirch: Fine scale measurements in the benthic boundary layer. In: The Benthic Boundary Layer: Transport Processes and Biogeochemistry. (Eds.) B. P. Boudreau, B. B. Jørgensen. Oxford University Press 2000, 44-77.

Rusch, A. and M. Huettel: Advective particle transport into permeable sediments - evidence from experiments in an intertidal sandflat. Limnology and Oceanography 45, 525-533 (2000).

Turnewitsch, R., U. Witte and G. Graf: Bioturbation in the abyssal Arabian Sea: influence of fauna and food supply. Deep-Sea Research II 47, 2877-2911 (2000).

Wenzhöfer, F., O. Holby, R. N. Glud, H. K. Nielsen and J. Gundersen: In situ microsensor studies of a shallow water hydrothermal vent at Milos, Greece. Marine Chemistry 69, 43-54 (2000).

Witte, U.: Vertical distribution of macrofauna within the sediment at four sites with contrasting food supply in the deep Arabian Sea. Deep-Sea Research II 47, 2979-2997 (2000).

Witte, U. and O. Pfannkuche: High rates of benthic carbon remineralisation in the deep Arabian Sea. Deep-Sea Research II 47, 2785-2804. 2000.

Diplomarbeiten

Köbrich, M.: Einfluss mikrobieller exopolymerer Substanzen auf die Permeabilität mariner Sedimente. Bremen 2000.

Treude, T.: Community structure and metabolism of scavenging amphipods in the deep Arabian Sea. Kiel 2000.

Dissertation

Rusch, A.: Dynamics of the fine fraction in the surface layer of permeable shelf sediments. Bremen 2000.

Leiter: Dr. Dirk De Beer

De Beer, D. and M. Kühl: Interfacial processes, gradients and metabolic activity in microbial mats and biofilms. In: The Benthic Boundary Layer. (Eds.) B. Boudreau, B. B. Jørgensen. Oxford University Press 2000, 374-394.

De Beer, D., M. Kühl, N. Stambler and L. Vaki: A microsensor study of light enhanced Ca²⁺ uptake and photosynthesis in the reef-building hermatypic coral Favia sp. Marine Ecology Progress Series 194, 75-85 (2000).

Edwards, H. G. M., F. Garcia-Pichel, E. M. Newton and D. D. Wynn-Williams: Vibrational Raman spectroscopic study of scytonemin, the UV-protective cyanobacterial pigment. Spectrochimica Acta Part A-Molecular Spectroscopy 56, 193-200 (2000).

Holst, G., I. Klimant, M. Kühl and O. Kohls: Optical microsensors and microprobes. In: Chemical sensors in Oceanography. (Ed.) M. S. Varney. Amsterdam, OPA 2000, 143-188.

Köhler-Rink, S. and M. Kühl: Microsensor studies of photosynthesis and respiration in larger foraminifera. I. The physico-chemical microenvironment of Marginopora vertebralis, Amphistegina lobifera and Amphisorus hemprichii. Marine Biology 137, 473-486 (2000).

Liebsch, G., I. Klimant, B. Frank, G. Holst and O. S. Wolfbeis: Luminescence Lifetime Imaging of Oxygen, pH and carbon dioxide distribution using optical sensors. Applied Spectroscopy 54, 548-559 (2000).

Portwich, A. and F. Garcia-Pichel: A novel procaryotic UVB photoreceptor in the cyanobacterium Chlorogloeopsis PCC6912. Photochemistry & Photobiology 71, 493-498 (2000).

Wieland, A. and M. Kühl: Short-term temperature effects on oxygen and sulfide cycling in a hypersaline cyanobacterial mat (Solar Lake, Egypt). Marine Ecology Progress Series 196, 87-102 (2000).

Wieland, A. and M. Kühl: Irradiance and temperature regulation of oxygenic photosynthesis and O₂ consumption in a hypersaline cyanobacterial mat (Solar Lake, Egypt). Marine Biology 137, 71-85 (2000).

Diplomarbeit

Zosgornik, H.: Interaktionen zwischen Cyanobakterien vom Stamm Aphanothece halophytica und aeroben heterotrophen Bakterien. Hochschule Anhalt 2000.

Department of microbiology

Direktor: Prof. Dr. Friedrich Widdel

Amann, R., R. Rosselló-Mora and D. Schüler: Phylogeny and in situ identification of magnetotactic bacteria. In: Biomineralization of nano- and microstructures. (Ed.) E. Baeuerlein. Wiley-VCH, Weinheim 2000, 47-60.

Bazylinski, D. A.; L. K. Kimble, D. Schüler, E. P. Phillips and D. R. Lovley: N₂-dependent growth and nitrogenase activity in the metal-metabolizing bacteria Geobacter metallireducens and Magnetospirillum species. Environmental Microbiology 2, 266-273 (2000).

Ehrenreich, P., A. Behrends, J. Harder and F. Widdel: Anaerobic oxidation of alkanes by newly isolated denitrifying bacteria. Archives of Microbiology 173, 58-64 (2000).

Harder, J., U. Heyen, C. Probian and S. Foß: Anaerobic utilization of essential oils by denitrifying bacteria. Biodegradation 11, 55-63 (2000).

Heyen, U. and J. Harder: Geranic acid formation, an initial reaction of anaerobic monoterpene metabolism in denitrifying Alcaligenes defragrans. Applied and Environmental Microbiology 66, 3004-3009 (2000).

Rabus, R., T. Hansen and F. Widdel: Dissimilatory sulfate- and sulfur-reducing prokaryotes. In: The prokaryotes, electronic edition. (Eds.) M. Dworkin, S. Falkow, E. Rosenberg, K.-H. Schleifer, E. Stackebrandt. Springer, New York 2000. http://link.springer-ny.com/link/service/books/10125.

Schüler, D.: Die Biomineralisation von magnetischen Nanokristallen in magnetotaktischen Bakterien. BioSpektrum 6, 445-449 (2000).

Schüler, D.: Characterization of the magnetosome membrane in Magnetospirillum gryphiswaldense. In: Biomineralization of nano- and microstructures. (Ed.) E. Baeuerlein. Wiley-VCH, Weinheim 2000, 109-118.

Sievert, S. M., T. Heidorn and J. Kuever: Halothiobacillus kellyi sp. nov., a mesophilic obligately chemolithoautotrophic sulfur-oxidizing bacterium isolated from shallow-water hydrothermal vent in the Aegean Sea and emended description of the genus Halothiobacillus. International Journal of Systematic and Evolutionary Microbiology 50, 1229-1237 (2000).

Sievert, S. M. and J. Kuever: Desulfacinum hydrothermale sp. nov., a thermophilic completely oxidizing sulfate-reducing bacterium from geothermally heated sediments near Milos Island (Greece). International Journal of Systematic and Evolutionary Bacteriology 50, 1239-1246 (2000).

Sievert, S., J. Kuever and G. Muyzer: Identification of 16S ribosomal DNA-defined bacterial populations at a shallow submarine hydrothermal vent near Milos island (Greece). Applied and Environmental Microbiology 66, 3102-3109 (2000).

Sievert, S., W. Ziebis, J. Kuever and K. Sahm: Relative abundance of Archaea and Bacteria along a thermal gradient of a shallow-water hydrothermal vent quantified by rRNA slot-blot hybridization. Microbiology 146, 1287-1293 (2000).

Surkov, A. V., M. E. Böttcher and J. Kuever: Stable sulfur isotope fractionation during the reduction of thiosulfate by Dethiosulfovibrio russensis. Archives of Microbiology 174, 448-451 (2000).

Wilkes H., C. Boreham, G. Harms, K. Zengler and R. Rabus: Anaerobic degradation and carbon isotopic fractionation of alkylbenzenes in crude oil by sulphate-reducing bacteria. Organic Geochemistry 31, 101-115 (2000).

Diplomarbeiten

Grünberg, K.: Untersuchungen zur mikroaeroben Kultivierung von M.gryphiswaldense sowie zur biochemischen Charakterisierung der Magnetosomenmembran. Bremen 2000.

Meinke, R.: Physiologische Untersuchungen zur Kälteanpassung bei chemolithoautotrophen schwefeloxidierenden Bakterien aus marinen Sedimenten. Bremen 2000.

Timke, M.: Initiale Reaktionen des Monoterpenstoffwechsels von Alcaligenes defragans. Bremen 2000.

Dissertationen

Detmers, J.: An aquifer in the deep subsurface – microbiology and sulfur isotope fractionation. Bremen 2000.

Molecular ecology group

Leiter Priv.-Doz. Dr. Rudolf I. Amann

Amann, R.: Who is out there? Microbial aspects of biodiversity. Systematic and Applied Microbiology 23, 1-8 (2000).

Amann, R.: Methoden zur Bestimmung der in situ-Funktion von Mikroorganismen. BIOspektrum 6, 274-276 (2000).

Amann, R.: Methodological Aspects of fluorescence in situ hybridization. Bioscience Microflora 19, 85-91 (2000).

Amann, R. and W. Ludwig: Ribosomal RNA-targeted nucleic acid probes for studies in microbial ecology. FEMS Microbiology Review 24, 555-565 (2000).

Amann, R., R. Rossello-Mora and D. Schüler: Phylogeny and in situ identification of magnetotactic bacteria, In: Biomineralisation. (Ed.) E. Bäuerlein. Wiley-VCH, Weinheim 2000, 47-60.

Anton, J., R. Rossello-Mora, F. Rodriguez-Valera and R. Amann: Extremely halophilic Bacteria in crystallizer ponds from solar salterns. Applied and Environmental Microbiology 66, 3052-3057 (2000).

Babenzien, H.-D., F. O. Glöckner and I. M. Head: Genus Achromatium Schewiakoff 1893. In: Bergey’s Manual of Systematic Bacteriology. (Eds.) J.T. Staley, M.P. Bryant, N. Pfennig, J. G. Holt. 2^nd Edition, Vol. II. Williams & Wilkens, Baltimore/USA.

Brand, B. C., R. I. Amann, M. Steinert, D. Grimm and J. Hacker: Identification and in situ detection of intracellular bacteria in the environment, In: Subcellular Biochemistry, Volume 33: Bacterial invasion into eukaryotic cells. (Eds.) T. A. Oelschlaeger and J. Hacker. Kluwer/Plenum, New York/USA 2000, 601-624.

Casamayor, E. O., H. Schäfer, L. Baneras, C. Pedros-Alio, and G. Muyzer: Identification of and spatio-temporal differences between microbial assemblages from two neighboring sulfurous lakes: comparison by microscopy and denaturing gradient gel electrophoresis. Applied and Environmental Microbiology 66, 499-508 (2000).

Eilers, H., J. Pernthaler and R. Amann: Succession of pelagic marine bacteria during enrichment: a close look at cultivation-induced shifts. Applied and Environmental Microbiology 66, 4634-4640 (2000).

Eilers, H., J. Pernthaler, F. O. Glöckner and R. Amann: Culturability and in situ abundance of pelagic bacteria from the North Sea. Applied and Environmental Microbiology 66, 3044-3051 (2000).

Fuchs, B. M., F. O. Glöckner, J. Wulf and R. Amann: Unlabeled helper oligonucleotides increase the in situ accessibility to 16S rRNA of fluorescently labeled oligonucleotide probes. Applied and Environmental Microbiology 66, 3603-3607 (2000).

Fuchs, B. M., M. V. Zubkov, K. Sahm, P. H. Burkill and R. Amann: Changes in community composition during dilution cultures of marine bacterioplankton as assessed by flow cytometric and molecular biological techniques. Environmental Microbiology 2, 191-201 (2000).

Glöckner, F. O., E. Zaichikov, N. Belkova, L. Denissova, J. Pernthaler, A. Pernthaler and R. Amann: Comparative 16S rRNA analysis of lake bacterioplankton reveals globally distributed phylogenetic clusters including an abundant group of actinobacteria. Applied and Environmental Microbiology 66, 5053-5065 (2000).

Groben, R., G. J. Doucette, M. Kopp, M. Kodama, R. Amann and L. K. Medlin: 16S rRNA targeted probes for the identification of bacterial strains isolated from cultures of the toxic dinoflagellate Alexandrium tamarense. Microbial Ecology 39, 186-196 (2000).

Head, I. M., N. D. Gray, H. D. Babenzien and F. O. Glöckner: Uncultured giant bacteria of the genus Achromatium. FEMS Microbiology Ecology 33, 171-180 (2000).

Jurgens, G., F. O. Glöckner, R. Amann, A. Saano, L. Montonen, M. Likolammi and U. Münster: Identification of novel Archaea in bacterioplankton of a boreal forest lake by phylogenetic analysis and fluorescent in situ hybridization. FEMS Microbiology Ecology 34, 45-56 (2000).

Krieger, J., O. Giere and N. Dubilier: Localization of RubisCO and sulfur in endosymbiotic bacteria of the gutless marine oligochaete Inanidrilus leukodermatus (Annelida). Marine Biology 137, 239-244 (2000).

Oerther, D. B., J. Pernthaler, A. Schramm, R. Amann and L. Raskin: Monitoring precursor 16S rRNAs of Acinetobacter spp. in activated sludge wastewater treatment systems. Applied and Environmental Microbiology 66, 2154-2165 (2000).

Ravenschlag, K., K. Sahm, C. Knoblauch, B. B. Jorgensen and R. Amann: Community structure, cellular rRNA content, and activity of sulfate-reducing bacteria in marine Arctic sediments. Applied and Environmental Microbiology 66, 3592-3602 (2000).

Weller, R., F.O. Glöckner and R. Amann: 16S rRNA-targeted oligonucleotide probes for the in situ detection of members of the phylum Cytophaga-Flavobacterium-Bacteroides. Systematic and Applied Microbiology 23, 107-114 (2000).

Wickham, S., A. Gieseke and U.-G. Berninger: Benthic ciliate identification and enumeration: an improved methodology and its application. Aquatic Microbial Ecology 22, 79-91 (2000).

Dissertationen

Ravenschlag, K.: Molekularbiologische Analyse der Diversität und Struktur mikrobielle Lebensgemeinschaften in marinen, arktischen Sedimenten (Svalbard). Bremen 2000.

Llobet-Brossa, E.: Microbial community structure and dynamics of Wadden Sea sediments (Dangast). Bremen 2000.

Eilers, H.: Pelagic microbial communities in the North Sea: cultivation, diversity and in situ dynamics. Bremen 2000.

Diplomarbeiten

Prilipp, A.: Charakterisierung von Ektosymbionten mariner Nematoden der Gattung Leptonemella und freilebender schwefel-oxidierender Bakterien anhand mikrobiologischer und molekularbiologischer Methoden. Bremen 2000.

Kolb, S.: Abundanz und vertikale Verteilung von sulfatreduzierenden und chemolithotrophen schwefeloxidierenden Bakterien in sandigen Wattenmeersedimenten. Göttingen 2000.

Peplies, J.: Gerichtete Isolierung von alpha-Proteobakterien aus der Nordsee und deren in situ-Nachweis. Bremen 2000.

Behrens, S.: Untersuchung der differentiellen Genexpression von Desulfotalea psychrophila. Bremen 2000.