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Publications

Publications

page last updated January 2014
2013Behrendt A, de Beer D, Stief P. 2013. Vertical activity distribution of dissimilatory nitrate reduction in coastal marine sediments. Biogeosciences:in press.
Chennu A, Färber P, Volkenborn N, Al-Najjar M, Janssen F, de Beer D, Polerecky L. 2013. Hyperspectral imaging of the microscale distribution and dynamics of microphytobenthos in intertidal sediments. Limnol Oceanogr Methods:accepted.
de Beer D, Haeckel M, Neumann J, Wegener G, Inagaki F, Boetius A. 2013. Saturated CO2 inhibits microbial processes in CO2-vented deep-sea sediments. Biogeosciences 10:5639-5649.
Heim C, Quéric NV, Ionescu D, Simon K, Thiel V. 2013. Chemolithotrophic microbial mats in an open pond in the continental subsurface – implications for microbial biosignatures, p. 175–188. In Wiese F, Reich M, Arp G (ed.), Göttingen Contributions to Geosciences, vol. 77. Geoscience Centre of the Georg-August University of Göttingen, Germany, Goettingen.
Heisterkamp IM, Schramm A, Larsen LH, Svenningsen NB, Lavik G, de Beer D, Stief P. 2013. Shell biofilm-associated nitrous oxide production in marine molluscs: processes, precursors and relative importance. Environmental Microbiology 15:1943-1959.
Kamp A, Stief P, Knappe J, de Beer D. 2013. Response of the ubiquitous pelagic diatom Thalassiosira weissflogii to darkness and anoxia. PLoS ONE 8(12):e82605. doi:82610.81371/journal.pone.0082605.
Knappe J. 2013. The pelagic diatom Thalassiosira weissfogii is capable of dissimilatory nitrate reduction to ammonium (DNRA)Master Thesis. Linköping University, Sweden.
Neumann J, Ramette A, de Beer D, Haeckel M, Inagaki F, Boetius A. 2013. Effects of subsurface CO2 leakage on deep-sea bacterial communities of the Yonaguni Knoll IV hydrothermal sediments (Okinawa Trough, 1350 m). Env. Microbiol.:in preparation.
Poulsen M, Kofoed MVW, Larsen LH, Schramm A, Stief P. 2013. Chironomus plumosus larvae increase fluxes of denitrification products and diversity of nitrate-reducing bacteria in freshwater sediment. Systematic and Applied Microbiology:in press.
Schutting S, Borisov SM, Klimant I. 2013. Diketo-pyrrolo-pyrrole dyes as new colorimetric and fluorescent pH indicators for optical carbon dioxide sensors. J. Anal. Chem. 85:3271-3279.
Stief P. 2013. Stimulation of microbial nitrogen cycling in aquatic ecosystems by benthic macrofauna: Mechanisms and environmental implications [Review article]. Biogeosciences:in press.
Stief P, Kamp A, de Beer D. 2013. Role of diatoms in the spatial-temporal distribution of intracellular nitrate in intertidal sediment. PLoS ONE 8(9):e73257. doi:73210.71371/journal.pone.0073257.
2012Abed RMM, Ramette A, Hubner V, De Deckker P, de Beer D. 2012. Microbial diversity of eolian dust sources from saline lake sediments and biological soil crusts in arid Southern Australia. Fems Microbiology Ecology:accepted.
Al-Najjar MAA, de Beer D, Kuhl M, Polerecky L. 2012. Light utilization efficiency in photosynthetic microbial mats. Environmental Microbiology:accepted.
Beutler M, Milucka J, Hinck S, Schreiber F, Brock J, Mußmann M, Schulz-Vogt HN, de Beer D. 2012. Vacuolar respiration of nitrate coupled to energy conservation in filamentous Beggiatoaceae. Environmental Microbiology 14:2911–2919.
Glas MS, Sato Y, Ulstrup K, Bourne D. 2012. Biogeochemical conditions determine virulence of Black Band Disease in corals. ISME J 6 1526–1534.
Heisterkamp IM, Kamp A, Schramm AT, de Beer D, Stief P. 2012. Indirect control of the intracellular nitrate pool of intertidal sediment by the polychaete Hediste diversicolor. Marine Ecology-Progress Series 445:181-192.
Ionescu D, Siebert C, Polerecky L, Munwes YY, Lott C, Hausler S, Bizic-Ionescu M, Quast C, Peplies J, Glockner FO, Ramette A, Rodiger T, Dittmar T, Oren A, Geyer S, Stark HJ, Sauter M, Licha T, Laronne JB, de Beer D. 2012. Microbial and Chemical Characterization of Underwater Fresh Water Springs in the Dead Sea. PLoS ONE 7:e38319.
Kofoed MVW, Stief P, Hauzmayer S, Schramm A, Herrmann M. 2012. Higher nitrate-reducer diversity in macrophyte-colonized compared to unvegetated freshwater sediment. Systematic and Applied Microbiology 35:8.
Lew B, Stief P, Beliavski M, Ashkenazi A, Svitlica O, Khan A, Tarre S, de Beer D, Green M. 2012. Characterization of denitrifying granular sludge with and without the addition of external carbon source. Bioresource Technology 124:8.
Lichtschlag A, Kamyshny A, Ferdelman TG, de Beer D. 2012. Intermediate Sulfur Oxidation State Compounds in the Euxinic Surface Sediments of the Dvurechenskii Mud Volcano (Black Sea). Geochimica et Cosmochimica Acta:accepted.
Long MH, Berg P, de Beer D, Zieman JC. 2012. In Situ Coral Reef Oxygen Metabolism: an Eddy Correlation Study. PLoS ONE:accepted.
Polerecky L, Adam B, Milucka J, Musat N, Vagner T, Kuypers MMM. 2012. [Bitte aktivieren Sie Javascript] – a tool for the analysis of nanoSIMS data in environmental microbiology. Environmental Microbiology.
Rao AMF, Polerecky L, Ionescu D, Meysman FJR, de Beer D. 2012. The influence of porewater advection, benthic photosynthesis and respiration on calciumcarbonate dynamics in reef sands. Limnol Oceanogr 57:809-825.
Schwedt A, Kreutzmann A-C, Polerecky L, Schulz-Vogt HN. 2012. Sulfur respiration in a marine chemolithoautotrophic Beggiatoa strain. Front. Microbio. 2:276.
Svenningsen NB, Heisterkamp IM, Sigby-Clausen M, Larsen LH, Nielsen LP, Stief P, Schramm A. 2012. Shell biofilm nitrification and gut denitrification contribute to emission of nitrous oxide by the invasive freshwater mussel Dreissena polymorpha (zebra mussel). Applied and Environmental Microbiology 78:5.
Wangpraseurt D, Weber M, Røy H, Polerecky L, de Beer D, Suharsono, Nugues MM. 2012. In situ oxygen dynamics in coral-algal interactions. PLoS ONE 7:1-8.
Weber M, de Beer D, Lott C, Polerecky L, Kohls K, Abed RMM, Ferdelman TG, Fabricius KE. 2012. Mechanisms of damage to corals exposed to sedimentation. PNAS 109:1558-1567.
2011Bissett A, Neu TR, De Beer D. 2011. Dissolution of Calcite in the Twilight Zone: Bacterial Control of Dissolution of Sinking Planktonic Carbonates Is Unlikely. PLoS ONE 6:e26404.
Grunke S, Felden J, Lichtschlag A, Girnth AC, de Beer D, Wenzhofer F, Boetius A. 2011. Niche differentiation among mat-forming, sulfide-oxidizing bacteria at cold seeps of the Nile Deep Sea Fan (Eastern Mediterranean Sea). Geobiology 9:330-348.
Hinck S, Mussmann M, Salman V, Neu TR, de Beer D, Jonkers H. 2011. Vacuolated Beggiatoa-like filaments from different hypersaline environments form a new genus. Environm. Microbiol. 13:3194-3205.
Schreiber F, Beutler M, Enning D, Lamprecht-Grandio M, Zafra O, Gonzalez-Pastor J, de Beer D. 2011. The role of nitric-oxide-synthase-derived nitric oxide in multicellular traits of Bacillus subtilis 3610: biofilm formation, swarming, and dispersal. BMC Microbiology 11:111.
de Beer, D. 2011. Microsensors for sediments, microbial mats, and biofilms. In V. Thiele (ed.), Encyclopedia of Geobiology, vol. 1. Springer Verlag.
Beck AJ, Janssen F, and de Beer D. 2011. The influence of phototrophic benthic biofilms on Cd, Cu, Ni, and Pb transport in permeable sediments. Biogeochemistry:102: 167-181.
Beck, M., T. Riedel, J. Graue, J. Köster, N. Kowalski, C. S. Wu, G. Wegener, Y. Lipsewers, H. Freund, M. E. Böttcher, H.-J. Brumsack, H. Cypionka, J. Rullkötter, and B. Engelen. 2011. Imprint of past and present environmental conditions on microbiology and biogeochemistry of coastal Quaternary sediments. Biogeosciences, 8, 55-68.
Girnth, A.-C., S. Grünke, A. Lichtschlag, J. Felden, K. Knittel, F. Wenzhöfer, D. de Beer, and A. Boetius. 2011. A novel, mat-forming Thiomargarita population associated with a sulfidic fluid flow from a deep-sea mud volcano. Environm. Micobiol.13:495-505. doi: 10.1111/j.1462-2920.2010.02353.x.
Kamp, A., de Beer, D., Nitsch, J.L., Lavik, G., and Stief, P. 2011. Diatoms respire nitrate to survive dark and anoxic conditions. PNAS 108 (14): 5649-5654.
Zedelius, J., R. Rabus, O. Grundmann, I. Werner, D. Brodkorb, F. Schreiber, P. Ehrenreich, A. Behrends, H. Wilkes, M. Kube, R. Reinhardt, and F. Widdel. 2011. Alkane degradation by a new type of denitrifying bacterium with possible involvement of the electron acceptor in substrate activation. Environmental Microbiology Reports 3:125–135.
2010Al-Najjar, M. A. A. 2010. Flow of light energy in benthic photosynthetic microbial mats. University of Bremen, Bremen, Germany.
Al-Najjar M.A.A., D. de Beer, B.B. Jørgensen, M. Kühl, and L. Polerecky. 2010. Conversion and conservation of light energy in a photosynthetic microbial mat ecosystem. The ISME Journal:4: 440-449 doi:10.1038/ismej.2009.121.
Barak, Y., F. Schreiber, S.H. Thorne, C.H. Contag, D. de Beer, and A.C. Matin. 2010. Role of nitric oxide in Salmonella typhimurium-mediated cancer cell killing. BMC Cancer 10:146.
Ettwig, K. F., M. K. Butler, D. Le Paslier, E. Pelletier, S. Mangenot, M.M.M. Kuypers, F. Schreiber, B. E. Dutilh, J. Zedelius, D. de Beer, J. Gloerich, H.J.C.T. Wessels, T. van Alen, F. Luesken, M.L. Wu, K.T. van de Pas-Schoonen, H.J.M. Op den Camp, E.M. Janssen-Megens, K.-J. Francoijs, H. Stunnenberg, J. Weissenbach, M.S.M. Jetten, M. Strous. 2010. Nitrite-driven anaerobic methane oxidation by oxygenic bacteria, Nature, 464, 543-548.
Gao, H., F. Schreiber, G. Collins, M. M. Jensen, J. E Kostka, G. Lavik, D. de Beer, H.-Y. Zhou, M. M. M. Kuypers. 2010. Aerobic denitrification in permeable Wadden Sea sediments, The ISME Journal, 4, 417-426.
Glas, M. S., C. A. Motti, A. P. Negri, Y. Sato, S. Froscio, A. R. Humpage, B. Krock, A. Cembella, and D. G. Bourne. 2010. Cyanotoxins are not implicated in the etiology of coral black band disease outbreaks on Pelorus Island, Great Barrier Reef. Fems Microbiology Ecology 73:43-54.
Grünke, S., A. Lichtschlag, D. de Beer, M. Kuypers, T. Lösekann, A. Ramette, and A. Boetius. 2010. Novel observations of Thiobacterium, a sulfur-storing Gammaproteobacterium producing gelatinous mats. ISME-Journal 4:1031-1043.
Ionescu, D., M. Hindiyeh, H. Malkawi, and A. Oren. 2010. Biogeography of thermophilic cyanobacteria: insights from the Zerka Ma'in hot springs (Jordan). Fems Microbiology Ecology 72:103-113.
Ionescu, D., B. Voss, A. Oren, W. R. Hess, and A. M. Muro-Pastor. 2010. Heterocyst-Specific Transcription of NsiR1, a Non-Coding RNA Encoded in a Tandem Array of Direct Repeats in Cyanobacteria. Journal of Molecular Biology 398:177-188.
Heisterkamp, I. M., A. Schramm, D. de Beer, P. Stief. 2010. Nitrous oxide production associated with coastal marine invertebrates. Mar Ecol Prog Ser 415: 1-9.
Jogler, C., M. Niebler, W. Lin, M. Kube, G. Wanner, S. Kolinko, P. Stief, A. Beck, D. de Beer, N. Petersen, Y. Pan, R. Amann, R. Reinhardt, D. Schüler. 2010. Cultivation-independent characterization of "Candidatus Magnetobacterium bavaricum" via ultrastructural, geochemical, ecological and metagenomic methods. Environmental Microbiology, 12: 2466-2478.
Kohls K, Abed RM, Polerecky L, Weber ME, and de Beer D. 2010. Halotaxis of cyanobacteria in an intertidal hypersaline microbial mat. Environmental Microbiology: 3: 567-575.
Larsen, L. H. 2010. Microbiology of nitrous oxide production from the marine mussel Mytilus edulis (Linnaeus). Master thesis:81 pages.
Lichtschlag A, Felden J, Brüchert V, Boetius A, and de Beer D. 2010. Geochemical processes and chemosynthetic primary production in different thiotrophic mats of the Håkon Mosby Mud Volcano (Barents Sea). Limnol Oceanogr:55, 931–949.
Nitsch, J. L. 2010. Nitrataufnahme, -speicherung und -verbrauch von Diatomeen. Diploma thesis:105 pages.
Pellicer i Nàcher, C., S. Sun, S. Lackner, A. Terada, F. Schreiber, Qi Zhou, and B.F. Smets. 2010. Sequential aeration of membrane-aerated biofilm reactors for high-rate autotrophic nitrogen removal. Environmental Science and Technology 44 (19), 7628-7643.
Schläppy, M.-L., M. Weber, D. Mendola, F. Hoffmann, and D. de Beer. 2010. Heterogeneous oxygenation resulting from active and passive flow in two Mediterranean sponges, Dysidea avara and Chondrosia reniformis. Limnol. Oceanogr. 55:1289-1300.
Schläppy, M. L., S. I. Schöttner, G. Lavik, M. M. M. Kuypers, D. de Beer, and F. Hoffmann. 2010. Evidence of nitrification and denitrification in high and low microbial abundance sponges. Mar Biol 157:593-602.
Schoon, R., A. Bissett, and D. de Beer. 2010. Resilience of pore-water chemistry and calcification in photosynthetic zones of calcifiying sediments. Limnol Oceanogr 55:377-385.
Schreiber, F. 2010. Bakterien bilden Stickstoffmonoxid und Lachgas im Zahnbelag. Zahnarzt und Praxis 5:350-352.
Schreiber, F., P. Stief, A. Gieseke, I. M. Heisterkamp, W. Verstraete, D. de Beer, P. Stoodley. 2010. Denitrification in human dental plaque. BMC Biology, 8: Art. No. 24.
Schwermer, C. U., T. G. Ferdelman, P. Stief, A. Gieseke, N. Rezakhani, J. van Rijn, D. de Beer, and A. Schramm. 2010. Effect of nitrate on sulfur transformations in sulfidogenic sludge of a marine aquaculture biofilter. Fems Microbiology Ecology 72:476-484.
Stief, P., A. Behrendt, G. Lavik, D. de Beer. 2010. Combined gel probe and isotope labeling technique for measuring Dissimilatory Nitrate Reduction to Ammonium in sediments at millimeter-level resolution. Applied and Environmental Microbiology, 76: 6239-6247.
Stief P, Polerecky L, Poulsen M, and Schramm A. 2010. Control of nitrous oxide emission from Chironomus plumosus larvae by nitrate and temperature. Limnol Oceanogr 55:872-884.
Stief P, and Schramm A. 2010. Regulation of nitrous oxide emission associated with benthic invertebrates. Freshwater Biology:55: 1647-1657.
Volkenborn N, Polerecky L, Wethey D, and Woodin SA. 2010. Oscillatory porewater bioadvection in marine sediments induced by hydraulic activities of Arenicola marina. Limnology and Oceanography: 55: 1231-1247
von Ohle C, Gieseke A, Nistico L, Decker EM, de Beer D, and Stoodley P. 2010. Real time microsensor measurement of local metabolic activities in ex vivo dental biofilms treated with chlorhexidine. Appl Environ Microbiol: 76: 2326-2334.
Wangpraseurt, D. 2010. In situ Characterization of Oxygen Microenvironments in Coral-algal Interactions. University of Bremen.
Wiedling, J. 2010. Biogeochemical investigations on a shallow-water methane seep in the Mediterranean Sea. University of Greifswald
Zedelius, J., and F. Schreiber. 2010. Anaerobe Methanoxidation durch oxygene Bakterien. Bioforum 33:28-30.
2009Beck A, Janssen F, Polerecky L, Herlory O, and de Beer D. 2009. Phototrophic biofilm activity and dynamics of diurnal Cd cycling in a freshwater stream. Env Sci Technol 43:7245-7251.
Beutler M, Hinck S, and de Beer D .2009. A method for imaging of low pH in live cells based on excited state saturation. J. Microb. Meth. 77:98-101.
Duperron S, de Beer D, Zbinden M, Boetius A, Schipani V, Kahil N, and Gaill F. 2009. Molecular characterization of bacteria associated with the trophosome and the tube of Lamellibrachia sp., a sibloglinid annelid from cold seeps in the eastern Mediiteranean. FEMS Microb Ecol: 69: 395-409.
Jansen S, Walpersdorf E, Werner U, Billerbeck M, Böttcher M, and de Beer D. 2009. Functioning of intertidal flats inferred from temporal and spatial dynamics of O2, H2S and pH in their surface sediments. Ocean Dynamics 59:317-332.
Nielsen M, Gieseke A, de Beer D, and Revsbech NP. 2009. Nitrate, nitrite, and nitrous oxide transformations in sediments along a salinity gradient in the Weser Estuary. Aq. Microb. Ecol. 55:39-52.
Polerecky L, Bissett A, Al-Najjar M, Faerber P, Osmers H, Suci PA, Stoodley P, and de Beer D. 2009. Modular spectral imaging system for discrimination of pigments in cells and microbial communities. Appl. Environm. Microbiol. 75:758-771.
Schreiber F, Loeffler B, Polerecky L, Kuypers MMM, and de Beer D. 2009. Mechanisms of transient nitric oxide and nitrous oxide production in a complex biofilm. ISME J 3:1301-1313.
Stief P, Poulsen M, Nielsen LP, Brix H, and Schramm A. 2009. Nitrous oxide emission by aquatic macrofauna. PNAS 106:4296-4300.
Stoodley P, de Beer D, Longwell M, Nistico L, Hall-Stoodley L, Wenig B, and Krespi YP. 2009. Tonsillolith: Not just a stone but a living biofilm. Otolaryngology–Head and Neck Surgery 141:316-321.
Weber, M. 2009. How sediment damages corals. University of Bremen.
2008Abed RMM, Kohls K, Schoon R, Scherf A, Schacht AK, Palinska AK, Al-Hassani H, Hamza W, Rullkötter J, and Golobic S. 2008. Lipid biomarkers, pigments and cyanobacterial diversity of microbial mats across intertidal flats of the arid coast of the Arabian Gulf (Abu Dhabi, UAE). FEMS Microb Ecol 65.
Beutler M, Makrogianneli K, Vermeij RJ, Keppler M, Ng T, Jovin TM, and Heintzmann R. 2008. satFRET: estimation of Förster resonance energy transfer by acceptor saturation. Eur. Biophys. J 38:69-82.
Bissett A, de Beer D, Schoon R, Reimer A, and Arp G. 2008. Microbial mediation of stromatolite formation in karst-water creeks. Limnol Oceanogr 53:1159-1168.
Bissett A, Reimer A, de Beer D, Shiraishi F, and Arp G. 2008. Metabolic microenvironmental control by photosynthetic biofilms under changing macroenvironmental temperature and pH conditions. Appl. Environm. Microbiol. 74:6306-6312.
de Beer D, Bissett A, de Wit R, Jonkers H, Köhler-Rink S, Nam H, Kim BH, Eickert G, and Grinstain M. 2008. A microsensor for carbonate ions suitable for microprofiling in freshwater and saline environments. Limnol Oceanogr Methods 6:532-541.
De Deckker P, Abed RMM, de Beer D, Hinrichs K, O'Loingsigh T, Schefuß E, Stuut JW, Tapper NJ, and van der Kaars S. 2008. Geochemical and microbiological fingerprinting of airborne dust that fell in Canberra, Australia, in October 2002. Geochem. Geophys. Geosyst. 9:doi:10.1029/2008GC002091.
Foesel BU, Gieseke A, Schwermer CU, Stief P, Koch L, Cytryn E, de la Torre JR, van Rijn J, Minz D, Drake HL, and Schramm A. 2008. Nitrosomonas Nm143-like ammonia oxidizers and Nitrospira marina-like nitrite oxidizers dominate the nitrifier community in a marine aquaculture biofilm. FEMS Microb Ecol 63:192-204.
Hoffmann F, Roy H, Bayer K, Hentschel U, Pfannkuchen M, Bruemmer F, and de Beer D. 2008. Oxygen dynamics and transport in the mediterranean sponge Aplysina aerophoba. Mar Biol 153:1257-1264.
Humphrey C, Weber M, Lott C, Cooper T, and Fabricius KE. 2008. Effects of different types of sediment, dissolved inorganic nutrients and salinity on fertilisation and embryo development in the coral Acropora millepora (Ehrenberg, 1834). Coral Reefs 27:837-850.
Kühl M, and Polerecky L. 2008. Functional and structural imaging of phototrophic microbial communities and symbioses. Aquatic Microbial Ecology 53:99-118.
Martinez-Garcia M, Stief P, Diaz-Valdes M, Wanner G, Ramos-Espla A, Dubilier N, and Anton J. 2008. Ammonia-oxidizing Crenarchaeota and nitrification inside the tissue of a colonial ascidian. Environmental Microbiology 10:2991-3001.
Polerecky L, Lott C, and Weber M. 2008. In situ measurement of gross photosynthesis using a microsensor-based light-shade shift method. Limnology and Oceanography-Methods 6:373-383.
Schreiber F, Polerecky L, and de Beer D. 2008. Nitric oxide microsensor for high spatial resolution measurements in biofilms and sediments. Anal. Chem. 80:1152-1158.
Schreiber, F., and U. Szewzyk. 2008. Environmentally relevant concentrations of pharmaceuticals influence the initial adhesion of bacteria. Aquatic Toxicology 87:227-233.
Shiraishi F, Bisset A, de Beer D, Reimer A, and Arp G. 2008. Photosynthesis, respiration and exopolymer calcium-binding in biofilm calcification (Westerhöfer and Deinschwanger Creek, Germany). Geomicrobiol. J.: 25: 83-94.
Schwermer CU, Lavik G, Abed RMM, Dunsmore B, Ferdelman TG, Stoodley P, Gieseke A, and de Beer D. 2008. Impact of nitrate on the structure and function of bacterial biofilm communities in pipelines used for injection of seawater into oil fields. Appl. Environm. Microbiol. 74:2841-2851.
Sher Y, Schneider K, Schwermer CU, and van Rijn J. 2008. Sulfide induced nitrate reduction in the sludge of an anaerobic digester of a zero-discharge recirculating mariculture system. Water Research 42:4386-4392.
Shiraishi F, Reimer A, Bisset A, de Beer D, and Arp G. 2008. Microbial effects on biofilm formation, ambient water chemistry and stable sotope records in a highly supersaturated setting (Westerhöfer Bach, Germany). Palaeogeography Palaeoclimatology Palaeoecology 262:91-106.
Werner U, Blazejak A, Bird P, Eickert G, Schoon R, Abed RMM, Bissett A, and de Beer D. 2008. Microbial photosynthesis in coral reef sediments (Heron Reef, Australia). Estuarine, Coastal and Shelf Science 76:876 – 888.
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