2009

Bissett A, de Beer D, Schoon R, Sharaishi F, Reimer A, and G. A (2009) Metabolic microenvironmental control by biofilms under changing macroenvironmental temperature and pH conditions. Appl Environ Microbiol 75:758-771.

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: in press.

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.

Stief P, Nazarova L, and de Beer D (2005) Chimney construction by Chironomus riparius larvae in response to hypoxia:Microbial implications for freshwater sediments. Microbial Ecology 48:145-153.

2008

Bachar A, Polerecky L, Fisher J, Vamvakopoulos K, de Beer D, and Jonkers HM (2008) Two-dimensional mapping of photopigments distribution and activity of Chloroflexus-like bacteria in a hypersaline microbial mat. FEMS Microb Ecol:1-
15.

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: accepted.

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.

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.

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.

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.

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.:Accepted.

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.

Stoodley P, Wefel J, Gieseke A, de Beer D, and von Ohle C (2008) Interactions Between Fluoride, Biofilm Plaque and Hydrodynamics on Caries. JADA 139:1182-1190.

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.

2007

Abed AMM, Zeina B, Al-Thukair A, and de Beer D (2007) Phylogenetic diversity and activity of aerobic heterotrophic bacteria from a hypersaline oil-polluted microbial mat. Syst. Appl. Microbiol. 30:319-330.

Abed R, Kohls K, and de Beer D (2007) Effect of salinity changes on the bacterial diversity, photosynthesis and oxygen consumption of cyanobacterial mats from an intertidal flat of the Arabian Gulf. Environm. Microbiol. 9:1384-1392.

Bissett A, de Beer D, Schoon R, Shaaishi F, Reimer A, and Arp G (2007) Microbial mediation of tufa formation in karst-water creeks. Limnol Oceanogr: Accepted.

Filthuth H, Eickert G, Faerber P, Jonkers HM, Polerecky L, and de Beer D (2007) A novel radioactivity microsensor for high spatial resolution measurements of beta radiation. Limnol Oceanogr Methods 5.

Hinck S, Neu T, Lavik G, Mussmann M, de Beer D, and Jonkers HM (2007) Physiological adaptation of a nitrate-storing Beggiatoa sp. to diel cycling in a phototrophic hypersaline mat. Appl Environ Microbiol 73:7013-7022.

Mußmann M, Hu FZ, Richter M, de Beer D, Preisler A, Jørgensen BB, Huntemann M, Glöckner FO, Amann R, Koopman WH, Lasken RS, Janto B, Hogg J, Stoodley P,
Boissy R, and Ehrlich GD (2007) Insights into the Genome of Large Sulfur Bacteria Revealed by Analysis of Single Filaments. PLoS Biology 5:1923-1937.

Polerecky L, Bachar A, Schoon R, Grinstein M, Jørgensen BB, de Beer D, and Jonkers H (2007) Contribution of Chloroflexus respiration to oxygen cycling in a hypersaline microbial mat from Lake Chiprana, Spain. Environmental Microbiology 9:2007–2024.

Polerecky L, Bissett A, Stoodley P, Suci P, and de Beer D. 2007. Presented at the 4th ASM conference on Biofilms, Quebec City, Canada.

Preisler A, de Beer D, Lichtschlag A, Lavik G, Boetius A, and Jørgensen BB (2007) Biological and chemical sulfide oxidation in a Beggiatoa inhabited marine sediment. ISME-Journal 1:341-353.

Røy H, Lee JS, Jansen S, and de Beer D (2007) Tide-driven deep pore-water flow in intertidal sand flats. Limnol Oceanogr 53:1521-1530.

Schläppy ML, Hoffmann F, Röy H, Wijffels RH, Mendola D, Sidri M, and de Beer D (2007) Oxygen dynamics and flow patterns of Dysidea avara (Porifera, Demospongiae). Journal of the Marine Biological Association of the United Kingdom. 87:1677-1682.

Schreiber F, Polerecky L, and de Beer D (2007) A Robust Nitric Oxide Microsensor for High Spatial Resolution Measurements in Biofilms and Sediments. Anal Chem 80:S1-8.

Volkenborn N, Polerecky L, Hedtkamp SIC, van Beusekom J, and de Beer D (2007) Bioturbation and bioirrigation extend the open exchange regions in permeable sediments. Limnol Oceanogr 52:1898-1909.

Weber M, Faerber P, Meyer V, Lott C, Eickert G, Fabricius KE, and de Beer D (2007) In situ applications of a new diver-operated motorized microsensor profiler. Env Sci Technol: in press.

2006

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

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

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

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

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

Green M, Beliavski M, Denekamp N, Gieseke A, de Beer D, and Tarre S (2006) 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.

Ludwig R, Pringault O, DeWit R, de Beer D, and Jonkers HM (2006) 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.

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

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

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

Stoodley P, Dodds I, de Beer D, Lappin Scott H, and Boyle JD (2006) The development and flow of biofilms through porous media under laminar and turbulent conditions.

Van Gaever S, Moodley L, de Beer D, and Vanreusel A (2006) Meiobenthos at the Arctic Håkon Mosby Mud Volcano, with a parental-caring nematode thriving in sulphide-rich sediments. Mar. Ecol. Prog. Ser 321:143–155.

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

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

2005

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

Collins G, Mahony T, McHugh S, Gieseke A, de Beer D, and O'Flaherty V (2005) Distribution, dynamics and in situ ecophysiology of Crenarchaeota in anaerobic wastewater treatment granular biofilms. Wat. Sci. Tech. 52:233-239.

Collins G, O'Connor L, Mahony T, Gieseke A, de Beer D, and O'Flaherty V (2005) Distribution, localization and phylogeny of abundant populations of Crenarchaeoty in anaerobic granular sludge. Appl. Environ. Microbiol. 71:7523- 7527.

Cytryn E, Minz D, Gelfand I, Neori A, Gieseke A, de Beer D, and van Rijn J (2005) Sulfide oxidising activity and bacterial community structure in a fluidized bed reactor from a zero-discharge mariculture system. Environ. Sci. Technol. 39:1802-1810.

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

Flies C, Jonkers HM, de Beer D, Bosselmann K, Böttcher ME, and Schüler D (2005) Diversity and vertical distribution of magnetotactic bacteria along chemical gradients in freshwater microcosms. FEMS Microb Ecol 52:185-195.

Gieseke A, Nielsen J, Amann R, and de Beer D (2005) In situ substrate conversion and assimilation by nitrifying bacteria in a model biofilm. Environm. Microbiol.: accepted.

Jonkers HM, Koh I-O, Behrend P, Muyzer G, and de Beer D (2005) Aerobic organic carbon mineralization by sulfate-reducing bacteria in the oxygen-saturated photic zone of a hypersaline microbial mat. Microbial Ecology 49:1-10.

Ludwig R, Al-Horani FA, de Beer D, and Jonkers HM (2005) Photosynthesis controlled calcification in a hypersaline microbial mat. Limnology & Oceanography 50:1836-1843.

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

Schoenberg C, de Beer D, and Lawton A (2005) Oxygen microsensor studies on zooxanthellate clionaid ponges from the Costa Brava, Mediteranean Sea. J. Phycol. 41:774-779.

2004	Stief, P., D. Altmann, D. de Beer, R. Bieg and A. Kureck (2004). "Microbial activities in the burrow environment of the potamal mayfly Ephoron virgo." Freshwater Biol. 49: 1152-1163.
2003	Al-Horani, F. A., S. M. Al-Mograbi and D. De Beer (2003). "Microsensor study of photosynthesis and calcification in the scleractinian coral Galaxea fascicularis: active internal carbon cycling." J. Exp. Mar. Biol. Ecol. 288: 1-15.
	Altmann, D., P. Stief, R. Amann, D. De Beer and A. Schramm (2003). " In situ distribution and activity of nitrifying bacteria in freshwater sediment." Environmental Microbiology 5(9): 798-803.
	Berg, P., H. Roey, F. Janssen, V. Meyer, B. B. Jørgensen, M. Huettel and D. De Beer (2003). Measuring oxygen uptake by marine sediments using a new eddy correlation technique. Aquatic Sciences Meeting, American Society of Limnology and Oceanography, Salt LAke City, USA.
	Berg, P., H. Roey, F. Janssen, V. Meyer, B. B. Jørgensen, M. Huettel and D. De Beer (2003). "Oxygen uptake by aquatic sediments measured with a novel non-invasive eddy correlation technique." Mar. Ecol. Prog. Ser. 261: 75-83.
	Jonkers, H. M., R. Ludwig, R. De Wit, O. Pringault, G. Muyzer, H. Niemann, N. Finke and D. De Beer (2003). "Structural and functional analysis of a microbial mat ecosystem from a unique permanent hypersaline inland lake: 'La Salada de Chiprana' (NE Spain)." FEMS Microbiology Ecology.
	Stief, P., A. Schramm, D. Altmann and D. De Beer (2003). "Temporal variation of nitrification rates in experimental freshwater sediments enriched with ammonia or nitrite." FEMS Microbiology Ecology 46: 63-71.
2002	Grötzschel, S. and D. De Beer (2002). "Effect of oxygen concentration on photosynthesis and respiration in two hypersaline microbial mats." Microbial Ecology 44(3): 208-216.
	Gieseke, A., J. L. Nielsen and D. De Beer (2002). Beta microimaging: a new high resolution technique to monitor in situ biomass production in biofilms. International Specialized Conference on Biofilm Monitoring, Porto.
	Schulz, H. and D. De Beer (2002). "Uptake rates of oxygen and sulfide measured with individual Thiomargarita namibiensis cells by using microelectrodes." Appl. Environm. Microbiol. 68(11): 5746-5749.
	Köhler-Rink, S. and D. De Beer (2002). Mikrosensoren für die Meeresbiologie. Der Ozean - Lebensraum und Klimasteuerung. G. Hempel, Hinrichsen, F. Bremen, Wittheit zu Bremen: 91-98.
	Grötzschel, S., J. Köster, R. M. M. Abed and D. De Beer (2002). "Degradation of petroleum model compounds immobilized on clay by a hypersaline microbial mat." Biodegradation 13(4): 273-283.
	Abed, R. M. M., N. M. D. Safi, J. Köster, D. De Beer, J. Rullkötter and F. Garcia-Pichel (2002). "Microbial Diversity of a Heavily Polluted Microbial Mat and Its Community Changes Following Degradation of Petroleum Compounds." Appl. Environm. Microbiol. 68(4): 1674-1683.
	Grötzschel, S., R. M. M. Abed and D. De Beer (2002). "Metabolic shifts in hypersaline cyanobacterial mats upon addition of organic substrates." Environmental Microbiology 4(11): 683-695
	Okabe, S., C. M. Santegoeds and D. De Beer (2002). "Effect of nitrite and nitrate on in situ sulfide production in an activated sludge immobilized agar gel film as determined by use of microelectrodes." Biotechnol. Bioeng. 81(5): 570-577.
	Okabe, S., C. M. Santegoeds, Y. Watanabe and D. De Beer (2002). "Successional Development of Sulfate-Reducing Bacterial Populations and Their Activities in An Activated Sludge Immobilized Agar Gel Film." Biotechnol. Bioeng. 78(2): 120-130.
	Stief, P. and D. De Beer (2002). "Bioturbation effects of Chironomus riparius (Diptera) on microbial nitrogen conversions in freshwater sediments as measured using microsensors and microbiological assays." Aquatic Microbial Ecology 27: 175-185.
	Stief, P., D. De Beer and D. Neumann (2002). "Small scale distribution of nitrite in freshwater microcosms: The role of nitrate and oxygen availability, and sediment permeability." Microbial Ecology 43(3): 367-378.
	Al-Horani, F. A., S. M. Al-Mograbi and D. De Beer (2002). "The mechanism of calcification and its relation to photosynthesis and respiration in the scleractian coral Galaxea fascicularis." Marine Biology 142(3): 419-426.
	Al-Horani, F. A., S. M. Al-Mograbi and D. De Beer (2002). "Microsensor study of photosynthesis and calcification in the scleractinian coral Galaxea fascicularis:active internal carbon cycling." J. Exp. Mar. Biol. Ecol. 288(1): 1-15.
2001	Wieland, A., D. De Beer, D. van Dusschoten, L. R. Damgaard, M. Kuehl and H. van As (2001). "Fine-scale measurement of diffusivity in a microbial mat with NMR imaging." Limnol. Oceanogr. 44(3): 248-259.
	De Beer, D. (2001). Microsensor studies of oxygen, carbon and nitrogen cycles in lake sediments and microbial mats. Environmental Electrochemistry: Analyses of Trace Element Biogeochemistry. M. Taillefert and T. F. Rozan. Washington DC. American Chemical Society Symposium Series 811: 227-246.
	De Beer, D. and A. J. W. Larkum (2001). "Photosynthesis and calcification in the calcifying algae Halimeda discoidea studied with microsensors." Plant, Cell & Environment 24(11): 1209-1217.
	Dubilier, N., C. Mülders, T. Ferdelman, D. De Beer, A. Pernthaler, M. Klein, M. Wagner, C. Erseus, F. Thiermann, J. Krieger, O. Giere and R. Amann (2001). "Endosymbiontic sulphate-reducing and sulphide-oxidising bacteria in an oligochaete worm." Nature 411: 298-302.
	Hanstein, S., D. De Beer and H. H. Felle (2001). "Miniaturised carbon dioxide sensor designed for measurements within plant leaves." Sensors and Actuators B 81: 107-114.
2000	De Beer, D., M. Kühl, N. Stambler and L. Vaki (2000). "A microsensor study of light enhanced Ca2+ uptake and photosynthesis in the reef-building hermatypic coral Favia sp." Mar. Ecol. Prog.Ser. 194: 75-85.
	Schramm, A., D. De Beer, A. Gieseke and R. Amann (2000). "Microenvironments and distribution of nitrifying bacteria in a membrane bound biofilm." Environm. Microbiol. 2(6): 680-686.
	De Beer, D. (2000). Potentiometric microsensors for in situ measurements in aquatic environments. In situ monitoring of aquatic systems: chemical analysis and speciation. J. Buffle and G. Horvai. London, Wiley & Sons: 161-194.
	De Beer, D. and M. Kühl (2000). Interfacial processes, gradients and metabolic activity in microbial mats and biofilms. The benthic boundary layer. B. Boudreau and B. B. Jørgensen: 374-394.
1999	De Beer, D. (1999). Use of microelectrodes to measure in situ microbial activities in biofilms, sediments and microbial mats. Molecular Microbial Ecology Manual. A. D. L. Akkermans, J. D. van Elsas and F. J. de Bruyn, Kluwer Academic Press. 8.1.3: 1-23.
	Schramm, A., D. De Beer, J. C. van den Heuvel, S. P. P. Ottengraf and R. Amann (1999). "Microscale distribution of populations and activities of Nitrosospira and Nitrospira spp. along a macroscale gradient in a nitryífying bioreactor: quantification by in situ hybridisation and the use of microsensors." Appl. Environ. Microbiol. 65(9): 3690-3696
	Santegoeds, C. M., L. R. Damgaard, G. Hesselink, J. Zopfi, P. Lens, G. Muyzer and D. De Beer (1999). "Distribution of sulfate-reducing and methanogenic bacteria in anaerobic aggregates determined by microsensor and molecular analysis." Appl. Environm. Microbiol. 65(10): 4618-4629.
	Verschuren, P. G., J. L. v. d. Baan, R. Blaauw, D. d. Beer and J. C. v. d. Heuvel (1999). "A nitrate-selective microelectrode based on a lipophilic derivative of iodocobalt (III) salen." Fresenius J Anal Chem 364: 595-598.
	De Beer, D. (1999). Micro-electrodes. Immobilized cells. R. Wijffels. Heidelberg, Germany, Springer Verlag: 85-100.
	De Beer, D. and A. Schramm (1999). "Micro-environments and mass transfer phenomena in biofilms studied with microsensors." Wat.Sci.Technol. 39(7): 173-178.
	Schramm, A., C. M. Santegoeds, H. K. Nielsen, H. Ploug, M. Wagner, M. Pribyl, J. Wanner, R. Amann and D. De Beer (1999). "On the occurrence of anoxic microniches, denitrification, and sulfate reduction in aerated activated sludge." Appl. Environ. Microbiol. 65(9): 4189-4196.