Publications

2015

1. Brocke HJ, Wenzhoefer F, de Beer D, Mueller B, van Duyl FC, Nugues MM. 2015. High dissolved organic carbon release by benthic cyanobacterial mats in a Caribbean reef ecosystem. Scientific Reports 5.
2. Christine Heim C, Simon K, Ionescu D, Reimer A, de Beer D, Quéric NV, Reitner J, Thiel V. 2015. Assessing the utility of trace and rare earth elements as biosignatures in microbial iron oxyhydroxides. Front. Earth Sci. 3.
3. Ionescu D, Heim C, Polerecky L, Ramette A, Haeusler S, Bizic-Ionescu M, Thiel V, D. dB. 2015. Diversity of Iron Oxidizing and Reducing Bacteria in Flow Reactors in the Äspö Hard Rock Laboratory. Geomicrobiology Journal 32:207-220.
4. Ionescu D, Heim C, Polerecky L, Thiel V, de Beer D. 2015. Biotic and abiotic oxidation and reduction of iron at circumneutral pH are inseparable processes under natural conditions. Geomicrobiology Journal 32:221-230.
5. Klatt J, M., Al-Najjar MAA, Yilmaz P, Lavik G, de Beer D, Polerecky L. 2015. Anoxygenic photosynthesis controls oxygenic photosynthesis in a cyanobacterium from a sulfidic spring. Appl Environ Microbiol:accepted.
6. Klatt JM, Haas S, Yilmaz P, de Beer D, Polerecky L. 2015. Hydrogen sulfide can inhibit and enhance oxygenic photosynthesis in a cyanobacterium from sulfidic springs. Environ. Microbiol.:accepted.
7. Schutting S, Jokic T, Strobl M, Borisov SM, de Beer D, Klimant I. 2015. NIR Optical Carbon Dioxide Sensors Based on Highly Photostable Dihydroxy-aza-BODIPY Dyes. J. Mater. Chem. C:accepted.

2014

1. Abed RMM, de Beer D, Stief P. 2014. Functional-structural analysis of nitrogen-cycle bacteria in a hypersaline mat from the Omani desert. Geomicrobiology Journal:in press.
2. Abed RMM, Polerecky L, Al-Habsi A, Oetjen J, Strous M, de Beer D. 2014. Rapid Recovery of Cyanobacterial Pigments in Desiccated Biological Soil Crusts following Addition of Water. PLoS ONE 9:e112372.
3. Al-Thani R, Al-Najjar MAA, Al-Raei A, Ferdelman A, Thang NM, Ali I, Al-Ansi M, de Beer D. 2014. Community structure and activity of highly dynamic and nutrient limited hypersaline microbial mat in Um Alhool Sabkha, Qatar. PLoS ONE:e92405.
4. Behrendt A, Tarre S, Beliavski M, Green M, Klatt J, de Beer D, Stief P. 2014. Effect of high electron donor supply on dissimilatory nitrate reduction pathways in a bioreactor for nitrate removal. Bioresource Technology 171:7.
5. Beutler M, Heisterkamp IM, Piltz B, Stief P, de Beer D. 2014. Microscopic oxygen imaging based on fluorescein bleaching efficiency measurements. Microscopy Research and Technique 77:7.
6. Chennu A, Färber P, Volkenborn N, Al-Najjar MAA, Janssen F, de Beer D. 2014. Hyperspectral imaging of the microscale distribution and dynamics of microphytobenthos in intertidal sediments. Limnol Oceanogr Methods 11:511-528.
7. Feseker T, Boetius A, Blandin J, Wenzhöfer F, Foucher JP, Harmegnies F, de Beer D. 2014. Eruption of the Håkon Mosby mud volcano recorded by the long-term observatory on mud-volcano eruptions (LOOME) between 2009 and 2010. , Pangaea.
8. Feseker T, Boetius A, Wenzhoefer F, Blandin J, Olu K, Yoerger D, Camilli R, German C, de Beer D. 2014. Eruption of a deep-sea mud volcano triggers rapid sediment movement. Nature Communications 5:1-8.
9. äusler S, Holtappel M, de Beer D, Ionescu D. 2014. Sulfate reduction and sulfide oxidation in extremely steep salinity gradients formed by freshwater springs emerging into the Dead Sea. FEMS Microb Ecol 90:956-969.
11. Häusler S, Noriega-Ortega BO, Polerecky L, Meyer V, de Beer D, Ionescu D. 2014. Microenvironments of reduced salinity harbour biofilms in Dead Sea underwater springs. Environmental Microbiology Reports 6:152–158.
12. Häusler S, Weber M, de Beer D, Ionescu D. 2014. Salinity adaptation of oxygenic phototrophs to salinity gradients formed by underwater freshwater springs in the Dead Sea. Extremophiles 18:1085-1094.
13. Ionescu D, Buchmann B, Heim C, Häusler S, de Beer D, Polerecky L. 2014. Oxygenic photosynthesis as a protection mechanism for cyanobacteria against iron-encrustation in environments with high Fe2+ concentrations. Front. Microbio. 5.
14. Ionescu D, Heim C, Thiel V, Ramette A, Reitner J, de Beer D. 2014. Diversity of iron oxidizing and reducing bacteria in bioreactors set in the Äspö Hard Rock Laboratory. Geomicrobiology Journal:in press.
15. onescu D, Polerecky L, Heim C, Thiel V, Reitner J, de Beer D. 2014. Biotic and abiotic iron precipitation in iron mineralization using the Äspö HRL as a model system. Geomicrobiology Journal:accepted.
16. Madden P, Al-Raei AM, Enright AM, Chinalia FA, de Beer D, O'Flaherty V, Collins G. 2014. Effect of sulfate on low-temperature anaerobic digestion. Front. Microbio. doi: 10.3389/fmicb.2014.00376
17. Raulf FF, Fabricius K, Uthicke S, de Beer D, Abed RMM, Ramette A. 2014. Changes in microbial communities in coastal sediments along natural CO2 gradients at a volcanic vent in Papua New Guinea. Environ. Miicrobiol.:in press.
18. Schreiber F, Stief P, Kuypers MMM, de Beer D. 2014. Nitric oxide turnover in permeable river sediment. Limnol Oceanogr 59:1310-1320.
19. Schutting S, Klimant I, de Beer D, Borisov SM. 2014. New highly fluorescent pH indicator for ratiometric RGB imaging of pCO2. Methods Appl. Fluoresc. 2 024001 2:024001.
20. Sevilgen DS, de Beer D, Al-Handal AY, Brey T, Polerecky L. 2014. Oxygen budgets in subtidal arctic (Kongsfjorden, Svalbard) and temperate (Helgoland, North Sea) microphytobenthic communities. MEPS 504:27-42.
21. Spitzer S, Brinkmann N, Reimer A, Ionescu D, Friedl T, de Beer D, Arp G. 2014. Effect of variable pCO2 on Ca2+ removal and potential calcification of cyanobacterial biofilms - an experimental microsensor study. Geomicrobiology Journal:in press.
22. Stemmer K, Brey T, Glas M, Beutler M, Schalkhausser B, de Beer D. 2014. In situ measurements of pH, Ca2+ and DIC dynamics within the extrapallial fluid of the ocean quahog Arctica islandica. Journal of Experimental Marine Biology and Ecology:accepted.
23. Stief P, Fuchs-Ocklenburg S, Kamp A, Manohar CS, Houbraken J, Boekhout T, de Beer D, Stoeck T. 2014. Dissimilatory nitrate reduction by Aspergillus terreus isolated from the seasonal oxygen minimum zone in the Arabian Sea. BMC Microbiology 14:http://www.biomedcentral.com/1471-2180/1414/1435.

2013

1.Abed RMM, Lam P, de Beer D, Stief P. 2013. High rates of denitrification and nitrous oxide emission in arid biological soil crusts from the Sultanate of Oman. ISME J 7:1862–1875.
2.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.
3.Ionescu D, Reimer A, Zippel B, Spring S, Schneider D, Spitzer S, Brinkmann N, de Beer D, Reitner J, Arp G. 2013. Calcium dynamics in microbialite-forming exopolymer-rich mats on the atoll of Kiritimati, Republic of Kiribati, Central Pacific. Geobiology.
4.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.
5.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.
6.Schutting S, Klimant I, de Beer D, Borisov SM. 2013. New highly fluorescent pH indicator for ratiometric RGB imaging of pCO2 Methods Appl. Fluoresc 2:024001.
7.Sevilgen DS, de Beer D, Al-Handal AY, Polerecky L. 2013. Oxygen dynamics in subtidal arctic (Kongsfjorden, Svalbard) and temperate (Helgoland, North Sea) microphytobenthos communities. Polar Biology:submitted.
8.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.
9.Winkel M, de Beer D, Lavik G, Peplies J, Mußmann M. 2013. Close association of active nitrifiers with Beggiatoa mats covering deep-sea hydrothermal sediments. Environmental Microbiology 16:1612–1626.

2012

1.Abed RMM, Ramette A, Hübner 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 80:294–304.
2.Al-Najjar MAA, de Beer D, Kuhl M, Polerecky L. 2012. Light utilization efficiency in photosynthetic microbial mats. Environmental Microbiology 14:982–992.
3.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.
4.Gao H, Matyka M, Liu B, Khalili A, Kostka JE, Collins G, Jansen S, Holtappels M, Jensen MM, Badewien TH, Beck M, Grunwald M, de Beer D, Lavik G, Kuypers MMM. 2012. Intensive and extensive nitrogen loss from intertidal permeable sediments of the Wadden Sea. Limnol Oceanogr 57:185-198.
5.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.
6.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.
7.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 124C:413-420.
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 105:130-145.
9.Long MH, Berg P, de Beer D, Zieman JC. 2012. In Situ Coral Reef Oxygen Metabolism: an Eddy Correlation Study. PLoS ONE:e58581.
10.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.
11.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:e31192.
12.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.
13.Yanagawa K, Morono Y, De Beer D, Haeckel M, Sunamura M, Futigami T, Hoshino T, Terada H, Nakamura KI, Urabe T, Rehder G, Boetius A, Inagaki F. 2012. Metabolically active microbial communities in marine sediment under high-CO2 and low-pH extremes. ISME J 7:555–567.

2011

1.Beck AJ, Janssen F, De Beer D. 2011. The influence of phototrophic benthic biofilms on Cd, Cu, Ni, and Pb transport in permeable sediments. Biogeochem. 102.
2.Bissett 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.
3.de Beer D. 2011. Microsensors for sediments, microbial mats, and biofilms, p. 658-662. In Reitner J, Thiel V (ed.), Encyclopedia of Geobiology, vol. XXVIII. Springer Verlag.
4.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.
5.Hamza W, Rizk M, Al-Hassini H, Stuut J, de Beer D. 2011. Dust Storms over the Arabian Gulf: An optimistic vision toward climate change consequences. Journal Aquatic Ecosystem Health and Management Society 14:260-268.
6.Hinck S, Mussmann M, Salman V, Neu TR, de Beer D, Jonkers H. 2011. Vacuolated Beggiatoa-like filaments from different hypersaline environments form a novel genus. Environm. Microbiol. 13:3194-3205.
7.Kamp A, de Beer D, Nitsch JL, Lavik G, Stief P. 2011. Diatoms respire nitrate to survive dark and anoxic conditions. Proc Natl Acad Sci U S A 108:5649-5654.
8.Lichtschlag A, Felden J, Wenzhoefer F, Schubotz F, Boetius A, De Beer D. 2011. Methane and sulfide fluxes in permanent anoxia: In situ studies at the Dvurechenskii mud volcano (Sorokin Trough, Black Sea). Geoch.Cosmoc.Acta 74:5002-5018.
9.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.

2010

1.Barak Y, Schreiber F, Thorne SH, Contag CH, de Beer D, Matin A. 2010. Role of nitric oxide in Salmonella typhimurium-mediated cancer cell killing. BMC Cancer 10:146-152.
2.Ettwig KF, Butler MK, Le Paslier D, Pelletier E, Mangenot S, Kuypers MMM, Schreiber F, Dutilh BE, Zedelius J, de Beer D, Gloerich J, Wessels HJCT, van Alen T, Luesken F, Wu ML, van de Pas-Schoonen KT, Op den Camp HJM, Janssen-Megens EM, Francoijs K, Stunnenberg H, Weissenbach J, Jetten MSM, Strous M. 2010. Nitrite-driven anaerobic methane oxidation by oxygenic bacteria. Nature 464:543-548.
3.Gao H, Schreiber F, Collins G, Jensen MM, Kostka JE, Lavik G, de Beer D, Zhou HY, Kuypers MMM. 2010. Aerobic denitrification in permeable Wadden Sea sediments. Isme Journal 4:417-426.
4.Gao H, Schreiber F, Collins G, Jensen MM, Kostka JE, Lavik G, de Beer D, Zhou HY, Kuypers MMM. 2010. Aerobic denitrification in permeable Wadden Sea sediments. Isme Journal 4:417-426.
5.Girnth AC, Gruenke S, Lichtschlag A, Felden J, Knittel K, Wenzhoefer F, de Beer D, Boetius A. 2010. Novel, mat-forming Thiomargarita spp. thrive on a sulfidic fluid outflow at the Amon mud volcano (Eastern Mediterranean). Geochimica Et Cosmochimica Acta 74:A335-A335.
6.Grünke S, Lichtschlag A, de Beer D, Kuypers M, Lösekann T, Ramette A, Boetius A. 2010. Novel observations of Thiobacterium, a sulfur-storing Gammaproteobacterium producing gelatinous mats. ISME-Journal 4:1031–1043.
7.Heisterkamp IM, Schramm A, de Beer D, Stief P. 2010. Nitrous oxide production associated with coastal marine invertebrates. Marine Ecology-Progress Series 415:1-9.
8.Jogler C, Niebler M, Lin W, Kube M, Wanner G, Kolinko S, Stief P, Beck AJ, de Beer D, Petersen N, Pan Y, Amann R, Reinhardt R, Schueller D. 2010. Cultivation-independent characterization of 'Candidatus Magnetobacterium bavaricum' via ultrastructural, geochemical, ecological and metagenomic methods. Environmental Microbiology 12:2466-2478.
9.Kohls K, Abed RM, Polerecky L, Weber ME, de Beer D. 2010. Halotaxis of cyanobacteria in an intertidal hypersaline microbial mat. Environmental Microbiology 12:567-574.
10.Lichtschlag A, Felden J, Brüchert V, Boetius A, 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.
11.Schläppy ML, Schottner SI, Lavik G, Kuypers MMM, de Beer D, Hoffmann F. 2010. Evidence of nitrification and denitrification in high and low microbial abundance sponges. Mar Biol 157:593-602.
12.Schläppy ML, Weber M, Mendola D, Hoffmann F, de Beer D. 2010. Heterogeneous oxygenation resulting from active and passive flow in two Mediterranean sponges, Dysidea avara and Chondrosia reniformis. Limnol Oceanogr 55:1289-1300.
13.Schoon R, Bissett A, de Beer D. 2010. Resilience of pore-water chemistry and calcification in photosynthetic zones of calcifying sediments. Limnology and Oceanography 55:377-385.
14.Schreiber F, Stief P, Gieseke A, Heisterkamp I, Verstraete W, De Beer D, Stoodley P. 2010. Denitrification in human plaque. BMC Biology 8.
15.Schwermer CU, Ferdelman TG, Stief P, Gieseke A, Rezakhani N, van Rijn J, de Beer D, Schramm A. 2010. Effect of nitrate on sulfur transformations in sulfidogenic sludge of a marine aquaculture biofilter. Fems Microbiology Ecology 72:476-484.
16.Stief P, Behrendt A, Lavik G, De Beer D. 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.
17.von Ohle C, Gieseke A, Nistico L, Decker EM, de Beer D, 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.

2009

1.Al-Najjar MAA, de Beer D, Jørgensen BB, Kühl M, Polerecky L. 2009. Conversion and conservation of light energy in a photosynthetic microbial mat ecosystem. The ISME Journal 4:440-449.
2.Beck A, Janssen F, Polerecky L, Herlory O, de Beer D. 2009. Phototrophic biofilm activity and dynamics of diurnal Cd cycling in a freshwater stream. Env Sci Technol 43:7245-7251.
3.Beutler M, Hinck S, 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.
4.Duperron S, de Beer D, Zbinden M, Boetius A, Schipani V, Kahil N, 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.
5.Jansen S, Walpersdorf E, Werner U, Billerbeck M, Böttcher M, 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.
6.Joye SB, de Beer D, Cook PLM. 2009. Biogeochemical dynamics of coastal tidal flats, p. 345-365. In Perillo GME (ed.), Coastal wetlands an intergrated ecosystem approach. Elsevier, Amsterdam.
7.Nielsen M, Gieseke A, de Beer D, 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.
8.Polerecky L, Bissett A, Al-Najjar M, Faerber P, Osmers H, Suci PA, Stoodley P, de Beer D. 2009. Modular spectral imaging system for discrimination of pigments in cells and microbial communities. Appl. Environm. Microbiol. 75:758-771.
9.Schreiber F, Loeffler B, Polerecky L, Kuypers MMM, de Beer D. 2009. Mechanisms of transient nitric oxide and nitrous oxide production in a complex biofilm. ISME J 3:1301-1313.
10.Stoodley P, de Beer D, Longwell M, Nistico L, Hall-Stoodley L, Wenig B, Krespi YP. 2009. Tonsillolith: Not just a stone but a living biofilm. Otolaryngology–Head and Neck Surgery 141:316-321.

2008

1.Bachar A, Polerecky L, Fisher J, Vamvakopoulos K, de Beer D, 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.
2.Bissett A, de Beer D, Schoon R, Reimer A, Arp G. 2008. Microbial mediation of stromatolite formation in karst-water creeks. Limnol Oceanogr 53:1159-1168.
3.Bissett A, Reimer A, de Beer D, Shiraishi F, Arp G. 2008. Metabolic microenvironmental control by photosynthetic biofilms under changing macroenvironmental temperature and pH conditions. Appl. Environm. Microbiol. 74:6306-6312.
4.de Beer D, Bissett A, de Wit R, Jonkers H, Köhler-Rink S, Nam H, Kim BH, Eickert G, Grinstain M. 2008. A microsensor for carbonate ions suitable for microprofiling in freshwater and saline environments. Limnol Oceanogr Methods 6:532-541.
5.De Deckker P, Abed RMM, de Beer D, Hinrichs K, O'Loingsigh T, Schefuß E, Stuut JW, Tapper NJ, 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.
6.Hoffmann F, Roy H, Bayer K, Hentschel U, Pfannkuchen M, Bruemmer F, de Beer D. 2008. Oxygen dynamics and transport in the mediterranean sponge Aplysina aerophoba. Mar Biol 153:1257-1264.
7.Schreiber F, Polerecky L, de Beer D. 2008. Nitric oxide microsensor for high spatial resolution measurements in biofilms and sediments. Anal. Chem. 80:1152-1158.
8.Schwermer CU, Lavik G, Abed RMM, Dunsmore B, Ferdelman TG, Stoodley P, Gieseke A, 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.
9.Shiraishi F, Bisset A, de Beer D, Reimer A, Arp G. 2008. Photosynthesis, respiration and exopolymer calcium-binding in biofilm calcification (Westerhöfer and Deinschwanger Creek, Germany). Geomicrobiol. J. 25:83-94.
10.Shiraishi F, Reimer A, Bisset A, de Beer D, 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.
11.Stoodley P, Wefel J, Gieseke A, de Beer D, von Ohle C. 2008. Interactions Between Fluoride, Biofilm Plaque and Hydrodynamics on Caries. JADA 139:1182-1190.
12.Werner U, Blazejak A, Bird P, Eickert G, Schoon R, Abed RMM, Bissett A, de Beer D. 2008. Microbial photosynthesis in coral reef sediments (Heron Reef, Australia). Estuarine, Coastal and Shelf Science 76:876 – 888.

2007

1.Abed AMM, Zeina B, Al-Thukair A, 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.
2.Abed R, Kohls K, 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.
3.Filthuth H, Eickert G, Faerber P, Jonkers HM, Polerecky L, de Beer D. 2007. A novel radioactivity microsensor for high spatial resolution measurements of beta radiation. Limnol Oceanogr Methods 5.
4.Hinck S, Neu T, Lavik G, Mussmann M, de Beer D, 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.
5.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, Ehrlich GD. 2007. Insights into the Genome of Large Sulfur Bacteria Revealed by Analysis of Single Filaments. PLoS Biology 5:1923-1937.
6.Polerecky L, Bachar A, Schoon R, Grinstein M, Jørgensen BB, de Beer D, Jonkers H. 2007. Contribution of Chloroflexus respiration to oxygen cycling in a hypersaline microbial mat from Lake Chiprana, Spain. Environmental Microbiology 9:2007–2024.
7.Polerecky L, Bissett A, Stoodley P, Suci P, de Beer D. 2007. 4th ASM conference on Biofilms, Quebec City, Canada.
8.Preisler A, de Beer D, Lichtschlag A, Lavik G, Boetius A, Jørgensen BB. 2007. Biological and chemical sulfide oxidation in a Beggiatoa inhabited marine sediment. ISME-Journal 1:341-353.
9.Røy H, Lee JS, Jansen S, de Beer D. 2007. Tide-driven deep pore-water flow in intertidal sand flats. Limnol Oceanogr 53:1521-1530.
10.Schläppy ML, Hoffmann F, Röy H, Wijffels RH, Mendola D, Sidri M, 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.
11.Volkenborn N, Polerecky L, Hedtkamp SIC, van Beusekom J, de Beer D. 2007. Bioturbation and bioirrigation extend the open exchange regions in permeable sediments. Limnol Oceanogr 52:1898-1909.
12.Weber M, Faerber P, Meyer V, Lott C, Eickert G, Fabricius KE, de Beer D. 2007. In situ applications of a new diver-operated motorized microsensor profiler. Env Sci Technol 41:6210-6215.

2006

1.Abed RMM, Al-Thukair A, de Beer D. 2006. Bacterial diversity of a cyanobacterial mat degrading petroleum compounds at elevated salinities and temperatures. FEMS Microb Ecol 57:290-301.
2.Abed RMM, Polerecky L, Al Najjar M, 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.
3.Billerbeck M, Werner U, Polerecky L, Walpersdorf E, de Beer D, 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.
4.de Beer D, Sauter E, Niemann H, Kaul N, Foucher JP, Witte U, Schlüter M, 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.
5.Gieseke A, Tarre S, Green M, 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.
6.Green M, Beliavski M, Denekamp N, Gieseke A, de Beer D, 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.
7.Ludwig R, Pringault O, DeWit R, de Beer D, 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.
8.Musat N, Werner U, Knittel K, Kolb S, Dodenhof T, van Beusekom JEE, de Beer D, Dubilier N, 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.
9.Niemann H, Lösekann T, de Beer D, Elvert M, Knittel K, Amann R, Sauter E, Schlüter M, Klages M, Foucher J, Boetius A. 2006. Novel methanotrophic communities of the Haakon Mosby mud volcano and their role as methane sink. Nature 443:854-858.
10.Stief P, 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.
11.Stoodley P, Dodds I, de Beer D, Lappin Scott H, Boyle JD. 2006. The development and flow of biofilms through porous media under laminar and turbulent conditions.
12.Van Gaever S, Moodley L, de Beer D, 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.
13.Werner U, Billerbeck M, Polerecky L, Franke U, Huettel M, van Beusekom JEE, 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.
14.Werner U, Bird P, Wild C, Ferdelman TG, Polerecky L, Eickert G, Jonstone R, Hoegh-Guldberg O, 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

1.Al-Horani F, Ferdelman TG, Al-Moghrabi SM, de Beer D. 2005. Spatial distribution of calcification and photosynthesis in the scleractinian coral Galaxea fascicularis. Coral Reefs 24:173-180.
2.Collins G, Mahony T, McHugh S, Gieseke A, de Beer D, O'Flaherty V. 2005. Distribution, dynamics and in situ ecophysiology of Crenarchaeota in anaerobic wastewater treatment granular biofilms. Wat. Sci. Tech. 52:233-239.
3.Collins G, O'Connor L, Mahony T, Gieseke A, de Beer D, O'Flaherty V. 2005. Distribution, localization and phylogeny of abundant populations of Crenarchaeoty in anaerobic granular sludge. Appl. Environ. Microbiol. 71:7523-7527.
4.Cytryn E, Minz D, Gelfand I, Neori A, Gieseke A, de Beer D, 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.
5.Cytryn E, van Rijn J, Schramm A, Gieseke A, de Beer D, 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.
6.Flies C, Jonkers HM, de Beer D, Bosselmann K, Böttcher ME, Schüler D. 2005. Diversity and vertical distribution of magnetotactic bacteria along chemical gradients in freshwater microcosms. FEMS Microb Ecol 52:185-195.
7.Gieseke A, Nielsen J, Amann R, de Beer D. 2005. In situ substrate conversion and assimilation by nitrifying bacteria in a model biofilm. Environm. Microbiol. 7:1392–1404.
8.Jonkers HM, Koh I-O, Behrend P, Muyzer G, 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.
9.Ludwig R, Al-Horani FA, de Beer D, Jonkers HM. 2005. Photosynthesis controlled calcification in a hypersaline microbial mat. Limnology & Oceanography 50:1836-1843.
10.Polerecky L, Franke U, Werner U, Grunwald B, de Beer D. 2005. High spatial resolution measurement of oxygen consumption rates in permeable sediments. Limnol. Oceanogr. Methods 3:75-85.
11.Rusch A, Walpersdorf E, de Beer D, Gurrieri S, Amend JP. 2005. Microbial communities near the oxic/anoxic interface in the hydrothermal system of Vulcano Island, Italy. Chem. Geol. 224:169-182.
12.Schoenberg C, de Beer D, Lawton A. 2005. Oxygen microsensor studies on zooxanthellate clionaid ponges from the Costa Brava, Mediteranean Sea. J. Phycol. 41:774-779.
13.Stief P, Nazarova L, de Beer D. 2005. Chimney construction by Chironomus riparius larvae in response to hypoxia:Microbial implications for freshwater sediments. Microbial Ecology 48:145-153.

2004

1.Altmann D, Stief P, Amann R, de Beer D. 2004. Distribution and activity of nitrifying bacteria in natural stream sediment versus laboratory sediment microcosms. Aquat. Microb. Ecol. 36:73-81.
2.Altmann D, Stief P, de Beer D, Amann R. 2004. Nitrification in freshwater sediments as influenced by insect larvae: Quantification by microsensors and fluorescence in situ hybridization. Microbial Ecology 48:145-153.
3.De Beer D, Al-Horani F. 2004. Marine calcification and decalcification studied with microsensors for calcium, pH and oxygen, p. 1107-1111. In Wanty RB, Seal RR (ed.), Water Rock Interaction, vol. 2. Taylor and Francis Group, London.
4.de Beer D, Wenzhöfer F, Ferdelman TG, Boehme S, Huettel M, van Beusekom J, Boettcher M, Musat N, Dubilier N. 2004. Transport and mineralization rates in North Sea sandy intertidal sediments (Sylt-Rømø Basin, Waddensea). Limnol. Oceanogr. 50:113-127.
5.Gieseke A, de Beer D. 2004. Use of microelectrodes to measure in situ microbial activities in biofilms, sediments, and microbial mats., p. 1581-1612. In Akkermans ADL, van Elsas D (ed.), Molecular Microbial Ecology Manual, 2 ed. Kluwer, Dordrecht (Nl).
6.Grötzschel S, Koester J, de Beer D. 2004. 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.
7.Stief P, Altmann D, de Beer D, Bieg R, Kureck A. 2004. Microbial activities in the burrow environment of the potamal mayfly Ephoron virgo. Freshwater Biol. 49:1152-1163.
8.Tarre S, Beliavski M, Denekamp N, Gieseke A, de Beer D, Green M. 2004. High nitrification rate at low pH in a fluidized bed reactor with chalk as the biofilm carrier. Wat.Sci.Technol. 49:99-105.

2003

1.Al-Horani FA, Al-Mograbi SM, de Beer D. 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.
2.Al-Horani FA, Al-Mograbi SM, de Beer D. 2003. The mechanism of calcification and its relation to photosynthesis and respiration in the scleractian coral Galaxea fascicularis. Marine Biology 142:419-426.
3.Altmann D, Stief P, Amann R, de Beer D, Schramm A. 2003. In situ distribution and activity of nitrifying bacteria in freshwater sediment. Environmental Microbiology 5:798-803.
4.Berg P, Roey H, Janssen F, Meyer V, Jørgensen BB, Huettel M, de Beer D. 2003, p 26. Aquatic Sciences Meeting, American Society of Limnology and Oceanography, Salt LAke City, USA.
5.Berg P, Roey H, Janssen F, Meyer V, Jørgensen BB, Huettel M, de Beer D. 2003. Oxygen uptake by aquatic sediments measured with a novel non-invasive eddy correlation technique. Mar. Ecol. Prog. Ser. 261:75-83.
6.Jonkers HM, Ludwig R, De Wit R, Pringault O, Muyzer G, Niemann H, Finke N, de Beer D. 2003. Structural and functional analysis of a microbial mat ecosystem from a unique permanent hypersaline inland lake: 'La Salada de Chiprana' (NE Spain). FEMS Microbiol. Ecol. 44:175-189.
7.Stief P, Schramm A, Altmann D, de Beer D. 2003. Temporal variation of nitrification rates in experimental freshwater sediments enriched with ammonia or nitrite. FEMS Microbiology Ecology 46:63-71.

2002

1.Abed RMM, Safi NMD, Köster J, de Beer D, Rullkötter J, Garcia-Pichel F. 2002. Microbial Diversity of a Heavily Polluted Microbial Mat and Its Community Changes Following Degradation of Petroleum Compounds. Appl. Environm. Microbiol. 68:1674-1683.
2.Gieseke A, Nielsen JL, de Beer D. 2002, p 1-4. International Specialized Conference on Biofilm Monitoring, Porto.
3.Grötzschel S, Abed RMM, de Beer D. 2002. Metabolic shifts in hypersaline cyanobacterial mats upon addition of organic substrates. Environmental Microbiology 4:683-695.
4.Grötzschel S, de Beer D. 2002. Effect of oxygen concentration on photosynthesis and respiration in two hypersaline microbial mats. Microbial Ecology 44:208-216.
5.Grötzschel S, Köster J, Abed RMM, de Beer D. 2002. Degradation of petroleum model compounds immobilized on clay by a hypersaline microbial mat. Biodegradation 13:273-283.
6.Kohler-Rink S, de Beer D. 2002. Mikrosensoren für die Meeresbiologie, p. 91-98. In Hempel G, Hinrichsen, F. (ed.), Der Ozean - Lebensraum und Klimasteuerung. Wittheit zu Bremen, Bremen.
7.Okabe S, Santegoeds CM, de Beer D. 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. 81:570-577.
8.Okabe S, Santegoeds CM, Watanabe Y, de Beer D. 2002. Successional Development of Sulfate-Reducing Bacterial Populations and Their Activities in An Activated Sludge Immobilized Agar Gel Film. Biotechnol. Bioeng. 78:120-130.
9.Schulz HN, de Beer D. 2002. Uptake rates of oxygen and sulfide measured with individual Thiomargarita namibiensis cells by using microelectrodes. Appl. Environm. Microbiol. 68:5746-5749.
10.Stief P, de Beer D. 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.
11.Stief P, de Beer D, Neumann D. 2002. Small scale distribution of nitrite in freshwater microcosms: The role of nitrate and oxygen availability, and sediment permeability. Microbial Ecology 43:367-378.

2001

1.de Beer D. 2001. Microsensor studies of oxygen, carbon and nitrogen cycles in lake sediments and microbial mats., p. 227-246. In Taillefert M, Rozan TF (ed.), Environmental Electrochemistry: Analyses of Trace Element Biogeochemistry., vol. American Chemical Society Symposium Series 811, Washington DC.
2.de Beer D, Larkum AJW. 2001. Photosynthesis and calcification in the calcifying algae Halimeda discoidea studied with microsensors. Plant, Cell & Environment 24:1209-1217.
3.Dubilier N, Mülders C, Ferdelman T, de Beer D, Pernthaler A, Klein M, Wagner M, Erseus C, Thiermann F, Krieger J, Giere O, Amann R. 2001. Endosymbiontic sulphate-reducing and sulphide-oxidising bacteria in an oligochaete worm. Nature 411:298-302.
4.Hanstein S, de Beer D, Felle HH. 2001. Miniaturised carbon dioxide sensor designed for measurements within plant leaves. Sensors and Actuators B 81:107-114.
5.Wieland A, de Beer D, van Dusschoten D, Damgaard LR, Kuehl M, van As H. 2001. Fine-scale measurement of diffusivity in a microbial mat with NMR imaging. Limnol. Oceanogr. 44:248-259.

2000

1.de Beer D. 2000. Potentiometric microsensors for in situ measurements in aquatic environments, p. 161-194. In Buffle J, Horvai G (ed.), In situ monitoring of aquatic systems: chemical analysis and speciation. Wiley & Sons, London.
2.de Beer D, Kühl M. 2000. Interfacial processes, gradients and metabolic activity in microbial mats and biofilms., p. 374-394. In Boudreau B, Jørgensen BB (ed.), The benthic boundary layer. Oxford University Press.
3.de Beer D, Kühl M, Stambler N, Vaki L. 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.
4.Schramm A, de Beer D, Gieseke A, Amann R. 2000. Microenvironments and distribution of nitrifying bacteria in a membrane bound biofilm. Environm. Microbiol. 2:680-686.

1999

1.de Beer D. 1999. Use of microelectrodes to measure in situ microbial activities in biofilms, sediments and microbial mats, p. 1-23. In Akkermans ADL, van Elsas JD, de Bruyn FJ (ed.), Molecular Microbial Ecology Manual, vol. 8.1.3. Kluwer Academic Press.
2.de Beer D. 1999. Micro-electrodes., p. 85-100. In Wijffels R (ed.), Immobilized cells. Springer Verlag, Heidelberg, Germany.
3.de Beer D, Schramm A. 1999. Micro-environments and mass transfer phenomena in biofilms studied with microsensors. Wat.Sci.Technol. 39: 173-178.
4.Santegoeds CM, Damgaard LR, Hesselink G, Zopfi J, Lens P, Muyzer G, de Beer D. 1999. Distribution of sulfate-reducing and methanogenic bacteria in anaerobic aggregates determined by microsensor and molecular analysis. Appl. Environm. Microbiol. 65:4618-4629.
5.Schramm A, de Beer D, van den Heuvel JC, Ottengraf SPP, Amann R. 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. 65:3690-3696.
6.Schramm A, Santegoeds CM, Nielsen HK, Ploug H, Wagner M, Pribyl M, Wanner J, Amann R, de Beer D. 1999. On the occurrence of anoxic microniches, denitrification, and sulfate reduction in aerated activated sludge. Appl. Environ. Microbiol. 65:4189-4196.

1998

1.de Beer D, Schramm A, Santegoeds CM, Nielsen HK. 1998. Anaerobic processes in activated sludge. Wat. Sci. Tech. 37:605-608.
2.Glud RN, Santegoeds CM, de Beer D, Kohls O, Ramsing NB. 1998. Oxygen dynamics at the base of a biofilm studied with planar optodes. Aq. Microb. Ecol. 14:223-233.
3.Santegoeds CCM, Schramm A, de Beer D. 1998. Microsensors as a tool to determine chemical microgradients and bacterial activity in wastewater biofilms and flocs. Biodegradation 9:159-167.
4.Santegoeds CM, Ferdelman TG, Muyzer G, de Beer D. 1998. Structural and functional dynamics of sulfate-reducing populations in bacterial biofilms. Appl. Environm. Microbiol.. 64:3731-3739.
5.Santegoeds CM, Muyzer G, de Beer D. 1998. Biofilm dynamics studied with microsensors and molecular techniques. Wat. Sci. Tech. 3:125-129.
6.Schramm A, de Beer D, van den Heuvel H, Ottengraf SPP, Amann R. 1998. In situ structure/function studies in wastewater treatment systems. Wat. Sci. Tech. 37:413-416.
7.Schramm A, de Beer D, Wagner M, Amann R. 1998. Identification and activities in situ of Nitrosospira and Nitrospira sp. as dominant populations in a nitrifying fluidized bed reactor. Appl. Environm. Microbiol. 64:3480-3485.

1997

1.de Beer D. 1997, p 217-224. International Symposium on Environmental Biotechnology, Oostende, Belgium.
2.de Beer D, Glud A, Epping E, Kühl M. 1997. A fast responding CO2 micro-electrode for profiling sediments, microbial mats and biofilms. Limnol. Oceanogr. 42:1590-1600.
3.de Beer D, Schramm A, Santegoeds CM, Kühl M. 1997. A nitrite microsensor for profiling environmental biofilms. Appl. Environ. Microbiol. 63:973-977.
4.de Beer D, Stoodley P, Lewandowski Z. 1997. Measurement of local diffusion coefficients in biofilms by microinjection and confocal microscopy. Biotechnol. Bioeng. 53:151-158.
5.O'Flaherty V, Lens PNL, De Beer D, Colleran EEOFCAUVOACIAURAAMB-, 1997. 1997. Effect of feed composition and upflow velocity on aggregate characteristics in anaerobic upflow reactors. Appl Microbiol Biotechnol. 47:102-107.
6.Stoodley P, de Beer D, Lappin-Scott HM. 1997. Influence of electric fields and pH on the biofilm structure as related to the bioelectric effect. Antimicrob. Agents Chemother. 41:1876-1879.

1996

1.de Beer D, O'Flaharty V, Thaveesri J, Lens P. 1996. Distribution of extracellular polysaccharides and flotation of anaerobic sludge. Appl. Microbiol. Biotechnol. 46:197-201.

1995

1.de Beer D, Stoodley P. 1995. Relation between the structure of an aerobic biofilm and transport phenomena. Wat. Sci. Technol. 32:11-18.
2.Lee W, de Beer D. 1995. Oxygen and pH microprofiles above corroding mild steel covered with a biofilm. Biofouling 8:273-280.
3.Lens P, de Beer D, Cronenberg C, Ottengraf SPP, Verstraete W. 1995. The use of microsensors to determine population distributions in UASB aggregates. Wat. Sci. Technol. 31:273-280.
4.Stewart PS, Murga R, Srinivasan R, de Beer D. 1995. Biofilm structural heterogeneity visualized by three microscopic methods. Wat. Res. 29:2006-2009.
5.Vandenabeele J, de Beer D, Germonpre R, van de Sande R, Verstraete W. 1995. Influence of nitrate on manganese removing microbial consortia from sand filters. Wat. Res. 28:579-587.
6.Wijffels RH, Eekhof MR, de Beer D, van den Heuvel JC, Tramper J. 1995. Pseudo-steady state oxygen-concentration profiles in an agar slab containing growing Nitrobacter agilis. J.Fermentation & Biotech 79:167-170.

1994

1.Costerton WJ, Lewandowski ZL, De Beer D, Caldwell D, Korber D, James G. 1994. Biofilms, the customized microniche. J. Bact. 176:2137-2142.
2.de Beer D, Srinivasan R, Stewart PS. 1994. Direct measurement of chlorine penetration into biofilms during disinfection. Appl. Environm. Microbiol. 60:4339-4344.
3.de Beer D, Stoodley P, Lewandowski Z. 1994. Liquid flow in heterogeneous biofilms. Biotechnol. Bioeng. 44:636-641.
4.de Beer D, Stoodley P, Roe F, Lewandowski Z. 1994. Effect of biofilm structures on oxygen distribution and mass transfer. Biotechnol. Bioeng. 43:1131-1138.
5.Lens P, de Beer D, Cronenberg CCH, Houwen FP, Ottengraf SPP, Verstraete W. 1994. Heterogeneous distribution of microbial activity in methanogenic aggregates: pH and glucose microprofiles. Appl. Environm. Microbiol. 59:3803-3815.
6.Stewart PS, Griebe T, Srinivasan R, Chen CI, Yu FP, de Beer D, McFeters GA. 1994. Comparison of respiratory activity and culturability during monochloramine disinfection of binary population biofilms. Appl. Environm. Micrbiol. 60:1690-1692.
7.Stoodley P, de Beer D, Lewandowski Z. 1994. Liquid flow in biofilm systems. Appl. Environm. Microbiol. 60:2711-2716.

1993

1.de Beer D, van den Heuvel JC, Ottengraf SPP. 1993. Microelectrode measurements of the activity distribution in nitrifying bacterial aggregates. Appl. Environm. Microbiol. 59:573-579.
2.De Boer JP, Cronenberg CCH, de Beer D, Van Den Heuvel JC, De Mattos MJT, Neijssel OM. 1993. pH and glucose profiles in aggregates of bacillus-laevolacticus. Appl. Environ. Microbiol. 59:2474-2478.

1992

1.de Beer D, Huisman JW, van den Heuvel JC, Ottengraf SSP. 1992. The effect of pH profiles in methanogenic aggregates on the kinetics of acetate conversion. Wat.Res. 26:1326-1336.
2.van den Heuvel JC, Verschuren PG, Beeftink HH, de Beer D. 1992. Determination of the critical concentration of inhibitory products in a repeated fed-batch culture. Biotechnol. Techniques 6:33-38.

1991

1.Cronenberg CCH, Van Groen H, de Beer D, Van den Heuvel JC. 1991. Oxygen-independent glucose microsensor based on glucose oxidase. Anal. Chim. Acta 242:275-278.
2.de Beer D, Sweerts J-PRA, van den Heuvel JC. 1991. Microelectrode measurement of ammonium profiles in freshwater sediments. FEMS Microbiol. Ecol. 86:1-6.

1990

1.de Beer D. 1990. Microelectrode studies in biofilms and sediments. University of Amsterdam, Amsterdam.
2.Sweerts J-PRA, de Beer D, Nielsen LP, Verdouw H, van den Heuvel JC, Cohen Y, Cappenberg TE. 1990. Denitrification by sulphur oxidizing Beggiatoa spp. mats on freshwater sediments. Nature 344:762-763.

1989

1.de Beer D, Sweerts JPRA. 1989. Measurements of nitrate gradients with an ion-selective microelectrode. Anal. Chim. Acta 219:351-356.
2.Sweerts J-PRA, de Beer D. 1989. Microelectrode measurements of nitrate gradients in the littoral and profundal sediments of a meso-eutrophic lake (lake Vechten, The Netherlands). Appl. Environ. Microbiol. 55:754-757.

1988

1.de Beer D, Van den Heuvel JC. 1988. Response of ammonium-selective microelectrodes based on the neutral carrier nonactin. Talanta 35:728-730.

1983

1.De Boer AH, de Beer D, Prins HBA, Kuiper PJC. 1983. Trans membrane potentials of root cortical cells of plantago-media as related to energy metabolism. Plant Physiology 72:140.
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