Holger Daims - Department of Microbial Ecology

	Dr. Holger Daims Department für Mikrobielle Ökologie Wiener Ökologiezentrum Universität Wien Althanstr. 14 A-1090 Wien Austria phone: +43 1 4277 54392 fax: +43 1 4277 54389 email:

Biodiversity and ecophysiology of nitrifying bacteria Nitrifying bacteria, also termed "nitrifiers", are widespread in nature and inhabit a great variety of aquatic and terrestrial habitats. They drive key processes of the biogeochemical nitrogen cycle and contribute to nitrogen removal from wastewater. Recent molecular surveys have revealed high biodiversity and abundance of yet uncultured ammonia- and nitrite-oxidizing bacteria in many natural and engineered ecosystems. These findings, experiments with cultured representatives, and first results of cultivation-independent physiological studies demonstrate that nitrifiers are surprisingly adaptable. Thus ammonia and nitrite oxidizers are prime examples of specialized prokaryotic guilds that occupy unique ecological niches, but nevertheless cope with a wide range of different environmental conditions. The physiology and ecological functions of these organisms must be studied in order to better understand the mechanisms of nitrogen turnover in nature and to improve the performance of biological nitrogen removal from wastewater. For this purpose, molecular methods are combined and applied to detect nitrifiers in environmental samples, to identify novel nitrifiers, and to study the physiology and ecological interactions of uncultured ammonia and nitrite oxidizers in situ. Biodiversity and function of nitrifying bacterial communities Environmental genomics Confocal laser scanning microscopy and digital image analysis Specific staining methods like fluorescence in situ hybridization (FISH) with rRNA-targeted probes enable microbiologists to detect and locate microorganisms directly in their natural habitats. Although FISH is actually not an invasive technique, the hybridization protocol must be modified to preserve the original three-dimensional structure of a sample. This effort pays off, because FISH is perfectly complemented by confocal laser scanning microscopy, which allows peeking into the most complex samples without mechanically disrupting their integrity. FISH and confocal microscopy are combined with 2D and 3D digital image analysis to quantify key features of microbial populations like their biovolume fraction or the surface to volume ratio of cell aggregates. New image analysis algorithms are developed and optimized for processing confocal images of probe-stained microbial cells. The resulting implementations become part of a novel image analysis software dedicated to meet the demands of microbial ecology. Confocal laser scanning microscopy and digital image analysis daime. digital image analysis in microbial ecology

Publications in peer reviewed journals Tatsuhiko Hoshino, L. Safak Yilmaz, Daniel R. Noguera, Holger Daims, and Michael Wagner. 2008. Quantification of target molecules needed to detect microorganisms by fluorescence in situ hybridization (FISH) and catalyzed reporter deposition-FISH. Appl. Environ. Microbiol. Online version Maixner F, Wagner M, Lücker S, Pelletier E, Schmitz-Esser S, Hace K, Spieck E, Konrat R, Le Paslier D, Daims H.. 2008. Environmental genomics reveals a functional chlorite dismutase in the nitrite-oxidizing bacterium "Candidatus Nitrospira defluvii". Environ. Microbiol. , in press. PDF PUBMED Supplementary material Reigstad LJ, Richter A, Daims H, Urich T, Schwark L, Schleper C. 2008. Nitrification in terrestrial hot springs of Iceland and Kamchatka. FEMS Microbiol. Ecol. 64: 167-174. Hatzenpichler R, Lebedeva EV, Spieck E, Stoecker K, Richter A, Daims H, Wagner M. 2008. A moderately thermophilic ammonia-oxidizing crenarchaeote from a hot spring. Proc. Natl. Acad. Sci. USA 105: 2134-2139. PDF PUBMED Lebedeva EV, Alawi M, Maixner F, Jozsa PG, Daims H, Spieck E. 2008. Physiological and phylogenetical characterization of a new lithoautotrophic nitrite-oxidizing bacterium 'Candidatus Nitrospira bockiana' sp. nov. Int. J. Syst. Evol. Microbiol. 58: 242-250. PDF [password required] PUBMED Huang WE, Stoecker K, Griffiths R, Newbold L, Daims H, Whiteley AS, Wagner M. 2007. Raman-FISH: Combining stable-isotope Raman spectroscopy and fluorescence in situ hybridization for the single cell analysis of identity and function. Environ. Microbiol. 9: 1878-1889. PDF PUBMED Daims H, Wagner M. 2007. Quantification of uncultured microorganisms by fluorescence microscopy and digital image analysis. Appl. Microbiol. Biotech. 75: 237-248. PDF PUBMED Battin TJ, Sloan WT, Kjelleberg S, Daims H, Head IM, Curtis TP, Eberl L. 2007. Microbial landscapes: new paths to biofilm research. Nature Rev. Microbiol. 5: 76-81. PDF PUBMED Daims H, Taylor MW, Wagner M. 2006. Wastewater treatment: a model system for microbial ecology. Trends Biotechnol. 24: 483-489. PUBMED Meyer H, Kaiser C, Biasi C, Hämmerle R, Rusalimova O, Lashchinsky N, Baranyi C, Daims H, Barsukov P, Richter A. 2006. Soil carbon and nitrogen dynamics along a latitudinal transect in Western Siberia, Russia. Biogeochemistry 81: 239-252. PDF Strous M, Pelletier E, Mangenot S, Rattei T, Lehner A, Taylor MW, Horn M, Daims H, Bartol-Mave D, Wincker P, Barbe V, Fonknechten N, Vallenet D, Segurens B, Schenowitz-Truong C, Médigue C, Collingro A, Snel B, Dutilh BE, Op den Camp HJM, van der Drift C, Cirpus I, van de Pas-Schoonen KT, Harhangi HR, van Niftrik L, Schmid M, Keltjens J, van de Vossenberg J, Kartal B, Meier H, Frishman D, Huynen MA, Mewes HW, Weissenbach J, Jetten MSM, Wagner M, Le Paslier D. 2006. Deciphering the evolution and metabolism of an anammox bacterium from a community genome. Nature 440: 790-794. PDF PUBMED Supplementary material [PDF] Maixner F, Noguera DR, Anneser B, Stoecker K, Wegl G, Wagner M, Daims H. 2006. Nitrite concentration influences the population structure of Nitrospira-like bacteria. Environ. Microbiol. 8: 1487-1495. PDF PUBMED Stoecker K, Bendinger B, Schöning B, Nielsen PH, Nielsen JL, Baranyi C, Toenshoff ER, Daims H, Wagner M. 2006. Cohn's Crenothrix is a filamentous methane oxidizer with an unusual methane monooxygenase. Proc. Natl. Acad. Sci. USA 7: 2363-2367 (Track II). PDF PUBMED Wagner M, Nielsen PH, Loy A, Nielsen JL, Daims H. 2006. Linking microbial community structure with function: fluorescence in situ hybridization-microautoradiography and isotope arrays. Curr. Opin. Biotechnol. 17: 1-9. PDF PUBMED Daims H, Maixner F, Lücker S, Stoecker K, Hace K, Wagner M. 2006. Ecophysiology and niche differentiation of Nitrospira-like bacteria, the key nitrite oxidizers in wastewater treatment plants. Wat. Sci. Tech. 54: 21-27. PUBMED Spieck E, Hartwig C, McCormack I, Maixner F, Wagner M, Lipski A, Daims H. 2006. Selective enrichment and molecular characterization of a previously uncultured Nitrospira-like bacterium from activated sludge. Environ. Microbiol. 8: 405-415. PDF PUBMED Daims H, Lücker S, Wagner M. 2006. daime, a novel image analysis program for microbial ecology and biofilm research. Environ. Microbiol. 8: 200-213. PDF PUBMED Ginige MP, Hugenholtz P, Daims H, Wagner M, Keller J, Blackall LL. 2004. Use of stable-isotope probing, full-cycle rRNA analysis, and fluorescence in situ hybridization-micrautoradiography to study a methanol-fed denitrifying microbial community. Appl. Environ. Microbiol. 70: 588-596 . PDF PUBMED Wagner M, Horn M, Daims H . 2003. Fluorescence in situ hybridisation for the identification and charcterisation of prokaryotes. Curr. Opin. Microbiol. 6: 302-309. PDF PUBMED Wagner M, Loy A, Nogueira R, Purkhold U, Lee N, Daims H. 2002. Microbial community composition and function in wastewater treatment plants. Antonie van Leeuwenhoek 81: 665-680 . PDF PUBMED Daims H, Ramsing NB, Schleifer KH, Wagner M. 2001. Cultivation-independent, semiautomatic determination of absolute bacterial cell numbers in environmental samples by fluorescence in situ hybridization. Appl. Environ. Microbiol. 67: 5810-5818. PDF PUBMED Daims H, Nielsen JL, Nielsen PH, Schleifer KH, Wagner M. 2001. In situ characterization of Nitrospira-like nitrite-oxidizing bacteria active in waste water treatment plants. Appl. Environ. Microbiol. 67: 5273-5284. PDF PUBMED Daims H, Purkhold U, Bjerrum L, Arnold E, Wilderer PA, Wagner M. 2001. Nitrification in sequencing biofilm batch reactors: lessons from molecular approaches. Wat. Sci. Tech. 43: 9-18. PDF PUBMED Daims H, Nielsen P, Nielsen JL, Juretschko S, Wagner M. 2000. Novel Nitrospira-like bacteria as dominant nitrite-oxidizers in biofilms from wastewater treatment plants: Diversity and in situ physiology. Wat. Sci. Tech. 41: 85-90. PDF Daims H, Bruhl A, Amann R, Schleifer KH, Wagner M. 1999. Probe EUB338 is insufficient for the detection of all Bacteria: Development and evaluation of a more comprehensive probe set. Syst. Appl. Microbiol. 22: 434-444. PDF PUBMED Book chapters and other publications Daims H, Wagner M. 2007. The microbiology of nitrogen removal. In The microbiology of activated sludge, in press. (Seviour RJ, Blackall LL, ed.). IWA Publishing, London, UK.. Daims H, Stoecker K, Wagner M. 2005. Fluorescence in situ hybridization for the detection of prokaryotes. In Advanced Methods in Molecular Microbial Ecology, pp. 213-239. (Osborn AM, Smith CJ, ed.). Bios-Garland, Abingdon, UK. PDF Daims H. 2005. Molecular analyses of microbial community structure and function of flocs. In Flocculation in natural and engineered environmental systems, pp. 317-338. (Droppo IG, Leppard GG, Liss SN, Milligan TG, ed.). CRC Press, Boca Raton. Daims H, Schleifer KH, Wagner M. 2002. Halbautomatische und kultivierungs-unabhängige Quantifizierung von Bakterien in komplexen Umweltproben. Laborwelt 1: 10-14. PDF Loy A, Daims H, Wagner M. 2002. Activated Sludge: Molecular techniques for determining community composition. In The Encyclopedia of Environmental Microbiology, pp. 26-43. (Bitton G, ed.). Wiley, New York . PDF

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