Dr. Holger Daims
Department of Microbial Ecology
Faculty Center of Ecology
Faculty of Life Sciences
University of Vienna
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
  1. Mußmann M, Brito I, Pitcher A, Damsté JSS, Hatzenpichler R, Richter A, Nielsen JL, Nielsen PH, Müller A, Daims H, Wagner M, Head IM. 2011. Thaumarchaeotes abundant in refinery nitrifying sludges express amoA but are not obligate autotrophic ammonia oxidizers. Proc. Natl. Acad. Sci. USA 108: 16771-16776.
     PUBMED
  2. Mlynek G, Sjöblom B, Kostan J, Füreder S, Maixner F, Gysel K, Furtmüller PG, Obinger C, Wagner M, Daims H, Djinovic-Carugo K. 2011. Unexpected diversity of chlorite dismutases: A catalytically efficient dimeric enzyme from Nitrobacter winogradskyi. J. Bacteriol. 193: 2408-2417.
     PUBMED
     Supplementary material [PDF]
  3. Daims H, Wagner M. 2011. In situ techniques and digital image analysis methods for quantifying spatial localization patterns of nitrifiers and other microorganisms in biofilm and flocs. Methods Enzymol. 496: 185-215.
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  4. Hall EK, Maixner F, Franklin O, Daims H, Richter A, Battin T. 2011. Linking microbial and ecosystem ecology using ecological stoichiometry: A synthesis of conceptual and empirical approaches. Ecosystems 14: 261-273.
  5. Lebedeva EV, Off S, Zumbrägel S, Kruse M, Shagzhina A, Lücker S, Maixner F, Lipski A, Daims H, Spieck S. 2011. Isolation and characterization of a moderately thermophilic nitrite-oxidizing bacterium from a geothermal spring. FEMS Microbiol. Ecol. 75: 195-204.
     PUBMED
  6. Hall EK, Singer GA, Pölzl M, Hämmerle I, Schwarz C, Daims H, Maixner F, Battin T. 2011. Looking inside the box: Using Raman microspectroscopy to deconstruct microbial biomass stoichiometry one cell at a time. ISME J. 5: 196-208.
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  7. Lücker S, Wagner M, Maixner F, Pelletier E, Koch H, Vacherie B, Rattei T, Sinninghe Damsté JS, Spieck E, Le Paslier D, Daims H. 2010. A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria. Proc. Natl. Acad. Sci. USA 107: 13479-13484.
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     Supporting information [PDF]
  8. Kostan J, Sjöblom B, Maixner F, Mlynek G, Furtmüller PG, Obinger C, Wagner M, Daims H, Djinovic-Carugo K. 2010. Structural and functional characterisation of the chlorite dismutase from the nitrite-oxidizing bacterium "Candidatus Nitrospira defluvii": Identification of a catalytically important amino acid residue. J. Struct. Biol. 172: 331-342.
     PUBMED
  9. Augspurger C, Karwautz C, Mussmann M, Daims H, Battin T. 2010. Drivers of bacterial colonization patterns in stream biofilms. FEMS Microbiol. Ecol. 72: 47-57.
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  10. Stoecker K, Dorninger C, Daims H, Wagner M. 2010. Double-labeling of oligonucleotide probes for fluorescence in situ hybridization (DOPE-FISH) improves signal intensity and increases rRNA accessibility. Appl. Environ. Microbiol. 76: 922–926.
     PUBMED
     Supplementary material [PDF]
  11. Daims, H. 2009. Use of fluorescence in situ hybridization and the daime image analysis program for the cultivation-independent quantification of microorganisms in environmental and medical samples. Cold Spring Harb. Protoc. , in press.
     Full text   
  12. Schwitalla P, Mennerich A, Austermann-Haun U, Müller A, Dorninger C, Daims H, Holm NC, Rönner-Holm SG. 2008. NH4+ ad-/desorption in sequencing batch reactors: simulation, laboratory and full-scale studies. Water Sci. Technol. 58: 345-350.
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  13. Biasi C, Meyer H, Rusalimova O, Hämmerle R, Kaiser C, Baranyi C, Daims H, Lashchinsky N, Barsukov P, Richter A. 2008. Initial effects of experimental warming on carbon exchange rates, plant growth and microbial dynamics of a lichen-rich dwarf shrub tundra in Siberia. Plant Soil 307: 191-205.
  14. Hoshino T, Yilmaz LS, Noguera DR, Daims H, Wagner M. 2008. Quantification of target molecules needed to detect microorganisms by fluorescence in situ hybridization (FISH) and catalyzed reporter deposition-FISH. Appl. Environ. Microbiol. 74: 5068-5077.
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  15. 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. 10: 3043-3056.
     PUBMED
     Supplementary material
  16. 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.
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  17. 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.
     PUBMED
  18. 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.
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  19. 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.
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  20. Daims H, Wagner M. 2007. Quantification of uncultured microorganisms by fluorescence microscopy and digital image analysis. Appl. Microbiol. Biotech. 75: 237-248.
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  21. 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.
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  22. Daims H, Taylor MW, Wagner M. 2006. Wastewater treatment: a model system for microbial ecology. Trends Biotechnol. 24: 483-489.
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  23. 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.
  24. 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 MC, 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.
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     Supplementary material [PDF]
  25. 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.
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  26. 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).
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  27. 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.
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  28. 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.
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  29. 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.
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  30. Daims H, Lücker S, Wagner M. 2006. daime, a novel image analysis program for microbial ecology and biofilm research. Environ. Microbiol. 8: 200-213.
     PUBMED
  31. 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 .
     PUBMED
  32. Wagner M, Horn M, Daims H . 2003. Fluorescence in situ hybridisation for the identification and charcterisation of prokaryotes. Curr. Opin. Microbiol. 6: 302-309.
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  33. 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 .
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  34. 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.
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  35. 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.
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  36. 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.
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  37. 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.
  38. Daims H, Brühl 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.
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Book chapters and other publications
  1. Daims H, Lücker S, Le Paslier D, Wagner M. 2010. Diversity, environmental genomics, and ecophysiology of nitrite-oxidizing bacteria. In Nitrification, pp. 295-322. (Ward BB, Arp DJ, Klotz MG, ed.). ASM Press, Washington, DC.
  2. Daims H, Wagner M. 2010. The microbiology of nitrogen removal. In The microbiology of activated sludge, pp. 259-280. (Seviour RJ, Nielsen PH, ed.). IWA Publishing, London, UK..
  3. Daims, H. 2009. Quantitative FISH for the cultivation-independent quantification of microbes in wastewater treatment plants In FISH Handbook for Biological Wastewater Treatment: Identification and quantification of microorganisms in activated sludge and biofilms by FISH, pp. 85-92. (Nielsen PH, Daims H, Lemmer H, ed.). IWA Publishing, London, UK.
  4. Daims H, Maixner F, Schmid MC. 2009. The nitrifying microbes: Ammonia oxidizers, nitrite oxidizers, and anaerobic ammonium oxidizers. In FISH Handbook for Biological Wastewater Treatment: Identification and quantification of microorganisms in activated sludge and biofilms by FISH, pp. 9-17. (Nielsen PH, Daims H, Lemmer H, ed.). IWA Publishing, London, UK.
  5. 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.
  6. 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.
  7. Daims H, Schleifer KH, Wagner M. 2002. Halbautomatische und kultivierungs-unabhängige Quantifizierung von Bakterien in komplexen Umweltproben. Laborwelt 1: 10-14.
  8. 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 .

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