Holger Daims

Summary

Affiliation: University of Vienna
Country: Austria

Publications

  1. ncbi request reprint Deciphering the evolution and metabolism of an anammox bacterium from a community genome
    Marc Strous
    Department of Microbiology, IWWR, Radboud University Nijmegen, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands
    Nature 440:790-4. 2006
  2. ncbi request reprint Wastewater treatment: a model system for microbial ecology
    Holger Daims
    Department of Microbial Ecology, University of Vienna, Althanstrasse 14, A 1090 Vienna, Austria
    Trends Biotechnol 24:483-9. 2006
  3. ncbi request reprint Quantification of uncultured microorganisms by fluorescence microscopy and digital image analysis
    Holger Daims
    Department für Mikrobielle Okologie, Universitat Wien, Althanstrasse 14, 1090, Vienna, Austria
    Appl Microbiol Biotechnol 75:237-48. 2007
  4. pmc Nitrification expanded: discovery, physiology and genomics of a nitrite-oxidizing bacterium from the phylum Chloroflexi
    Dimitry Y Sorokin
    Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
    ISME J 6:2245-56. 2012
  5. doi request reprint Use of fluorescence in situ hybridization and the daime image analysis program for the cultivation-independent quantification of microorganisms in environmental and medical samples
    Holger Daims
    Department of Microbial Ecology, Vienna Ecology Centre, University of Vienna, A 1090 Vienna, Austria
    Cold Spring Harb Protoc 2009:pdb.prot5253. 2009
  6. ncbi request reprint daime, a novel image analysis program for microbial ecology and biofilm research
    Holger Daims
    Department für Mikrobielle Okologie, Universitat Wien, Vienna, Austria
    Environ Microbiol 8:200-13. 2006
  7. pmc A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria
    Sebastian Lücker
    Department of Microbial Ecology, Ecology Centre, University of Vienna, 1090 Vienna, Austria
    Proc Natl Acad Sci U S A 107:13479-84. 2010
  8. doi request reprint Environmental genomics reveals a functional chlorite dismutase in the nitrite-oxidizing bacterium 'Candidatus Nitrospira defluvii'
    Frank Maixner
    Department für Mikrobielle Okologie, Universitat Wien, Vienna, Austria
    Environ Microbiol 10:3043-56. 2008
  9. pmc Impact of subunit and oligomeric structure on the thermal and conformational stability of chlorite dismutases
    Stefan Hofbauer
    University of Natural Resources and Life Sciences, Vienna, Austria
    Biochim Biophys Acta 1824:1031-8. 2012
  10. pmc Double labeling of oligonucleotide probes for fluorescence in situ hybridization (DOPE-FISH) improves signal intensity and increases rRNA accessibility
    Kilian Stoecker
    Department of Microbial Ecology, University of Vienna, Vienna, Austria
    Appl Environ Microbiol 76:922-6. 2010

Collaborators

Detail Information

Publications34

  1. ncbi request reprint Deciphering the evolution and metabolism of an anammox bacterium from a community genome
    Marc Strous
    Department of Microbiology, IWWR, Radboud University Nijmegen, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands
    Nature 440:790-4. 2006
    ..Most significantly, we identified candidate genes responsible for ladderane biosynthesis and biological hydrazine metabolism, and discovered unexpected metabolic versatility...
  2. ncbi request reprint Wastewater treatment: a model system for microbial ecology
    Holger Daims
    Department of Microbial Ecology, University of Vienna, Althanstrasse 14, A 1090 Vienna, Austria
    Trends Biotechnol 24:483-9. 2006
    ..Here, we consider selected key findings to illustrate the past and future roles of molecular ecophysiology and genomics in the development of wastewater microbiology as an important subdiscipline of microbial ecology...
  3. ncbi request reprint Quantification of uncultured microorganisms by fluorescence microscopy and digital image analysis
    Holger Daims
    Department für Mikrobielle Okologie, Universitat Wien, Althanstrasse 14, 1090, Vienna, Austria
    Appl Microbiol Biotechnol 75:237-48. 2007
    ..This article provides an overview of these methods and some of their applications with emphasis on (semi-)automated image analysis solutions...
  4. pmc Nitrification expanded: discovery, physiology and genomics of a nitrite-oxidizing bacterium from the phylum Chloroflexi
    Dimitry Y Sorokin
    Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
    ISME J 6:2245-56. 2012
    ..The surprising discovery of N. hollandicus significantly extends the known diversity of nitrifying organisms and likely will have implications for future research on nitrification in natural and engineered ecosystems...
  5. doi request reprint Use of fluorescence in situ hybridization and the daime image analysis program for the cultivation-independent quantification of microorganisms in environmental and medical samples
    Holger Daims
    Department of Microbial Ecology, Vienna Ecology Centre, University of Vienna, A 1090 Vienna, Austria
    Cold Spring Harb Protoc 2009:pdb.prot5253. 2009
    ....
  6. ncbi request reprint daime, a novel image analysis program for microbial ecology and biofilm research
    Holger Daims
    Department für Mikrobielle Okologie, Universitat Wien, Vienna, Austria
    Environ Microbiol 8:200-13. 2006
    ..This image analysis method complements recent molecular techniques for analysing structure-function relationships in microbial communities and will help to characterize symbiotic interactions among microorganisms...
  7. pmc A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria
    Sebastian Lücker
    Department of Microbial Ecology, Ecology Centre, University of Vienna, 1090 Vienna, Austria
    Proc Natl Acad Sci U S A 107:13479-84. 2010
    ....
  8. doi request reprint Environmental genomics reveals a functional chlorite dismutase in the nitrite-oxidizing bacterium 'Candidatus Nitrospira defluvii'
    Frank Maixner
    Department für Mikrobielle Okologie, Universitat Wien, Vienna, Austria
    Environ Microbiol 10:3043-56. 2008
    ....
  9. pmc Impact of subunit and oligomeric structure on the thermal and conformational stability of chlorite dismutases
    Stefan Hofbauer
    University of Natural Resources and Life Sciences, Vienna, Austria
    Biochim Biophys Acta 1824:1031-8. 2012
    ..By contrast the dimeric protein starts to unfold already at 53°C. The observed unfolding pathways are discussed with respect to the known subunit structure and subunit interaction...
  10. pmc Double labeling of oligonucleotide probes for fluorescence in situ hybridization (DOPE-FISH) improves signal intensity and increases rRNA accessibility
    Kilian Stoecker
    Department of Microbial Ecology, University of Vienna, Vienna, Austria
    Appl Environ Microbiol 76:922-6. 2010
    ..Furthermore, Cy3-doubly labeled probes strongly increase in situ accessibility of rRNA target sites and thus provide more flexibility for probe design...
  11. pmc Unexpected diversity of chlorite dismutases: a catalytically efficient dimeric enzyme from Nitrobacter winogradskyi
    Georg Mlynek
    Department for Structural and Computational Biology, Max F Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A 1030 Vienna, Austria
    J Bacteriol 193:2408-17. 2011
    ..Interestingly, proteins that contain all these signatures and are phylogenetically closely related to the novel-type Cld of N. winogradskyi exist in a large number of other microbes, including other nitrite oxidizers...
  12. ncbi request reprint Nitrite concentration influences the population structure of Nitrospira-like bacteria
    Frank Maixner
    , , Althanstrasse 14, A 1090 Vienna, Austria
    Environ Microbiol 8:1487-95. 2006
    ..Consistent with the observed localization patterns, a higher nitrite concentration selected for sublineage I but suppressed sublineage II Nitrospira...
  13. doi request reprint Colonization of freshwater biofilms by nitrifying bacteria from activated sludge
    Marc Mußmann
    Department of Microbial Ecology, Ecology Center, University of Vienna, Vienna, Austria
    FEMS Microbiol Ecol 85:104-15. 2013
    ..Measured nitrification activities were high in the microcosms and the stream. Our results show that nitrifiers from WWTPs can colonize freshwater biofilms and confirm that WWTP-affected streams are hot spots of nitrification...
  14. pmc Thaumarchaeotes abundant in refinery nitrifying sludges express amoA but are not obligate autotrophic ammonia oxidizers
    Marc Mussmann
    Department of Microbial Ecology, University of Vienna, 1090 Vienna, Austria
    Proc Natl Acad Sci U S A 108:16771-6. 2011
    ..These data demonstrate that some amoA-carrying group I.1b Thaumarchaeota are not obligate chemolithoautotrophs...
  15. pmc A moderately thermophilic ammonia-oxidizing crenarchaeote from a hot spring
    Roland Hatzenpichler
    Department of Microbial Ecology, University of Vienna, Althanstrasse 14, A 1090 Vienna, Austria
    Proc Natl Acad Sci U S A 105:2134-9. 2008
    ..1b for which ammonium oxidation has been verified on a cellular level. Its preference for thermophilic conditions reinvigorates the debate on the thermophilic ancestry of AOA...
  16. pmc Interactions of nitrifying bacteria and heterotrophs: identification of a Micavibrio-like putative predator of Nitrospira spp
    Jan Dolinsek
    Department of Microbial Ecology, Ecology Centre, University of Vienna, Vienna, Austria
    Appl Environ Microbiol 79:2027-37. 2013
    ..In silico screening of published next-generation sequencing data sets revealed a broad environmental distribution of the uncultured Micavibrio-like lineage...
  17. pmc Quantification of target molecules needed to detect microorganisms by fluorescence in situ hybridization (FISH) and catalyzed reporter deposition-FISH
    Tatsuhiko Hoshino
    Department für Mikrobielle Okologie, Universitat Wien, Althanstrasse 14, A 1090 Wien, Austria
    Appl Environ Microbiol 74:5068-77. 2008
    ..These results suggest that optimized FISH protocols using oligonucleotide probes could be suitable for more recent applications of FISH (for example, to detect mRNA in situ in microbial cells)...
  18. doi request reprint Isolation and characterization of a moderately thermophilic nitrite-oxidizing bacterium from a geothermal spring
    Elena V Lebedeva
    Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
    FEMS Microbiol Ecol 75:195-204. 2011
    ..6-96.1% 16S rRNA gene sequence similarity). The findings confirmed that Nitrospira drive nitrite oxidation in moderate thermophilic habitats and also indicated an unexpected diversity of heat-adapted Nitrospira in geothermal hot springs...
  19. ncbi request reprint Linking microbial community structure with function: fluorescence in situ hybridization-microautoradiography and isotope arrays
    Michael Wagner
    Department of Microbial Ecology, University of Vienna, Althanstrasse 14, 1090 Wien, Austria
    Curr Opin Biotechnol 17:83-91. 2006
    ..Isotope arrays have also been developed that exploit the parallel detection offered by DNA microarrays to measure incorporation of labelled substrate into the rRNA of many community members in a single experiment...
  20. doi request reprint Structural and functional characterisation of the chlorite dismutase from the nitrite-oxidizing bacterium "Candidatus Nitrospira defluvii": identification of a catalytically important amino acid residue
    Julius Kostan
    Department for Structural and Computational Biology, Max F Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A 1030 Vienna, Austria
    J Struct Biol 172:331-42. 2010
    ..Finally, our analysis indicates that all Clds and Cld-like enzymes employ a non-covalently bound heme as a cofactor...
  21. pmc Cohn's Crenothrix is a filamentous methane oxidizer with an unusual methane monooxygenase
    Kilian Stoecker
    Department für Mikrobielle Okologie, Universitat Wien, A 1090 Wien, Austria
    Proc Natl Acad Sci U S A 103:2363-7. 2006
    ..Our findings demonstrate a previously unrecognized complexity of the evolutionary history and cell biology of methane-oxidizing bacteria...
  22. doi request reprint Drivers of bacterial colonization patterns in stream biofilms
    Clemens Augspurger
    Department of Freshwater Ecology, University of Vienna, Vienna, Austria
    FEMS Microbiol Ecol 72:47-57. 2010
    ..Our results show that colonization of biofilms in a model stream environment is a heterogeneous process differently affected by biological and physical factors...
  23. pmc Depletion of unwanted nucleic acid templates by selective cleavage: LNAzymes, catalytically active oligonucleotides containing locked nucleic acids, open a new window for detecting rare microbial community members
    Jan Dolinsek
    Department of Microbial Ecology, Vienna Ecology Centre, University of Vienna, Vienna, Austria
    Appl Environ Microbiol 79:1534-44. 2013
    ....
  24. pmc The Genome of Nitrospina gracilis Illuminates the Metabolism and Evolution of the Major Marine Nitrite Oxidizer
    Sebastian Lücker
    Department of Microbial Ecology, Ecology Centre, University of Vienna Vienna, Austria
    Front Microbiol 4:27. 2013
    ..Further, detailed phylogenetic analyses using concatenated marker genes provided evidence that Nitrospina forms a novel bacterial phylum, for which we propose the name Nitrospinae...
  25. pmc Looking inside the box: using Raman microspectroscopy to deconstruct microbial biomass stoichiometry one cell at a time
    Edward K Hall
    Department of Limnology and WasserKluster Lunz GmbH, University of Vienna, Vienna, Austria
    ISME J 5:196-208. 2011
    ..This includes the ability to partition microbial biomass into its constituent macromolecules and increase our understanding of how microorganisms in the environment respond to resource heterogeneity...
  26. doi request reprint In situ techniques and digital image analysis methods for quantifying spatial localization patterns of nitrifiers and other microorganisms in biofilm and flocs
    Holger Daims
    Department of Microbial Ecology, Ecology Center, University of Vienna, Vienna, Austria
    Methods Enzymol 496:185-215. 2011
    ....
  27. pmc Enrichment and genome sequence of the group I.1a ammonia-oxidizing Archaeon "Ca. Nitrosotenuis uzonensis" representing a clade globally distributed in thermal habitats
    Elena V Lebedeva
    Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
    PLoS ONE 8:e80835. 2013
    ..N. uzonensis", which potentially include genetic determinants of ecological niche differentiation. ..
  28. ncbi request reprint Microbial landscapes: new paths to biofilm research
    Tom J Battin
    Department of Freshwater Ecology, University of Vienna, Althanstrasse 14, A 1090 Vienna, Austria
    Nat Rev Microbiol 5:76-81. 2007
    ..Here, we suggest a concept for biofilm research that is spatially explicit and solidly rooted in ecological theory, which might serve as a universal approach to the study of the numerous facets of biofilms...
  29. ncbi request reprint Fluorescence in situ hybridisation for the identification and characterisation of prokaryotes
    Michael Wagner
    Department of Microbial Ecology, Institute of Ecology and Conservation Biology, University of Vienna, Althanstrasse 14, A 1090 Vienna, Austria
    Curr Opin Microbiol 6:302-9. 2003
    ....
  30. ncbi request reprint Raman-FISH: combining stable-isotope Raman spectroscopy and fluorescence in situ hybridization for the single cell analysis of identity and function
    Wei E Huang
    Biodiversity and Ecosystem Function Group, Molecular Microbial Ecology Section, Centre for Ecology and Hydrology Oxford, Mansfield Road, Oxford, OX1 3SR, UK
    Environ Microbiol 9:1878-89. 2007
    ....
  31. ncbi request reprint Selective enrichment and molecular characterization of a previously uncultured Nitrospira-like bacterium from activated sludge
    Eva Spieck
    Universitat Hamburg, Biozentrum Klein Flottbek, Mikrobiologie, Ohnhorststr 18, D 22609 Hamburg, Germany
    Environ Microbiol 8:405-15. 2006
    ..The enriched strain is provisionally classified as 'Candidatus Nitrospira defluvii'...
  32. pmc Use of stable-isotope probing, full-cycle rRNA analysis, and fluorescence in situ hybridization-microautoradiography to study a methanol-fed denitrifying microbial community
    Maneesha P Ginige
    Advanced Wastewater Management Centre, The University of Queensland, St Lucia 4072, Queensland, Australia
    Appl Environ Microbiol 70:588-96. 2004
    ..We conclude that Methylophilales bacteria are the dominant denitrifiers in our SBR system and likely are important denitrifiers in full-scale methanol-fed denitrifying sludges...
  33. ncbi request reprint Microbial community composition and function in wastewater treatment plants
    Michael Wagner
    Microbial Ecology Group, Lehrstuhl fur Mikrobiologie, Technische Universitat Munchen, Freising, Germany
    Antonie Van Leeuwenhoek 81:665-80. 2002
    ..Here we provide an overview of what is currently known about the identity and physiology of some of the microbial key players in activated sludge and biofilm systems...
  34. doi request reprint Nitrification in terrestrial hot springs of Iceland and Kamchatka
    Laila J Reigstad
    Department of Biology, Center for Geobiology, University of Bergen, Bergen, Norway
    FEMS Microbiol Ecol 64:167-74. 2008
    ..Our data provide evidence for an active role of archaea in nitrification of hot springs in a wide range of pH values and at a high temperature...