Personal information

microbial ecology; nitrification; nitrite-oxidizing bacteria; single-cell techniques
Austria

Biography

Holger Daims is Full Professor at the Centre for Microbiology and Environmental Systems Science at the University of Vienna, Austria. He received his PhD in Microbiology at the Technical University in Munich, Germany where he studied the ecology of nitrifying bacteria (especially nitrite-oxidizing bacteria) in biological wastewater treatment plants and developed tools to detect these mainly uncultured organisms in situ. In 2003, he became a founding member of the Department of Microbial Ecology at the University of Vienna in Austria. As University Assistant he established his own research group based on third-party grants. Subsequently, he was Assistant Professor from 2010 to 2012, obtained his “Habilitation” (venia docendi) for Microbiology in 2012, was Associate Professor from 2012 to 2017, and became Full Professor in 2017. His research addresses the ecology, physiology, and evolution of nitrogen-cycling microorganisms with focus on nitrite-oxidizing bacteria, and the development of molecular and imaging methods to study uncultured microorganisms in natural and engineered ecosystems as well as medical samples.

Activities

Employment (1)

University of Vienna: Vienna, AT

2003-03-01 to present | Full Professor (Department of Microbiology and Ecosystem Science)
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Holger Daims

Works (50 of 100)

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Enhanced nitrogen and carbon removal in natural seawater by electrochemical enrichment in a bioelectrochemical reactor

Journal of Environmental Management
2022 | Journal article
Contributors: De la Fuente, Maria Jose; De la Iglesia, Rodrigo; Farias, Laura; Glasner, Benjamin; Torres-Rojas, Felipe; Munoz, Diana; Daims, Holger; Lukumbuzya, Michael; Vargas, Ignacio T.
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A nitrite-oxidising bacterium constitutively consumes atmospheric hydrogen

The ISME Journal
2022-09-01 | Journal article
Contributors: Pok Man Leung; Anne Daebeler; Eleonora Chiri; Iresha Hanchapola; David L Gillett; Ralf B Schittenhelm; Holger Daims; Chris Greening
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Ammonia-oxidizing archaea possess a wide range of cellular ammonia affinities

The ISME Journal
2022-01 | Journal article
Part of ISSN: 1751-7362
Part of ISSN: 1751-7370
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Holger Daims

Nitrogen Kinetic Isotope Effects of Nitrification by the Complete Ammonia Oxidizer Nitrospira inopinata

mSphere
2021-12-22 | Journal article
Contributors: Shurong Liu; Man-Young Jung; Shasha Zhang; Michael Wagner; Holger Daims; Wolfgang Wanek; Jorge L. M. Rodrigues
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Sustained nitrogen loss in a symbiotic association of Comammox Nitrospira and Anammox bacteria

Water Research
2021-09 | Journal article
Part of ISSN: 0043-1354
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Holger Daims

Electrochemical enrichment of marine denitrifying bacteria to enhance nitrate metabolization in seawater

Journal of Environmental Chemical Engineering
2021-08 | Journal article
Contributors: María José De La Fuente; Rodrigo De la Iglesia; Laura Farias; Holger Daims; Michael Lukumbuzya; Ignacio T. Vargas
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Genomic and kinetic analysis of novel Nitrospinae enriched by cell sorting

The ISME Journal
2021-03-01 | Journal article
Contributors: Anna J Mueller; Man-Young Jung; Cameron R Strachan; Craig W Herbold; Rasmus H Kirkegaard; Michael Wagner; Holger Daims
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Exploring the upper pH limits of nitrite oxidation: diversity, ecophysiology, and adaptive traits of haloalkalitolerant Nitrospira

The ISME Journal
2020-12 | Journal article
Part of ISSN: 1751-7362
Part of ISSN: 1751-7370
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Holger Daims

A refined set of rRNA-targeted oligonucleotide probes for in situ detection and quantification of ammonia-oxidizing bacteria

Water Research
2020-11 | Journal article
Contributors: Michael Lukumbuzya; Jannie Munk Kristensen; Katharina Kitzinger; Andreas Pommerening-Röser; Per Halkjær Nielsen; Michael Wagner; Holger Daims; Petra Pjevac
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Activity and Metabolic Versatility of Complete Ammonia Oxidizers in Full-Scale Wastewater Treatment Systems

mBio
2020-03-17 | Journal article
Part of ISSN: 2150-7511
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Holger Daims

Single cell analyses reveal contrasting life strategies of the two main nitrifiers in the ocean.

Nature communications
2020-02-07 | Journal article
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Holger Daims

Transcriptomic Response of Nitrosomonas europaea Transitioned from Ammonia- to Oxygen-Limited Steady-State Growth.

mSystems
2020-01-14 | Journal article
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Holger Daims

A Multicolor Fluorescence in situ Hybridization Approach Using an Extended Set of Fluorophores to Visualize Microorganisms

Frontiers in Microbiology
2019 | Journal article
Contributors: Daims, Holger; Pjevac, Petra; Schmid, Markus; Lukumbuzya, Michael
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An automated Raman-based platform for the sorting of live cells by functional properties

Nature Microbiology
2019 | Journal article
Contributors: Lee, Kang Soo; Palatinszky, Marton; Pereira, Fatima C.; Nguyen, Jen; Fernandez, Vicente, I; Mueller, Anna J.; Menolascina, Filippo; Daims, Holger; Berry, David; Wagner, Michael et al.
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Low yield and abiotic origin of N2O formed by the complete nitrifier Nitrospira inopinata

Nature Communications
2019 | Journal article
Contributors: Kits, K. Dimitri; Jung, Man-Young; Vierheilig, Julia; Pjevac, Petra; Sedlacek, Christopher J.; Liu, Shurong; Herbold, Craig; Stein, Lisa Y.; Richter, Andreas; Wissel, Holger et al.
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A fiber-deprived diet disturbs the fine-scale spatial architecture of the murine colon microbiome

Nature Communications
2019-12 | Journal article
Part of ISSN: 2041-1723
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Holger Daims

Characterization of the First "<i>Candidatus</i> Nitrotoga" Isolate Reveals Metabolic Versatility and Separate Evolution of Widespread Nitrite-Oxidizing Bacteria

mBio
2018 | Journal article
Contributors: Kitzinger, Katharina; Koch, Hanna; Lucker, Sebastian; Sedlacek, Christopher J.; Herbold, Craig; Schwarz, Jasmin; Daebeler, Anne; Mueller, Anna J.; Lukumbuzya, Michael; Romano, Stefano et al.
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Cultivation and Genomic Analysis of "<i>Candidatus</i> Nitrosocaldus islandicus," an Obligately Thermophilic, Ammonia-Oxidizing Thaumarchaeon from a Hot Spring Biofilm in Graendalur Valley, Iceland

Frontiers in Microbiology
2018 | Journal article
Contributors: Daebeler, Anne; Herbold, Craig W.; Vierheilig, Julia; Sedlacek, Christopher J.; Pjevac, Petra; Albertsen, Mads; Kirkegaard, Rasmus H.; de la Torre, Jose R.; Daims, Holger; Wagner, Michael
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Draft Genome Sequence of Telmatospirillum siberiense 26-4b1, an Acidotolerant Peatland Alphaproteobacterium Potentially Involved in Sulfur Cycling

Microbiology Resource Announcements
2018 | Journal article
Contributors: Loy, Alexander; Wagner, Michael; Daims, Holger; Herbold, Craig W.; Schreck, Katharina; Pjevac, Petra; Hausman, Bela
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Nitrospira

Trends in Microbiology
2018 | Journal article
Contributors: Wagner, Michael; Daims, Holger
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The draft genome sequence of "Nitrospira lenta" strain BS10, a nitrite oxidizing bacterium isolated from activated sludge

Standards in Genomic Sciences
2018 | Journal article
Contributors: Sakoula, Dimitra; Nowka, Boris; Spieck, Eva; Daims, Holger; Lucker, Sebastian
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<i>Crenothrix</i> are major methane consumers in stratified lakes

The ISME Journal
2017 | Journal article
Contributors: Oswald, Kirsten; Graf, Jon S.; Littmann, Sten; Tienken, Daniela; Brand, Andreas; Wehrli, Bernhard; Albertsen, Mads; Daims, Holger; Wagner, Michael; Kuypers, Marcel M. M. et al.
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Adaptability as the key to success for the ubiquitous marine nitrite oxidizer <i>Nitrococcus</i>

Science Advances
2017 | Journal article
Contributors: Fuessel, Jessika; Luecker, Sebastian; Yilmaz, Pelin; Nowka, Boris; van Kessel, Maartje A. H. J.; Bourceau, Patric; Hach, Philipp F.; Littmann, Sten; Berg, Jasmine; Spieck, Eva et al.
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AmoA-Targeted Polymerase Chain Reaction Primers for the Specific Detection and Quantification of Comammox Nitrospira in the Environment

Frontiers in Microbiology
2017 | Journal article
Contributors: Sebastian Lücker; Michaela Steinberger; Craig W. Herbold; Petra Pjevac; Holger Daims; Michael Wagner; Mike S. M. Jetten; Anne Daebeler; Maartje A. H. J. van Kessel; Lianna Poghosyan et al.
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Giant viruses with an expanded complement of translation system components

Science
2017 | Journal article
Contributors: Schulz, Frederik; Yutin, Natalya; Ivanova, Natalia; Ortega, Davi; Lee, Tae Kwon; Vierheilig, Julia; Daims, Holger; Horn, Matthias; Wagner, Michael; Jensen, Grant et al.
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Kinetic analysis of a complete nitrifier reveals an oligotrophic lifestyle

Nature
2017 | Journal article
Contributors: Kits, K. Dimitri; Sedlacek, Christopher J.; Lebedeva, Elena V.; Han, Ping; Bulaev, Alexandr; Pjevac, Petra; Daebeler, Anne; Romano, Stefano; Albertsen, Mads; Stein, Lisa Y. et al.
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A New Perspective on Microbes Formerly Known as Nitrite-Oxidizing Bacteria

Trends in Microbiology
2016 | Journal article
Contributors: Michael Wagner; Sebastian Lücker; Holger Daims
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Genomics of a phototrophic nitrite oxidizer: insights into the evolution of photosynthesis and nitrification

The ISME Journal
2016 | Journal article
Contributors: Holger Daims; Laura A Pace; Woodward W Fischer; Bernhard Schink; Jena E Johnson; Joachim Schott; Sebastian Lücker; James Hemp
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Relative Abundance of Nitrotoga spp. in a Biofilter of a Cold-Freshwater Aquaculture Plant Appears To Be Stimulated by Slightly Acidic pH

Applied and Environmental Microbiology
2016 | Journal article
Contributors: Carsten Kühn; Yvonne Bedarf; Sebastian Lücker; Sandra Off; Eva Spieck; Holger Daims; Simone Wegen; Jennifer Hüpeden
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Comparison of Oxidation Kinetics of Nitrite-Oxidizing Bacteria: Nitrite Availability as a Key Factor in Niche Differentiation

Applied and Environmental Microbiology
2015 | Journal article
Contributors: Eva Spieck; Holger Daims; Boris Nowka
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Complete nitrification by <i>Nitrospira</i> bacteria

Nature
2015 | Journal article
Contributors: Daims, Holger; Lebedeva, Elena V.; Pjevac, Petra; Han, Ping; Herbold, Craig; Albertsen, Mads; Jehmlich, Nico; Palatinszky, Marton; Vierheilig, Julia; Bulaev, Alexandr et al.
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Cyanate as an energy source for nitrifiers

Nature
2015 | Journal article
Contributors: Palatinszky, Marton; Herbold, Craig; Jehmlich, Nico; Pogoda, Mario; Han, Ping; von Bergen, Martin; Lagkouvardos, Ilias; Karst, Soren M.; Galushko, Alexander; Koch, Hanna et al.
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Dimeric chlorite dismutase from the nitrogen-fixing cyanobacterium Cyanothece sp PCC7425

Molecular Microbiology
2015 | Journal article
Contributors: Gianantonio Battistuzzi; Georg Mlynek; Christian Obinger; Holger Daims; Paul G. Furtmüller; Kristina Djinovic-Carugo; Marzia Bellei; Gerhard Stadlmayr; Michael Krutzler; Stefan Hofbauer et al.
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Expanded metabolic versatility of ubiquitous nitrite-oxidizing bacteria from the genus <i>Nitrospira</i>

Proceedings of the National Academy of Sciences
2015 | Journal article
Contributors: Koch, Hanna; Luecker, Sebastian; Albertsen, Mads; Kitzinger, Katharina; Herbold, Craig; Spieck, Eva; Nielsen, Per Halkjaer; Wagner, Michael; Daims, Holger
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Functionally relevant diversity of closely related Nitrospira in activated sludge

The ISME Journal
2015 | Journal article
Contributors: Michael Pester; Michael Wagner; Thomas Rattei; Alexander Loy; Domenico F Savio; Katharina Kitzinger; Holger Daims; Christiane Gruber-Dorninger
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Improved isolation strategies allowed the phenotypic differentiation of two Nitrospira strains from widespread phylogenetic lineages

FEMS Microbiology Ecology
2015 | Journal article
Contributors: Eva Spieck; Sandra Off; Boris Nowka; Holger Daims
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Nitrotoga-like bacteria are previously unrecognized key nitrite oxidizers in full-scale wastewater treatment plants

The ISME Journal
2015 | Journal article
Contributors: Holger Daims; Michael Wagner; Eva Spieck; Christiane Gruber-Dorninger; Jasmin Schwarz; Sebastian Lücker
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Structure and heme-binding properties of HemQ (chlorite dismutase-like protein) from Listeria monocytogenes

Archives of Biochemistry and Biophysics
2015 | Journal article
Contributors: Holger Daims; Michael Krutzler; Georg Mlynek; Kristina Djinović-Carugo; Gerhard Stadlmayr; Paul G. Furtmüller; Christian Obinger; Katharina F. Pirker; Irene Schaffner; Andreas Hagmüller et al.
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<i>Nitrolancea</i> <i>hollandica</i> gen. nov., sp nov., a chemolithoautotrophic nitrite-oxidizing bacterium isolated from a bioreactor belonging to the phylum <i>Chloroflexi</i>

International Journal of Systematic and Evolutionary Microbiology
2014 | Journal article
Contributors: Sorokin, Dimitry Y.; Vejmelkova, Dana; Luecker, Sebastian; Streshinskaya, Galina M.; Rijpstra, W. Irene C.; Damste, Jaap S. Sinninghe; Kleerbezem, Robbert; van Loosdrecht, Mark; Muyzer, Gerard; Daims, Holger
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Growth of nitrite-oxidizing bacteria by aerobic hydrogen oxidation

Science
2014 | Journal article
Contributors: Koch, Hanna; Galushko, Alexander; Albertsen, Mads; Schintlmeister, Arno; Gruber-Dorninger, Christiane; Luecker, Sebastian; Pelletier, Eric; Le Paslier, Denis; Spieck, Eva; Richter, Andreas et al.
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Manipulating Conserved Heme Cavity Residues of Chlorite Dismutase: Effect on Structure, Redox Chemistry, and Reactivity

Biochemistry
2014 | Journal article
Contributors: Hofbauer, Stefan; Gysel, Kira; Bellei, Marzia; Hagmueller, Andreas; Schaffner, Irene; Mlynek, Georg; Kostan, Julius; Pirker, Katharina F.; Daims, Holger; Furtmueller, Paul G. et al.
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NxrB encoding the beta subunit of nitrite oxidoreductase as functional and phylogenetic marker for nitrite-oxidizing Nitrospira

Environmental Microbiology
2014 | Journal article
Contributors: Pester, Michael; Maixner, Frank; Berry, David; Rattei, Thomas; Koch, Hanna; Luecker, Sebastian; Nowka, Boris; Richter, Andreas; Spieck, Eva; Lebedeva, Elena et al.
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Spatial distribution analyses of natural phyllosphere-colonizing bacteria on <i>A</i> <i>rabidopsis thaliana</i> revealed by fluorescence <i>in situ</i> hybridization

Environmental Microbiology
2014 | Journal article
Contributors: Mitja N. P. Remus-Emsermann; Julia A. Vorholt; Eva Potthoff; Sebastian Lücker; Holger Daims; Daniel B. Müller
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Thermophilic biological nitrogen removal in industrial wastewater treatment

Applied Microbiology and Biotechnology
2014 | Journal article
Contributors: Lopez-Vazquez, C. M.; Kubare, M.; Saroj, D. P.; Chikamba, C.; Schwarz, J.; Daims, H.; Brdjanovic, D.
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Three-Dimensional Stratification of Bacterial Biofilm Populations in a Moving Bed Biofilm Reactor for Nitritation-Anammox

International Journal of Molecular Sciences
2014 | Journal article
Contributors: Britt-Marie Wilén; Frank Persson; Magnus Christensson; Maria Ekenberg; Holger Daims; Robert Almstrand; Malte Hermansson; Fred Sörensson
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Understanding Chlorite Dismutase from Candidatus Nitrospira defluvii

Journal of Biological Inorganic Chemistry
2014 | Journal article
Contributors: Hofbauer, S.; Gruber, C.; Pirker, K. F.; Schaffner, I.; Furtmueller, P. G.; Obinger, C.; Hagmueller, A.; Gysel, K.; Mlynek, G.; Kostan, J. et al.
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Colonization of freshwater biofilms by nitrifying bacteria from activated sludge

FEMS Microbiology Ecology
2013 | Journal article
Contributors: Mussmann, Marc; Ribot, Miquel; von Schiller, Daniel; Merbt, Stephanie N.; Augspurger, Clemens; Karwautz, Clemens; Winkel, Matthias; Battin, Tom J.; Marti, Eugenia; Daims, Holger
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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

Applied and Environmental Microbiology
2013 | Journal article
Contributors: Holger Daims; Michael Wagner; Ilias Lagkouvardos; Christiane Dorninger; Jan Dolinšek
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Enrichment and Genome Sequence of the Group I. 1a Ammonia-Oxidizing Archaeon "Ca. Nitrosotenuis uzonensis" Representing a Clade Globally Distributed in Thermal Habitats

Plos One
2013 | Journal article
Contributors: Lebedeva, Elena V.; Hatzenpichler, Roland; Pelletier, Eric; Schuster, Nathalie; Hauzmayer, Sandra; Bulaev, Aleksandr; Grigor'eva, Nadezhda V.; Galushko, Alexander; Schmid, Markus; Palatinszky, Marton et al.
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Interactions of Nitrifying Bacteria and Heterotrophs: Identification of a Micavibrio-Like Putative Predator of Nitrospira spp

Applied and Environmental Microbiology
2013 | Journal article
Contributors: Daims, Holger; Wagner, Michael; Wanek, Wolfgang; Lagkouvardos, Ilias; Dolinsek, Jan
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