DOME

Univ.-Prof. Dr. Holger Daims

Deputy Head of the Department of Microbiology and Ecosystem Science
Deputy Head of the Division of Microbial Ecology

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✉ holger.daims(at)univie.ac.at

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CeMESS/Ludwig Schedl

Our research centers on microorganisms that drive the biogeochemical nitrogen cycle, with a particular focus on key nitrifiers: nitrite-oxidizing bacteria (NOB) and complete ammonia oxidizers (comammox). Using a combination of molecular, omics, and microbial physiology approaches, we identify new nitrifying microbes and investigate their metabolism, ecophysiology, and evolution. Our goal is to achieve a fundamental understanding of nitrification in natural and engineered ecosystems, with implications for improving agricultural and wastewater management practices and reducing nitrous oxide emissions.

We are also interested in microbe-microbe interactions within complex microbiomes, such as biofilms in natural and engineered environments. By integrating omics, fluorescence and chemical imaging, and computational analyses, we identify microbial partners and study their interactions in situ. These efforts aim to uncover core principles of microbial interaction that shape the composition, spatial organization, and functional adaptability of microbial communities.

Research Topics

Biology of complete ammonia oxidizers (comammox)

We contributed to the discovery of complete ammonia oxidizers (comammox), microorganisms belonging to the diverse and environmentally widespread genus Nitrospira. Unlike all other known nitrifiers, comammox perform complete nitrification (the oxidation of ammonia to nitrate) within a single organism. This discovery resolved a century-old question in nitrogen cycling and transformed our understanding of this fundamental biogeochemical process. It also opened new research directions on the ecology, evolution, kinetics, regulation, and biochemistry of complete nitrification. Comammox Nitrospira are particularly well adapted to oligotrophic environments: their kinetic traits allow them to outcompete other ammonia oxidizers, including many ammonia-oxidizing archaea, under strong substrate limitation. We investigate the biology of these remarkable organisms using our primary comammox isolate (Nitrospira inopinata), new enrichment cultures, and cultivation-independent approaches in close collaboration with the group of Michael Wagner.

Anne Daebeler

Ecophysiology of nitrite-oxidizing bacteria

Nitrite-oxidizing bacteria (NOB), which catalyze the second step of nitrification, remain among the most elusive and least understood players in the nitrogen cycle. Our research aims to uncover the biology and ecological roles of NOB in natural habitats and engineered systems such as wastewater treatment plants. We combine (meta)genomic analyses with laboratory experiments to test genome-based hypotheses.

Traditionally viewed as highly specialized with narrow metabolic capacities, NOB are now recognized as remarkably versatile. Our work has revealed that many NOB can oxidize not only nitrite but also alternative substrates such as hydrogen or formate, and can use oxygen or nitrate as terminal electron acceptors. Our research explores how this impressive metabolic flexibility underpins their niche adaptations and survival strategies in diverse and fluctuating environments.

CeMESS\Holger Daims

Microbe-microbe interactions

Microbiomes consist of diverse microorganisms that interact in many functionally distinct ways, including the exchange of metabolites, syntrophic substrate degradation, molecular signaling, stress mitigation, competition, and predation. These interactions shape community structure and influence key processes that sustain ecosystem functioning. Our research seeks to unravel how such microbial relationships affect growth, activity, and resilience within microbiomes.

A focus lies on interactions involving nitrifying organisms. As chemolithoautotrophic primary producers, nitrifiers provide organic matter that supports heterotrophic partners, while in turn benefiting from other microbes that supply essential cofactors or alleviate environmental stress. By studying these associations, we aim to understand the ecology of nitrifiers beyond their role in nitrification and to reveal the mechanisms that govern their coexistence and population dynamics within complex microbial communities.

Jan Dolinšek, Holger Daims

Microscopy and image analysis in microbiology

Fluorescence labeling techniques are essential tools in microbial ecology and related microbiological disciplines. A prominent example is fluorescence in situ hybridization (FISH) with rRNA-targeted probes, which enables the cultivation-independent identification, detection, and quantification of microorganisms. Combined with advanced imaging systems such as confocal laser scanning microscopes, FISH allows three-dimensional analyses of labeled microbial populations in biofilms and other spatially complex samples.

The full potential of fluorescence labeling is realized through quantitative digital image analysis. We develop algorithms for the analysis of fluorescence-labeled microorganisms, implemented in our software daime (digital image analysis in microbial ecology). It provides accurate quantification of microbial population and community features in diverse sample types, including biofilms, flocs, and animal or plant tissues. It also offers advanced tools for interactive three-dimensional visualization of confocal image stacks, seamlessly integrated with its quantitative image analysis capabilities.

CeMESS\Holger Daims, Markus Schmid

Group Members

Sarah Al-Ajeel

PhD Student

Dr. Nicole Geerlings

Postdoc

Dr. Ruizhe Pei

Senior Postdoc

Jakob Rauter

Master's Student

Dr. Anton Strunov

Senior Scientist

Dr. Stefan Thiele

Technician

Dr. Meng Zhang

Postdoc

Publications

Daims H, Nielsen JL, Nielsen PH, Schleifer KH, Wagner M. In Situ Characterization of Nitrospira-Like Nitrite-Oxidizing Bacteria Active in Wastewater Treatment Plants. Applied and Environmental Microbiology. 2001;67(11):5273-5284.

Daims H, Purkhold U, Bjerrum L, Arnold E, Wilderer PA, Wagner M. Nitrification in sequencing biofilm batch reactors: Lessons from molecular approaches. In Water Science and Technology: Volume 43. Unknown publisher. 2001. p. 9-18. (Water Science and Technology).

Daims H, Nielsen PH, Nielsen JL, Juretschko S, Wagner M. Novel Nitrospira-like bacteria as dominant nitrite-oxidizers in biofilms from wastewater treatment plants: Diversity and in situ physiology. In Water Science and Technology: Volume 41. Unknown publisher. 2000. p. 85-90. (Water Science and Technology).

Daims H, Brühl A, Amann R, Schleifer KH, Wagner M. The domain-specific probe EUB338 is insufficient for the detection of all Bacteria: Development and evaluation of a more comprehensive probe set. Systematic and Applied Microbiology. 1999;22:434-444.

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Microbiomes Drive Planetary Health

Holger Daims is part of the FWF-funded Cluster of Excellence (CoE)

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