Michael Wagner

Michael Wagner
University of Vienna | UniWien · Department of Microbiology and Ecosystem Science

Prof. Dr.

About

616
Publications
124,983
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Introduction
Michael Wagner is full professor for Microbial Ecology at the University of Vienna, Austria and serves also as Director of the Centre for Microbiology and Environmental Systems Science. He also holds a position as a distinguished professor (20%) at Aalborg University, Denmark. Michael and his team is interested in all aspects of nitrification with a particular focus on the biology of ammonia-oxidizing archaea and bacteria as well as on complete nitrifiers of the genus Nitrospira (Comammox). Furthermore, he and his group continuously develop innovative single cell tools (Raman microspectroscopy, microfluidics or NanoSIMS) for investigating the identity and function of individual microbial cells within their natural habitats.
Additional affiliations
February 2003 - present
University of Vienna
Position
  • Managing Director

Publications

Publications (616)
Article
Full-text available
One of the biggest challenges in microbiome research in environmental and medical samples is to better understand functional properties of microbial community members at a single-cell level. Single-cell isotope probing has become a key tool for this purpose, but the current detection methods for determination of isotope incorporation into single ce...
Article
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The bacterial genus Tetrasphaera encompasses abundant polyphosphate accumulating organisms (PAOs) that are responsible for enhanced biological phosphorus removal (EBPR) in wastewater treatment plants. Recent analyses of genomes from pure cultures revealed that 16S rRNA genes cannot resolve the lineage, and that Tetrasphaera spp. are from several di...
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Nitrification is an important nitrogen cycle process in terrestrial and aquatic environments. The discovery of comammox has changed the view that canonical AOA, AOB, and NOB are the only chemolithoautotrophic organisms catalyzing nitrification.
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Raman microspectroscopy offers microbiologists a rapid and non-destructive technique to assess the chemical composition of individual live microorganisms in near real time. In this Primer, we outline the methodology and potential for its application to microbiology. We describe the technical aspects of Raman analyses and practical approaches to app...
Article
Raman microspectroscopy offers microbiologists a rapid and non-destructive technique to assess the chemical composition of individual live microorganisms in near real time. In this Primer, we outline the methodology and potential for its application to microbiology. We describe the technical aspects of Raman analyses and practical approaches to app...
Article
Raman microspectroscopy offers microbiologists a rapid and non-destructive technique to assess the chemical composition of individual live microorganisms in near real time. In this Primer, we outline the methodology and potential for its application to microbiology. We describe the technical aspects of Raman analyses and practical approaches to app...
Article
Heterotrophic nitrifiers are able to oxidize and remove ammonia from nitrogen‐rich wastewaters but the genetic elements of heterotrophic ammonia oxidation are poorly understood. Here, we isolated and identified a novel heterotrophic nitrifier, Alcaligenes ammonioxydans sp. nov. strain HO‐1, oxidizing ammonia to hydroxylamine and ending in the produ...
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Albumin-targeting of a maleimide-containing oxaliplatin-releasing platinum( iv ) prodrug results in tumor-specific drug delivery and activity as shown by LA-ICP-MS, isotope-labeling and NanoSIMS in cell culture and in vivo .
Article
This study evaluates the performance of the antigen-based anterior nasal screening programme implemented in all Austrian schools to detect SARS-CoV-2 infections. We combined nationwide antigen-based screening data obtained in March 2021 from 5,370 schools (Grade 1–8) with an RT-qPCR-based prospective cohort study comprising a representative sample...
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Cyanate can serve as a nitrogen and/or carbon source for different microorganisms and as an energy source for autotrophic ammonia oxidizers. However, the extent of cyanate availability and utilisation in terrestrial ecosystems and its role in biogeochemical cycles is poorly known. Here we analyse cyanate concentrations in soils across a range of so...
Preprint
Full-text available
One of the biggest challenges in microbiome research in environmental and medical samples is to better understand functional properties of microbial community members at a single cell level. Single cell isotope probing has become a key tool for this purpose, but the currently applied detection methods for measuring isotope incorporation into single...
Article
Full-text available
Extracellular DNA is a major macromolecule in global element cycles, and is a particularly crucial phosphorus, nitrogen and carbon source for microorganisms in the seafloor. Nevertheless, the identities, ecophysiology and genetic features of DNA-foraging microorganisms in marine sediments are largely unknown. Here, we combined microcosm experiments...
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Ectomycorrhizal plants trade plant-assimilated carbon for soil nutrients with their fungal partners. The underlying mechanisms are, however, not fully understood. Here we investigated the exchange of carbon for nitrogen in the ectomycorrhizal symbiosis of Fagus Sylvatica across different spatial scales from the root-system to the cellular scale. We...
Article
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Nitrification, the oxidation of ammonia to nitrate, is an essential process in the biogeochemical nitrogen cycle. The first step of nitrification, ammonia oxidation, is performed by three, often co-occurring guilds of chemolithoautotrophs: ammonia-oxidizing bacteria (AOB), archaea (AOA), and complete ammonia oxidizers (comammox). Substrate kinetics...
Article
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Background The role of schools in the SARS-CoV-2 pandemic is much debated. We aimed to quantify reliably the prevalence of SARS-CoV-2 infections at schools detected with reverse-transcription quantitative polymerase-chain-reaction (RT-qPCR). Methods This nationwide prospective cohort study monitors a representative sample of pupils (grade 1–8) and...
Preprint
Full-text available
Nitrification, the oxidation of ammonia to nitrate, is an essential process in the biogeochemical nitrogen cycle. The first step of nitrification, ammonia oxidation, is performed by three, often co-occurring guilds of chemolithoautotrophs: ammonia-oxidizing bacteria (AOB), archaea (AOA), and complete ammonia oxidizers (comammox). Substrate kinetics...
Article
A multi‐omics approach including proteomics, transcriptomics and imaging, was applied to comprehensively investigate the mode of action of the anticancer ruthenium(III) drug candidate BOLD‐100. In their Communication (DOI: 10.1002/anie.202015962), Samuel M. Meier‐Menches, Christopher Gerner et al. found the ribosomal proteins RPL10, RPL24 and the t...
Article
Ein Multiomics‐Ansatz, der Proteomik, Transkriptomik und Bildgebung umfasst, wurde angewendet, um die Wirkungsweise des Antikrebs‐Ruthenium(III)‐Wirkstoffkandidaten BOLD‐100 umfassend zu untersuchen. In ihrer Zuschrift (DOI: 10.1002/ange.202015962) identifizieren Samuel M. Meier‐Menches, Christopher Gerner et al. die ribosomalen Proteine RPL10, RPL...
Article
Oxaliplatin shows a superior clinical activity in colorectal cancer compared to cisplatin. Nevertheless, the knowledge about its cellular distribution and the mechanisms responsible for the different range of oxaliplatin-responsive tumors is far from complete. In this study, we combined highly sensitive element specific and isotope selective imagin...
Preprint
Full-text available
Background Thee is much debate about the role of schools and children in the SARS-CoV-2 pandemic. We aimed to quantify reliably the prevalence of SARS-CoV-2 infections at schools detected with reverse-transcription polymerase-chain-reaction (RT-PCR). Methods This nationwide prospective cohort study monitors a representative sample of pupils (grade...
Article
Full-text available
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Article
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Multi‐Omik‐Analysen zeigen, dass der tumorinhibierende Wirkstoffkandidat BOLD‐100/KP1339 gezielt mit den ribosomalen Proteinen RPL10/RPL24 sowie GTF2I wechselwirken könnte. Schwellungen des endoplasmatischen Retikulums (ER) und der Nachweis der Bildung von Polyribosomen durch bildgebende Verfahren weisen darauf hin, dass eine Behandlung mit BOLD‐10...
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The ruthenium‐based anticancer agent BOLD‐100/KP1339 has shown promising results in several in vitro and in vivo tumour models, as well as in early clinical trials. However, its mode of action remains to be fully elucidated. Recent evidence identified ER stress‐induction and concomitant down‐modulation of HSPA5 (GRP78) as key drug effects. By explo...
Article
Stable isotope labeling of microbial taxa of interest and their sorting provide an efficient and direct way to answer the question “who does what?” in complex microbial communities when coupled with fluorescence in situ hybridization or downstream ‘omics’ analyses. We have developed a platform for automated Raman-based sorting in which optical twee...
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Full-text available
Abstract The field of microbiome research has evolved rapidly over the past few decades and has become a topic of great scientific and public interest. As a result of this rapid growth in interest covering different fields, we are lacking a clear commonly agreed definition of the term “microbiome.” Moreover, a consensus on best practices in microbi...
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The class Deltaproteobacteria comprises an ecologically and metabolically diverse group of bacteria best known for dissimilatory sulphate reduction and predatory behaviour. Although this lineage is the fourth described class of the phylum Proteobacteria , it rarely affiliates with other proteobacterial classes and is frequently not recovered as a m...
Preprint
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Microbiome research has consistently been placed in the spotlight over the past two decades, and has shown tremendous promise in the fields of medicine, environmental science, food production, and agriculture. Life on Earth does not exist without microbes, and we may benefit from learning more about them. Yet, there is no common understanding among...
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Chemolithoautotrophic nitrite-oxidizing bacteria (NOB) are key players in global nitrogen and carbon cycling. Members of the phylum Nitrospinae are the most abundant, known NOB in the oceans. To date, only two closely affiliated Nitrospinae species have been isolated, which are only distantly related to the environmentally abundant uncultured Nitro...
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Many intestinal pathogens, including Clostridioides difficile, use mucus-derived sugars as crucial nutrients in the gut. Commensals that compete with pathogens for such nutrients are therefore ecological gatekeepers in healthy guts, and are attractive candidates for therapeutic interventions. Nevertheless, there is a poor understanding of which com...
Article
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Ammonia-oxidizing bacteria (AOB) of the betaproteobacterial genera Nitrosomonas and Nitrosospira are key nitrifying microorganisms in many natural and engineered ecosystems. Since many AOB remain uncultured, fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes has been one of the most widely used approaches to study t...
Article
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Stable isotope probing (SIP) is a key tool for identifying the microorganisms catalyzing the turnover of specific substrates in the environment and to quantify their relative contributions to biogeochemical processes. However, SIP-based studies are subject to the uncertainties posed by cross-feeding, where microorganisms release isotopically labele...
Article
Full-text available
An amendment to this paper has been published and can be accessed via the original article.
Preprint
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Hydroxylamine is a key intermediate of microbial ammonia oxidation and plays an important role in the biogeochemical cycling of N-compounds. Hydroxylamine is oxidized to NO or N2O by hydroxylamine oxidases or cytochrome P460 from heterotrophic or autotrophic bacteria, but its enzymatic oxidation to N2 has not yet been observed. Here, we report on t...
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Nitrification is a fundamental process in terrestrial nitrogen cycling. However, detailed information on how climate change affects the structure of nitrifier communities is lacking, specifically from experiments in which multiple climate change factors are manipulated simultaneously. Consequently, our ability to predict how soil nitrogen (N) cycli...
Article
Full-text available
Nitrite-oxidizing bacteria of the genus Nitrospira are key players of the biogeochemical nitrogen cycle. However, little is known about their occurrence and survival strategies in extreme pH environments. Here, we report on the discovery of physiologically versatile, haloalkalitolerant Nitrospira that drive nitrite oxidation at exceptionally high p...
Preprint
Full-text available
Cyanate (NCO ⁻ ) can serve as a nitrogen and/or carbon source for different microorganisms and even additionally as an energy source for autotrophic ammonia oxidizers. Despite the widely distributed genetic potential for direct cyanate utilization among bacteria, archaea and fungi, the availability and environmental significance of cyanate is large...
Preprint
Full-text available
Chemolithoautotrophic nitrite-oxidizing bacteria (NOB) are key players in global nitrogen and carbon cycling. Members of the phylum Nitrospinae are the dominant, known NOB in the oceans. To date, only two closely affiliated Nitrospinae species have been isolated, which are only distantly related to the environmentally dominant uncultured Nitrospina...
Article
Full-text available
The assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International Code of Nomenclature of Prokaryotes (ICNP) only recog...
Preprint
Full-text available
Ammonia-oxidizing bacteria (AOB) of the betaproteobacterial genera Nitrosomonas and Nitrosospira are key nitrifying microorganisms in many natural and engineered ecosystems. Since many AOB remain uncultured, fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes has been one of the most widely used approaches to study t...
Preprint
Full-text available
Chemosynthetic symbioses occur worldwide in marine habitats. However, physiological studies of chemoautotrophic bacteria thriving on animals are scarce. Stilbonematinae are coated by monocultures of thiotrophic Gammaproteobacteria. As these nematodes migrate through the redox zone, their ectosymbionts experience varying oxygen concentrations. Here,...
Preprint
Nitrite-oxidizing bacteria of the genus Nitrospira are key players of the biogeochemical nitrogen cycle. However, little is known about their occurrence and survival strategies in extreme pH environments. Here, we report on the discovery of physiologically versatile, haloalkalitolerant Nitrospira that drive nitrite oxidation at exceptionally high p...
Article
Full-text available
In our recent work, we developed an optofluidic platform that allows a direct link to be made between the phenotypes (functions) and the genotypes (genes) of microbial cells within natural communities. By combining stable isotope probing, optical tweezers, Raman microspectroscopy, and microfluidics, the platform performs automated Raman-based sorti...
Article
Full-text available
Nitrification, the oxidation of ammonia via nitrite to nitrate, is a key process in marine nitrogen (N) cycling. Although oceanic ammonia and nitrite oxidation are balanced, ammonia-oxidizing archaea (AOA) vastly outnumber the main nitrite oxidizers, the bacterial Nitrospinae. The ecophysiological reasons for this discrepancy in abundance are uncle...
Article
Full-text available
Nitrification is a ubiquitous microbially mediated process in the environment and an essential process in engineered systems such as wastewater and drinking water treatment plants. However, nitrification also contributes to fertilizer loss from agricultural environments, increasing the eutrophication of downstream aquatic ecosystems, and produces t...
Article
Full-text available
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Article
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Consistent with the observation that ammonia-oxidizing bacteria (AOB) outnumber ammonia-oxidizing archaea (AOA) in many eutrophic ecosystems globally, AOB typically dominate activated sludge aeration basins from municipal wastewater treatment plants (WWTPs). In this study, we demonstrate that the growth of AOA strains inoculated into sterile-filter...
Preprint
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Ammonia-oxidizing microorganisms perform the first step of nitrification, the oxidation of ammonia to nitrite. The bacterium Nitrosomonas europaea is the best characterized ammonia oxidizer to date. Exposure to hypoxic conditions has a profound effect on the physiology of N. europaea , e.g. by inducing nitrifier denitrification, resulting in increa...
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Thaumarchaeota are responsible for a significant fraction of ammonia oxidation in the oceans and in soils that range from alkaline to acidic. However, the adaptive mechanisms underpinning their habitat expansion remain poorly understood. Here we show that expansion into acidic soils and the high pressures of the hadopelagic zone of the oceans is ti...
Article
Cable bacteria of the family Desulfobulbaceae form centimeter-long filaments comprising thousands of cells. They occur worldwide in the surface of aquatic sediments, where they connect sulfide oxidation with oxygen or nitrate reduction via long-distance electron transport. In the absence of pure cultures, we used single-filament genomics and metage...
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For Thaumarchaeota , the ratio of their glycerol dialkyl glycerol tetraether (GDGT) lipids depends on growth temperature, a premise that forms the basis of the widely applied TEX 86 paleotemperature proxy. A thorough understanding of which GDGTs are produced by which Thaumarchaeota and what the effect of temperature is on their GDGT composition is...
Article
The recently discovered complete ammonia-oxidizing (comammox) bacteria are occurring in various environments, including wastewater treatment plants. To better understand their role in micropollutant biotransformation in comparison with ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), we investigated the biotransformation capabi...
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Marine sponges represent one of the few eukaryotic groups that frequently harbor symbiotic members of the Thaumarchaeota, which are important chemoautotrophic ammonia‐oxidizers in many environments. However, in most studies, direct demonstration of ammonia‐oxidation by these archaea within sponges is lacking, and little is known about sponge‐specif...
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Microorganisms in wastewater treatment plants (WWTPs) are essential for water purification to protect public and environmental health. However, the diversity of microorganisms and the factors that control it are poorly understood. Using a systematic global-sampling effort, we analysed the 16S ribosomal RNA gene sequences from ~1,200 activated sludg...
Article
Full-text available
Stable-isotope probing is widely used to study the function of microbial taxa in their natural environment, but sorting of isotopically labelled microbial cells from complex samples for subsequent genomic analysis or cultivation is still in its early infancy. Here, we introduce an optofluidic platform for automated sorting of stable-isotope-probing...
Article
Full-text available
Nitrous oxide (N2O) is a key climate change gas and nitrifying microbes living in terrestrial ecosystems contribute significantly to its formation. Many soils are acidic and global change will cause acidification of aquatic and terrestrial ecosystems, but the effect of decreasing pH on N2O formation by nitrifiers is poorly understood. Here, we used...
Article
The abilities of three phylogenetically distant ammonia oxidizers, Nitrososphaera gargensis, an ammonia-oxidizing archaeon (AOA); Nitrosomomas nitrosa Nm90, an ammonia-oxidizing bacterium (AOB); and Nitrospira inopinata, the only complete ammonia oxidizer (comammox) available as a pure culture, to biotransform seven sulfonamides (SAs) were investig...