A5030719944- Microbial Community Ecology and Physiology
- Methane Hydrates and Related Phenomena
- Wastewater Treatment and Nitrogen Removal
- Genomics and Phylogenetic Studies
- Atmospheric and Environmental Gas Dynamics
- Protist diversity and phylogeny
- Anaerobic Digestion and Biogas Production
- Biofuel production and bioconversion
- Microbial metabolism and enzyme function
- Hydrocarbon exploration and reservoir analysis
- Peatlands and Wetlands Ecology
- Microbial Metabolic Engineering and Bioproduction
- Microbial Fuel Cells and Bioremediation
- biodegradable polymer synthesis and properties
- Marine and coastal ecosystems
- Extracellular vesicles in disease
- Geology and Paleoclimatology Research
- Enzyme Catalysis and Immobilization
- Bacteriophages and microbial interactions
- Ammonia Synthesis and Nitrogen Reduction
- Mine drainage and remediation techniques
- Tracheal and airway disorders
- Coastal wetland ecosystem dynamics
- Soil Carbon and Nitrogen Dynamics
- Arsenic contamination and mitigation
University of Vienna
2023-2025
Max Planck Institute for Marine Microbiology
2022-2024
California Institute of Technology
2018-2024
Radboud University Nijmegen
2012-2021
Massachusetts Institute of Technology
2012-2017
Metagenomics, or sequencing of the genetic material from a complete microbial community, is promising tool to discover novel microbes and viruses. Viral metagenomes typically contain many unknown sequences. Here we describe discovery previously unidentified bacteriophage present in majority published human faecal metagenomes, which refer as crAssphage. Its ~97 kbp genome six times more abundant publicly available than all other known phages together; it comprises up 90% 22% reads virus-like...
Anaerobic oxidation of methane (AOM) is crucial for controlling the emission this potent greenhouse gas to atmosphere. Nitrite-, nitrate-, and sulfate-dependent well-documented, but AOM coupled reduction oxidized metals has so far been demonstrated only in environmental samples. Here, using a freshwater enrichment culture, we show that archaea order Methanosarcinales, related "Candidatus Methanoperedens nitroreducens," couple environmentally relevant forms Fe3+ Mn4+ methane. We obtained an...
Partial-nitritation anammox (PNA) is a novel wastewater treatment procedure for energy-efficient ammonium removal. Here we use genome-resolved metagenomics to build genome-based ecological model of the microbial community in full-scale PNA reactor. Sludge from bioreactor examined here used seed reactors plants around world; however, role most its removal remains unknown. Our analysis yielded 23 near-complete draft genomes that together represent majority community. We assign these distinct...
Summary Anaerobic ammonium‐oxidizing (anammox) bacteria are responsible for a significant portion of the loss fixed nitrogen from oceans, making them important players in global cycle. To date, marine anammox found water columns and sediments worldwide belong almost exclusively to ‘ Candidatus Scalindua’ species, but molecular basis their metabolism competitive fitness is presently unknown. We applied community sequencing enrichment culture dominated by Scalindua profunda’ construct genome...
Methane oxidation is an important process to mitigate the emission of greenhouse gas methane and further exacerbating climate forcing. Both aerobic anaerobic microorganisms have been reported catalyze with only a few possible electron acceptors. Recently, new were identified that could couple nitrate or nitrite reduction. Here we investigated such enrichment culture at (meta)genomic level establish metabolic model nitrate-driven (nitrate-AOM). Nitrate-AOM catalyzed by archaeon closely...
Abstract Nitrogen (N 2 ) fixation in oligotrophic surface waters is the main source of new nitrogen to ocean 1 and has a key role fuelling biological carbon pump . Oceanic N been attributed almost exclusively cyanobacteria, even though genes encoding nitrogenase, enzyme that fixes into ammonia, are widespread among marine bacteria archaea 3–5 Little known about these non-cyanobacterial fixers, direct proof they can fix so far lacking. Here we report discovery -fixing symbiont, ‘ Candidatus...
Nitric oxide (NO) and nitrous (N2O) are among Nature's most powerful electron acceptors. In recent years it became clear that microorganisms can take advantage of the oxidizing power these compounds to degrade recalcitrant aliphatic aromatic hydrocarbons. For two unrelated bacterial species, 'NC10' phylum bacterium 'Candidatus Methylomirabilis oxyfera' γ-proteobacterial strain HdN1 has been suggested under anoxic conditions with nitrate and/or nitrite, monooxygenases used for methane...
Oxygen minimum zones (OMZ) are areas in the global ocean where oxygen concentrations drop to below one percent. Low allow alternative respiration with nitrate and nitrite as electron acceptor become prevalent these areas, making them main contributors oceanic nitrogen loss. The contribution of anammox denitrification loss seems vary different OMZs. In Arabian Sea, both processes were reported. Here, we performed a metagenomics study upper core zone Sea OMZ, provide comprehensive overview...
Several recent studies have indicated that members of the phylum Planctomycetes are abundantly present at brine-seawater interface (BSI) above multiple brine pools in Red Sea. include bacteria capable anaerobic ammonium oxidation (anammox). Here, we investigated possibility anammox BSI sites using metagenomic shotgun sequencing DNA obtained from Discovery Deep pool. Analysis reads matching 16S rRNA and hzsA genes confirmed presence genus Scalindua. Phylogenetic analysis gene this Scalindua...
Methane is a potent greenhouse gas, which can be converted by microorganism at the expense of oxygen, nitrate, nitrite, metal-oxides or sulfate. The bacterium 'Candidatus Methylomirabilis oxyfera', member NC10 phylum, capable nitrite-dependent anaerobic methane oxidation. Prolonged enrichment 'Ca. M. oxyfera' with cerium added as trace element and without nitrate resulted in shift dominant species. Here, we present high quality draft genome new species lanthanophilum' use comparative...
Eukaryotic genomes are known to have garnered innovations from both archaeal and bacterial domains but the sequence of events that led complex gene repertoire eukaryotes is largely unresolved. Here, through enrichment hydrothermal vent microorganisms, we recovered two circularized Heimdallarchaeum species belong an Asgard archaea clade phylogenetically closest eukaryotes. These reveal diverse mobile elements, including integrative viral genome bidirectionally replicates in a circular form...
Abstract ‘ Candidatus Methanophagales’ (ANME-1) is an order-level clade of archaea responsible for anaerobic methane oxidation in deep-sea sediments. The diversity, ecology and evolution ANME-1 remain poorly understood. In this study, we use metagenomics on hydrothermal samples to expand diversity uncover the effect virus–host dynamics. Phylogenetic analyses reveal a deep-branching, thermophilic family, Methanospirareceae’, closely related short-chain alkane oxidizers. Global phylogeny...
Lacustrine methane emissions are strongly mitigated by aerobic methane-oxidizing bacteria (MOB) that typically most active at the oxic-anoxic interface. Although oxygen is required MOB for first step of oxidation, their occurrence in anoxic lake waters has raised possibility they capable oxidizing further anaerobically. Here, we investigate activity and growth Lake Zug, a permanently stratified freshwater lake. The rates anaerobic oxidation hypolimnion reached up to 0.2 µM d
Since their discovery, extracellular vesicles (EVs) have changed our view on how organisms interact with world. EVs are able to traffic a diverse array of molecules across different species and even domains, facilitating numerous functions. In this study, we investigate EV production in
Anammox bacteria are key players in the global nitrogen cycle and responsible for up to 50% of loss. Because their cost effective application anaerobic removal, anammox widely implemented wastewater treatment. Currently, five genera have been identified, together forming a deep branching order Planctomycetes-Verrucomicrobium- Chlamydiae (PVC) superphylum. Members all detected treatment plants, but metagenomic information is not yet available genera. Here we report analysis an enrichment...
Summary Fixed nitrogen is released by anaerobic ammonium oxidation (anammox) and/or denitrification from (marine) ecosystems. Nitrite, the terminal electron acceptor of anammox process, occurs in nature at very low concentrations and produced via (micro)aerobic or nitrate reduction. The coupling sulfide‐dependent to particularly interesting because besides hydrogen, sulfide most important reductant chemocline anoxic marine basins abundant within sediments. Although μ M concentrations, may be...
Abstract Hydrothermal vents have been key to our understanding of the limits life, and metabolic phylogenetic diversity thermophilic organisms. Here we used environmental metagenomics combined with analysis physicochemical data 16S rRNA gene amplicons characterize sediment-hosted microorganisms at recently discovered Auka in Gulf California. We recovered 325 metagenome assembled genomes (MAGs) representing 54 phyla, over 30% those currently known, showing microbial community hydrothermal...
Sulfate-coupled anaerobic oxidation of methane (AOM) is performed by multicellular consortia methanotrophic archaea (ANME) in obligate syntrophic partnership with sulfate-reducing bacteria (SRB). Diverse ANME and SRB clades co-associate but the physiological basis for their adaptation diversification not well understood. In this work, we used comparative metagenomics phylogenetics to investigate metabolic among 4 main (HotSeep-1, Seep-SRB2, Seep-SRB1a, Seep-SRB1g) identified features...
Poly(3-hydroxybutyrate) (PHB) production and mobilization in Ralstonia eutropha are well studied, but only a few instances has PHB been explored relation to other cellular processes. We examined the global gene expression of wild-type R. throughout cycle: growth on fructose, using fructose following ammonium depletion, utilization absence exogenous carbon after was resupplied. Our results confirm or lend support previously reported regarding PHB-related genes enzymes. Additionally, for many...
Anaerobic ammonium oxidizing (anammox) bacteria are responsible for a significant portion of the loss fixed nitrogen from oceans, making them important players in global cycle. To date, marine anammox found both water columns and sediments worldwide belong almost exclusively to "Candidatus Scalindua" species. Recently genome assembly enrichment culture dominated by Scalindua profunda" became available can now be used as template study metagenome data obtained various oxygen minimum zones...
Nitric oxide (NO) is a highly reactive and climate-active molecule key intermediate in the microbial nitrogen cycle. Despite its role evolution of denitrification aerobic respiration, high redox potential capacity to sustain growth, our understanding NO-reducing microorganisms remains limited due absence cultures obtained directly from environment using NO as substrate. Here, continuous bioreactor constant supply sole electron acceptor, we enriched characterized community dominated by two...
Bacteria of the phylum Planctomycetes are special interest for study compartmental cellular organization. Members this share a very unusual prokaryotic cell plan, featuring several membrane-bound compartments. Recently, it was shown that organization might extend to certain members Verrucomicrobia. The Planctomycete plan has been defined as proteinaceous wall, cytoplasmic membrane surrounding paryphoplasm and an intracytoplasmic defining riboplasm. So far presumed did not have asymmetric...