A5021660345- Microbial Community Ecology and Physiology
- Wastewater Treatment and Nitrogen Removal
- Genomics and Phylogenetic Studies
- Microbial Fuel Cells and Bioremediation
- Polar Research and Ecology
- Methane Hydrates and Related Phenomena
- Gut microbiota and health
- Protist diversity and phylogeny
- Water Treatment and Disinfection
- Probiotics and Fermented Foods
- Soil Carbon and Nitrogen Dynamics
- Environmental DNA in Biodiversity Studies
- Anaerobic Digestion and Biogas Production
- Groundwater and Isotope Geochemistry
- Marine Sponges and Natural Products
- Marine and coastal ecosystems
- Biocrusts and Microbial Ecology
- Isotope Analysis in Ecology
- Marine Biology and Ecology Research
- Photosynthetic Processes and Mechanisms
- Marine Bivalve and Aquaculture Studies
- Microbial Natural Products and Biosynthesis
- Sulfur Compounds in Biology
- Atmospheric and Environmental Gas Dynamics
- Mine drainage and remediation techniques
University of Canterbury
2023-2025
University of Vienna
2015-2024
University of Waikato
2012-2024
Université de Lille
2024
Max Planck Institute for Marine Microbiology
2022
Medical University of Vienna
2022
Antarctica New Zealand
2013-2020
Ecologie Microbienne Lyon
2019
NASA Astrobiology Institute
2005-2009
University of California, Los Angeles
2007-2009
Significance Nitrification, the sequential aerobic oxidation of ammonia via nitrite to nitrate, is a key process biogeochemical nitrogen cycle and catalyzed by two microbial guilds (nitrifiers): oxidizers nitrite-oxidizing bacteria (NOB). NOB are generally considered as metabolically restricted dependent on oxidizers. Here, we report that, surprisingly, many ecosystems ( Nitrospira ) convert urea, an important source in nature, CO 2 . Thus, supply urease-negative with receive produced...
Chemosynthetic symbioses are partnerships between invertebrate animals and chemosynthetic bacteria. The latter the primary producers, providing most of organic carbon needed for animal host's nutrition. We sequenced genomes symbionts from lucinid bivalve Loripes lucinalis stilbonematid nematode Laxus oneistus. both host species encoded nitrogen fixation genes. This is remarkable as no marine symbiont was previously known to be capable fixation. detected nitrogenase expression by clams at...
Microorganisms are critical in mediating carbon (C) and nitrogen (N) cycling processes soils. Yet, it has long been debated whether the underlying biogeochemical cycles affected by composition diversity of soil microbial community or not. The communities can be influenced various environmental factors, which turn known to impact processes. objectives this study were test effects multiple edaphic drivers individually represented as multivariate environment interacting with diversity,...
Nitrification, the oxidation of ammonia via nitrite to nitrate, has always been considered be catalyzed by concerted activity ammonia- and nitrite-oxidizing microorganisms. Only recently, complete oxidizers ('comammox'), which oxidize nitrate on their own, were identified in bacterial genus Nitrospira, previously assumed contain only canonical oxidizers. Nitrospira are widespread nature, but for assessments distribution functional importance comammox ecosystems, cultivation-independent tools...
Members of the phylum Acidobacteria are abundant and ubiquitous across soils. We performed a large-scale comparative genome analysis spanning subdivisions 1, 3, 4, 6, 8 23 (n = 24) with goal to identify features help explain their prevalence in soils understand ecophysiology. Our revealed that bacteriophage integration events along transposable mobile elements influenced structure plasticity these genomes. Low- high-affinity respiratory oxygen reductases were detected multiple genomes,...
Many intestinal pathogens, including Clostridioides difficile, use mucus-derived sugars as crucial nutrients in the gut. Commensals that compete with pathogens for such are therefore ecological gatekeepers healthy guts, and attractive candidates therapeutic interventions. Nevertheless, there is a poor understanding of which commensals mucin-derived situ well their potential to impede pathogen colonization. Here, we identify mouse gut utilize monosaccharides within complex communities using...
Climate change is altering the frequency and severity of drought events. Recent evidence indicates that may produce legacy effects on soil microbial communities. However, it unclear whether precedent events lead to ecological memory formation, i.e., capacity past influence current ecosystem response trajectories. Here, we utilize a long-term field experiment in mountain grassland central Austria with an experimental layout comparing 10 years recurrent single event ambient conditions. We show...
The global atmospheric level of methane (CH 4 ), the second most important greenhouse gas, is currently increasing by ∼10 million tons per year. Microbial oxidation in unsaturated soils only known biological process that removes CH from atmosphere, but so far, bacteria can grow on have eluded all cultivation efforts. In this study, we isolated a pure culture bacterium, strain MG08 grows air at concentrations [1.86 parts volume (p.p.m.v.)]. This organism, named Methylocapsa gorgona , globally...
Nitrous oxide (N2O) and nitric (NO) are atmospheric trace gases that contribute to climate change affect stratospheric ground-level ozone concentrations. Ammonia oxidizing bacteria (AOB) archaea (AOA) key players in the nitrogen cycle major producers of N2O NO globally. However, nothing is known about production by recently discovered widely distributed complete ammonia oxidizers (comammox). Here, we show comammox bacterium Nitrospira inopinata sensitive inhibition an scavenger, cannot...
Abstract Sulfur-cycling microorganisms impact organic matter decomposition in wetlands and consequently greenhouse gas emissions from these globally relevant environments. However, their identities physiological properties are largely unknown. By applying a functional metagenomics approach to an acidic peatland, we recovered draft genomes of seven novel Acidobacteria species with the potential for dissimilatory sulfite (dsrAB, dsrC, dsrD, dsrN, dsrT, dsrMKJOP) or sulfate respiration (sat,...
Abstract Nitrification, the oxidation of ammonia to nitrate, is an essential process in biogeochemical nitrogen cycle. The first step nitrification, oxidation, performed by three, often co-occurring guilds chemolithoautotrophs: ammonia-oxidizing bacteria (AOB), archaea (AOA), and complete oxidizers (comammox). Substrate kinetics are considered be a major niche-differentiating factor between these guilds, but few AOA strains have been kinetically characterized. Here, kinetic properties 12...
Microorganisms are responsible for nutrient removal and resource recovery in wastewater treatment plants (WWTPs), their diversity is often studied by 16S rRNA gene amplicon sequencing. However, this approach underestimates the abundance of Patescibacteria due to low coverage commonly used PCR primers highly divergent bacterial phylum. Therefore, our current understanding global diversity, distribution, ecological role WWTPs very incomplete. This particularly relevant as considered be...
Analysis of microbial communities by high-throughput pyrosequencing SSU rRNA gene PCR amplicons has transformed ecology research and led to the observation that many contain a diverse assortment rare taxa–a phenomenon termed Rare Biosphere. Multiple studies have investigated effect read quality on operational taxonomic unit (OTU) richness for contrived communities, yet there is limited information fidelity community structure estimates obtained through this approach. Given biases are widely...
High throughput sequencing of phylogenetic and functional gene amplicons provides tremendous insight into the structure potential complex microbial communities. Here, we introduce a highly adaptable economical PCR approach to barcoding pooling libraries numerous target genes. In this approach, replace gene- platform-specific fusion primers with general, interchangeable primers, enabling nearly limitless customized barcode-primer combinations. Compared long our multiple-target is more because...
ABSTRACT Nitrification is a key process of the biogeochemical nitrogen cycle and biological wastewater treatment. The second step, nitrite oxidation to nitrate, catalyzed by phylogenetically diverse, chemolithoautotrophic nitrite-oxidizing bacteria (NOB). Uncultured NOB from genus “ Candidatus Nitrotoga” are widespread in natural engineered ecosystems. Knowledge about their biology sparse, because no genomic information pure Ca . culture was available. Here we obtained first isolate...
Obligate acidophilic members of the thaumarchaeotal genus Candidatus Nitrosotalea play an important role in nitrification acidic soils, but their evolutionary and physiological adaptations to environments are still poorly understood, with only a single member this (Ca. N. devanaterra) having its genome sequenced. In study, we sequenced genomes two additional cultured Ca. strains, extracted almost complete metagenome-assembled from fen, performed comparative genomics four 19 other archaeal...
Two strains, 30N-5 and 30VD-1, identified as Bacillus simplex B. subtilis, were isolated from the rhizospheres of two different plants, a Podocarpus palm, respectively, growing in University California, Los Angeles (UCLA) Mildred E. Mathias Botanical Garden. subtilis is well-known plant-growth promoting bacterial species, but not. was initially on nitrogen-free medium, no evidence for nitrogen fixation found. Nevertheless, pea plants inoculated with showed change root architecture due to...
Abstract Compartmentalization of the gut microbiota is thought to be important system function, but extent spatial organization in ecosystem remains poorly understood. Here, we profile murine colonic along longitudinal and lateral axes using laser capture microdissection. We found fine-scale structuring marked by gradients composition diversity length colon. Privation fiber reduces disrupts composition. Both mucus-adjacent luminal communities are influenced absence dietary fiber, with loss a...
Abstract Nitrification, the oxidation of ammonia via nitrite to nitrate, is a key process in marine nitrogen (N) cycling. Although oceanic and are balanced, ammonia-oxidizing archaea (AOA) vastly outnumber main oxidizers, bacterial Nitrospinae. The ecophysiological reasons for this discrepancy abundance unclear. Here, we compare substrate utilization growth Nitrospinae AOA Gulf Mexico. Based on our results, more than half cellular N-demand met by organic-N compounds urea cyanate, while...