A5036215076- Microbial Community Ecology and Physiology
- Environmental DNA in Biodiversity Studies
- Ecology and Vegetation Dynamics Studies
- Forest Insect Ecology and Management
- Legume Nitrogen Fixing Symbiosis
- Gut microbiota and health
- Identification and Quantification in Food
- Forest Ecology and Biodiversity Studies
- Protist diversity and phylogeny
- Plant and animal studies
- Genomics and Phylogenetic Studies
- Aquatic Ecosystems and Phytoplankton Dynamics
- Chromosomal and Genetic Variations
- Species Distribution and Climate Change
- Evolution and Genetic Dynamics
- Lichen and fungal ecology
- Nematode management and characterization studies
- Mycorrhizal Fungi and Plant Interactions
- Botany and Plant Ecology Studies
- Agronomic Practices and Intercropping Systems
- Water Treatment and Disinfection
- RNA Research and Splicing
- Allelopathy and phytotoxic interactions
- Agricultural Development and Management
- Aquaculture disease management and microbiota
ETH Zurich
2016-2025
École Polytechnique Fédérale de Lausanne
2015-2024
National Institute of Diabetes and Digestive and Kidney Diseases
2008-2020
National Institutes of Health
2008-2020
University of Basel
2009-2019
University of Chicago
2005-2007
Swiss Federal Institute for Forest, Snow and Landscape Research
2001-2006
Krankenhaus Oberndorf
1991
Georgetown University
1976
Purdue University West Lafayette
1973
Harnessing beneficial microbes presents a promising strategy to optimize plant growth and agricultural sustainability. Little is known which extent how specifically soil microbiomes can be manipulated through different cropping practices. Here, we investigated wheat root microbial communities in system experiment consisting of conventional organic managements, both with tillage intensities. While richness was marginally affected, found pronounced effects on community composition, were...
Abstract DNA sampled from the environment (eDNA) is a useful way to uncover biodiversity patterns. By combining conceptual model and empirical data, we test whether eDNA transported in river networks can be used as an integrative assess eukaryotic for broad spatial scales across land–water interface. Using metabarcode approach, detect 296 families of eukaryotes, spanning 19 phyla catchment river. We show subset these that samples overcome autocorrelation biases associated with classical...
Diverse assemblages of microbes colonize plant roots and collectively function as a microbiome. Earlier work has characterized the root microbiomes numerous species, but little information is available for legumes despite their key role in ecosystems including agricultural systems. Legumes form nodule symbiosis with nitrogen-fixing Rhizobia bacteria thereby account large, natural nitrogen inputs into soils. Here, we describe microbiome legume Trifolium pratense combining culture-dependent...
A fructose-rich diet can induce metabolic syndrome, a combination of health disorders that increases the risk diabetes and cardiovascular diseases. Diet is also known to alter microbial composition gut, although it not clear whether such alteration contributes development syndrome. The aim this work was assess possible link between gut microbiota diet-induced syndrome in rat model obesity. Rats were fed either standard or high-fructose diet. Groups fructose-fed rats treated with antibiotics...
Here we used flow cytometry (FCM) and filtration paired with amplicon sequencing to determine the abundance composition of small low nucleic acid (LNA)-content bacteria in a variety freshwater ecosystems. We found that FCM clusters associated LNA-content were ubiquitous across several ecosystems, varying from 50 90% aquatic bacteria. Using filter-size separation, separated (passing 0.4 µm filter) large (captured on characterized communities 16S sequencing. Small each represented different...
Abstract Assessing individual components of biodiversity, such as local or regional taxon richness, and differences in community composition is a long‐standing challenge ecology. It especially relevant spatially structured diverse ecosystems. Environmental DNA (eDNA) has been suggested novel technique to detect taxa therefore may allow accurately measure biodiversity. However, we do not yet fully understand the comparability eDNA‐based assessments classical morphological approaches. We...
Abstract Background Plants influence their root and rhizosphere microbial communities through the secretion of exudates. However, how specific classes exudate compounds impact assembly root-associated microbiotas is not well understood, especially under realistic field conditions. Maize roots secrete benzoxazinoids (BXs), a class indole-derived defense compounds, thereby microbiota. Here, we investigated broader impacts BX exudation on adult maize plants grown natural conditions at different...
Abstract Through the development of environmental DNA (eDNA) metabarcoding, in situ monitoring organisms is becoming easier and promises a revolution our approaches to detect changes biodiversity over space time. A cornerstone eDNA approach primer pairs that allow amplifying specific taxonomic groups, which then used link sequence identification. Here, we propose framework for comparing regarding (a) their capacity bind amplify broad coverage species within target clade using silico PCR, (b)...
Abstract Accurate characterisation of ecological communities with respect to their biodiversity and food-web structure is essential for conservation. However, combined empirical study multi-trophic food webs at a large spatial temporal resolution has been prohibited by the lack appropriate access such data from natural systems. Here, we assessed characteristics across 700 km 2 riverine network over seasons using environmental DNA. We found contrasting patterns between major taxonomic groups....
Abstract Many lichen species produce both sexual and asexual propagules, but, aside from being minute, these diaspores lack special adaptations for long‐distance dispersal. So far, molecular studies have not directly addressed isolation genetic differentiation of populations, affected by gene flow, at a regional scale. We used six mycobiont‐specific microsatellite loci to investigate the population structure epiphytic Lobaria pulmonaria in two regions that strongly differed with respect...
We reconstructed cyanobacterial community structure and phylogeny using DNA that was isolated from layers of stratified sediments spanning 200 years lake history in the perialpine lakes Greifensee Lake Zurich (Switzerland). Community analysis based on amplification sequencing a 400-nucleotide (nt)-long 16S rRNA fragment specific to Cyanobacteria revealed operational taxonomic units (OTUs) capturing whole phylum, including representatives newly characterized clade termed Melainabacteria,...
Flexible polymeric pipe materials are commonly used as shower hoses or connections to faucets in the last meters of building plumbing, but these tend leach high concentrations carbon that encourage bacterial growth.
Methods to estimate microbial diversity have developed rapidly in an effort understand the distribution and of microorganisms natural environments. For bacterial communities, 16S rRNA gene is phylogenetic marker choice, but most studies select only a specific region diversity. Whereas biases derived from DNA extraction, primer choice PCR amplification are well documented, we here address how variable can influence wide range standard ecological metrics, such as species richness, diversity,...
Abstract Soil nematode communities and food web indices can inform about the complexity, nutrient flows decomposition pathways of soil webs, reflecting quality. Relative abundance feeding life‐history groups are used for calculating indices, i.e., maturity index (MI), enrichment (EI), structure (SI) channel (CI). Molecular methods to study potentially offer advantages compared traditional in terms resolution, throughput, cost time. In spite such advantages, molecular data have not often been...
Anthropogenic activities are changing the state of ecosystems worldwide, affecting community composition and often resulting in loss biodiversity. Rivers among most impacted ecosystems. Recording their current with regular biomonitoring is important to assess future trajectory Traditional monitoring methods for ecological assessments costly time-intensive. Here, we compared macroinvertebrates based on environmental DNA (eDNA) sampling traditional kick-net biodiversity patterns at 92 river...
Abstract We investigated microbial methane oxidation in the water column of two connected but hydrodynamically contrasting basins Lake Lugano, Switzerland. Both accumulate large amounts below their chemoclines, efficiently prevents from reaching surface waters. Here we show that meromictic North Basin column, a substantial fraction was eliminated through anaerobic (AOM) coupled to nitrite reduction by Candidatus Methylomirabilis. Incubations with 14CH4 and concentrated biomass this basin...
Propagation, whether sexual or asexual, is a fundamental step in the life cycle of every organism. In lichenized fungi, great variety vegetative propagules have evolved order for symbiotic partners to disperse simultaneously. For lichens with ability and asexual reproduction, relative contribution dispersal unknown but could, nonetheless, be inferred by studying genotype distribution. The genetic structure three Lobaria pulmonaria (Lobariaceae) populations from Switzerland was investigated...
Abstract Background The invasive benthic round goby ( Neogobius melanostomus) is the most successful temperate fish and has spread in aquatic ecosystems on both sides of Atlantic. Invasive species constitute powerful situ experimental systems to study fast adaptation directional selection short ecological timescales present promising case studies understand factors involved impressive ability some colonize novel environments. We seize unique opportunity presented by invasion genomic...
Abstract Environmental DNA (eDNA) metabarcoding is raising expectations for biomonitoring of organisms that have hitherto been neglected. To bypass current limitations in taxonomic assignments due to incomplete or erroneous reference databases, taxonomy‐free approaches are proposed at the level operational units (OTUs). This challenging, because OTUs cannot be annotated and directly compared against classically derived data. The application good stringency treatments infer validity clear...
Phosphorus (P) is a limiting element for plant growth. Several root microbes, including arbuscular mycorrhizal fungi (AMF), have the capacity to improve nutrition and their abundance known depend on P fertility. However, how complex root-associated bacterial fungal communities respond various levels of supplementation remains ill-defined. Here we investigated responses bacteria varying supply using 16S rRNA gene internal transcribed spacer amplicon sequencing. We grew Petunia, which forms...
Sleep disorders have been linked to alterations of gut microbiota composition in adult humans and animal models, but it is unclear how this link develops. With longitudinal assessments 162 healthy infants, we present a so far unrecognized sleep-brain-gut interrelationship. First, report between sleep habits microbiota: daytime associated with bacterial diversity, nighttime fragmentation variability are maturity enterotype. Second, demonstrate link: diversity enterotype neurophysiology....