A5044355096- Microbial Community Ecology and Physiology
- Mycorrhizal Fungi and Plant Interactions
- Soil Carbon and Nitrogen Dynamics
- Plant Pathogens and Fungal Diseases
- Genomics and Phylogenetic Studies
- Gut microbiota and health
- Forest Ecology and Biodiversity Studies
- Environmental DNA in Biodiversity Studies
- Peatlands and Wetlands Ecology
- Yeasts and Rust Fungi Studies
- Legume Nitrogen Fixing Symbiosis
- Polar Research and Ecology
- Lower Extremity Biomechanics and Pathologies
- Foot and Ankle Surgery
- Plant-Microbe Interactions and Immunity
- Lichen and fungal ecology
- Forest Insect Ecology and Management
- Agronomic Practices and Intercropping Systems
- Nematode management and characterization studies
- Urban Agriculture and Sustainability
- Heavy metals in environment
- Soil Management and Crop Yield
- Plant Ecology and Soil Science
- Species Distribution and Climate Change
- Orthoptera Research and Taxonomy
Universitätsklinik Balgrist
2024-2025
University of Zurich
2024-2025
ETH Zurich
2018-2025
Swiss Federal Institute for Forest, Snow and Landscape Research
2012-2023
Goethe University Frankfurt
2020
Agroscope
2005-2016
Institute for Sustainability
2015
University of British Columbia
2009-2015
Federal Office for Agriculture
2005-2006
ABSTRACT mothur aims to be a comprehensive software package that allows users use single piece of analyze community sequence data. It builds upon previous tools provide flexible and powerful for analyzing sequencing As case study, we used trim, screen, align sequences; calculate distances; assign sequences operational taxonomic units; describe the α β diversity eight marine samples previously characterized by pyrosequencing 16S rRNA gene fragments. This analysis more than 222,000 was...
Abstract The nuclear ribosomal internal transcribed spacer ( ITS ) region is the formal fungal barcode and in most cases marker of choice for exploration diversity environmental samples. Two problems are particularly acute pursuit satisfactory taxonomic assignment newly generated sequences: (i) lack an inclusive, reliable public reference data set (ii) means to refer species, which no Latin name available a standardized stable way. Here, we report on progress these regards through further...
Low-input agricultural systems aim at reducing the use of synthetic fertilizers and pesticides in order to improve sustainable production ecosystem health. Despite integral role soil microbiome production, we still have a limited understanding complex response microbial diversity organic conventional farming. Here report on structural more than two decades different management long-term field experiment using high-throughput pyrosequencing approach bacterial fungal ribosomal markers. Organic...
Summary The nuclear ribosomal internal transcribed spacer ( ITS ) region is the primary choice for molecular identification of fungi. Its two highly variable spacers 1 and 2) are usually species specific, whereas intercalary 5.8S gene conserved. For sequence clustering blast searches, it often advantageous to rely on either one but not conserved gene. To identify extract 2 from large taxonomic environmental data sets is, however, difficult, many sequences incorrectly delimited in public...
Microorganisms are vital in mediating the earth's biogeochemical cycles; yet, despite our rapidly increasing ability to explore complex environmental microbial communities, relationship between community structure and ecosystem processes remains poorly understood. Here, we address a fundamental unanswered question ecology: 'When do need understand accurately predict function?' We present statistical analysis investigating value of data independently combination for explaining rates carbon...
Abstract The ribosomal rRNA genes are widely used as genetic markers for taxonomic identification of microbes. Particularly the small subunit ( SSU ; 16S/18S) gene is frequently species‐ or genus‐level identification, but also large LSU 23S/28S) employed in assignment. metaxa software tool a popular utility extracting partial sequences from sequencing data sets and assigning them to an archaeal, bacterial, nuclear eukaryote, mitochondrial chloroplast origin. This study describes...
Permafrost represents a largely understudied genetic resource. Thawing of permafrost with global warming will not only promote microbial carbon turnover direct feedback on greenhouse gases, but also unlock an unknown diversity. Pioneering metagenomic efforts have shed light the microbiome in polar regions, temperate mountain is understudied. We applied unique experimental design coupled to high-throughput sequencing ribosomal markers characterize microbiota at long-term alpine study site...
The nuclear ribosomal internal transcribed spacer (ITS) region is the most commonly chosen genetic marker for molecular identification of fungi in environmental sequencing and ecology studies. Several analytical issues complicate such efforts, one which formation chimeric—artificially joined—DNA sequences during PCR amplification or sequence assembly. software tools are currently available chimera detection, but rely to various degrees on presence a chimera-free reference dataset optimal...
Despite the importance of Arctic soils in global carbon cycle, we know very little impacts warming on soil microbial communities that drive and nutrient cycling these ecosystems. Over a 2-year period, monitored structure fungal bacterial organic mineral horizons plots warmed by greenhouses for 18 years control plots. We found were stable over time but strongly structured warming. Warming led to significant reductions evenness communities, while increased significantly. These patterns...
The impact of climate change on the soil microbiome potentially alters biogeochemical cycle terrestrial ecosystems. In semi-arid environments, water availability is a major constraint cycles due to combination high summer temperatures and low rainfall. Here, we explored how 10 years irrigation water-limited pine forest in central European Alps altered associated ecosystem functioning. A decade stimulated tree growth, resulting higher crown cover, larger yearly increments biomass, increased...
Human wellbeing depends on ecosystem services, highlighting the need for improving ecosystem-service multifunctionality of food and feed production systems. We study Swiss agricultural grasslands to assess how employing combining three widespread aspects grassland management their interactions can enhance 22 plot-level service indicators, as well multifunctionality. The we are i) organic system, ii) an eco-scheme prescribing extensive (without fertilization), iii) harvest type (pasture vs....
Summary Disturbances caused by timber harvesting have critical long‐term effects on the forest soil microbiota and alter fundamental ecosystem services provided these communities. This study assessed of organic matter removal compaction microbial community structures in different horizons 13 years after at productivity site Skulow Lake, British Columbia. A harvested stand was compared with an unmanaged stand. Ribosomal intergenic spacer profiles bacteria, archaea eukarya indicated...
ABSTRACT Changes in the diversity and structure of soil microbial communities may offer a key to understanding impact environmental factors on quality agriculturally managed systems. Twenty-five years biodynamic, bio-organic, or conventional management DOK long-term experiment Switzerland significantly altered bacterial community structures, as assessed by terminal restriction fragment length polymorphism (T-RFLP) analysis. To evaluate these results, relation between structures their...
Climate warming is leading to shrub expansion in Arctic tundra. Shrubs form ectomycorrhizal (ECM) associations with soil fungi that are central ecosystem carbon balance as determinants of plant community structure and decomposers organic matter. To assess potential climate change impacts on ECM communities, we analysed fungal internal transcribed spacer sequences from root tips the dominant tundra Betula nana growing treatments plots had received long-term by greenhouses and/or fertilization...
Molecular data form an important research tool in most branches of mycology. A non-trivial proportion the public fungal DNA sequences are, however, compromised terms quality and reliability, contributing noise bias to sequence-borne inferences such as phylogenetic analysis, diversity assessment, barcoding. In this paper we discuss various aspects pitfalls sequence assessment. Based on our observations, provide a set guidelines assist manual management newly generated, near-full-length...
Abstract Spatial patterns of microbial communities have been extensively surveyed in well‐developed soils, but few studies investigated the vertical distribution micro‐organisms newly developed soils after glacier retreat. We used 454‐pyrosequencing to assess whether bacterial and fungal community structures differed between stages soil development ( SSD ) characterized by an increasing vegetation cover from barren (vegetation cover: 0%/age: 10 years), sparsely vegetated (13%/60 transient...
Agricultural productivity relies on a wide range of ecosystem services provided by the soil biota. Plowing is fundamental component conventional farming, but long-term detrimental effects such as erosion and loss organic matter have been recognized. Moving towards more sustainable management practices reduced tillage or crop residue retention can reduce these effects, will also influence structure function microbiota with direct consequences for associated services. Although there increasing...
Decomposition is a major flux of the carbon cycle in forest soils and understanding involved processes key for budgeting turnover. constrained by presence biological agents such as microorganisms underlying environmental conditions water availability. A metabarcoding approach ribosomal markers was chosen to study succession bacterial fungal decomposers on root litter. Litterbags containing pine roots were buried two years sequentially sampled. associated communities surveyed under ambient...