A5060524938- Microbial Community Ecology and Physiology
- Protist diversity and phylogeny
- Environmental DNA in Biodiversity Studies
- Plant Pathogens and Fungal Diseases
- Mycorrhizal Fungi and Plant Interactions
- Forest Ecology and Biodiversity Studies
- Lichen and fungal ecology
- Gut microbiota and health
- Actinomycetales infections and treatment
- Genomics and Phylogenetic Studies
- Plant and animal studies
- Ecology and Vegetation Dynamics Studies
- Marine and coastal ecosystems
- Biocrusts and Microbial Ecology
- Plant Parasitism and Resistance
- Yeasts and Rust Fungi Studies
- Parasite Biology and Host Interactions
- Polar Research and Ecology
- Fermentation and Sensory Analysis
- Microbial metabolism and enzyme function
- Identification and Quantification in Food
- Geology and Paleoclimatology Research
- Invertebrate Taxonomy and Ecology
- Insect and Arachnid Ecology and Behavior
- Parasitic Infections and Diagnostics
University of Neuchâtel
2020-2025
University of Kaiserslautern
2016-2021
Helmholtz Centre for Environmental Research
2014-2019
Leipzig University
2013-2015
Laboratoire d'Écologie Alpine
2011
Centre National de la Recherche Scientifique
2011
Université Joseph Fourier
2011
Université Grenoble Alpes
2011
Soil management is fundamental to all agricultural systems and fertilization practices have contributed substantially the impressive increases in food production. Despite pivotal role of soil microorganisms agro-ecosystems, we still a limited understanding complex response microbiota organic mineral very long-term. Here report effects different regimes (mineral, combined fertilization), carried out for more than century, on structure activity microbiome. Organic matter content, nutrient...
Microorganisms play a crucial role in the biological decomposition of plant litter terrestrial ecosystems. Due to permanently changing quality during decomposition, studies both fungi and bacteria at fine taxonomic resolution are required whole process. Here we investigated microbial community succession decomposing leaf temperate beech forest using pyrotag sequencing bacterial 16S fungal internal transcribed spacer (ITS) rRNA genes. Our results reveal that communities underwent rapid...
Abstract Urbanisation is an important global driver of biodiversity change, negatively impacting some species groups whilst providing opportunities for others. Yet its impact on ecosystem services poorly investigated. Here, using a replicated experimental design, we test how Central European cities flying insects and the service pollination. City sites have lower insect richness, particularly Diptera Lepidoptera, than neighbouring rural sites. In contrast, Hymenoptera, especially bees, show...
Protists dominate eukaryotic diversity and play key functional roles in all ecosystems, particularly by catalyzing carbon nutrient cycling. To date, however, a comparative analysis of their taxonomic that compares the major ecosystems on Earth (soil, freshwater marine systems) is missing. Here, we present comparison protist based standardized high throughput 18S rRNA gene sequencing soil, environmental DNA. Soil communities were more similar to each other than communities, with virtually no...
To understand the fine-scale effects of changes in nutrient availability on eukaryotic soil microorganisms communities, a multiple barcoding approach was used to analyse samples from four different treatments long-term fertilization experiment. We performed PCR amplification DNA with primer pairs specifically targeting 18S rRNA genes all eukaryotes and three protist groups (Cercozoa, Chrysophyceae-Synurophyceae Kinetoplastida) as well ITS gene fungi 23S plastid photoautotrophic...
Several fungi-specific primers target the 18S rRNA gene sequence, one of prominent markers for fungal classification. The design most goes back to last decades. Since then, number sequences in public databases increased leading discovery new groups and changes taxonomy. However, no reevaluation was carried out relevant information on is missing. With this study, we aimed develop an sequence primer toolkit allowing easy selection best pair appropriate different sequencing platforms, research...
Increasing anthropogenic impact and global change effects on natural ecosystems has prompted the development of less expensive more efficient bioassessments methodologies. One promising approach is integration DNA metabarcoding in environmental monitoring. A critical step this process inference ecological quality (EQ) status from identified molecular bioindicator signatures that mirror classification based standard macroinvertebrate surveys. The most approaches to infer EQ biotic indices...
The rhizosphere encompasses the soil surrounding surface of plants' fine roots. Accordingly, microbiome present is influenced by both type and plant species. Furthermore, microbial communities respond to land-use intensity due effects on conditions performance. However, there limited knowledge about impact grassland management practices under field composition bacteria fungi in different functional groups. In spring 2014 we planted four phytometer species, two forbs (Plantago lanceolata,...
Despite the important role of wood-inhabiting fungi (WIF) in deadwood decomposition, our knowledge factors shaping dynamics their species richness and community composition is scarce. This due to limitations regarding resolution classical methods used for characterizing WIF communities a lack well-replicated long-term experiments with sufficient numbers tree species. Here, we large scale experiment logs 11 at an early stage distributed across three regions Germany, identify Operational...
Tropical animals and plants are known to have high alpha diversity within forests, but low beta between forests. By contrast, it is unknown whether microbes inhabiting the same ecosystems exhibit similar biogeographic patterns. To evaluate biogeographies of tropical protists, we used metabarcoding data species sampled in soils three lowland Neotropical rainforests. Taxa-area distance-decay relationships for dominant protist taxa their subtaxa were estimated at both OTU phylogenetic levels,...
Summary Effective and precise grouping of highly similar sequences remains a major bottleneck in the evaluation high‐throughput sequencing datasets. Amplicon sequence variants (ASVs) offer promising alternative that may supersede widely used operational taxonomic units (OTUs) environmental studies. We compared performance recently developed pipeline based on algorithm DADA2 for obtaining ASVs against SWARM OTUs. Illumina‐sequencing 29 individual ciliate species resulted up to 11 per species,...
Ciliates are single celled eukaryotes recognized as key players in the microbial loop of aquatic ecosystems. The present study was carried out on Krka River (Croatia), a karst freshwater ecosystem characterized by tufa barriers, biomineralization and highly diverse communities. main aims were to investigate ciliate community structure biofilm (i.e. periphyton) samples collected from light- dark-exposed lithified tufa/stones. Furthermore, establishing links between patterns environmental...
Methanol is an abundant atmospheric volatile organic compound that released from both living and decaying plant material. In forest other aerated soils, methanol can be consumed by methanol-utilizing microorganisms constitute a known terrestrial sink. However, the environmental factors drive biodiversity of such methanol-utilizers have been hardly resolved. Soil-derived isolates also often assimilate multicarbon compounds as alternative substrates. Here, we conducted comparative DNA stable...
The deadwood mycobiome, also known as wood-inhabiting fungi (WIF), are among the key players in wood decomposition, having a large impact on nutrient cycling forest soils. However, our knowledge of WIF richness and distribution patterns different biomes is limited. Here, we used pyrotag sequencing fungal internal transcribed spacer (ITS2) region to characterize mycobiome two tree species with greatly characteristics (Schima superba Pinus massoniana) Chinese subtropical ecosystem....
Deconvoluting the relative contributions made by specific biotic and abiotic drivers to soil fungal community compositions facilitates predictions about functional responses of ecosystems environmental changes, such as losses plant diversity, but it is hindered complex interactions involved. Experimental assembly tree species allows separation respective effects composition (biotic components) properties (abiotic components), enabling much greater statistical power than can be achieved in...
Soil biodiversity is immense, with an estimated 10-100 million organisms belonging to over 5000 taxa in a handful of soil. In spite the importance soil for ecosystem functions and services, information on species, from taxonomy biogeographical patterns, incomplete there no infrastructure connect pre-existing or future data. Here, we propose global platform allow greater access by linking databases repositories through single open portal. The proposed would first time, link data different...
Summary Nitrogen deposition can strongly affect biodiversity, but its specific effects on terrestrial microbial communities and their roles for ecosystem functions processes are still unclear. Here, we investigated the impacts of N wood‐inhabiting fungi (WIF) related ecological in a highly N‐limited deadwood habitat. Based high‐throughput sequencing, enzymatic activity assay measurements wood decomposition rates, show that addition has no significant effect overall WIF community composition...
ABSTRACT The soil eukaryome constitutes a significant portion of Earth's biodiversity that drives major ecosystem functions, such as controlling carbon fluxes and plant performance. Currently, however, we miss standardised approach to functionally classify the in holistic way. Here compiled EukFunc, first functional reference database characterises most abundant important eukaryotic groups: fungi, nematodes protists. We classified 14,060 species based on their mode nutrient acquisition into...
Due to the high diversity of bacteria in many ecosystems, their slow generation times, specific but mostly unknown nutrient requirements and syntrophic interactions, isolation based approaches microbial ecology fail describe community structure. Thus, cultivation independent techniques, which rely on directly extracted nucleic acids from environment, are a well-used alternative. For example, bacterial automated ribosomal intergenic spacer analysis (B-ARISA) is one widely used methods for...
Abstract Aim Assembly of protist communities is known to be driven mainly by environmental filtering, but the imprint phylogenetic relatedness unknown. In this study, we aimed test degree which co‐occurrences and co‐exclusions protists in different classes deviate from random expectation two ecosystems, order link them ecological processes. Location Global open oceans Neotropical rain‐forest soils. Major taxa Protists. Time period 2009–2013. Methods Protist metabarcoding data originated...
A large part of the soil protist diversity is missed in metabarcoding studies based on 0.25 g environmental DNA (eDNA) and universal primers due to ca. 80% co-amplification non-target plants, animals fungi. To overcome this problem, enrichment substrate used for eDNA extraction an easily implemented option but its effect has not yet been tested. In study, we evaluated a 150 μm mesh size filtration sedimentation method improve recovery eDNA, while reducing co-extraction plant, animal fungal...