A5041059608- Genomics and Phylogenetic Studies
- Mycorrhizal Fungi and Plant Interactions
- Microbial Community Ecology and Physiology
- Plant Pathogens and Fungal Diseases
- Fungal Biology and Applications
- Methane Hydrates and Related Phenomena
- Marine Biology and Ecology Research
- Bacteriophages and microbial interactions
- Single-cell and spatial transcriptomics
- Epigenetics and DNA Methylation
- Animal Behavior and Reproduction
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- RNA modifications and cancer
- Lichen and fungal ecology
- Nematode management and characterization studies
- Insect and Pesticide Research
- Genetic diversity and population structure
- Marine Ecology and Invasive Species
- Legume Nitrogen Fixing Symbiosis
- Sperm and Testicular Function
- Yeasts and Rust Fungi Studies
- Aquatic Invertebrate Ecology and Behavior
- Genomics and Chromatin Dynamics
- Marine Biology and Environmental Chemistry
- Coral and Marine Ecosystems Studies
Science for Life Laboratory
2017-2023
Uppsala University
2013-2023
Max Planck Society
2006-2008
Max Planck Institute for Marine Microbiology
2006
Termites effectively feed on many types of lignocellulose assisted by their gut microbial symbionts. To better understand the decomposition biomass with varied chemical profiles, it is important to determine whether termites harbor different symbionts specialized functionalities geared toward feeding regimens. In this study, we compared microbiota in hindgut paunch Amitermes wheeleri collected from cow dung and Nasutitermes corniger sound wood 16S rRNA pyrotag, comparative metagenomic...
Bathymodiolus azoricus and puteoserpentis are symbiont-bearing mussels that dominate hydrothermal vent sites along the northern Mid-Atlantic Ridge (MAR). Both species live in symbiosis with two physiologically phylogenetically distinct Gammaproteobacteria: a sulfur-oxidizing chemoautotroph methane-oxidizer. A detailed analysis of collected from four MAR (Menez Gwen, Lucky Strike, Rainbow, Logatchev) using comparative 16S rRNA sequence fluorescence situ hybridization (FISH) showed mussel...
Prokaryotes dominate the biosphere and regulate biogeochemical processes essential to all life. Yet, our knowledge about their biology is for most part limited minority that has been successfully cultured. Molecular techniques now allow obtaining genome sequences of uncultivated prokaryotic taxa, facilitating in-depth analyses may ultimately improve understanding these key organisms. We compared results from two culture-independent strategies recovering bacterial genomes: single-amplified...
Morphological characters and nuclear ribosomal DNA (rDNA) phylogenies have so far been the basis of current classifications arbuscular mycorrhizal (AM) fungi. Improved understanding evolutionary history AM fungi requires extensive ortholog sampling analyses genome transcriptome data from a wide range taxa. To circumvent need for axenic culturing we gathered combined genomic single nuclei to generate de novo assemblies covering seven families We successfully sequenced genomes 15 fungal...
Abstract The advent of novel sequencing techniques has unraveled a tremendous diversity on Earth. Genomic data allow us to understand ecology and function organisms that we would not otherwise know existed. However, major methodological challenges remain, in particular for multicellular with large genomes. Arbuscular mycorrhizal (AM) fungi are important plant symbionts cryptic complex life cycles, thus representing suitable model system method development. Here, report scale, unbiased...
Abstract. Scientific drilling expeditions offer a unique opportunity to characterize microbial communities in the subsurface that have long been isolated from surface. With biomass being low general, biological contamination fluid, sample processing, or molecular work is major concern. To address this, characterization of contaminant populations fluid and negative extraction controls are essential for assessing evaluating such sequencing data. Here, rock cores down 2250 m depth,...
Abstract Arbuscular mycorrhizal (AM) fungi are ubiquitous mutualistic symbionts of most terrestrial plants and many complete their lifecycles underground. Whole genome analysis AM has long been restricted to species strains that can be maintained under controlled conditions facilitate collection biological samples. There is some evidence suggesting adapt culture resulting in phenotypic possibly also genotypic changes the fungi. In this study, we used field isolated spores identified them as...
Abstract DNA methylation is a central epigenetic mark that has diverse roles in gene regulation, development, and maintenance of genome integrity. 5 methyl cytosine (5mC) can be interrogated at base resolution single cells by using bisulfite sequencing (scWGBS). Several different scWGBS strategies have been described recent years to study cells. However, there remain limitations with respect cost-efficiency yield. Herein, we present new development the field library preparation; cell...
Arbuscular mycorrhizal (AM) fungi are arguably the most important symbionts of plants, offering a range benefits to their hosts. However, provisioning these does not appear be uniform among AM fungal individuals, with genetic variation between having substantial impact on plant performance. Interestingly, has also been reported within which contain millions haploid nuclei sharing common cytoplasm. In model fungus, Rhizophagus irregularis, several isolates have dikaryotes, containing two...
Abstract Spermatogenesis is a complex process where spermatogonia develop into haploid, mobile sperm cells. The genes guiding this are subject to an evolutionary trade-off between preserving basic functions of while acquiring new traits ensuring advantages in competition over fertilization female gametes. In species with XY sex chromosomes, the outcome found vary across stages spermatogenesis but remains unexplored for ZW chromosomes. Here we characterize avian at single cell resolution from...
Abstract Identifying genes involved in genetic incompatibilities causing hybrid sterility or inviability is a long-standing challenge speciation research, especially studies based on natural zones. Here we present the first high-probability candidate for male birds by using combination of whole genome sequence data, histology sections testis and single cell transcriptomics samples from pied-, collared-, flycatchers. We reveal failure meiosis males propose this failure. Based identification...
Abstract Background Prokaryotes dominate the biosphere and regulate biogeochemical processes essential to all life. Yet, our knowledge about their biology is for most part limited minority that has been successfully cultured. Molecular techniques now allow obtaining genome sequences of uncultivated prokaryotic taxa, facilitating in-depth analyses may ultimately improve understanding these key organisms. Results We compared results from two culture-independent strategies recovering bacterial...
Summary A large proportion of Earth's biodiversity constitutes organisms that cannot be cultured, have cryptic life-cycles and/or live submerged within their substrates 1–4 . Genomic data are key to unravel both identity and function 5 The development metagenomic methods 6,7 the advent single cell sequencing 8–10 revolutionized study life by upending need for pure biological material, allowing generation genomic from complex or limited environmental samples. Genome assemblies so far been...
Abstract Background Arbuscular mycorrhizal (AM) fungi are arguably the most important symbionts of plants, offering a range benefits to their hosts. However, provisioning these does not appear be uniform among AM fungal individuals, with genetic variation between having substantial impact on plant performance. Interestingly, has also been reported within which contain millions haploid nuclei sharing common cytoplasm. In model fungus, Rhizophagus irregularis, several isolates have dikaryotes,...
Summary Morphological characters and nuclear ribosomal DNA (rDNA) phylogenies have so far been the basis of current classifications arbuscular mycorrhizal (AM) fungi. Improved understanding phylogeny evolutionary history AM fungi requires extensive ortholog sampling analyses genome transcriptome data from a wide range taxa. To circumvent need for axenic culturing we gathered combined genomic single nuclei to generate de novo assemblies covering seven families Comparative analysis previously...
Abstract. Scientific drilling expeditions offer a unique opportunity to characterize the microbial communities in subsurface that have been long-term isolated from surface. With biomass being low general, biological contamination fluid, sample processing, or molecular work is major concern. To address this, characterization of contaminant populations fluid and negative extraction controls are essential for assessing evaluating such sequencing data. Here, crystalline rock cores down 2250 m...
This protocol describes fluorescence-activated single cell sorting using a MoFlo Astrios EQ sorter (Beckman Coulter) and whole genome amplification of sorted cells in plate formats the REPLI-g Single Cell kit (Qiagen).