A5080215717- Microbial Community Ecology and Physiology
- Protist diversity and phylogeny
- Environmental DNA in Biodiversity Studies
- Marine and coastal ecosystems
- Aquatic Invertebrate Ecology and Behavior
- Aquatic Ecosystems and Phytoplankton Dynamics
- Single-cell and spatial transcriptomics
- Genomics and Phylogenetic Studies
- Algal biology and biofuel production
- Geochemistry and Elemental Analysis
- Marine Biology and Ecology Research
- Diatoms and Algae Research
Science for Life Laboratory
2020-2024
KTH Royal Institute of Technology
2020-2024
Stockholm University
2022-2024
Czech Academy of Sciences, Biology Centre
2015-2023
Institute of Hydrobiology, Biology Centre, Academy of Sciences of the Czech Republic
2015-2023
Czech Academy of Sciences
2017-2019
University of South Bohemia in České Budějovice
2015-2018
Abstract Background The phytoplankton spring bloom in freshwater habitats is a complex, recurring, and dynamic ecological spectacle that unfolds at multiple biological scales. Although enormous taxonomic shifts microbial assemblages during after the have been reported, genomic information on community of remains scarce. Results We performed high-resolution spatio-temporal sampling reservoir describe multitude previously unknown taxa using metagenome-assembled genomes eukaryotes, prokaryotes,...
Abstract Small bacterivorous eukaryotes play a cardinal role in aquatic food webs and their taxonomic classification is currently hot topic microbial ecology. Despite increasing interest diversity, core questions regarding predator–prey specificity remain largely unanswered, e.g., which heterotrophic nanoflagellates (HNFs) are the main bacterivores freshwaters prokaryotes support growth of small HNFs. To answer these questions, we fed natural communities HNFs from Římov reservoir (Czech...
Abstract Despite the importance of shallow lakes worldwide, knowledge microbial components, base their food webs, remains scarce. To close this gap, we investigated planktonic in particular protistan bacterivory (for both ciliates and heterotrophic nanoflagellates [HNF]), 10 hypertrophic fishponds South Bohemia (Czech Republic). We used fluorescently labeled bacteria as tracers to estimate how abundant populations (4–25 × 3 HNF mL −1 55–770 ) contribute total bacterial mortality....
High-throughput sequencing-based analysis of microbial diversity has evolved vastly over the last decade. Currently, go-to method for studying eukaryotes is short-read metabarcoding variable regions 18S rRNA gene with <500 bp amplicons. However, there a growing interest in applying long-read sequencing amplicons covering operon improving taxonomic resolution. For both methods, choice primers crucial. It determines if community members are covered, they can be identified at satisfactory...
Single-cell transcriptomics has the potential to provide novel insights into poorly studied microbial eukaryotes. Although several such technologies are available and benchmarked on mammalian cells, few have been tested protists. Here, we applied a microarray single-cell sequencing (MASC-seq) technology, that generates microscope images of cells in parallel with capturing their transcriptomes, three species representing important plankton groups different cell structures; ciliate Tetrahymena...
A few genera of diatoms are widespread in the oceans and form stable partnerships with N2-fixing filamentous cyanobacteria Richelia spp. unique feature diatom-Richelia symbioses is symbiont cellular location spans a continuum integration (epibiont, periplasmic, endobiont) that reflected genome size content. In this study we analyzed genomes derived from cultures environmental metagenome-assembled focusing on characters indicative evolution. Our results show an enrichment short length...
Abstract Different bacterioplankton species represent different food quality resources for heterotrophic nanoflagellate (HNF) communities, potentially affecting HNF growth, community dynamics and carbon flow to higher trophic levels. However, our knowledge of such is still very limited. Here, we describe the results 11 experiments with natural communities from distinct seasonal phases in two freshwater habitats. The were released predation pressure zooplankton incubated 16 ecologically...
Diplonemids are considered marine protists and have been reported among the most abundant diverse eukaryotes in world oceans. Recently we detected presence of freshwater diplonemids Japanese deep lakes. However, their distribution abundances ecosystems remain unknown. We assessed abundance diversity from several geographically distant lakes by amplicon-sequencing, shotgun metagenomics catalysed reporter deposition-fluorescent situ hybridization (CARD-FISH). found all studied lakes, albeit...
Heterotrophic nanoflagellates (HNF) are considered as major planktonic bacterivores, however, larger HNF taxa can also be important predators of eukaryotes. To examine this trophic cascading, natural protistan communities from a freshwater reservoir were released grazing pressure by zooplankton via filtration through 10- and 5-µm filters, yielding microbial food webs different complexity. Protistan growth was stimulated amendments five Limnohabitans strains, thus prey-specific treatments...
Because their large growth potential is counterbalanced with grazing by heterotrophic nanoflagellates (HNF), bacteria of the genus Limnohabitans, which are common in many freshwater habitats, represent a valuable model for examining bacterial carbon flow to grazer food chain. We conducted experiments natural HNF communities taken from two distinct meso-eutrophic Římov Reservoir and oligo-mesotrophic Lake Cep (South Bohemia). each habitat at seasonal phases, late April algal bloom May clear...
Studying microbes from a single-cell perspective has become major theme and interest within the field of aquatic microbiology. One emerging trend is unfailing observation heterogeneity in activity levels microbial populations. Wherever researchers have looked, intra-population variability biochemical composition, growth rates, responses to varying environmental conditions been evident probably reflect coexisting genetically distinct strains same species. Such observations require shift away...
Abstract Background Protists are essential contributors to eukaryotic diversity and exert profound influence on carbon fluxes energy transfer in freshwaters. Despite their significance, there is a notable gap research protistan dynamics, particularly the deeper strata of temperate lakes. This study aimed address this by integrating protists into well-described spring dynamics Římov reservoir, Czech Republic. Over 2-month period covering transition from mixing established stratification, we...
Background Protists are essential contributors to eukaryotic diversity and exert profound influence on carbon fluxes energy transfer in freshwaters. Despite their significance, there is a notable gap research protistan dynamics, particularly the deeper strata of temperate lakes. This study aimed address this by integrating protists into well-described spring dynamics Rimov reservoir, Czech Republic. Over two-month period covering transition from mixing established stratification, we...
Abstract Diplonemids are considered marine protists and have been reported among the most abundant diverse eukaryotes in world oceans. Recently we detected presence of freshwater diplonemids Lake Biwa, Japan. However, their distribution abundances ecosystems remain unknown. We assessed abundance diversity from several geographically distant deep lakes by amplicon-sequencing, shotgun metagenomics CARD-FISH. found all studied lakes, albeit with low diversity. assembled long 18S rRNA sequences...
High-throughput sequencing for analysis of environmental microbial diversity has evolved vastly over the last decade. Currently go-to method eukaryotes is short-read metabarcoding variable regions 18S rRNA gene with <500 bp amplicons. However, there a growing interest in long-read amplicons covering operon improving taxonomic resolution. For both methods, choice primers crucial. It determines if community members are covered, they can be identified at satisfactory level, and obtained...
Abstract Single-cell transcriptomics has the potential to provide novel insights into poorly studied microbial eukaryotes. Although several such technologies are available and benchmarked on mammalian cells, few have been tested protists. Here, we optimized a microarray single-cell sequencing (MASC-seq) technology that generates microscope images of cells in parallel with capturing their transcriptomes. We method three species representing important plankton groups different cell structures,...