Karel Šimek

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• Prof, Dr, PhD
• Professor Emeritus, senior scientist at Czech Academy of Sciences, Biology Centre

Bacterioplankton from a meso-eutrophic dam reservoir was size fractionated to reduce (<0.8-microm treatment) or enhance (<5-microm treatment) protistan grazing and then incubated in situ for 96 h in dialysis bags. Time course samples were taken from the bags and the reservoir to estimate bacterial abundance, mean cell volume, production, protistan...

Different bacterial strains can have different value as food for heterotrophic nanoflagellates (HNF), thus modulating HNF growth and community composition. We examined the influence of prey food quality using four Limnohabitans strains, one Polynucleobacter strain and one freshwater actinobacterial strain on growth (growth rate, length of lag phase...

We employed high frequency sampling to determine the major factors modulating microbial food web composition and dynamics through the spring phytoplankton bloom and clear water phases in a freshwater reservoir. We examined effects of a changing trophic structure of the planktonic community cascading from the level of zooplankton, through phytoplank...

Despite the importance of shallow lakes worldwide, knowledge of microbial components, the base of their food webs, remains scarce. To close this gap, we investigated planktonic microbial food webs, in particular protistan bacterivory (for both ciliates and heterotrophic nanoflagellates [HNF]), in 10 shallow hypertrophic fishponds in South Bohemia (...

Phagotrophic protists are key players in aquatic food webs. Although sequencing-based studies have revealed their enormous diversity, ecological information on in situ abundance, feeding modes, grazing preferences, and growth rates of specific lineages can be reliably obtained only using microscopy-based molecular methods, such as Catalyzed Reporte...

In aquatic microbial food webs, ciliates represent an important trophic link in the energy transfer from prokaryotes, algae, and heterotrophic nanoflagellates (HNF) to higher trophic levels. However, the trophic role of abundant small ciliates (< 20 µm) is not clearly understood. To unveil their trophic linkages, we conducted two experiments manipu...

Telonemia are one of the oldest identified marine protists that for most part of their history have been recognized as a distinct incertae sedis lineage. Today, their evolutionary proximity to the SAR supergroup (Stramenopiles, Alveolates, and Rhizaria) is firmly established. However, their ecological distribution and importance as a natural predat...

The perception of the importance of ciliate in freshwater has changed dramatically since the “microbial loop” conceptualisation, reflecting methodological attempts. The data from two decades (1994–2018) on the surface (0–3 m) ciliate assemblage in the Slapy reservoir (Vltava River, Czech Republic) during two different nutrient-load defined periods...

Current eutrophication-based approaches to fish production cannot be applied to high-flow oligotrophic mountain ponds, whose oligotrophic status is crucial for sustaining water quality in drinking water reservoirs. Here, we exemplified the impacts of eutrophication and inappropriate fish stocking projects conducted on oligotrophic ponds in Novohrad...

Background Protists are essential contributors to eukaryotic diversity and exert profound influence on carbon fluxes and energy transfer in freshwaters. Despite their significance, there is a notable gap in research on protistan dynamics, particularly in the deeper strata of temperate lakes. This study aimed to address this gap by integrating proti...

Background Protists are essential contributors to eukaryotic diversity and exert profound influence on carbon fluxes and energy transfer in freshwaters. Despite their significance, there is a notable gap in research on protistan dynamics, particularly in the deeper strata of temperate lakes. This study aimed to address this gap by integrating proti...

We investigated the effects of strong top-down control by high fish stock on structure and seasonal dynamics of plankton in nine fishponds under conventional fishery management based on auxiliary feeding during two vegetation seasons. Mean concentrations of total nitrogen, phosphorus, and high densities of phytoplankton, bacteria, heterotrophic nan...

Introduction High-trophy shallow lakes, both natural and artificial, have become the most common type of lentic waterbodies worldwide. They are key for maintaining landscape ecological stability; however, we still have very limited understanding of processes driven by the microbes at the lowest trophic levels in these systems, especially fungi, or...

Background Planktonic microbial communities have critical impacts on the pelagic food web and water quality status in freshwater ecosystems, yet no general model of bacterial community assembly linked to higher trophic levels and hydrodynamics has been assessed. In this study, we utilized a 2-year survey of planktonic communities from bacteria to z...

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 in microbial assemblages during and after the bloom have been reported, genomic information on the microbial community of the spring bloom remains s...

Morphology-based microscopic approaches are insufficient for a taxonomic classification of bacterivorous heterotrophic nanoflagellates (HNF) in aquatic environments since their cells do not display reliably distinguishable morphological features. This leads to a considerable lack of ecological insights into this large and taxonomically diverse func...

Diplonemids are one of the most abundant groups of heterotrophic planktonic microeukaryotes in the world ocean and, thus, are likely to play an essential role in marine ecosystems. So far, only few species have been introduced into a culture, allowing basic studies of diplonemid genetics, morphology, ultrastructure, metabolism, as well as endosymbi...

Heterotrophic nanoflagellates (HNF) and ciliates are major protistan planktonic bacterivores. The term HNF, however, describes a functional guild only and, in contrast to the morphologically distinguishable ciliates, does not reflect the phylogenetic diversity of flagellates in aquatic ecosystems. Associating a function with taxonomic affiliation o...

Small lakes and ponds occupy an enormous surface area of inland freshwater and represent an important terrestrial–water interface. Disturbances caused by extreme weather events can have substantial effects on these ecosystems. Here, we analysed the dynamics of nutrients and the entire plankton community in two flood events and afterwards, when quas...

Bioindication has become an indispensable part of water quality monitoring in most countries of the world, with the presence and abundance of bioindicator taxa, mostly multicellular eukaryotes, used for biotic indices. In contrast, microbes (bacteria, archaea and protists) are seldom used as bioindicators in routine assessments, although they have...

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 from grazing pressure by zooplankton via filtration through 10-µm and 5-µm filters, yi...

Diplonemids are considered marine protists and have been reported among the most abundant and diverse eukaryotes in the world oceans. Recently we detected the presence of freshwater diplonemids in Japanese deep freshwater lakes. However, their distribution and abundances in freshwater ecosystems remain unknown. We assessed abundance and diversity o...

Highly abundant, small waterbodies contribute substantially to global freshwater shoreline and surface area. They are strongly interlinked with the terrestrial surrounding, thus controlling the flow of energy, nutrients and organisms through the landscape. Disturbance events can have severe consequences for these ecosystems and the entire downstrea...

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 from grazing pressure by zooplankton via filtration through 10-µm and 5-µm filters, yi...

Diplonemids are considered marine protists and have been reported among the most abundant and diverse eukaryotes in the world oceans. Recently we detected the presence of freshwater diplonemids in Lake Biwa, Japan. However, their distribution and abundances in freshwater ecosystems remain unknown. We assessed abundance and diversity of diplonemids...

High-throughput sequencing (HTS) of gene amplicons is a preferred method of assessing microbial community composition, because it rapidly provides information from a large number of samples at high taxonomic resolution and low costs. However, mock community studies show that HTS data poorly reflect the actual relative abundances of individual phylo...

he effect of flagellate grazing on bacterioplankton community composition, e.g. cell size and diversity, has been well studied in fresh waters, but much less is known for marine sys- tems. We conducted experiments with communities from an oligotrophic bay in the NW Mediter- ranean Sea; size fractionation was used to alter grazing by flagellates, an...

Elucidating trophic interactions, such as predation and its effects, is a frequent task for many researchers in ecology. The study of microbial communities has many limitations, and determining a predator, prey, and predatory rates is often difficult. Presented here is an optimized method based on the addition of fluorescently labelled prey as a tr...

Despite the importance of shallow lakes worldwide, knowledge of microbial components, the base of their food webs, remains scarce. To close this gap, we investigated planktonic microbial food webs, in particular protistan bacterivory (for both ciliates and heterotrophic nanoflagellates [HNF]), in 10 shallow hypertrophic fishponds in South Bohemia (...

The attached file documents the way how ciliate food vacuole contents were analyzed in our recent study: Šimek K., Grujčić V., Nedoma J., Jezberová J., Šorf M., Matoušů A., Pechar L., Posch T., Bruni E. P., Vrba J. 2019: Microbial food webs in hypertrophic fishponds: omnivorous ciliate taxa are major protistan bacterivores. Limnol. Oceanogr. 64: 2...

Just a link to Open Access: https://aslopubs.onlinelibrary.wiley.com/doi/epdf/10.1002/lno.11260

ODespite the importance of shallow lakes worldwide, knowledge of microbial components, the base of their food webs, remains scarce. To close this gap, we investigated planktonic microbial food webs, in particular protistan bacterivory (for both ciliates and heterotrophic nanoflagellates [HNF]), in 10 shallow hypertrophic fishponds in South Bohemia...

The effect of flagellate grazing on bacterioplankton community composition, e.g. cell size and diversity, has been well studied in fresh waters, but much less is known for marine systems. We conducted experiments with communities from an oligotrophic bay in the NW Mediterranean Sea; size fractionation was used to alter grazing by flagellates, and i...

• Multiple factors operate simultaneously and interact in complex ways to shape community assembly. Understanding the organisation of communities including species interactions and the importance of driving factors (food, temperature, nutrients, oxygen concentration, etc.) is a central topic in ecology. Intra‐annual variation in zooplankton and the...

Following publication of the original article [1], the author reported an error in Fig. 3.

We conducted multiple small (2011–2012) and one large sampling campaign (2013) at selected profiles along the Elbe River. With the data we were able to outline spatial and temporal variability of methane concentration, oxidation and emissions in one of the major rivers of Central Europe. The highest methane concentrations were found in human-altere...

Background Utricularia are rootless aquatic carnivorous plants which have recently attracted the attention of researchers due to the peculiarities of their miniaturized genomes. Here, we focus on a novel aspect of Utricularia ecophysiology—the interactions with and within the complex communities of microorganisms colonizing their traps and external...

Background: Representatives of the phylum Chloroflexi, though reportedly highly abundant in the extensive deep water habitats of both marine (SAR202 up to 30% of total prokaryotes) and freshwater (CL500-11 up to 26% of total prokaryotes), remain uncultivated and uncharacterized. There are few metagenomic studies on marine Chloroflexi representativ...

Background: Representatives of the phylum Chloroflexi, though reportedly highly abundant (up to 30% of total prokaryotes) in the extensive deep water habitats of both marine (SAR202) and freshwater (CL500-11), remain uncultivated and uncharacterized. There are few metagenomic studies on marine Chloroflexi representatives, while the pelagic freshwat...

Small bacterivorous eukaryotes play a cardinal role in aquatic food webs and their taxonomic classification is currently a hot topic in aquatic microbial ecology. Despite increasing interest in their diversity, core questions regarding predator-prey specificity remain largely unanswered, e.g. which heterotrophic nanoflagellates (HNFs) are the main...

The growth rate is a fundamental characteristic of bacterial species, determining its contributions to the microbial community and carbon flow. High throughput sequencing can reveal bacterial diversity, but its quantitative inaccuracy precludes estimation of abundances and growth rates from the read numbers. Here, we overcame this limitation by nor...

The genus Limnohabitans (Comamonadaceae, Betaproteobacteria) is a common and a highly active component of freshwater bacterioplankton communities. So far, the genus has been considered to contain only heterotrophic species. In this study, we detected photosynthesis genes pufLM and bchY in 28 out of 46 strains from three Limnohabitans lineages. The...

We studied the diversity of Limnohabitans using Reverse Line Blot Hybridization with Limnohabitans lineage-specific probes in the freshwater canyon-shaped Římov Reservoir (CZ). To examine the succession of distinct lineages we performed two studies: (i) an intensive spring sampling program at the lacustrine part of the Římov Reservoir (from ice mel...

All higher eukaryotes live in a relationship with diverse microorganisms which colonize their bodily surfaces; plants are no exception. However, we still lack a satisfactory understanding of how these loosely associated microbiomes with immense diversity and functional potential interact with their hosts or how these interactions shape processes wi...

We investigated changes in quality and quantity of extracellular and biomass-derived organic matter (OM) from three axenic algae (genera Rhodomonas, Chlamydomonas, Coelastrum) during growth of Limnohabitans parvus, Limnohabitans planktonicus and Polynucleobacter acidiphobus representing important clusters of freshwater planktonic Betaproteobacteria...