World's Best Scientists 2026 revealed!

D-Index & Metrics

Biology and Biochemistry

D-Index
62
Citations
10110
World Ranking
11056
National Ranking
13

Overview

Karel Šimek is affiliated with the Institute of Hydrobiology at the Biology Centre of the Academy of Sciences of the Czech Republic. Their research primarily focuses on Environmental Science and Biochemistry, Genetics and Molecular Biology, with significant contributions in subfields such as Ecology, Molecular Biology, Oceanography, and Environmental Chemistry.

The main topics of their work include:

  • Microbial Community Ecology and Physiology
  • Protist diversity and phylogeny
  • Marine and coastal ecosystems
  • Environmental DNA in Biodiversity Studies
  • Genomics and Phylogenetic Studies
  • Aquatic Ecosystems and Phytoplankton Dynamics
  • Aquatic Ecosystems and Biodiversity

Šimek has published extensively, with notable contributions to journals such as bioRxiv (Cold Spring Harbor Laboratory), The ISME Journal, Environmental Microbiology, Microbiome, and Water Research. The top venues by number of publications include:

  • bioRxiv (Cold Spring Harbor Laboratory)
  • The ISME Journal
  • Environmental Microbiology
  • Microbiome
  • Water Research

Recent selected papers include:

  • "Expanding ecological assessment by integrating microorganisms into routine freshwater biomonitoring," 2020, Water Research
  • "Recovery of freshwater microbial communities after extreme rain events is mediated by cyclic succession," 2021, Nature Microbiology
  • "Bacterial and Eukaryotic Small-Subunit Amplicon Data Do Not Provide a Quantitative Picture of Microbial Communities, but They Are Reliable in the Context of Ecological Interpretations," 2020, mSphere
  • "High-resolution metagenomic reconstruction of the freshwater spring bloom," 2023, Microbiome
  • "CARD-FISH in the Sequencing Era: Opening a New Universe of Protistan Ecology," 2021, Frontiers in Microbiology

Frequent co-authors associated with Šimek include Indranil Mukherjee, Tanja Shabarova, Michaela M. Salcher, Petr Znachor, and Vojtěch Kasalický. Collaborations with these colleagues span multiple projects and publications, reflecting active engagement in microbial ecology and environmental microbiology research.

Best Publications

  • Changes in Bacterial Community Composition and Dynamics and Viral Mortality Rates Associated with Enhanced Flagellate Grazing in a Mesoeutrophic Reservoir

    Karel Šimek;Karel Šimek;Jakob Pernthaler;Markus G. Weinbauer;Karel Hornák

  • Ciliategrazing on picoplankton in a eutrophic reservoir during the summer phytoplankton maximum: A study at the species and community level

    Karel Šimek;Jitka Bobková;Miroslav Macek;Jiři Nedoma

  • Prey-size selection by freshwater flagellated protozoa

    Thomas H. Chrzanowski;Karel Šimek

  • Morphological and compositional shifts in an experimental bacterial community influenced by protists with contrasting feeding modes.

    K Simek;J Vrba;J Pernthaler;T Posch

  • Direct and indirect evidence of size-selective grazing on pelagic bacteria by freshwater nanoflagellates.

    Karel Šimek;Thomas H. Chrzanowski

  • Contrasting bacterial strategies to coexist with a flagellate predator in an experimental microbial assemblage.

    J Pernthaler;T Posch;K Simek;J Vrba

  • Expanding ecological assessment by integrating microorganisms into routine freshwater biomonitoring

    M. Sagova-Mareckova;J. Boenigk;A. Bouchez;K. Cermakova

  • Selective feeding behaviour of key free-living protists: avenues for continued study

    David J. S. Montagnes;Ana B. Barbosa;Jens Boenigk;Keith Davidson

  • The diversity of the Limnohabitans genus, an important group of freshwater bacterioplankton, by characterization of 35 isolated strains.

    Vojtěch Kasalický;Jan Jezbera;Martin W. Hahn;Karel Šimek

  • Maximum growth rates and possible life strategies of different bacterioplankton groups in relation to phosphorus availability in a freshwater reservoir

    Karel Šimek;Karel Šimek;Karel Horňák;Karel Horňák;Jan Jezbera;Jan Jezbera;Jiří Nedoma

  • Shifts in bacterial community composition associated with different microzooplankton size fractions in a eutrophic reservoir

    Karel Šimek;Karel Šimek;Petra Kojecká;Petra Kojecká;Jiří Nedoma;Petr Hartman

  • Predator-specific enrichment of actinobacteria from a cosmopolitan freshwater clade in mixed continuous culture.

    Jakob Pernthaler;Thomas Posch;Karel Simek;Karel Simek;Jaroslav Vrba

  • Food selection by bacterivorous protists: insight from the analysis of the food vacuole content by means of fluorescence in situ hybridization

    Jan Jezbera;Jan Jezbera;Karel Horňák;Karel Horňák;Karel Šimek;Karel Šimek

  • Top-down effects on the size-biomass distribution of a freshwater bacterioplankton community

    Pernthaler J;Sattler B;Simek K;Schwarzenbacher A

  • Synergistic and antagonistic effects of viral lysis and protistan grazing on bacterial biomass, production and diversity.

    Markus G. Weinbauer;Karel Hornák;Jan Jezbera;Jiři Nedoma

  • Unveiling Distribution Patterns of Freshwater Phytoplankton by a Next Generation Sequencing Based Approach

    Alexander Eiler;Stina Drakare;Stefan Bertilsson;Jakob Pernthaler

  • Response of Alteromonadaceae and Rhodobacteriaceae to glucose and phosphorus manipulation in marine mesocosms

    Elke Allers;Laura Gómez-Consarnau;Jarone Pinhassi;Josep M. Gasol

  • Investigations on pelagic food webs in mountain lakes - aims and methods

    Viera Straškrabová;Cristiana Callieri;Presentacion Carrillo;Luis Cruz-Pizarro

  • Predator-induced changes of bacterial size-structure and productivity studied on an experimental microbial community

    Thomas Posch;Karel Simek;Jaroslav Vrba;Jakob Pernthaler

  • Ecological role and bacterial grazing of Halteria spp.: small freshwater oligotrichs as dominant pelagic ciliate bacterivores.

    Karel Šimek;Klaus Jürgens;Jiří Nedoma;Marta Comerma

Frequent Co-Authors

John R. Dolan
John R. Dolan Université Paris Cité
Jakob Pernthaler
Jakob Pernthaler University of Zurich
Martin W. Hahn
Martin W. Hahn University of Innsbruck
Josef Hejzlar
Josef Hejzlar Czech Academy of Sciences
Markus G. Weinbauer
Markus G. Weinbauer Centre national de la recherche scientifique, CNRS
Roland Psenner
Roland Psenner University of Innsbruck
Josep M. Gasol
Josep M. Gasol Spanish National Research Council
Hans-Peter Grossart
Hans-Peter Grossart University of Potsdam
Lubomír Adamec
Lubomír Adamec Czech Academy of Sciences
Rudolf Amann
Rudolf Amann Max Planck Institute for Marine Microbiology

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