prof. RNDr. Karel Šimek, CSc.

Job Position: Research Scientist - Department of Aquatic Microbial Ecology (AME)

Contact details

Phone: +420 387775873
Room: 015



Limnology, Microbial ecology, Bacteria-protozoa-virus interactions, Carbon flow through microbial food webs, Food web structure in eutrophic and hypertrophic lakes and fishponds

Current research and interests include: (i) lake and reservoir ecology, responses of microbial communities to changes in nutrients availability and predation pressure, protistan bacterivory and selective grazing; (ii) interactions of bacteria-protozoa-viruses as the key drivers shaping dynamics and community composition of bacterioplankton; (iii) microbial food web dynamics, carbon flow to higher trophic levels; (iv) food web structure in eutrophic and hypertrophic lakes and fishponds; (v) new methods for in situ identification of flagellated protists in freshwaters.


  • Citations (WOS, January 2023):  6501 SCI citations
  • Total publications (WOS): 156
  • H-index (WOS, January 2023): 49
Curriculum vitae


  • Bachelor of Arts, 1979, Charles University in Prague.
  • Master of Sciences, 1980, Charles University in Prague. Emphasis in microbiology.
  • Doctor of Philosophy, (PhD), 1986, Charles University in Prague. Emphasis in limnology and microbial ecology. Dissertation title: "Factors regulating bacterial abundance and activity in the Římov reservoir: relationships to phyto- and zooplankton".
  • Habilitation, 1997, University of South Bohemia, České Budějovice. Thesis title: "Protozoan grazing as one of the principal factors controlling structure and production of bacterioplankton assemblages".
  • Professor of hydrobiology, 2003, Charles University in Prague.

Professional Experience:

  • Institute of Landscape Ecology CAS, since 1 April, 1990 Hydrobiological Institute CAS
  • Research Assistant, 1979-1985
  • Research Associate, 1986-1990
  • Since 1990 – 2018, Head of the Department of Aquatic Microbial Ecology
  • Since 1994 – 2001, Scientific secretary of the Hydrobiological Institute CAS
  • Since 1996 – 1999 - Faculty of Science, University of South Bohemia in České Budějovice, a chairperson for the master studies in limnology
  • Since 1999-2009, a chairperson of the committee for PhD studies in hydrobiology - Faculty of Science, University of South Bohemia in České Budějovice
  • Since 2003 – 2009, a guarantor for the full professorship program in hydrobiology. University of South Bohemia is the only one in the Czech Republic having this accreditation.
  • 2010 – Vice-director of Hydrobiological Institute CAS

Research coordination:

Leading the team of the Department of Aquatic Microbial Ecology (1990 – 2018), with 28-40 staff members, divided into (1) Microbial ecology and (2) Phytoplankton ecology subgroups.

The most important projects awarded to K. Šimek by the Czech grant agency:

• 2013 – 2017, leading the project (GA CR No. 13-00243S): “Unveiling life strategies of important groups of planktonic Betaproteobacteria in relationship to carbon flow to higher trophic levels”

• 2008 – 2012, leading the project (GA CR No. 206/08/0015): “Ecophysiological traits and grazing- and virus-induced mortality of bacterial strains representing major bacterioplankton groups in a reservoir”

• 2005 – 2007, leading the project (GA CR No. 206/05/0007): “Changes in bacterioplankton structure and functioning in a reservoir related to single-cell activities of major phylogenetic groups of bacteria”

• 2002 – 2004, leading the project (GA CR No. 206/02/0003): “Top-down and bottom-up factors controlling bacterial community composition and dynamics in different parts of a meso-eutrophic canyon-shaped reservoir”

• 1999 – 2001, leading the research project (GA CR): “Mechanisms of microbial transformation of pollution with biodegradable organic carbon and nutrients in the inflow zone of canyon-shaped reservoirs”. A part of the project was conducted on the Sau Reservoir (Spain); a collaboration with Prof. Joan Armegol (co-supervising Ph.D. students - Marta Comerma and Juan-Carlos Garcia).

• 1996 – 1998, leading the project (GA CR): "Impact of protozoan grazing on community structure and cell morphology of aquatic bacteria by using RNA probes and image analysis"
• 1993 – 1995, leading the project (GA CR) "Microbial pathways of utilizing phytoplankton production: Indication via ectoenzyme assays". 

• 1991 – 1993, leading the project (GA CR) "Size selective grazing by freshwater ciliates and its impact on structure and production of bacterial assemblage".

International projects awarded and coordinated together with a foreign partner:

• 2017 – 2018, a bilateral project Japan Center for Ecological Research, Kyoto University (Japan Society for the Promotion of Science) – the Czech Academy of Sciences, Hydrobiological Institute of Biology Centre. K. Šimek coordinated the project together with Prof. Shin-ichi Nakano: “Unveiling flagellate and bacterial community dynamics and trophic interactions in two deep freshwater ecosystems by a unique methodological combination”

• 2011 – 2012, a bilateral CZ-French project CRNS, coordinated together with Dr. Markus Weinbauer from Laboratoire d'Océanographie de Villefranche-sur-mer, CRNS, France: “Controlling mechanisms of bacterioplankton diversity and activity: Viruses versus flagellates”

• 2007 – 2008, a KONTAKT project between Czech Republic and Austria, coordinated together with Dr. Martin Hahn (Institute for Limnology, Austrian Academy of Sciences, Mondsee): “Eco-physiological characteristics of two important groups of Betaproteobacteria abundant in freshwater bacterioplankton”

• 2005 – 2006, a joint project of CSIC (Spain) and the Czech Academy of Sciences coordinated with Dr. Josep Gasol (Institut de Ciències del Mar, CMIMA, CSIC, Barcelona): “Taxonomic characterization and metabolic capabilities of key groups of bacterioplankton in two different aquatic systems

• 2005 – 2006, BARRANDE project, coordinated together with Dr. John Dolan (Laboratoire d'Océanographie de Villefranche-sur-mer, CRNS, France), “Sources of mortality in Synechococcus, a common planktonic, autotrophic prokaryote”

• 2002 – 2004, a joint project of CSIC and the Czech Academy of Sciencies coordinated together with Dr. Josep Gasol (Institut de Ciències del Mar, CMIMA, CSIC, Barcelona): “Single-cell analysis of aquatic bacterioplankton: comparing methods and transferring expertise

• 2000 – 2002, Project CRNS – PICS, financed by the CNRS - Directions des Relations Internationales (DRI) and coordinated together with Dr. J. Dolan (Laboratoire d'Océanographie de Villefranche-sur-mer, CRNS, France) and Prof. T. Sime-Ngando, Biologie des Protistes Universite Blaise Pascal, Clermont-Ferrand):"Régulation des populations picoplanctoniques prokaryotiques hétérotrophes"

• 2000 – 2001, a bilateral research project: Czech Republic – Greece; coordinated with Dr. Urania Christaki (National Center for Marine Research, Athens, Greece), “Protistan control of autochthonous and allochthonous bacterial populations through grazing in polluted and non-polluted aquatic environments”

• 1997 – 1999, AKCION - bilateral project between CZ - Austria, coordinated with Doc. T. Posch (University of Innsbruck, Austria): "Ecological aspects of genetic and functional diversity of aquatic bacteria under grazer control: the use of in situ hybridization and fluorescent rRNA-targeted probes"

• 1996 – 1999, a bilateral project CRNS – the Czech Academy of Sciences, coordinated with Dr. J. Dolan (Laboratoire d'Océanographie de Villefranche-sur-mer, CRNS, France), “Factors controlling development of prokaryotic picoplankton”

• 1993 – 1994, EAST-WEST PROGRAM between Czech Republic and Austria, a bilateral project coordinated with Prof. Roland Psenner: (University of Innsbruck, Austria): "Determination of the grazing impact of ciliates and heterotrophic flagellates on bacterioplankton and phytoplankton by means of fluorescent labelling and image analysis techniques".

International experience – the most important research stays:

The University of Texas at Arlington, USA

March-November 1989, POST-DOCT FELLOW, the lab of Prof. T.H. Chrzanowski, a research project "Microbial processes in reservoirs: Regulation of bacteria by grazers".

Institute of Limnology, University of Constance, Germany

Joint experiments ("SPRING BLOOM", May 1991) with Dr. T. Weisse and Dr. M. Simon, dial cycles of (1) grazing of protozoans on bacteria and (2) grazing of macrozooplankton on protozoans.

University of Innsbruck, Austria

Joint experiment "Microbial loop in forested alpine Lake Piburger See". (EAST-WEST PROGRAM, May-June 1994), two follow-up projects during 1998-2002. Collaboration with Prof. Roland Psenner and Dr. Thomas Posch

Station Zoologique, Villefranche-sur-Mer, France

Exchange program CRNS - AS CR, stays - 2-3 weeks every year (1995 - 2011), collaboration with Dr. J. Dolan a M. Weinbauer

Department of Ecology, University of Barcelona, Spain

An invited professor stay - 8 weeks (June - July 1996), collaboration with Prof. Joan Armengol

Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar-CMIMA, CSIC, Barcelona, Spain

Exchange program CSIC – AS CR, collaboration with Dr. Josep Gasol, two follow-up 2-year projects (2 months during 2003-2006)

Laboratoire Microorganisme: Génome & Environnement, Université Blaises Pascal, Clermont-Ferrand, France

A collaboration with Prof. T. Sime-Ngando, covered by the project CRNS – PICS (1999 – 2002), Directions des Relations Internationales (DRI) and coordinated together with Dr. John Dolan (Laboratoire d'Océanographie de Villefranche-sur-mer, CRNS, France). Project: "Régulation des populations picoplanctoniques prokaryotiques hétérotrophes"

Recognition of Professional Excellence Award

2015 - Received a medal of the Czech Academy of Sciences "The Gregor Johann Mendel Honorary Medal for Merits in Biological Sciences".

2010 - Received a title: Docteurs HONORIS CAUSA, the University of Clermont Ferrand, France, on the basis of his outstanding publication and educational results in the field of hydrobiology.

1991 - International Recognition of Professional Excellence Award (IRPE), selected as the Prize winner (International Recognition of Professional Excellence in Ecology) awarded to young scientists in the field of limnetic ecology.

Other scientific activities

  • Subject editor in the journal of Aquatic Microbial Ecology (1995 – 2018), covering the field of "Microbial dynamics in freshwaters".
  • Selected as the president of the Otto Kinne Foundation (OKF, 2006-2008) that supports promising young environmental scientists in eastern European countries.
  • Six invited lectures were presented abroad during 2016 – 2020 (Japan, Austria, Germany, France).

Teaching activities in the Czech Republic

1990 – 1998, teaching General Microbiology and Limnology in the Pedagogical faculty of the University of South Bohemia.

Since 1994 – teaching several subjects in limnology and aquatic microbial ecology at the Faculty of Science, University of South Bohemia in České Budějovice.

Aside, as an external professor, since 2001 K. Šimek has been teaching selected subjects in limnology in Charles University in Prague and Masaryk University, Faculty of Science, Brno.

Students supervised: 7 Master thesis students and 9 PhD thesis students, 3 PhD co-supervised abroad (2 in Spain, one in Austria).

Teaching and collaboration with foreign universities

University of Texas at Arlington, USA 

1989, the lab of Prof. T.H. Chrzanowski. Contracted via a NSF US project; a part of the contract I was teaching selected techniques in aquatic microbial ecology.

The University of Innsbruck, AUSTRIA

1990, leading a workshop for students and graduates in limnology from University of Innsbruck focused on fluorescent methods for protozoan grazing experiments.

1992-2002, within the collaboration established with Prof. R. Psenner, Dr. J. Pernthaler, and Dr. T. Posch, covered by several follow-up projects, we conducted a frequent exchange of master and PhD students between both institutions.

2011 - 2012, K. Šimek lectured a 10-day course M.Sc. in Environmental Science, specialization in Limnology & Wetland Ecosystems 2012; International Postgraduate Training Programmes in Limnology (IPGL) of the Austrian Academy of Sciences in Lunz.

Department of Ecology, University of Barcelona, Spain

Invited professor - teaching Microbial processes and Reservoir Limnology, collaboration with Prof. Joan Armengol.

Professional Associations

Czechoslovak Society of Limnology

Czechoslovak Society of Microbiology

American Society of Limnology and Oceanography (1999-2006)

Total found: 144 records
Mukherjee I., Grujčić V., Salcher M., Znachor P., Seďa J., Devetter M., Rychtecký P., Šimek K., Shabarova T. (2024) Integrating depth-dependent protist dynamics and microbial interactions in spring succession of a freshwater reservoir. Environmental Microbiome 19 : 31.
DOI: 10.1186/s40793-024-00574-5
Vrba J., Šorf M., Nedoma J., Benedová Z., Kröpfelová L., Šulcová J., Tesařová B., Musil M., Pechar L., Potužák J., Regenda J., Šimek K., Řeháková K. (2024) Top‑down and bottom‑up control of plankton structure and dynamics in hypertrophic fishponds. Hydrobiologia 851 : 1095–1111.
DOI: 10.1007/s10750-023-05312-5
Kavagutti V., Bulzu P., Chiriac M., Salcher M., Mukherjee I., Shabarova T., Grujčić V., Mehrshad M., Kasalický V., Andrei A.S., Jezberová J., Seďa J., Rychtecký P., Znachor P., Šimek K., Ghai R. (2023) High‑resolution metagenomic reconstruction of the freshwater spring bloom. Microbiome 11 : 15.
DOI: 10.1186/s40168-022-01451-4
Park H., Shabarova T., Salcher M., Kosová L., Rychtecký P., Mukherjee I., Šimek K., Porcal P., Seďa J., Znachor P., Kasalický V. (2023) In the right place, at the right time: the integration of bacteria into the Plankton Ecology Group model. Microbiome 11 : 112.
DOI: 10.1186/s40168-023-01522-0
Šimek K., Mukherjee I., Szöke-Nagy T., Haber M., Salcher M., Ghai R. (2023) Cryptic and ubiquitous aplastidic cryptophytes are key freshwater flagellated bacterivores. ISME Journal 17 : 84–94.
DOI: 10.1038/s41396-022-01326-4
Prokopchuk G., Korytář T., Juricová V., Horák A., Majstorović J., Šimek K., Lukeš J. (2022) Trophic flexibility of marine diplonemids - switching from osmotrophy to bacterivory The ISME Journal 16 : 1409–1419.
DOI: 10.1038/s41396-022-01192-0

Documents to download:
Prokopchuk_2022_ISMEJ (pdf)
Šimek K., Mukherjee I., Nedoma J., Pires de Paula C., Jezberová J., Sirová D., Vrba J. (2022) CARD-FISH and prey tracer techniques reveal the role of overlooked flagellate groups as major bacterivores in freshwater hypertrophic shallow lakes. Environmental Microbiology 24 : 4256–4273.
DOI: 10.1111/1462-2920.15846
Piwosz K., Mukherjee I., Salcher M., Grujčić V., Šimek K. (2021) CARD-FISH in the sequencing era: Opening a new universe of protistan ecology. Frontiers in Microbiology 12 : 640066.
DOI: 10.3389/fmicb.2021.640066
Ságová-Marečková M., Boenigk J., Bouchez A., Cermakova K., Chonova T., Cordier T., Eisendle U., Elersek T., Fazi S., Fleituch T., Frühe L., Gajdosova M., Graupner N., Haegerbaeumer A., Kelly A.-M., Kopecký J., Nõges P., Orlic S., Panksep K., Pawlowski J., Petrusek A., Piggot J.J., Rusch J.C., Salis R., Schenk J., Šimek K., Stovicek A., Strand D.A., Vasquez M.I., Vralstad T., Zlatkovic S., Zupancic M., Stoeck T. (2021) Expanding ecological assessment by integrating microorganisms into routine freshwater biomonitoring. Water Research 191 : 116767.
Shabarova T., Salcher M., Porcal P., Znachor P., Nedoma J., Grossart H., Seďa J., Hejzlar J., Šimek K. (2021) Recovery of freshwater microbial communities after extreme rain events is mediated by cyclic succession. Nature Microbiology 6 : 479–488.
DOI: 10.1038/s41564-020-00852-1
Mukherjee I., Salcher M., Andrei A., Kavagutti V., Shabarova T., Grujčić V., Haber M., Layoun P., Hodoki Y., Nakano S., Šimek K., Ghai R. (2020) A freshwater radiation of diplonemids Environmental Microbiology 22 : 4658–4668.
Piwosz K., Shabarova T., Pernthaler J., Posch T., Šimek K., Porcal P., Salcher M. (2020) 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 mSphere 5 : e00052-20.
DOI: 10.1128/mSphere.00052-20
Šimek K., Grujčić V., Mukherjee I., Kasalický V., Nedoma J., Posch T., Mehrshad M., Salcher M. (2020) Cascading effects in freshwater microbial food webs by predatory Cercozoa, Katablepharidacea and ciliates feeding on aplastidic bacterivorous cryptophytes FEMS Microbiology Ecology 96 : fiaa121.
Bednařík A., Blaser M., Matoušů A., Tušer M., Chaudhary P.P. , Šimek K., Rulík M. (2019) Sediment methane dynamics along the Elbe River Limnologica 79 : 125716.
DOI: 10.1016/j.limno.2019.125716
Gabaldon Tebar C., Devetter M., Hejzlar J., Šimek K., Znachor P., Nedoma J., Seďa J. (2019) Seasonal strengths of the abiotic and biotic drivers of a zooplankton community Freshwater Biology 64 : 1326–1341.
DOI: 10.1111/fwb.13308
Matoušů A., Rulík M., Tušer M., Bednařík A., Šimek K., Bussmann I. (2019) Methane dynamics in a large river: a case study of the Elbe River Aquatic Sciences 81 : UNSP 12.
DOI: 10.1007/s00027-018-0609-9
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 Limnology and Oceanography 64 : 2295–2309.
DOI: 10.1002/lno.11260
Šimek K., Sirová D. (2019) Fluorescently Labeled Bacteria as a Tracer to Reveal Novel Pathways of Organic Carbon Flow in Aquatic Ecosystems Jove - Journal of Visualized Experiments 151 : e59903.
DOI: 10.3791/59903
Weinbauer M., Suominen S., Jezbera J., Kerros M.E., Marro S., Dolan J., Šimek K. (2019) Shifts in cell size and community composition of bacterioplankton due to grazing by heterotrophic flagellates: evidence from a marine system Aquatic Microbial Ecology 83 : 295–308.
DOI: 10.3354/ame01919
Grujčić V., Nuy J. K., Salcher M., Shabarova T., Kasalický V., Boenigk J., Jensen M. , Šimek K. (2018) Cryptophyta as major bacterivores in freshwater summer plankton ISME Journal 12 : 1668-1681.
DOI: 10.1038/s41396-018-0057-5

More publications


Biology Centre CAS
Institute of Hydrobiology
Na Sádkách 702/7
370 05 České Budějovice

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