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, Bacterial diversity, Betaproteobacteria

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 factors shaping bacterioplankton dynamics and community composition, exploring a variety of molecular, flow cytometric, fluorescence microscopy, and isolation and cultivation approaches; (iii) microbial food web dynamics, carbon flow to higher trophic levels; (iv) factors shaping population dynamics, occurrence and geographical distribution and of Betaproteobacteria in freshwaters.

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 1991 - 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 part-time contract, a chair person for the master studies in limnology
  • Since 1999-2009, a chair person 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. Currently, University of South Bohemia is the only one in the Czech Republic having this accreditation, giving the unique position to the Faculty of Science in the field of hydrobiology.
  • 2010 – Vice-director of Hydrobiological Institute CAS

More information

Research activities


Leading and coordinating the team of the Department of Aquatic Microbial Ecology (HBI-BC) with 28 staff members divided into (1) microbial ecology and (2) phytoplankton ecology subgroups.


The most important projects awarded to Karel Šimek by the Czech grant agencies:

• 2013 – 2017, leading the research 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 research 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 research 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 research 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 research 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 research project (CAS) "Microbial pathways of utilizing phytoplankton production: Indication via ectoenzyme assays". 
• 1991 – 1993, leading the research project (CAS) "Size selective grazing by freshwater ciliates and its impact on structure and production of bacterial assemblage".


International projects awarded and coordinated together with a partner from abroad:

• 2011 – 2012, a bilateral project CRNS – the Czech Academy of Sciences, coordinated together with Dr. Markus Weinbauer (Laboratoire d'Océanographie de Villefranche-sur-mer, CRNS, France), Controlling mechanisms of bacterioplankton diversity and activity: Viruses versus flagellates”

• 2007 – 2008, 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, coordinated with Dr. Josep Gasol (Institut de Ciències del Mar, CMIMA, CSIC, Barcelona) a joint project of CSIC and the Czech Academy of Sciencies: 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, coordinated together with Dr. Josep Gasol (Institut de Ciències del Mar, CMIMA, CSIC, Barcelona) a joint project of CSIC and the Czech Academy of Sciencies: 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. John Dolan (Laboratoire d'Océanographie de Villefranche-sur-mer, CRNS, France)  and Dr. Télesphore 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 together 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 Czech Republic and Austria, coordinated together with Dr. Thomas 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 together with Dr. John 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

April-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 ÖAW, Mondsee, AUSTRIA

1990, Leading the workshop ("Protozoan grazing on bacteria: field and laboratory studies") for students and graduates in limnology from the University of Innsbruck focused on fluorescent methods in microbial ecology.

Institute of Limnology, The 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

Invited professor stay - 6 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”, UMR CNRS 6023, Université Blaises Pascal, Clermont-Ferrand, France

Since 1999 – a collaboration with Dr. Télesphore Sime-Ngando, officially covered by the project CRNS – PICS (2000 – 2002), financed by the CNRS - Directions des Relations Internationales (DRI) and coordinated together with Dr. John Dolan (Laboratoire d'Océanographie de Villefranche-sur-mer, CRNS, France) and Dr. Télesphore Sime-Ngando: "Régulation des populations picoplanctoniques prokaryotiques hétérotrophes".


Recognition of Professional Excellence Award

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


International Recognition of Professional Excellence Award

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


In 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.


Other scientific activities


  • Subject editor (since 1995) covering the field of "Microbial dynamics in freshwaters" in the journal AQUATIC MICROBIAL ECOLOGY
  • Selected as the president of the Otto Kinne Foundation (OKF, 2006-2008) that supports promising young environmental scientists in eastern European countries
  • Five invited lectures were presented abroad during 2011 - 2015
  • Citations (WOS):  3545 SCI citations (without autocitations, Core collection)
  • H-index (WOS, February 2016):  37

Teaching activities in the Czech Republic

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

Since 1994 – until now, teaching several subjects in limnology and aquatic microbial ecology in Faculty of Science, University of South Bohemia in České Budějovice, where is my major pedagogical affiliation.

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


Students supervised: 5 Master thesis students and 7 PhD thesis students, 3 PhD co-supervised abroad (2 in Spain, one in Austria).

Total found: 130 records
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
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
Kasalický V., Zeng Y. H. , Piwosz K., Šimek K., Kratochvilová H., Koblížek M. (2018) Aerobic Anoxygenic Photosynthesis Is Commonly Present within the Genus Limnohabitans Applied and Environmental Microbiology 84 : e02116-17.
DOI: 10.1128/AEM.02116-17
Mehrshad M., Salcher M.M., Okazaki Y., Nakano S., Šimek K., Andrei A., Ghai R. (2018) Hidden in plain sight—highly abundant and diverse planktonic freshwater Chloroflexi Microbiome 6 : 176.
DOI: 10.1186/s40168-018-0563-8
Piwosz K., Shabarova T., Tomasch J., Šimek K., Kopejtka K., Kahl S., Pieper D.H. , Koblížek M. (2018) Determining lineage-specific bacterial growth curves with a novel approach based on amplicon reads normalization using internal standard (ARNIS) ISME Journal 12 : 2640-2654.
DOI: 10.1038/s41396-018-0213-y
Šimek K., Grujčić V., Hahn M., Horňák K., Jezberová J., Kasalický V., Nedoma J., Salcher M., Shabarova T. (2018) Bacterial prey food characteristics modulate community growth response of freshwater bacterivorous flagellates Limnology and Oceanography 63 : 484–502.
DOI: 10.1002/lno.10759
Sirová D., Bárta J., Šimek K., Posch T., Pech J., Stone J., Borovec J., Adamec L., Vrba J. (2018) Hunters or farmers? Microbiome characteristics help elucidate the diet composition in an aquatic carnivorous plant Microbiome 6 : 225.
DOI: 10.1186/s40168-018-0600-7
Vrba J., Benedová Z., Jezberová J., Matoušů A., Musil M., Nedoma J., Pechar L., Potužák J., Řeháková K., Šimek K., Šorf M., Zemanová J. (2018) Nevstoupíš dvakrát do téhož rybníka – předběžná zpráva o stavu dnešních hypertrofních rybničních ekosystémů [You cannot step into the same fishpond twice – A preliminary report on the current status of hypertrophic fishpond ecosystems] Vodní hospodářství 68 (8) : 1-5.
Vrba J., Benedová Z., Jezberová J., Matoušů A., Musil M., Nedoma J., Pechar L., Potužák J., Řeháková K., Šimek K., Šorf M., Zemanová J. (2018) Nevstoupíš dvakrát do téhož rybníka aneb vývoj rybničních ekosystémů od Šusty k hypertrofii [You cannot step into the same fishpond twice - an evolution of fishpond ecosystems to hypertrophy] Sborník konference Rybníky 2018 2-11.
Gabaldon Tebar C., Devetter M., Hejzlar J., Šimek K., Znachor P., Nedoma J., Seďa J. (2017) Repeated flood disturbance enhances rotifer dominance and diversity in a zooplankton community of a small dammed mountain pond Journal of Limnology 76 : 292–304 .
DOI: 10.4081/jlimnol.2016.1544
Horňák K., Kasalický V., Šimek K., Grossart H. (2017) Strain-specific consumption and transformation of alga-derived dissolved organic matter by members of the Limnohabitans-C and Polynucleobacter-B clusters of Betaproteobacteria Environmental Microbiology 19 : 4519–4535 .
DOI: 10.1111/1462-2920.13900
Jezberová J., Jezbera J., Znachor P., Nedoma J., Kasalický V., Šimek K. (2017) The Limnohabitans genus harbors generalistic and opportunistic subtypes: evidence from spatiotemporal succession in a canyon-shaped reservoir Applied and Environmental Microbiology 83 : e01530-17.
DOI: 10.1128/AEM.01530-17
Matoušů A., Osudar R., Šimek K., Bussmann I. (2017) Methane distribution and methane oxidation in the water column of the Elbe estuary, Germany Aquatic Sciences 79 : 443–458. .
DOI: 10.1007/s00027-016-0509-9
Pitsch G., Adamec L., Dirren S., Nitsche F. , Šimek K., Sirová D., Posch T. (2017) The Green Tetrahymena utriculariae n. sp. (Ciliophora, Oligohymenophorea) with its endosymbiotic algae (Micractinium sp.), living in traps of a carnivorous aquatic plant Journal of Eukaryotic Microbiology 64 : 322–335 .
DOI: 10.1111/jeu.12369

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

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