prof. RNDr. Karel Šimek, CSc.

Funkce: Vedoucí oddělení - Oddělení mikrobiální ekologie vody

Kontaktní údaje

Telefon: +420 387775873
E-mail: ksimek@hbu.cas.cz
Místnost: 015

Popis

Specializace

Limnologie, mikrobiální ekologie, interakce bakterie-prvoci-viry, mikrobiální potravní řetězce v planktonu, bakteriální diverzita, Betaproteobacteria

Odborný životopis

Education:

  • 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

 

Research activities

 

Leading and coordinating the team of the Department of Aquatic Microbial Ecology 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).

 

Teaching and collaboration with universities abroad

 

University of Texas at Arlington, USA. 

1989, the lab of Prof. T.H. Chrzanowski. I was contracted via a NSF project; a part of the contract I was teaching of 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. Roland Psenner, Dr. Jakob Pernthaler, and Dr. Thomas 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 stay - 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)

Czech and Spanish Society of Entomology

Spanish Lepidopterological society - SOCIEDAD HISPANO-LUSO-AMERICANA DE

LEPIDOPTEROLOGÍA (SHILAP)

Publikace
Celkem nalezeno: 109 záznamů
Shabarova T., Kasalický V., Šimek K., Nedoma J., Znachor P., Posch T., Pernthaler J., Salcher M. (2017) Distribution and ecological preferences of the freshwater lineage LimA (genus Limnohabitans) revealed by a new double hybridization approach Environmental Microbiology 19 (3) : 1296–1309 .
DOI: 10.1111/1462-2920.13663
Baltar F., Palovaara J., Unrein U., Catala P., Horňák K., Šimek K., Vaqué D., Massama R., Gasol J., Pinhassi J. (2016) Marine bacterial community structure resilience to changes in protist predation under phytoplankton bloom conditions. ISME J. 10 : 568-581.
DOI: doi:10.1038/ismej.2015.135
Salcher M., Ewert C., Šimek K., Kasalický V., Posch T. (2016) Interspecific competition and protistan grazing affect the coexistence of freshwater betaproteobacterial strains. FEMS Microbiology Ecology 92 : -.
DOI: 10.1093/femsec/fiv156
Salcher M., Šimek K. (2016) Isolation and cultivation of planktonic freshwater microbes is essential for a comprehensive understanding of their ecology. Aquatic Microbial Ecology 77 : 183–196..
DOI: 10.3354/ame01796
Šimek K. (2016) Metody studia vodních bakterií pomocí fluorescenční mikroskopie [Methods of fluorescence microscopy to study aquatic bacteria]. Živa 64 (2) : 76.
Šimek K., Kubečka J. (2016) Rozhovor s hydrobiologem Karlem Šimkem, držitelem medaile G.J. Mendela [An interview with a hydrobiologist, Karel Šimek, who received a medal of the Czech Academy of Sciences "The Gregor Johann Mendel Honorary Medal for Merits in Biological Sciences"]. Živa 64 (2) : 27-29.
Znachor P., Hejzlar J., Vrba J., Nedoma J., Seďa J., Šimek K., Komárková J., Kopáček J., Šorf M., Kubečka J., Matěna J., Říha M., Peterka J., Čech M., Vašek M. (2016) Brief history of long-term ecological research into aquatic ecosystems and their catchments in the Czech Republic. Part I: Manmade reservoirs. Biology Centre CAS, v. v. i., Institute of Hydrobiology, České Budějovice, ISBN 978–80–86668–38–3: 80 p.
Adamec L., Sirová D., Vrba J., Bárta J., Šantrůček J., Šimek K. (2015) Lovci, nebo zahradníci? Komplexní výzkum vodních masožravých bublinatek [Hunters or gardeners? A complex research of aquatic carnivorous bladderworts]. Živa 63 : 286-288.
Grujčić V., Kasalický V., Šimek K. (2015) Prey-specific growth responses of freshwater flagellate communities induced by morphologicallly distinct bacteria from the genus Limnohabitans. Applied and Environmental Microbiology 81 : 4993–5002 .
DOI: 10.1128/AEM.00396-15
Weinbauer M.G. , Dolan J., Šimek K. (2015) A population of giant tailed virus-like particles associated with heterotrophic flagellates in a lake-type reservoir. Aquatic Microbial Ecology 76 : 111–116.
DOI: 10.3354/ame01769
Šimek K., Nedoma J., Znachor P., Kasalický V., Jezbera J., Horňák K., Seďa J. (2014) A finely tuned symphony of factors modulates the microbial food web of a freshwater reservoir in spring. Limnology and Oceanography 59 : 1477–1492..
Eiler A., Drakare S., Bertilsson S., Pernthaler J., Peura S., Rofner C., Šimek K., Yang Y., Znachor P., Lindström E. (2013) Unveiling distribution patterns of freshwater phytoplankton by a next generation sequencing based approach. PLOS ONE 8 : e53516..
Jezbera J., Jezberová J., Kasalický V., Šimek K., Hahn M. (2013) Patterns of Limnohabitans microdiversity across a large set of freshwater habitats as revealed by reverse line blot hybridization. PLOS ONE 8 : e58527..
DOI: DOI: 10.1371/journal.pone.0058527
Kasalický V., Jezbera J., Hahn M., Šimek K. (2013) The diversity of the Limnohabitans genus, an important group of freshwater bacterioplankton, by characterization of 35 isolated strains. PLOS ONE 8 : e58209..
Rulík M., Baudišová D., Růžička J., Šimek K. (2013) Mikrobiální ekologie vod [Aquatic mnicrobial ecology (textbook)]. In: Univerzita Palackého v Olomouci (Skripta) ISBN 978–80–244–3477–3 292 p.
Šimek K., Kasalický V., Jezbera J., Horňák K., Nedoma J., Hahn M., Bass D., Jost S., Boenigk J. (2013) Differential freshwater flagellate community response to bacterial food quality with a focus on Limnohabitans bacteria. The ISME Journal 7 : 1519–1530..
Hahn M., Scheuerl T., Jezberová J., Koll U., Jezbera J., Šimek K., Vannini C., Petroni G., Wu Q. (2012) The passive yet successful way of planktonic life: genomic and experimental analysis of the ecology of a free-living Polynucleobaster population. PLOS ONE 7 : e32772..
DOI: DOI: 10.1371/journal.pone.0032772
Jezbera J., Jezberová J., Koll U., Horňák K., Šimek K., Hahn M. (2012) Contrasting trends in distribution of four major planktonic betaproteobacterial groups along a pH gradient of epilimnia of 72 freshwater habitats. FEMS Microbiology Ecology 81 : 467–479..
DOI: DOI: 10.1111/j.1574-6941.2012.01372.x
Kasalický V., Jezbera J., Hahn M., Jezberová J., Hejzlar J., Šimek K. (2012) Ecology of planktonic freshwater bacteria of the Limnohabitans genus (Betaproteobacteria). In: Zborník príspevkov XVI. Konferencia SLS a ČLS Od molekúl po ekosystémy, Jasná, June 25–29, 2012, ISBN 978–80–971056–0–0: pp. 59–62.
Zeng Y., Kasalický V., Šimek K., Koblížek M. (2012) Genome sequences of two freshwater betaproteobacterial isolates, Limnohabitans species strains Rim28 and Rim47, indicate their capabilities as both photoautotrophs and ammonia oxidizers. Journal of Bacteriology 194 : 6302-6303..

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