Biology Centre of the Academy of Sciences of the Czech Republic, Institute of Hydrobiology

Prof. Dr. Karel Šimek, PhD.
Personal data: Date of birth: 5 March 1955 Marital status: Married Affiliations: Faculty of Biological Sciences, University of South Bohemia, 370 05 České Budějovice & Biology Centre of the Academy of Sciences of the Czech Republic, v.v.i., Institute of Hydrobilology, Na Sádkách 7, České Budějovice CZ-370 05, Czech Republic

Contacts:

PHONE-Nr. 00420 38 7775873
MOBIL-Nr. 00420 606 927118
FAX-Nr. 00420 38 5310248
E-MAIL. ksimek@hbu.cas.cz

Areas of Competence:

Limnology, Microbial Ecology, Bacteria-Protozoa-Virus Interactions, Bacterial Diversity

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 selection; (ii) interactions of bacteria-protozoa-viruses as factors shaping bacterioplankton dynamics and community composition exploring a variety of molecular, flow cytometric, fluorescence microscopy and isolation and cultivation approaches; (iii) population dynamics and occurrence of Betaproteobacteria in freshwaters.

Education:

• Bachelor of Arts, 1979, Charles University in Prague
• Master of Sciences, 1980, Charles University in Prague. Emphasis in microbiology. Thesis title: "Influence of large-scale duck breeding on bacterial faecal pollution in a carp pond".
• 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, 1979-1990, Section of Hydrobiology, since 1 April, 1990 Hydrobiological Institute CAS
• Research Assistant, 1979-1985
• Research Associate, 1986-1990
• Since 1 Febr., 1991 - Head of the Department of Aquatic Microbial Ecology
• Since 1994 – 2001, Scientific secretary of the Hydrobiological Institute CAS
• Since 1996 – 1999, Faculty of Biological Sciences, University of South Bohemia in České Budějovice, a chair person for the master studies in limnology
• Since 1999, a chair person of the committee for Ph.D. studies in hydrobiology - Faculty of Sciences, University of South Bohemia in České Budějovice.

Research activities

Heading the team of the Department of Aquatic Microbial Ecology with 23 staff members divided into (1) microbial ecology and (2) phytoplankton ecology subgroups.

Projects awarded – Czech Grant Agency:

• January 2008 – December 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”

• January 2005 - December 2007, leading of 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”

• January 2002 - December 2004, leading of 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”
• January 1999 - December 2001, leading of 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”
• November 1997 - December 1998, AKCION project between Czech Republic and Austria, leading the project: “Ecological aspects of genetic and functional diversity of aquatic bacteria under grazer control: the use of in situ hybridisation and fluorescent rRNA-targeted probes"
• January 1996 - December 1998, leading of 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"
• April 1993 - December 1995, leading of the research project (CAS) "Microbial pathways of utilizing phytoplankton production: Indication via ectoenzyme assays".
• March 1991 - March 1993, leading of 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:

• 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 together 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 (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, Projekt CRNS – PICS, financed by the CNRS - Directions des Relations Internationales (DRI) and coordinated together with Dr. John Dolan (CRNS, France), "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, AKTION project between Czech Republic and Austria, coordinated together with Dr. Thomas Posch (University of Innsbruck, Austria) a bilateral project: "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 projekt CRNS – the Czech Academy of Sciences, coordinated together with Dr. John Dolan (CRNS, France), “Factors controlling development of preokaryotic 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 - 7 months, the lab of Prof. T.H. Chrzanowski, the research project "Microbial processes in reservoirs: Regulation of bacteria by grazers".
Institute of Limnology ÖAW, Mondsee, AUSTRIA
Leading the workshop ("Protozoan grazing on bacteria: field and laboratory studies") for students and graduates of limnology from The University of Innsbruck focused on fluorescent methods for protozoan grazing experiments (15-19 November, 1990, invited by Dr. R. Psenner).
Institute of Limnology, The University of Constance, FRG
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 - always 2-3 weeks every year (1995 - 2005), 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 Ci?ncies del Mar-CMIMA, CSIC, Barcelona, Spain
Exchange program CSIC – AS CR, collaboration with Dr. J. M Gasol, two follow-up 2-year projects (2 months during 2003-2006).

International Recognition of Professional Excellence Award:
In 1991 selected as the IRPE (International Recognition of Professional Excellence) Prize winner in the field of limnetic ecology

Twenty invited and keynote lectures were presented abroad during 2000 - 2009

Subject editor (since 1995) in the field of expertise "Microbial dynamics in freshwaters" in the journal of AQUATIC MICROBIAL ECOLOGY

Citations (WOS): 1810 SCI citations

H-index (2009): 24

Teaching activities at the University of South Bohemia:

Lecturing "Aquatic Microbial Ecology" and "Modern limnological approaches" at the Biological Faculty, University of South Bohemia, České Budějovice. Since 2006, co-lecturing “Special limnology” with Jaroslav Vrba and Josef Hejzlar.

Professional Associations:

Czechoslovak Society for Microbiology, Czechoslovak Society for Limnology
American Society of Limnology and Oceanography (1999-2004)

Hobbies:

Gardening, hiking, entomology – an amateur butterfly collector, participating in several ongoing international (European) and Czech national projects focused on mapping of European butterfly fauna supplying the data also for the EU program NATURA 2000.

Papers...

Prof. Dr. Karel Šimek, PhD.