Přírodovědecká fakulta JU
Hydrobiologický ústav BC AVČR
dagmara_sirova [at] hotmail.com

Mikrobiální ekologie, Interakce mezi rostlinami a mikroorganismy

Přírodovědecká fakulta JU
joacim.naslund [at] gmail.com
aquatic ecology
Přírodovědecká fakulta JU
tahovska [at] centrum.cz
soil (micro)biology and ecology

I study how nutrients (especially N & P) & carbon flow through forest ecosystems and which is the impact of human activity on the cycles, primarily on nitrogen retention and C-N(P) cycle interactions. I use field observations in combination with field and lab manipulative experiments (bio-chemical soil analyses, stable isotopes, ion resins etc.).

running projects:

- The effect of natural dieback of mountain spruce forest on microclimate, chemistry, and bio-diversity of terrestrial and aquatic ecosystems - member of the research team, P504/12/1218, Jiří Kopáček, 2012 - 2016, GAČR

- Acidity and nutrient constraints on organic matter balance and nitrogen saturation in forest soils, acidity/N availability manipulative experiments in area of formerly high S/N deposition - co-investgater of the project, 14-33311S, Filip Oulehle, 2014 - 2016, GAČR

finished projects:

What are the main mechanisms affecting N flow through soil N pools in N saturated mountain soils? - co-investigator, KJB600960907, 2009-2011, GAAV, Jiří Kaňa





Brief CV: 

2012 Ph.D. Ecosystem Biology, dissertation thesis: N availability and transformation in soils of acidified and nitrogen saturated mountain forest ecosystems

2005 M.Sc. Applied ecology

More information: 

konference (list of participation in conferences):

2016   ISME– 16th International Symposium on microbial Ecology (poster): Microbial community regulates N loss in mountain forests after decades of acid deposition recovery (Tahovská et al.) (Montreal, Canada)

2015    Ecology of Soil Microorganisms - Microbes as Important Drivers of Soil Processes (poster): Microbial activity in the context of acid deposition – field manipulations with sulphur and/or nitrogen inputs to the forest soils (Tahovská et al.) (Czech Republic)     

             Aktuelle Ergebnisse der Böhmerwaldforschung (poster):  In situ nitrogen availability in mountain soils following forest disturbances – N saturation symptoms mitigated (Tahovská et al.) (Germany)

2014    Biogeomon (2x poster): In-situ nitrogen availability in mountain soils following forest disturbances (Tahovská et al.); The importance of being DOC - microbial N immobilization in mountain soils (Tahovská et al.) (Bayreuth, Germany)

2012    Biogeomon (talk): Microbial N immobilization is of great importance in acidified and N-saturated mountain forest soils if carbon is available, USA (Maine)

2011    Ecology of Soil Microorganisms - Microbes as Important Drivers of Soil Processes (talk): „Are microorganisms adapted for mineral N assimilation in acidified soils, Czech Republic (Prague)

2011    Czech Ecological Society (CSPE) conference (poster): „Microbial N assimilation in primeval and N saturated forest soils (in Czech), Czech Republic (Kostelec nad Č. Lesy)

2010    EGU conference (2 posters): „Aluminum availability in forest floor of two acidified mountain watersheds“ (Kaňa and Tahovská) and „Nitrogen availability in mountain spruce forest floor after forest defoliation“ (Tahovská et al.), Austria (Vienna)

2009    Biogeomon (poster): “Microbial N transformations in N loaded spruce forest soils:  immobilization of different 15N forms into microbial biomass”, Finland (Helsinki)

2008    Mountain soils under a changing climate and land-use (poster & short presentation): Microbial assimilation of nitrogen in N saturated mountain forest soils - 15N tracer study, Switzerland (Zürich)

2008    CSPE conference (poster): “N availability in mountain forest soils after forest defoliation” (in Czech), Czch Republic (Třeboň)

2007    Soil processes under extreme meteorological conditions (2x poster & 1x short presentation): „Nitrogen availability and fluxes in acidified mountain forest soils – in situ measurement“ (Tahovská et al.) and “N pools and seasonal fluxes in acidified mountain spruce forest soil” (Šantrůčková & Tahovská), Germany (Bayreuth)

2007    GORDON conference  (poster): “Nitrogen pools and fluxes in the catchment-lake ecosystem of Plešné Lake (Czech Republic) prior to and after a bark beetle infestation“ (Kopáček et al.), USA (New Hampsire)


Publikace (list of publications):

Tahovská, K., Čapek, P., Kaňa, J., Kopáček, J., Šantrůčková, H., 2016. Measurement of  in situ phosphorus availability in acidified soils using iron infused resin, Communications in Soil Science and Plant Analysis 47 (4), 487 - 494. 

Staňková P., Tahovská K., Šantrůčková H., in press: Anthropogenic impact on nitrogen transformation in spruce forests of central European mountains - a review. Silva Gabreta 21 (1) 

Vrba, J., Kopáček, J., Tahovská, K., Šantrůčková, H., 2015. Long-term ecological research of glacial lakes in the Bohemian Forest and their catchments. Silva Gabreta 21, 53-71.

Kaňa, J., Tahovská, K., Kopáček, J., Šantrůčková, H., 2015. Excess of organic carbon in mountain spruce forest soils after bark beetle outbreak altered microbial N transformations and mitigated N-saturation. Plos One DOI:10.1371/journal.pone.0134165

Kopáček, J., Cosby, B.J., Evans, C.D., Hruška, J., Moldan, F., Oulehle, F., Šantrůčková, H., Tahovská, K., Wright, R.F., 2013. Nitrogen, organic carbon and sulphur cycling in terrestrial ecosystems: linking nitrogen saturation to carbon limitation of soil microbial processes. Biogeochemistry 115 (1-3), 33-51.

Tahovská, K., Kaňa, J., Bárta, J., Oulehle, F., Richter, A., Šantrůčková, H., 2013. Microbial N immobilization is of great importance in acidified mountain spruce forest soils, Soil Biology and Biochemistry 59, 58-71.

Kaňa, J., Tahovská, K., Kopáček, J., 2013.  Changes in soil chemistry after bark beetle infestation and forest dieback, Biogeochemistry (in press)  DOI: 10.1007/s10533-012-9765-5.

Hruška J., Oulehle F., Šamonil P., Šebesta J., Tahovská K., Hleb R., Houška J., Šikl (2012). Long term forest soil acidification, nutrient leaching and vegetation development: Linking modelling and surveys of a primeval spruce forest in the Ukrainian Transcarpathian Mts. Ecological Modelling 244: 28-37.

Oulehle F., Evans C.D., Hofmeister J., Krejčí R., Tahovská K., Persson T., Cudlín P., Hruška J. (2011) Major changes in forest carbon and nitrogen cycling caused by declining sulphur deposition. Global Change Biology 17: 3115-3129.

Tahovská, K., Šantrůčková, H., Kopáček , J., 2010. Nitrogen availability in Norway spruce forest floor - the effect of forest defoliation induced by bark beetle infestation. Boreal Environment Research 15 (6): 553 – 564.

Šantrůčková, H., Tahovská, K., Kopáček , J., 2009. Nitrogen transformations and pools in N saturated mountain spruce forest soils. Biology and Fertility of Soils 45 (4): 395 – 404.

Skopcová, K., Šantrůčková, H., 2006. The effect of temperature on nitrogen transformations in mountain forest soils of Plešné, Černé, and Čertovo Lake watersheds, Silva Gabreta 12 (1), 3 - 14.

Přírodovědecká fakulta JU
Entomologický ústav BC AVČR
michal.sorf [at] prf.jcu.cz
zooplankton ecology

Research interests include taxonomy (Rotifera, Cladocera, Cyclopoida, Calanoida), seasonal dynamics of zooplankton and predator-prey interactions among zooplankton species.

Brief CV: 


2001-2004 BSc. study at University of South Bohemia, Faculty of Biological Sciences, České Budějovice

2004-2007 MSc. study at University of South Bohemia, Faculty of Biological Sciences, České Budějovice

2007-2014 Ph.D. study at University of South Bohemia, Faculty of Science, České Budějovice


Professional qualification:

2004 - BSc. in Biology, Thesis: Seasonal changes of zooplankton in the Kačležský rybník (Supervisors: RNDr. Miloslav Devetter, Ph.D. & RNDr. Jaromír Seďa, CSc.)

2007 - MSc. in Ecology, Thesis: Animal component in a diet of two Eudiaptomus species (Copepoda: Calanoida) (Supervisor: prof. RNDr. Zdeněk Brandl, CSc.)

2014 - Ph.D. in Hydrobiology, Thesis: The impact of fish and planktonic invertebrate predation on zooplankton in experimental mesocosms (supervisors: prof. RNDr. Zdeněk Brandl, CSc., prof. RNDr. Jaroslav Vrba, CSc. & Mgr. Mojmír Vašek, Ph.D.)



since 2008 Faculty of Science, University of South Bohemia

since 2014 Institute of Entomology, Biology Centre of the Academy of Sciences of the Czech Republic (part-time job within the project EU FP-7 Theme 6 project REFRESH (Adaptive strategies to Mitigate the Impacts of Climate Change on European Freshwater Ecosystems,

Contract No.: 244121))

2010-2013 Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic (part-time job within the project EU FP-7 Theme 6 project REFRESH (Adaptive strategies to Mitigate the Impacts of Climate Change on European Freshwater Ecosystems)

REFRESH Project Meetings: Aberdeen, United Kingdom (3.-8.4.2011); Sitges, Spain (19.-23.3.2012) and Antalya, Turkey (22.-26.4.2013)

Přírodovědecká fakulta JU
jmocq [at] prf.jcu.cz
Abiotic and biotic effects on trophic interactions

I focus on the effect of biotic (conspecifics, top predator, prey density, chemical cues) and abiotic (temperature, habitat complexity) factors on trophic (predation success, functional responses) and non-trophic (mutual interference) interactions of aquatic invertebrates in connection with their functional traits.

Brief CV: 


Water Sciences PhD Program, Institut National de la Recherche Scientifique INRS, Québec, Canada,
Fuzzy modelling of Atlantic Salmon (Salmo salar) habitat

2007- 2008

Island Conservation Society, Mahé, Seychelles. Reintroduction project of Pelusios castanoides and P. subniger (Anapsids Peludomedusidae): study and determination of benthic macroinvertebrates as food resource


Master 2nd year ‘Wetland Eco-Engineering and Biodiversity’ (equivalent to the 2nd year of an M.Sc.)
Angers University- National School of Horticulture, Angers, France


CERSP « Conservation, Restoration and Population Monitoring », National Museum of Natural History, Paris, France
Biodiversity and biological value of stormwater detention ponds: study of macroinvertebrates of motorway A11’s ponds.


Master 2nd year ‘Ecosystems and Anthropisation’
Paul Sabatier University/ École Nationale Supérieure Agronomique, Toulouse, France


LADYBIO- LAboratory of BIOdiversity DYnamics, Toulouse, France
Study on fragmentation impact on fishes, macroinvertebrate and diatom community structures.

More information: 

Scientific presentations

Mocq J., St-Hilaire A. & Cunjak R.A.(2010) Modeling of Atlantic salmon habitat using fuzzy coding method: a brief introduction, Canadian Rivers Institute (CRI) conference, 9th of July, Fredericton (NB), Canada

Mocq J., St-Hilaire A. & Cunjak R.A.(2013) Influences et conséquences de l’expérience personnelle des experts dans un modèle de logique floue, Conference of the Centre Interuniversitaire de Recherche sur le Saumon Atlantique (CIRSA), 2nd of May, Québec (QC), Canada – Best presentation award.

Mocq J., St-Hilaire A. & Cunjak R.A.(2013) Atlantic Salmon (Salmo salar) Habitat Models and Uncertainty Assessment Using Fuzzy Logic Modeling, American Fisheries Society (AFS) conference, 10th of July, Little Rock (AR), USA

Mocq J., Egon J. & Boukal D. (2017) Multiple biotic influences  on functional response in an intraguild predation system, FreshBlood for Freshwater conference, 11th of April, Ceske Budejovice, Czech Republic

Mocq J., Soukup P. & Boukal D. (2017) Unexpected nonlinear effect of habitat complexity on functional responses, Symposium for European Freshwater Sciences (SEFS), 7th of July, Olomouc, Czech Republic

Přírodovědecká fakulta JU
petacapek [at] gmail.com
Ecology, soil biology and microbiology

Based on site-based research I try to find out the role of soil microbial community in the ecosystem scale processes. I use the knowledge and concepts of general microbiology and ecological stoichiometry to trace imprints of soil microbial community behavoir in soil organic carbon mineralization, humification and nutrient cycling. At the same time I try to quantify constraints possessed by physical and chemical properties of soil to microbial metabolism and growth.  

Brief CV: 

2005 – 2008: Bachelor of Biology (Bc, České Budějovice, (Faculty of Science, Department of Ecosystem Biology) - student of environmental care (supervisor: prof. Ing. Hana Šantrůčková, CSc.)

2008 – 2010: Master of Biology (Mgr.), University of South Bohemia, České Budějovice, (Faculty of Science, Department of Ecosystem Biology) – student of soil biology (supervisor: prof. Ing. Hana Šantrůčková, CSc.)

2011 – present: Ph.D. program at University of South Bohemia, České Budějovice, (Faculty of Science, Department of Ecosystem Biology) – student of ecosystem biology (supervisor: prof. Ing. Hana Šantrůčková, CSc.)



More information: 

Work and science experience:

Collaborator on the CryoCARB project (Long-term Carbon Storage in Cryoturbated Arctic Soils). http://www.univie.ac.at/cryocarb/the-cryocarb-project/.

Member of joint sampling trip 2011 of CryoCARB project to Taymyr peninsula (Russia).

Member of a field works in the Himalaya, Ladakh, 2013 (India).

Member of a field works in the Svalbard, 2014.


Scientific skills:

Using stable isotopes in biological research.

Using high level statistics and simple mathematical modelling in biological research with program R.


Publications in peer-reviewed scientific journals:


Manzoni, S., P. Čapek, M. Mooshammer, B. D. Lindahl, A. Richter, & H. Šantrůčková, 2017. Optimal metabolic regulation along resource stoichiometry gradients. Ecology Letters , http://doi.wiley.com/10.1111/ele.12815.

Choma, M., M. O. Rappe-George, J. Bárta, P. Čapek, E. Kaštovská, A. I. Gärdenäs, & H. Šantrůčková, 2017. Recovery of the ectomycorrhizal community after termination of long-term nitrogen fertilisation of a boreal Norway spruce forest. Fungal Ecology , http://linkinghub.elsevier.com/retrieve/pii/S1754504816301106.

Diáková K, Biasi C, Čapek P, Martikainen PJ, Marushchak ME, Patova EN, Šantrůčková H. (2016). Variation in N2 fixation in subarctic tundra in relation to landscape position and nitrogen pools and fluxes. Arctic Antarctic and Alpine Research, 48, 111–125.

Čapek P., Kotas P., Manzoni S., Šantrůčková H. (2016). Drivers of phosphorus limitation across soil microbial communities. Functional Ecology (in press). http://onlinelibrary.wiley.com/doi/10.1111/1365-2435.12650/abstract

Čapek, P., Diáková, K., Dickopp, J.-E., Bárta, J., Wild, B., Schnecker, J., Alves, R.J.E., Aiglsdorfer, S., Guggenberger, G., Gentsch, N., Hugelius, G., Lashchinsky, N., Gittel, A., Schleper, C., Mikutta, R., Palmtag, J., Shibistova, O., Urich, T., Richter, A., Šantrůčková, H., 2015. The effect of warming on the vulnerability of subducted organic carbon in arctic soils. Soil Biology and Biochemistry 90, 19-29. - http://authors.elsevier.com/a/1RWOv8g1337Yu

Hauer, T., Čapek, P., Böhmová, P., 2015. Main photoautotrophic components of biofilms in natural draft cooling towers. Folia Microbiologica, 1-6.

Řeháková, K., Chroňáková, A., Krištůfek, V., Kuchtová, B., Čapková, K., Scharfen, J., Čapek, P., Doležal, J., 2015. Bacterial community of cushion plant Thylacospermum ceaspitosum on elevational gradient in the Himalayan cold desert. Frontiers in Microbiology 6. - http://journal.frontiersin.org/article/10.3389/fmicb.2015.00304/abstract

Gentsch, N., Mikutta, R., Alves, R.J.E., Barta, J., Čapek, P., Gittel, A., Hugelius, G., Kuhry, P., Lashchinskiy, N., Palmtag, J., Richter, A., Šantrůčková, H., Schnecker, J., Shibistova, O., Urich, T., Wild, B., Guggenberger, G., 2015. Storage and transformation of organic matter fractions in cryoturbated permafrost soils across the Siberian Arctic. Biogeosciences 12, 4525-4542. - http://www.biogeosciences.net/12/4525/2015/bg-12-4525-2015.html

Gittel, A., Bárta, J., Kohoutova, I., Schnecker, J., Wild, B., Čapek, P., Kaiser, C., Torsvik, V.L., Richter, A., Schleper, C. & Urich, T. (2014) Site- and horizon-specific patterns of microbial community structure and enzyme activities in permafrost-affected soils of Greenland. Frontiers in Microbiology, 5. - http://journal.frontiersin.org/article/10.3389/fmicb.2014.00541/abstract

Gittel, A., Barta, J., Kohoutova, I., Mikutta, R., Owens, S., Gilbert, J., Schnecker, J., Wild, B., Hannisdal, B., Maerz, J., Lashchinskiy, N., Capek, P., Šantrůčková H, Gentsch, N., Shibistova, O., Guggenberger, G., Richter, A., Torsvik, V.L., Schleper, C. & Urich, T. (2014) Distinct microbial communities associated with buried soils in the Siberian tundra. Isme Journal, 8, 841-853.

Schädel, C., Bader, M.K.-F., Schuur, E.A.G., Biasi, C., Bracho, R., Čapek, P., De Baets, S., Diáková, K., Ernakovich, J., Estop-Aragones, C., Graham, D.E., Hartley, I.P., Iversen, C.M., Kane, E., Knoblauch, C., Lupascu, M., Martikainen, P.J., Natali, S.M., Norby, R.J., O’Donnell, J.A., Chowdhury, T.R., Šantrůčková, H., Shaver, G., Sloan, V.L., Treat, C.C., Turetsky, M.R., Waldrop, M.P. & Wickland, K.P. (2016) Potential carbon emissions dominated by carbon dioxide from thawed permafrost soils. Nature Climate Change, advance on.

Schnecker, J., Wild, B., Hofhansl, F., Alves, R.J.E., Bárta, J., Čapek, P., Fuchslueger, L., Gentsch, N., Gittel, A., Guggenberger, G., Hofer, A., Kienzl, S., Knoltsch, A., Lashchinskiy, N., Mikutta, R., Santruckova, H., Shibistova, O., Takriti, M., Urich, T., Weltin, G. & Richter, A. (2014) Effects of Soil Organic Matter Properties and Microbial Community Composition on Enzyme Activities in Cryoturbated Arctic Soils. Plos One, 9. - http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0094076

Tahovská, K., Čapek, P., Kaňa, J., Kopáček, J. & Šantrůčková, H. Measurement of in situ phosphorus availability in acidified soils using iron infused resin. Communications in Soil Science and Plant Analysis.

Wild, B., Gentsch, N., Čapek, P., Diáková, K., Alves, R.J.E., Bárta, J., Gittel, A., Hugelius, G., Knoltsch, A., Kuhry, P., Lashchinskiy, N., Mikutta, R., Palmtag, J., Schleper, C., Schnecker, J., Shibistova, O., Takriti, M., Torsvik, V.L., Urich, T., Watzka, M., Šantrůčková, H., Guggenberger, G. & Richter, A. (2016) Plant-derived compounds stimulate the decomposition of organic matter in arctic permafrost soils. Scientific Reports, 6, 25607.

Wild, B., Schnecker, J., Alves, R.J.E., Barsukov, P., Bárta, J., Čapek, P., Gentsch, N., Gittel, A., Guggenberger, G., Lashchinskiy, N., Mikutta, R., Rusalimova, O., Šantrůčková, H., Shibistova, O., Urich, T., Watzka, M., Zrazhevskaya, G. & Richter, A. (2014) Input of easily available organic C and N stimulates microbial decomposition of soil organic matter in arctic permafrost soil. Soil Biology and Biochemistry, 75, 143-151. - http://www.sciencedirect.com/science/article/pii/S0038071714001345

Wild, B., Schnecker, J., Bárta, J., Čapek, P., Guggenberger, G., Hofhansl, F., Kaiser, C., Lashchinsky, N., Mikutta, R., Mooshammer, M.,Šantrůčková H, Shibistova, O., Urich, T., Zimov, S.A. & Richter, A. (2013) Nitrogen dynamics in Turbic Cryosols from Siberia and Greenland. Soil Biology & Biochemistry, 67, 85-93. - http://www.sciencedirect.com/science/article/pii/S0038071713002691

Zimmermann, M., Bird, M.I., Wurster, C., Saiz, G., Goodrick, I., Bárta, J., Čapek, P., Šantrůčková, H. & Smernik, R. (2012) Rapid degradation of pyrogenic carbon. Global Change Biology, 18, 3306-3316. - http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2486.2012.02796.x/abst...


Přírodovědecká fakulta JU
urbanz00 [at] prf.jcu.cz
wetland ecology


Peatland ecology

Effect of drainage and restoration on peatland functioning with a focus on greenhouse gasses production a emissions, vegetation, microbial community composition, nutrient transformation and organic matter quality in peatlands.  

Carbon fluxes and balance on pristine, drained and restored peatlands. 

Brief CV: 


1996 - 2001 high school Gymnázium Vimperk

2001 - 2007 Faculty of Science, Masaryk University in Brno, Czech Republic; graduated in biology, geology and geography; Master thesis: Mire flora and vegetation and their human alternation in the right-side Lipno area (Czech Republic).

2007 - 2012 Department of Ecosystem Biology, Faculty of Science, University of South Bohemia in Ceske Budejovice, postgraduate study, specialization Ecosystem biology;                     Ph.D. thesis: Effect of drainage and restoration on the ecology of peatlands in the Šumava Mountains

2008 - present time: Department of Ecosystem Biology employee, Faculty of Science,  University of South Bohemia in Ceske Budejovice, research worker


More information: 

Study stays: 

Department of Forest Sciences, Peatland Ecology group, University of Helsinki, Finland in 2009/2010 (three months).
Greencycles II Summer School, May 2011, Peyresq, France. Feedbacks in the Earth System: the stateof the art.
Faculty of Science and Forestry, University of Eastern Finland, Joensuu, Finland, August 2012, sprucemire study under the supervision of Eeva-Stiina Tuittila

Teaching at international course Soil and Water: Tartu, Estonia, September 2013; Marseille, France 2014; Ulm, Germany 2015; Ceske Budejovice, Czechia 2016; 


Finished projects:

Effect of hydrological restoration of long-term drained peatlands on functional diversity of soil microorganisms in relation to organic matter quality, postdok project GAČR (Czech Science Foundation),  2014 - 2016, investigator of the project


Mastný, J., Urbanová, Z., Kaštovská, E., Straková, P., Šantrůčková, H. and Picek, T. 2016. Soil

organic matter quality and microbial activities in spruce swamp forests affected by drainage and water

 regime restoration. Soil Use and Management 32, 200–209. 

Urbanová, Z. and Bárta, J. 2016. Effects of long-term drainage on microbial community composition

vary between peatland types. Soil Biol Biochem 92, 16-26.

Urbanová, Z. and Bárta, J. 2014. Microbial community composition and in silico predicted metabolic

potential reflect biogeochemical gradients between distinct peatland types. FEMS Microbiol Ecol 90, 633-646.

Urbanová, Z., Picek, T., I., Tuittila, E.-S., 2013. Sensitivity of carbon gas fluxes to weather 

variability on pristine, drained and rewetted temperate bogs. Mires and Peat 11, article 04.

Urbanová, Z., Bárta, J., Picek, T., 2013. Methane emissions and methanogenic Archaea on
pristine, drained and restored mountain peatlands, Central Europe. Ecosystems 16, 664-677.

Urbanová, Z., Picek, T., Hájek, T., Bufková, I., Tuittila, E.-S., 2012. Vegetation and carbon gas
dynamics under a changed hydrological regime in central European peatlands. Plant Ecology &
Diversity 5, 89-103.

Urbanová, Z., Picek, T., Bárta, J., 2011. Effect of peat re-wetting on carbon and nutrient fluxes,
greenhouse gas production and diversity of methanogenic archaeal community. Ecological
Engineering 37:1017–1026.