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: 


Mocq J., St-Hilaire A. & Cunjak RA (2018 Do habitat measurements in the vicinity of Atlantic salmon (Salmo salar) parr matter?  Fisheries Management and Ecology. 25(1), 22-30

Mocq J. & Hare L. (2018) Influence of Acid Mine Drainage, and Its Remediation, on Lakewater Quality and Benthic Invertebrate Communities. Water, Air, & Soil Pollution 229 (2), 28

Mocq J., St-Hilaire A. & Cunjak RA (2015) Influences of Experts' Personal Experiences in Fuzzy Logic Modeling of Atlantic Salmon Habitat. North American Journal of Fisheries Management 35 (2), 271-280

Mocq J., St-Hilaire A. & Cunjak RA (2013) Assessment of Atlantic salmon (Salmo salar) habitat quality and its uncertainty using a multiple-expert fuzzy model applied to the Romaine River (Canada). J Ecological modelling 265, 14-25

le Viol I., Mocq J., Julliard R. & Kerbiriou C. (2009) The contribution of motorway stormwater retention ponds to the biodiversity of aquatic macroinvertebrates, Biological Conservation, 142(12). 3163-3171


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
+387 772 361; 2361
Biogeochemistry, soil ecology, ecological stoichiometry

The main focus of my research is small and large scale soil processes such as organic material decomposition or nutrient mineralization. I frequently use the knowledge and concepts of general microbiology and ecological stoichiometry to study the rate and direction of these processes as mediated by the activity of the soil microbial community.

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 – 2016: 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.)

2017 – 2019: Postdoc position at Environmental Molecular Sciences Laboratory in Richland, Washington, USA.

2019 - present: Researcher at the Department of Ecosystem Biology.



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 mathematical modelling in biological research using program R and python.


Publications in peer-reviewed scientific journals:


Starke Robert, Capek Petr, Morais Daniel, Jehmlich Nico, Baldrian Petr, 2020. Explorative Meta-Analysis of 377 Extant Fungal Genomes Predicted a Total Mycobiome Functionality of 42.4 Million KEGG Functions. Frontiers in Microbiology (11), 143, ISSN=1664-302X, DOI=10.3389/fmicb.2020.00143, URL=https://www.frontiersin.org/article/10.3389/fmicb.2020.00143

Starke, R., Capek, P., Morais, D., Callister, S. J., & Jehmlich, N. (2019). The total microbiome functions in bacteria and fungi. Journal of Proteomics, 103623. https://doi.org/10.1016/J.JPROT.2019.103623

Starke, R., Jehmlich, N., Alfaro, T., Dohnalkova, A., Capek, P., Bell, S. L., & Hofmockel, K. S. (2019). Incomplete cell disruption of resistant microbes. Scientific Reports, 9(1), 5618. https://doi.org/10.1038/s41598-019-42188-9

Čapek, P., Starke, R., Hofmockel, K. S., Bond-Lamberty, B., & Hess, N. (2019). Apparent temperature sensitivity of soil respiration can result from temperature driven changes in microbial biomass. Soil Biology and Biochemistry, 135, 286–293. https://doi.org/10.1016/J.SOILBIO.2019.05.016


Čapek, P., Manzoni, S., Kaštovská, E., Wild, B., Diáková, K., Bárta, J., … Šantrůčková, H. (2018). A plant–microbe interaction framework explaining nutrient effects on primary production. Nature Ecology & Evolution, 2, 1588–1596. https://doi.org/10.1038/s41559-018-0662-8

Wild, B., Alves, R. J. E., Bárta, J., Čapek, P., Gentsch, N., Guggenberger, G., … Richter, A. (2018). Amino acid production exceeds plant nitrogen demand in Siberian tundra. Environmental Research Letters, 13(3). https://doi.org/10.1088/1748-9326/aaa4fa

Thao Thi Dao, Norman Gentsch, Robert Mikutta, Leopold Sauheitl, Olga Shibistova, Birgit Wild, Jörg Schnecker, Jiří Bárta, Petr Čapek, Antje Gittel, Nikolay Lashchinskiy, Tim Urich, Hana Šantrůčková, Andreas Richter, Georg Guggenberger, 2018. Fate of carbohydrates and lignin in north-east Siberian permafrost soils, Soil Biology and Biochemistry (116), 311-322, ISSN 0038-0717, https://doi.org/10.1016/j.soilbio.2017.10.032. (http://www.sciencedirect.com/science/article/pii/S0038071717300019)

Tahovská, K., Čapek, P., Šantrůčková, H., & Kopáček, J. (2018). In situ phosphorus dynamics in soil: long-term ion-exchange resin study. Biogeochemistry, 1–14. https://doi.org/10.1007/s10533-018-0470-x

Manzoni, S., Čapek, P., Porada, P., Thurner, M., Winterdahl, M., Beer, C., … Way, D. (2018). Reviews and syntheses: Carbon use efficiency from organisms to ecosystems – definitions, theories, and empirical evidence. Biogeosciences, 15(19), 5929–5949. https://doi.org/10.5194/bg-15-5929-2018.

Hana Šantrůčková, Petr Kotas, Jiří Bárta, Tim Urich, Petr Čapek, Juri Palmtag, Ricardo J. Eloy Alves, Christina Biasi, Kateřina Diáková, Norman Gentsch, Antje Gittel, Georg Guggenberger, Gustaf Hugelius, Nikolaj Lashchinsky, Pertti J. Martikainen, Robert Mikutta, Christa Schleper, Jörg Schnecker, Clarissa Schwab, Olga Shibistova, Birgit Wild, Andreas Richter, 2018. Significance of dark CO2 fixation in arctic soils, Soil Biology and Biochemistry (119), 11-21, ISSN 0038-0717, https://doi.org/10.1016/j.soilbio.2017.12.021. (http://www.sciencedirect.com/science/article/pii/S0038071717307010)

Gentsch, N., Wild, B., Mikutta, R., Čapek, P., Diáková, K., Schrumpf, M., … Guggenberger, G., 2018. Temperature response of permafrost soil carbon is attenuated by mineral protection. Global Change Biology. https://doi.org/10.1111/gcb.14316
M.O. Rappe-George, M. Choma, P. Čapek, G. Börjesson, E. Kaštovská, H. Šantrůčková, A.I. Gärdenäs, 2017. Indications that long-term nitrogen loading limits carbon resources for soil microbes, Soil Biology and Biochemistry (115), 310-321, ISSN 0038-0717, https://doi.org/10.1016/j.soilbio.2017.07.015. (http://www.sciencedirect.com/science/article/pii/S003807171630325X)
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
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.
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.
Tahovská, K., Čapek, P., Šantrůčková, H., Kaňa, J., & Kopáček, J. (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. https://doi.org/10.1080/00103624.2015.1123721
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.
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

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


Urbanová, Z., Straková, P., Kaštovská, E., 2018. Response of peat biogeochemistry and soil organic matter

quality to rewetting in bogs and spruce swamp forests. European J. of Soil Biology 85, 12-22.

Kaštovská, E., Straková, P., Edwards, K., Urbanová, Z., Bárta, J., Mastný, J., Šantrůčková, H., Picek, T., 2017. 

Cotton-grass and blueberry have opposite effect on peat characteristics and nutrient transformation in peatland. Ecosystems, online.

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.