Department of Ecosystem Biology

The Department of Ecosystem Biology is responsible for the Environmental Ecology Bachelor’s programme, the Ecosystem Biology Master’s and Doctoral programmes, and the Hydrology Doctoral programme. Within the scope of the Ecosystem Biology programme students can chose one of five specializations: Theoretical Ecology, Conservation Biology, Applied Ecology, Hydrology and Soil Biology.

Head of the Department: Assoc. Prof. David Boukal

Research and education activities

The Department of Ecosystem Biology is responsible for the Environmental Ecology Bachelor’s programme, the Ecosystem Biology Master’s and Doctoral programmes, and the Hydrology Doctoral programme. Within the Ecosystem Biology programme, students can choose one of five specializations: Ecology, Conservation Biology, Applied Ecology, Hydrobiology and Soil Biology. Our faculty is the only one in the Czech Republic that offers a study programme focused on soil biology in the ecosystem context.

Our research deals with a wide range of questions in applied and fundamental ecology. It covers both terrestrial and aquatic ecosystems and their interactions including catchment–lake approaches, ecology of aquatic and soil organisms, microbial ecology, processes in soil, studies of aquatic and wetland ecosystems disturbed by human activities, and consequences of climate change and exploitation for terrestrial and aquatic biota. 

We combine a wide range of approaches including advanced molecular techniques, short-term laboratory and mesocosm experiments on model organisms, long-term field observations, mathematical modelling and the use of remote sensing in ecology. The department is involved in a number of national and international projects including the Soil and Water Research Infrastructure.

Freshwater Ecology and Hydrobiology

Our research ranges from processes at microscopic scales to whole-lake surveys. We study carbon and nutrient fluxes, aquatic microbial ecology, biotic interactions in aquatic food webs, and community ecology of zooplankton, aquatic insects and fish. Empirical research is complemented by modelling of life histories and community dynamics. We maintain active study sites in man-made reservoirs, acidified headwater lakes and small standing waters across the Czech Republic and in neighbouring countries. 

Ecosystem and Soil Biology

Our research deals with carbon, nitrogen, and phosphorus fluxes and transformations in wetland, forest, and pasture ecosystems with a focus on plant-soil interactions, primary production, C and nutrient transformations in soil and the composition of soil microbial communities. We also use experimental data to detect forest disturbances and their subsequent regeneration using remote sensing.

Conservation Biology

The research focuses on the ecology and management of endangered species, using orchids in terrestrial systems and aquatic insects in freshwaters as model groups.

Landscape Ecology

We deal with main ecosystem processes and spatio-temporal change detection in landscape. Main topics include forest ecosystem disturbances, land use and landscape structure changes in relation to biodiversity, importance of green infrastructure in urban areas, land-use scenario modelling and landscape politics.

Examples of results 


DE BELLO F., ŠMILAUER P., DINIZ-FILHO J.A.F., CARMONA C.P., LOSOSOVÁ Z., HERBEN T. and GOETZENBERGER L. (2017): Decoupling phylogenetic and functional diversity to reveal hidden signals in community assembly. Methods in Ecology and Evolution, in press (doi: 10.1111/2041-210X.12735).

SENTIS A., BINZER A. and BOUKAL D.S. (2017): Temperature-size responses alter food chain persistence across environmental gradients. Ecology Letters, in press (doi: 10.1111/ele.12779).

ČAPEK P., KOTAS P., MANZONI S. and ŠANTRŮČKOVÁ H. (2016): Drivers of phosphorus limitation across soil microbial communities. Functional Ecology 30: 1705-1713.

VRBA J., BOJKOVÁ J., CHVOJKA P., FOTT J., KOPÁČEK J., MACEK M., NEDBALOVÁ L., PAPÁČEK M., RÁDKOVÁ V., SACHEROVÁ V., SOLDÁN T. and ŠORF M. (2016): Constraints of biological recovery of the Bohemian Forest lakes from acid stress. Freshwater Biology 61: 376–395.

KAŠTOVSKÁ E., EDWARDS K.R., PICEK T. and ŠANTRŮČKOVÁ H. (2015): A larger investment into exudation by competitive versus conservative plants is connected to more coupled plant–microbe N cycling. Biogeochemistry 122: 47-59.

RASMUSSEN H.N., DIXON K.W., JERSÁKOVÁ J. and TĚŠITELOVÁ T. (2015): Germination and seedling establishment in orchids: a complex of requirements. Annals of Botany 116: 391–402.

SENTIS A., MORISSON J., BOUKAL D.S. (2015): Thermal acclimation modulates the impacts of temperature and enrichment on trophic interaction strengths and population dynamics. Global Change Biology 21: 3290-3298.

SIROVÁ D., ŠANTRŮČEK J., ADAMEC L., BÁRTA J., BOROVEC J., PECH J., OWENS S.M., SCHÄUFELE R., STORCHOVÁ H. and VRBA J. (2014): Dinitrogen fixation associated with shoots of aquatic carnivorous plants: is it ecologically important? Annals of Botany 114: 125-133.

ŠIMEK K., NEDOMA J., ZNACHOR P., KASALICKÝ V., JEZBERA J., HORŇÁK K. and 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. 

ŠMILAUER P. and LEPŠ J. (2014): Multivariate Analysis of Ecological Data using Canoco 5, Cambridge University Press.


Ph.D. theses:

ČAPKOVÁ K. (2016) Biological soil crusts of cold deserts of Western Himalaya.

ČAPEK P. (2016) Amount and transformation of phosphorus in permafrost affected soils.

KOUBOVÁ A. (2016) Regulation potential of earthworms as related to diversity and functioning of soil microbial community.

JAN J. (2015) Determination of eutrophication potential of particles in rivers and waterbody sediments.

SVOBODOVÁ Z. (2015) Effect of GM maize on entomofauna.

FARSKÁ J. (2015) Effects of management and natural disturbance on oribatid mites in montane forests.

RYCHTECKÝ P. (2014) Application of modern fluorescence techniques in studying growth, viability and phosphatase production of phytoplankton.

ŠORF M. (2014) The impact of fish and planktonic invertebrate predation on zooplankton in experimental mesocosms.

VANÍČKOVÁ I. (2013): The dynamics of sexual reproduction and ephippia production of Daphnia in reservoirs.

KRATOCHVÍL M. (2013): Spatio-temporal distribution and feeding of age 0+ fish in different reservoir habitats.

KROLOVÁ M. (2013): Factors affecting the occurrence of littoral vegetation in a reservoir with storage fiction.

TUŠER M. (2013): Fish detection with modern sonar systems.

KLEČKA J. (2013): The role of species traits in predator-prey interactions and food web structure.