Department of Experimental Plant Biology

The Department of Plant Physiology offers study on the Experimental Plant Biology Master’s programme and the Doctoral specialization of Plant Physiology. The research covers environmental plant physiology, biochemistry, and the biophysics of photosynthesis, and is focused to several dominant areas.

Head of the Department: Assoc. Prof. Jiří Šantrůček

Research and education activities

 The Department of Experimental Plant Biology provides education in the Experimental Plant Biology Master’s programme and the Doctoral programme of Plant Physiology. The research topics cover environmental plant physiology, biochemistry and the biophysics of photosynthesis and plant-water relations, and are focused on several dominant areas.

Photosynthesis of higher plants, algae and cyanobacteria

The regulation of photosynthesis in higher plants, algae, and cyanobacteria is studied on a molecular, cellular and organ level, with respect to environmentally important natural variability of CO2 concentration, temperature, irradiance and nutrients. In higher plants, leaf internal limitations to CO2 fixation (mesophyll conductance for CO2) are studied using gas exchange, chlorophyll fluorescence and stable isotope mass spectrometry techniques.

Contact persons: Jiří Šantrůček (, Ondřej Prášil (

Stomatal development, leaf cuticle and plant–atmosphere interactions

Environmental factors controlling stomatal development and patterning in leaf epidermis are studied using gas exchange, thermography, mass spectrometry, and microscopy. Transport and structural properties of the cuticle as a leaf water loss barrier are studied in cooperation with the Institute of Cellular and Molecular Botany, University of Bonn.         

Contact person: Jiří Šantrůček (, Marie Hronková (

Stable isotopes fractionation in biosphere

Fractionation of water isotopes (18O and D) in the soil–plant–atmosphere continuum and stable carbon isotopes (13C/12C) in leaves and stems (tree rings) is applied in the assessment of plant growth conditions, water use and in the tracing of the geographical origin of plant products. In cooperation with Technical University Munich (Chair of Grassland Science, Freising), we organize the International Spring School on Stable Isotopes in Environmental Sciences, Ecology and Physiology (      

Contact persons: Jiří Květoň (, Jiří Šantrůček (

Bryophyte ecophysiology

Bryophytes, the earliest land plants, thrive through a huge range of environmental conditions. Their physiological adaptations are studied with respect to their ecology in extreme habitats, typically under stress from limiting or excess availability of water, mineral nutrients and photosynthetic light. Ecophysiology of peat mosses (Sphagnum) is of special interest.

Contact person: Tomáš Hájek (

Thermal stability of type II photosynthetic reaction centres

A highly collaborative, interdisciplinary approach that combines biophysical, analytical, molecular biology and computational methods is used to investigate molecular mechanisms behind the adaptation of photosynthesis to ambient temperature. The discovered stabilization mechanisms are being exploited together with our partner team at Weizmann Institute of Science in engineering of thermotolerant strains of algae while mutagenesis studies on tobacco are performed at our University. Thermal adaptation of photosynthesis in cryotolerant algae and thermotolerant photosynthetic bacteria is carried out in collaboration with teams at the Institute of Microbiology CAS.
Contact person: David Kaftan (

Biophysics and biochemistry of plants with a focus on metal metabolism

Many metals are essential for all organisms as active centres of enzymes and other proteins, but in higher concentrations they become toxic. Metal deficiency as well as metal toxicity frequently occurs in many parts of the world, incl. Czech Republic. Using the example of photosynthetic organisms, in particular plants, the projects of this team enhance the knowledge of mechanisms of metal deficiency / toxicity stress and metal metabolism in general. This mechanistic knowledge is decisive for environmental risk assessment, for improved agriculture through more targeted fertilization and breeding, phytoremediation of polluted soils and aquifers, for understanding evolutionary processes and for more realistic estimation of the productivity of ecosystems.

Contact person: Hendrik Küpper (

Example of results


ANDRESEN E., KAPPEL S., STÄRK H.J., RIEGGER U., BOROVEC J., MATTUSCH J., HEINZ A., SCHMELZER C.E.H., MATOUŠKOVÁ Š., DICKINSON B., KÜPPER H. (2016): Cadmium toxicity investigated on physiological and biophysical level under environmentally relevant conditions using the aquatic model plant Ceratophyllum demersum L. New Phytologist 210, 1244-1258.

KÜPPER H., ANDRESEN E. (2016): Mechanisms of metal toxicity in plants. Metallomics 8, 269-285.

MISHRA S., ALFELD M., SOBOTKA R., ANDRESEN E., FALKENBERG G., KÜPPER H. (2016): Analysis of sub-lethal arsenic toxicity to Ceratophyllum demersum: Subcellular distribution of arsenic and inhibition of chlorophyll biosynthesis. Journal of Experimental Botany 67, 4639-4646.

VICHEROVÁ E., HÁJEK M. and HÁJEK T. (2015): Calcium intolerance of fen mosses: physiological evidences, effects of nutrient availability and successional drivers. Perspectives in Plant Ecology, Evolution and Systematics. Provisionally accepted.

BÁRTA J., STONE J.D., PECH J., SIROVÁ D., ADAMEC L., CAMPBELL M.A. and ŠTORCHOVÁ H. (2015): The transcriptome of Utricularia vulgaris, a rootless plant with minimalist genome, reveals extreme alternative splicing and only moderate sequence similarity wityh Utricularia gibba. BMC Plant Biology 15: 78 DOI10.1186/s12870-015-0467-8.

HRONKOVÁ M., WIESNEROVÁ D., ŠIMKOVÁ M., SKŮPA P., DEWITTE W., VRÁBLOVÁ M., ZAŽÍMALOVÁ E., ŠANTRŮČEK J. (2015): Light induced STOMAGEN-mediated stomatal development in Arabidopsis leaves. Journal of Experimental Botany, 66: 4621-4630, 2015.

HÁJEK T. and VICHEROVÁ E. (2014): Desiccation tolerance of Sphagnum revisited: a puzzle resolved. Plant Biology 16: 765-773.

KUBÁSEK J., HÁJEK T. and GLIME J.M. (2014): Bryophyte photosynthesis in sunflecks: greater relative induction rate than in tracheophytes. Journal of Bryology, 36: 110–117.

HÁJEK T. (2014): Physiological Ecology of Peatland Bryophytes. In Hanson D.T. & Rice S.K. (Eds.): Photosynthesis in Bryophytes and Early Land Plants, Advances in Photosynthesis and Respiration 37: 233–252.

LUKEŠ M., PROCHÁZKOVÁ L., SHMIDT V., NEDBALOVÁ L. and KAFTAN D. (2014): Temperature dependence of photosynthesis and thylakoid lipid composition in the red snow alga Chlamydomonas cf. nivalis (Chlorophyceae). FEMS Microbiology Ecology 89: 303-315. doi: 10.1111/1574-6941.12299.

ŠANTRŮČEK J., VRÁBLOVÁ M., ŠIMKOVÁ M., HRONKOVÁ M., DRTINOVÁ M., KVĚTOŇ J., VRÁBL D., KUBÁSEK J., MACKOVÁ J., WIESNEROVÁ D., NEUWIRTHOVÁ J. and SCHREIBER L. (2014): Stomatal and pavement cell density linked to leaf internal CO2 concentration. Annals of Botany114: 191-202, 114: 191-202.

VOELKER S.L., BROOKS J.R., MEINZER F.C., RODEN J., PAZDUR A., PAWELCZYK S., HARTSOUGH P., SNYDER K., PLAVCOVÁ L. and ŠANTRŮČEK J. (2014): Isolating relative humidity: dual isotopes δ18O and δD as deuterium deviations from the global meteoric water line. Ecological Applications 24: 960-975.

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

TAZOE Y. and ŠANTRŮČEK J. (2014): Superimposed behavior of gm under ABA-induced stomata closing and low CO2. Plant, Cell and Environment, doi: 10.1111/pce.12437 2014.

THOMAS G., STÄRK H-J., WELLENREUTHER G., DICKINSON B.C., KÜPPER H. (2013): Effects of nanomolar copper on water plants - comparison of biochemical and biophysical mechanisms of deficiency and sublethal toxicity under environmentally relevant conditions. Aquatic toxicology 140-141, 27-36

LEITENMAJER B., KÜPPER H. (2013): Compartmentation and complexation of metals in hyperaccumulator plants. Frontiers in Plant Science, doi: 10.3389/fpls.2013.00374

KUBÁSEK J., URBAN O., ŠANTRŮČEK J. (2013): C4 plants use fluctuating light less efficiently than do C3 plants: a study of growth, photosynthesis and carbon isotope discrimination. Physiologia Plantarum 149: 528-539.

MACKOVÁ J., VAŠKOVÁ M., MACEK P., Hronková M., SCHREIBER L. and ŠANTRŮČEK J. (2013): Plant response to drought stress simulated by ABA application: changes in chemical composition of cuticular waxes. Environmental and Experimental Botany 86: 70-75.



SCHERZ A., SHLYK-KERNER O., SAMISH I., KAFTAN D. and DINAMARCA J. (2014): Photosynthetic organisms and compositions and methods of generating same. US 8629259.

KAFTAN D., LUKEŠ M. and NEDBALOVÁ L. (2012): The photosynthetic microorganism for production of phospahatidylglycerol and ways to increase the content of phosphatidylglycerol in the said photosynthetic microorganism. CZ2001-705.


Ph.D. theses:

KUBÁSEK J. (2014) Photosynthesis, production and growth of plants under temporal light hererogeneity.

VRÁBL D. (2013) Carbon dioxide transport within the leaf mesophyll: physico-chemical and biological aspects.

TOMŠÍČKOVÁ J. (2013) Fungicidal activity of cyanobacteria from the genus Nostoc.