III. Domain of Environmental Effects on Terrestrial Ecosystems

The activities of this domain focus on the study and assessment of the effects of environmental factors (primarily increased CO2 concentration, temperature, water availability, spectral composition of solar radiation, and modification in mineral nutrition) and their mutual interactions on metabolism, physiology, and production processes in plants at various hierarchical levels (ecosystem, plant, tissue) comprise a key condition for more accurately forecasting the impacts of global change on terrestrial ecosystems and formulating proposals for appropriate measures to mitigate these impacts.

The domain’s main objectives are as follow:

a) clarification of adaptive and regulatory mechanisms associated with the effects of global climate change (especially with increased concentrations of greenhouse gases, rise in temperature, drought, and changes in the spectral composition of radiation) on physiology, metabolism, and production processes in plants and development of methods for early diagnosis of the effects of stress factors; and

b) innovation in the methodological approach consists in the description of changes in the metabolic profile of plants when exposed to environmental stresses and in finding functional connections between the metabolic profile of plants and their physiological and/or phenological properties; identification of the main metabolic pathways in plants involved in plants’ physiological adaptation and in the functional stability of ecosystems under the effects of global change.

Ing. Karel Klem, PhD.

Bělidla 986/4a, 603 00 Brno

It includes:
Laboratory of Ecological Plant Physiology
Laboratory of Metabolomics and Isotope Analyses
Department of Xylogenesis and Biomass Allocation
Department of Ecosystem Trace Gas Exchange

Laboratory of Ecological Plant Physiology

Urban Otmar, Assoc., prof., Dr., Ph.D. - head

Scientists :
Ač Alexander, Mgr., Ph.D.
Calfapietra Carlo, Dr.
Gargallo Garriga Albert, Dr.
Grace John, prof.
Holub Petr, Mgr., Ph.D.
Jansen Marcel, prof., Ph.D.
Juráň Stanislav, Ing., Ph.D.
Karlický Václav, Mgr., Ph.D.
Klem Karel, Ing., Ph.D.
Kováč Daniel, MSc., Ph.D.
Kurasová Irena, Mgr., Ph.D.
Mishra Anamika, Mgr., Ph.D.
Mishra Kumud, Dr., PhD
Šprtová Mirka, Mgr., Ph.D.
Špunda Vladimír, doc., RNDr., CSc.
Štroch Michal, Mgr., Ph.D.
Večeřová Kristýna, Mgr., Ph.D.
Veselá Barbora, Mgr.
Vítek Petr, Mgr., Ph.D.
Záhora Jaroslav, Ing., CSc.

Others :
Hodaňová Petra, Ing., et Ing.
Novotná Kateřina, Ing.
Pernicová Natálie, Bc.
Pozhidaeva Daria
Rajsner Lukáš
Roshka Inna
Vavříková Jana, Ing.

Ph.D. students :


The Laboratory of Ecological Plant Physiology is engaged in the study of selected physiological processes of plants across a broad time range (activation of physiological processes in seconds to processes in biomass production over the course of years) and spatial scale (enzyme activities to substance fluxes in ecosystems). Special emphasis is given to studying the ecophysiology of photosynthesis. These processes are studied with emphasis on the productive activity of plants exposed to modified growth conditions according to projected climate change scenarios.

The laboratory’s main objectives include to:

a) use top-down analysis of substance and energy fluxes in various types of ecosystems based on detailed analysis of the vertical profile of physiological stand properties in steady and dynamic growth environments;

b) understand the impacts of global change on plant physiology and production processes on the plant–ecosystem scale, especially based on multi-factorial impact experiments;

c) understand the adaptive and regulatory mechanisms associated with global change impacts, including to identify species and genotype variation in terms of adaptive capacity;

d) in collaboration with the Laboratory of Metabolomics, to monitor changes in the content of primary and secondary metabolites in plants that may be important for changes in qualitative production parameters (amino acids, simple sugars, essential fatty acids), which may influence change in resistance to fungal diseases and pests (phenolics , phytoalexins, jasmonates), or may perform regulatory and signalling functions in plants (plant hormones, ergosterol, AOS); and

e) develop optical diagnostic methods intended for the diagnosis of stress effects through evaluation of physiological processes based on the selection of sensitive excitation–emission fluorescence spectra, sensitive bands, and spectral reflectance indices in the UV/VIS/NIR ranges and to utilize FTIR and Raman spectroscopy.

To fulfil these objectives, the following infrastructure is used:

a) portable gasometric systems for determining the rate of assimilation/dissimilation of CO2 and transpiration rate, or, more precisely, stomatal conductance, at the level of individual leaves (annual shoots);

b) fluorometers (integration and imaging) for detecting the fluorescence signal of chlorophyll a, which allows rapid monitoring of damage or change in the functional condition of plants;

c) spectrophotometers for determining the content of pigments, enzyme activity, and concentrations of selected metabolites in the studied plants and for determining spectral reflectance curves and transmittance at leaf and stand levels; and

d) FTIR and Raman imaging spectrometer for evaluating changes in the areal distribution of metabolites at leaf level and for metabolic fingerprinting.

Laboratory of Metabolomics and Isotope Analyses

Tříska Jan, Prof., Ing., CSc. - head

Scientists :
Kozáčiková Michaela, Ing.
Oravec Michal, Mgr., Ph.D.
Svobodová Kateřina, Mgr.
Vrchotová Naděžda, RNDr., CSc.

Ph.D. students :
Sendecká Katarína, Ing.

Others :
Bednář Jan
Vilímková Olga, Ing.


The biochemical profile of plants, which is studied within the filed of metabolomics, is the result of interaction between genotype, environment and regulatory mechanisms, and thus it creates a unique biochemical “fingerprint” of the growth environment in plants. Environmental metabolomics comprise a relatively new research direction which allows us, for example, to identify the effect of environmental stress on plants and/or whole ecosystems and to understand the internal (molecular) mechanisms for how plants respond to external stimuli (response), how they adapt to changes in growth conditions (adaptability, plasticity), and how functional stability (robustness) is formed in plants.

The laboratory’s main objectives are:

a) using chromatographic techniques in conjunction with mass spectrometry, to comprehensively analyse, identify and quantify metabolites in plants and soils (rhizosphere) in order to describe the overall metabolomes of selected plants and the rhizosphere (broad-spectrum screening of metabolic profile);

b) to describe changes in the metabolic profile of plants when exposed to environmental stresses;

c) to find functional links between the metabolic profile of plants and their physiological (e.g. photosynthesis) and phenological (e.g. growth) properties;

d) to detect stable isotopes ratios in the soil–plant–atmosphere system and in individual selected metabolites; and

e) to identify the main metabolic pathways involved in the physiological adaptation of plants to the effects of global change and the formation of their functional stability.

To fulfil these objectives, the following key instrumentation will be used:

a) high-pressure liquid chromatography with mass spectrometry (HPLC–MS) for broad-spectrum screening of metabolites (non-target analyses) and analysis of selected metabolite groups (target analysis);

b) gas chromatography with mass spectrometry (GC–MS) for the detection of volatile and easily derived metabolites, complemented with a thermogravimetric analyser to study the dynamics of the carbon cycle in soils; and

c) isotope-ratio mass spectrometry (irMS) coupled with gas and liquid chromatography for the detection of stable isotope ratios (13C/12C, 15N/14N, 34S/32S, D/H, 18O/16O) in gaseous and solid samples of the soil–plant–atmosphere system and isotope ratios in individual selected metabolites.

Department of Xylogenesis and Biomass Allocation

Horáček Petr, Prof., Dr., Ing. - head

Scientists :
Bellan Michal, Ing.
Krejza Jan, Ing., Ph.D.
Nezval Ondřej, Mgr.
Noyer Estelle, M.Sc, Ph.D
Stojanović Marko, M.Sc., Ph.D.
Světlík Jan, Ing., Ph.D.

Ph.D. students :
Fajstavr Marek, Ing.
Uchytilová Tereza, Ing.

Others :
Benc Martin, Ing.
Šlížek Jiří


The department’s research activities proceed in two basic directions: i) study of water regime and ii) study of the process of creating and allocating biomass in forest ecosystems. The water regime is quantified by the classical water balance – namely, the amount of precipitation input and the output in the form of runoff and evapotranspiration. Evapotranspiration is determined both by measuring microclimatic parameters in the vertical profile of the stand canopy and from analysis of turbulent fluxes between the stand and the adjacent layer of the atmosphere. Transpiration is quantified at the level of individual plants using so-called “thermal” methods. The phenology of stand units is studied using imaging cameras, and the production of biomass is estimated using automatic dendrometers and through application of special allometric equations. Stand structure is observed using remote sensing methods – LiDar.

The department’s two basic research directions are primarily associated with the active physiological processes of photosynthesis, respiration and transpiration, which are controlled by environmental parameters. Therefore, the modified influence of these parameters (e.g. due to drought or increased temperature) or simulation of other stressful conditions (e.g. reduced availability of nitrogen in the soil, increased air concentration of CO2 or O3 in the atmosphere, and increased input of UV-B radiation) affecting the water regime and biomass production also are examined. In pursuing its research activities, the department cooperates with research domains II to V.

The department’s main objectives are to:

a) describe and quantify the energy balance of selected stands of a given structure;

b) describe and quantify the carbon balance of selected stands of a given structure;

c) identify temporally and spatially the stand’s productive activity, depending on the effect of environmental factors;

d) model the development of an ecosystem with respect to climate change; and

e) develop new methods or instrumentation primarily applicable in forestry practice.

Department of Ecosystem Trace Gas Exchange

Macháčová Kateřina, Dr., rer.nat., Mgr. - head

Scientists :
Hrdlička Jan, Ing., MSc.
Schindler Thomas, M.Sc.

Ph.D. students :
Agyei Thomas, MSc.
Ofori-Amanfo Kojo Kwakye, MSc.

Others :
Borák Libor, RNDr., Mgr., Ph.D.


The Department of Ecosystem Trace Gas Exchange is engaged in the research of fluxes of methane (CH4), nitrous oxide (N2O), and to a lesser extent also carbon dioxide (CO2), from various tree species, soils and ecosystems. CH4, N2O and CO2 are major greenhouse gases contributing to the global climate change. In addition to the soil, CH4 and N2O can also be emitted by the surface of the plants. However, data on emissions of these gases from trees are more than insufficient. The long-term goal of the Department is to quantify CH4 and N2O fluxes from adult trees of different species and to clarify their dynamics and mechanisms. We managed to identify boreal forests trees (pine, spruce, birch) as missing CH4 and N2O resources in ecosystem greenhouse gas exchange and point out their surprising seasonal dynamics. Furthermore, we have proved that trees (beech trees) can be both emitters and also N2O sinks from the atmosphere. An interdisciplinary approach linking plant physiology with soil biology and atmospheric sciences enables us to study this issue in detail. The results of the research will be crucial for estimating the future CH4 and N2O fluxes in European forests and thus for the inventory of greenhouse gas fluxes. Studying the impact of environmental parameters on the fluxes of these gases will contribute to the prediction of global change.

Main objectives of the department:

a) characterization and quantification of CH4 and N2O fluxes from adult woody plants of various species and from soil in different types of ecosystems (forest ecosystems mainly temperate and boreal zones, wetlands, agricultural land)

b) studies of species and spatial variability and the seasonal and daily dynamics of these fluxes

c) studies of the impact of environmental parameters (e.g. humidity and temperature of soil and air, PAR, UV, elevated CO2 concentration) on CH4 and N2O exchange in the soil-tree-atmosphere continuum and understanding the relations between greenhouse gas fluxes from trees and physiological activity of trees

d) research on the origin of CH4 and N2O emitted by trees

e) parameterization of models of transport of these substances in the soil-plant-atmosphere system

f) clarification of the role of photo-autotrophic organisms associated with woody plants (algae, lichens, mosses) in the CH4 and N2O cycle

g) clarification of the role of woody species in the overall exchange of CH4 and N2O within forest ecosystems

h) measurement of fluxes of nitrogen gases in the agricultural land-vegetation-atmosphere continuum

Long-term goals of the department:

a) identification of missing sources and sinks for the above mentioned gases in the greenhouse gases balance in forest ecosystems

b) finding common characteristics of CH4 and N2O fluxes for individual tree species groups (e.g. upland vs. wetland tree species, deciduous trees vs. conifers) in a wider geographic and climatic gradient

To meet these objectives the following infrastructure is used:

a) ecosystem stations in the Czech Republic and abroad (extensive cooperation with foreign research centers)

b) static chamber systems (soil, stem, leaf) for measuring the fluxes of gases from individual components of the ecosystem

c) gas chromatograph and portable FTIR analyzers (Fourier Infrared Transformation Principle) to determine the concentrations of the studied gases

d) various supporting systems and instruments for measurements, laboratory facilities for incubation experiments, etc.