II. Domain of Ecosystems Analysis

The Domain of Ecosystem Analyses receives, gathers and analyses information on carbon fluxes, sequestration and storage at various hierarchical levels (from molecules to landscape) primarily at the level of terrestrial ecosystems. Furthermore, it studies the impact of global climate change on particular ecosystems, such as forests and small catchment basins, as well as on selected animal communities.

The domain’s main objectives are as follow:

a) long-term monitoring of greenhouse gas fluxes and meteorological parameters, conversion of quantitative and dynamic data to country-wide scale, and model estimation of their future development; proposals for measures to enhance ecosystems’ abilities to capture CO2 from the atmosphere and to deposit carbon over the long term;

b) development of synchronization methods for aerial data imaging using passive imaging spectroscopy and active LiDAR scanning and their evaluation in order to obtain spectral–spatial characteristics of vegetation and ecosystems for generating maps of biochemical and biophysical parameters of vegetation as well as detecting stress in plants caused by various natural and anthropogenic factors; and

c) evaluation and modelling of changes in the hydrological cycle of forest catchment basins, biogeochemistry of nitrogen in the forest ecosystem, forms and export of dissolved organic and inorganic carbon, and the amount of base cations in forest soils and waters as influenced by expected global climate and forest management changes; proposals for measures to reduce the negative impacts of global climate change on the hydrological and biogeochemical cycles of forest catchment basins;

d) assessment of the impact of global climate change mainly on the population dynamics of insect pests, their natural enemies as well as population dynamics of certain rare species; analysis of the significance of bio-corridors in facilitating species migration and their survival under global climate change; proposals for biodiversity conservation measures.

Mgr. Marian Pavelka, Ph.D
Tel.: +420 511192255

Bělidla 986/4a 60300 Brno

It includes the following:
Department of Matters and Energy Fluxes
Department of Remote Sensing
Department of Biogeochemical and Hydrological Cycles
Department of Biodiversity Research

Department of Matters and Energy Fluxes

Pavelka Marian, Mgr., Ph.D. - head

Scientists :
Acosta Manuel, Ph.D.
Dařenová Eva, Mgr., Ph.D.
Dušek Jiří, MSc., Ph.D.
Fischer Milan, Ing., Ph.D.
Foltýnová Lenka, Mgr., Ph.D.
Holata Filip, Ing.
Jocher Georg, Dr.
Kowalska Natalia, MSc., Ph.D.
Květ Jan, RNDr., CSc.
Montagová Hana, Mgr.
Olejnik Janusz, Prof.
Sedlák Pavel, RNDr., CSc.
Šigut Ladislav, Ph.D.
Vágner Lukáš, Ing.

Ph.D. students :
Guerra Torres Carlos, MSc.
Kyselová Ina, Mgr.
Mensah Caleb, MSc.
Nguyen Vinh , MSc.

Others :
Czerný Radek, Mgr.
Stellner Stanislav
Trusina Jan, Mgr.


The Earth’s ecosystems are today strongly influenced by ongoing global climate change. This change is related to the increasing atmospheric concentrations of greenhouse gases (especially CO2, N2O, CH4). The basis of our research is to achieve a deeper understanding of the carbon cycle in the environment, its sources, destiny and sinks, and to find opportunities for mitigating global climate change through increased ability of terrestrial ecosystems to capture atmospheric carbon (mainly in the form of CO2).

The basic methods consist of precise long-term monitoring of fluxes in greenhouse gases and meteorological parameters at the level of specific ecosystems. The impact of greenhouse gases on the production activity of selected ecosystems is analysed. Quantitative and dynamic data is converted to a country-wide scale and model estimation of their future development is created.

The section’s main objectives are to:

a) describe and quantify the substances and energy fluxes in different types of ecosystems;

b) evaluate the ability of ecosystems to capture and deposit atmospheric carbon, both under current conditions as well as under the conditions of expected global climate change;

c) evaluate the environmental burden at the level of mechanisms of substance and energy fluxes between ecosystems and the atmosphere;

d) conduct modelling to estimate future development of ecosystems in the Czech Republic;

e) develop new methodologies for measures to enhance the ability of ecosystems to capture CO2 from the atmosphere and deposit carbon over the long term.

To fulfil these objectives, a network of ecosystem stations covering selected types of ecosystems (spruce mountain forest, mountain meadow, beech forest, spruce forest of medium altitudes, agroecosystem, wetland, floodplain forest) is used. Ecosystem stations are equipped with systems measuring substance and energy fluxes (using eddy covariance method), water balance, respiratory losses of CO2, and micrometeorological phenomena, as well as the systems conducting  phenological monitoring. A detailed inventory of biomass is carried out periodically.

Selected ecosystem stations are part of the international project ICOS (www.icos-infrastructure.eu).

Department of Remote Sensing

Homolová Lucie, Ing., M.Sc., Ph.D. - head

Scientists :
Brovkina Olga, Ing., CSc.
Janoutová Růžena, Ing., Ph.D.
Lukeš Petr, Ing., Ph.D.
Novotný Jan, M.Sc., Ph.D.
Pikl Miroslav, Ing.
Raj Rahul, Dr.
Zemek František, Assoc., prof., Ph.D.

Ph.D. students :
Loayza Fernandez Rolling Richard, Ing.
Švik Marian, Mgr.

Others :
Navrátilová Barbora, Ing.


The Department of Remote Sensing is incorporated into the Domain of Ecosystems Analyses and has been developing its current focus since 2006. The department is focused on the evaluation of selected types of ecosystems at different spatial and temporal scales. In addressing its research objectives the department uses satellite data in combination with hyperspectral and thermal sensor data acquired with its own airborne platform. Special emphasis is placed on developing methods to quantitatively assess biochemical parameters of vegetation (e.g. forest stands, agricultural crops, etc.) based on these data.

A new challenge associated with the development of CzechGlobe infrastructure is incorporation of airborne hyperspectral, LiDAR and thermal data into physically based radiative transfer (RT) models. This data synergy will enable us to address new and more complex tasks.

Key objectives of the research:

  • Using LiDAR data to determine ecosystem structural parameters (e.g. tree crown shape, height) as input to RT models
  • Elucidating the relationships between biochemical properties of plants, their structural features and water and thermal performance
  • Linking and upscalling information on physiological functioning of individual trees with that obtained from air/space borne data
  • Investigating the thermal regime of landscapes and urban heat islands

Department of Biogeochemical and Hydrological Cycles

Hruška Jakub, Prof., RNDr., CSc. - head

Scientists :
Bohdálková Leona, Mgr., Ph.D.
Chuman Tomáš, RNDr., Ph.D.
Hofmeister Jeňýk, RNDr., Ph.D.
Krám Pavel, RNDr., Ph.D.
Lamačová Anna, Mgr., Ph.D.
Moldan Filip, RNDr., Ph.D.
Oulehle Filip, Ph.D.

Ph.D. students :
Zamazalová Kateřina, Mgr.

Others :
Čuřík Jan, Mgr.
Glovinová Eliška, Ing., Ph.D.
Myška Oldřich, Ing.
Novotná Zlata


A variety of direct and indirect influences on climate, soil, water and forests may be encountered in Central Europe. They are evident in changes in biogeochemical cycles of ecologically significant elements. These changes in turn affect individual components of ecosystems and often act through very complicated mechanisms and pathways. Knowledge of individual cycles and their interconnection and mutual influence is essential for a proper understanding of how ecosystems function and how they respond to climate change in combination with such other factors as forestry management and acidification. Only by better understanding these phenomena can we deduce their future development and make appropriate decisions in carrying out such important activities as managing forests, soils and waters.

The department’s main objectives are to:

a) assess changes in the hydrological cycle of forest catchments under various GCC scenarios;

b) study the impacts of GCC on the nitrogen cycle (its leaching, fixation in soils, availability, and direct losses back into the atmosphere);

c) analyse the impacts of GCC and other anthropogenic influences (changes in atmospheric deposition) on the concentration, form and export of dissolved organic and inorganic carbon from ecosystems;

d) study the impacts of GCC and other anthropogenic influences on sufficiency or insufficiency of base cations in forest soils;

e) evaluate in terms of the chemistry of forest soils the phenomenon of intentions to eliminate GCC’s influence by utilization of post-logging residues for energy purposes; and

f) carry out modelling to forecast developments in the hydrology of water and soil chemistry to 2100 under various scenarios of GCC development.

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

a) ion-exchange liquid chromatograph for determination of anions and cations in waters and extracts;

b) automatic titrator for determining pH, alkalinity and acid–base characteristics of dissolved organic carbon in waters;

c) UV/VIS spectrophotometer for measuring the spectra of dissolved organic carbon and determining the concentrations of ammonia, dissolved phosphorous and aluminium fractions;

d) mercury analyser for measuring Hg concentrations in waters and soils;

e) limnigraphs with a device for remote transmission of data to improve hydrological measurements of flow rates in river basins;

f) rain gauges and lysimeters to retrofit basins for extractions of deposition and soil waters;

g) elemental analyser of C, N, and H to determine the total content in biomass and soils;

h) analyser of dissolved organic carbon and nitrogen in waters;

i) automatic portable field measurement system for CO2 emissions to quantify fluxes of gaseous CO2 from soils for the measurement of carbon emissions on a limed and reference area; and

j) computers, statistical software, the MAGIC biogeochemical model, and ArcView GIS software

Department of Biodiversity Research

Kindlmann Pavel, Prof., RNDr., DrSc. - head

Scientists :
Bílá Karolína, Ph.D.
Dixon Anthony, Prof., Ph.D., dr.h.c.
Kolanowska Marta, MSc., Ph.D.
Křenová Zdenka, Dr.
Rokaya Maan, Mgr., Ph.D.
Sivila Wojtasiak Susanne, MSc.
Traxmandlová Iva, RNDr., Ph.D.
Tsiftsis Spyros, Dr.

Ph.D. students :
Rokaya Binu, Mgr.
Shrestha Bikram, MSc.
Štípková Zuzana, Mgr.

Others :
Atexingerová Lenka


The task of the Department of Biodiversity Research is to perform basic research in fields including evolution ecology (in particular the evolution of life strategies), population dynamics (especially predator–prey and plant–pollinator systems), and stability of ecological communities using theoretical, experimental and field approaches, particularly in the context of current climate changes, and to pass on such knowledge through teaching and publications. The results of this research will be applied in the protection of biodiversity, nature conservation, and biological control of pests. At present, the main model groups are terrestrial orchids, aphids, aphidophagous insects and large mammals. Besides the Czech Republic, the department conducts field research also in France, Nepal, Bolivia and Papua New Guinea.

The department’s main objectives are to:

a) study the impact of GCC on population dynamics of insect pests of agricultural crops (mainly aphids) and their predators (e.g. such model groups as ladybugs and ground beetles) while applying different scenarios of landscape use, GCC, and intensification of agricultural activities in the landscape;

b) evaluate the impact of GCC on ecosystem functions, particularly at the level of relations between an insect pest and its natural enemy under various schemes of agroecosystem management;

c) analyse the impact of changes in temperature (possible consequence of GCC) on the population dynamics of some rare species;

d) evaluate the importance of bio-corridors in facilitating species migration necessary for their survival under GCC and their importance as shelters and overwintering sites for the monitored organisms;

e) evaluate the dependence of changes in biodiversity (especially species loss) and ecosystem services caused by the effects of GCC on landscape connectivity; and

f) analyse changes in basic laws governing the dynamics of ecosystems and the interactions between species with changing temperature.