Press "Enter" to skip to content
Global Change Research Institute, CAS

Department of Matters and Energy Fluxes


Keeping our finger on the pulse of ecosystems

We investigate basic physiological processes, such as photosynthesis, respiration and transpiration (loss of water vapour from plants) in various types of ecosystems. Our main goal is to reveal the effect of current climate changes on the ecosystems’ vitality and their capability to fix atmospheric carbon, and also to predict their future development. We monitor the mentioned processes continuously “online” from the level of individual trees up to the whole ecosystem. This way, we investigate not only the current status of trees or ecosystems but also the response of trees and ecosystems to changes in environmental conditions. Those include both regular weather fluctuation and impacts of the climate change, such as extreme temperatures, drought or, on the contrary, torrential rains, but also ecosystem disturbances (e.g. bark beetle outbreak).

The main method we use is so called eddy-covariance. That allows high-frequency measurements (20 times per second) of airflow (eddies) and monitored substances – greenhouse gases (CO2, water vapour, and in relevant ecosystems also CH4 and N2O). From these data, we calculate the exchange of these substances between the ecosystem and the atmosphere. The measurements are carried out continuously 24 hours per day and 365 days per year. We can therefore say with exaggeration that we “keep our finger on the pulse of the ecosystems”. Similarly, we measure a number of other important parameters (meteorological elements, biomass increment etc.). For supplementary measurements, we have developed our special systems – automatic chamber systems for monitoring CO2 or CH4 from soils, tree stems and wetland and grassland ecosystems.

Our research is realized within a frame of a net of ecosystem stations CzeCOS which includes fundamental ecosystem types of the Czech Republic (agricultural, forest, grassland and wetland ecosystems). Selected stations of the CzeCOS are also a part of the prestigious infrastructure of worldwide significance ICOS (Integrated Carbon Observation System). We are also one of the founding members and important co-authors of the unified measurement methodologies. This European research infrastructure reached also the prestige ERIC statute (European Research Infrastructure Consortium).

Global impacts of the climate change on ecosystems result in necessity of international collaboration. Therefore, we applied our experiences in the cooperation with local universities and institutes to establish ecosystem stations in Vietnam (agroecosystem – rice field) and Ghana (tropical forest). We share data from our stations with the whole scientific community on the basis of open access principles through freely accessible databases, e.g. FLUXNET, DEIMS-SDR.

Key words

Greenhouse gases, CO2, CH4, N2O, carbon cycle, primary production, photosynthesis, soil respiration, biomass respiration, ecosystem respiration, carbon, sequestration, eddy-covariance, chamber measurements, carbon flux models, climate change impacts.

Main activities of the department

  • Deeper understanding of the carbon dynamics in individual ecosystems and looking for ways to mitigate climate change due to increased capability of terrestrial ecosystem to fix and sequester atmospheric carbon in the biomass of plants, especially trees, under both current and future climatic conditions.
  • Investigation of the ecosystem water regime with the focus on forest ecosystems and their ability to resist drought stress.
  • Long-term precise monitoring of greenhouse gases and meteorological elements, which is the basis for analyses of climate change impacts on terrestrial ecosystems and on their production activity at different spatial scales.
  • Modeled estimations of future development of terrestrial ecosystems
  • Innovation of methods for monitoring of greenhouse gases and energy between ecosystems and the atmosphere

Selected publications

Kowalska, Natalia; Šigut, Ladislav; Stojanović, M.; Fischer, Milan; Kyselová, Ina; Pavelka, Marian: Analysis of floodplain forest sensitivity to drought (in printing). Philosophical Transactions of the Royal Society B 1(1): 1-1, Article number 1, 2020.

Dařenová, Eva; Čater, M.: Effect of spatial scale and harvest on heterogeneity of forest floor CO2 efflux in a sessile oak forest. Catena 188: Article number 104455, 2020

Acosta, Manuel; Dušek Jiří; Chamizo S.; Serrano-Ortiz P.; Pavelka Marian: Autumnal fluxes of CH4 and CO2 from Mediterranean reed wetland based on eddy covariance and chamber methods. Catena. 2019 (183) 104191.

Crabbe, Richard A.; Janouš, Dalibor; Dařenová, Eva; Pavelka, Marian: Exploring the potential of LANDSAT-8 for estimation of forest soil CO2 efflux. International Journal of Applied Earth Observation and Geoinformation. 2019, 77(May), 42-52. ISSN 0303-2434

Dařenová, Eva; Szatniewska, Justyna; Acosta, Manuel; Pavelka, Marian: Variability of stem CO2 efflux response to temperature over the diel period. Tree Physiology. 2019, 39(5), 877-887. ISSN 0829-318X

McGloin, Ryan; Šigut, Ladislav; Fischer, Milan; Foltýnová, Lenka; Chawla, Shilpy; Trnka, M., Pavelka, Marian; Marek, M. V.: Available Energy Partitioning During Drought at Two Norway Spruce Forests and a European Beech Forest in Central Europe. Journal of Geophysical Research: Atmospheres. 2019, 124(7), 3726-3742. ISSN 2169-897X

Acosta, Manuel; Dařenová, Eva; Foltýnová, Lenka; Pavelka, Marian: Seasonal and inter-annual variability of soil CO2 efflux in a Norway spruce forest over an eight-year study. Agricultural and Forest Meteorology. 2018, 256(jun), 93-103. ISSN 0168-1923

Dařenová, Eva; Acosta, Manuel; Pokorný, R., Pavelka, Marian: Variability in temperature dependence of stem CO2 efflux from Norway spruce trees. Tree Physiology. 2018, 38(9), 1333-1344. ISSN 0829-318X

Dušek, Jiří; Acosta, Manuel; Stellner, Stanislav; Šigut, Ladislav: Consumption of atmospheric methane by soil in a lowland broadleaf mixed forest. Plant, Soil and Environment. 2018, 64(8), 400-406. ISSN 1214-1178

Pavelka, Marian; Acosta, Manuel; Kiese, R., Altimir, N., Brümmer, C., Crill, P., Dařenová, Eva, Fuß, R., Gielen, B., Graf, A., Klemedtsson, L., Lohila, A., Longdoz, B., Lindroth, A., Nilsson, M., Maraňón Jiménez, S., Merbold, L., Montagnani, L., Peichl, M., Pihlatie, M., Pumpanen, J., Serrano Oritz, P., Silvennoinen, H., Skiba, U., Vestin, P., Weslien, P., Janouš, Dalibor, Kutsch, W. Standardisation of chamber technique for CO2, N2O and CH4 fluxes measurements from terrestrial ecosystems. International Agrophysics. 2018, 32(4), 569-587. ISSN 0236-8722

McGloin, Ryan; Šigut, Ladislav; Havránková, Kateřina; Dušek, Jiří; Pavelka, Marian; Sedlák, Pavel: Energy balance closure at a variety of ecosystems in Central Europe with contrasting topographies. Agricultural and Forest Meteorology. 2018, 248(jan), 418-431. ISSN 0168-1923

Acosta, Manuel; Juszczak, R., Chojnicki, B. H., Pavelka, Marian; Havránková, Kateřina; Leśny, J., Foltýnová, Lenka; Urbaniak, M., Macháčová, Kateřina, Olejnik, Janusz: CO2 Fluxes from Different Vegetation Communities on a Peatland Ecosystem. Wetlands. 2017, 37(3), 423-435. ISSN 0277-5212

Acosta, Manuel; Dařenová, Eva; Dušek, Jiří; Pavelka, Marian: Soil carbon dioxide fluxes in a mixed floodplain forest in the Czech Republic. European Journal of Soil Biology. 2017, 82(SEP), 35-42. ISSN 1164-5563

Dařenová, Eva; Holub, Petr, Foltýnová, Lenka; Pavelka, Marian: Effect of repeated spring drought and summer heavy rain on managed grassland biomass production and CO2 efflux. Journal of Plant Ecology. 2017, 10(3), 475-485. ISSN 1752-9921

Dušek, Jiří; Hudecová, S., Stellner, Stanislav: Extreme precipitation and long-term precipitation changes in a Central European sedge-grass marsh in the context of flood occurrence. Hydrological Sciences Journal. 2017, 62(11), 1796-1808. ISSN 0262-6667

Foltýnová, Lenka; Marková, I., Havránková, Kateřina; Pokorný, Radek, Urban, Otmar, Šigut, Ladislav; Pavelka, Marian; Cienciala, E., Marek, M. V.: Comparison of different approaches of radiation use efficiency of biomass formation estimation in Mountain Norway spruce. Trees: structure and function. 2017, 31(1), 325-337. ISSN 0931-1890