The coupling of the Earth's surface and the overlying atmosphere through mass and energy fluxes has an important role in atmospheric chemistry and physics in addition to boundary layer meteorology and ecosystem research. We aim to increase the fundamental understanding of physical and chemical land surface processes and interactions and atmosphere–biosphere–hydrosphere coupling for different ecosystems and surfaces. We apply the gained information for practical applications and purposes. Ecosystems can act as sources or sinks of several trace gases and biogenic volatile organic compounds. All these gases play an important role in climate change. We focus on studying effects of climate change and land use change on the biogeochemical cycles and on dynamics of gases important in the atmosphere. The conducted research spans various scales from molecules to ecosystems to landscape.