Seasonal dynamics of CO2, CH4 and N2O fluxes and evapotranspiration in an organically managed cropping system

Fluxes of carbon dioxide (CO₂), methane (CH₄) and nitrous oxide (N₂O) from croplands, as well as evapotranspiration (ET) are regulated by complex interactions among abiotic and biotic factors, which are strongly modified by environmental conditions, crop growth and management practices. This study investigated how CO₂, CH₄ and N₂O fluxes and ET developed during the cultivation of spring wheat and the subsequent cover crop (oil radish) in an organic farming field at the Wiesengut experimental farm of the University of Bonn, located in Rhein-Sieg district of Germany. Since March 2025, we continuously monitor net ecosystem CO₂ exchange and evapotranspiration using the eddy covariance technique. In parallel, we conducted weekly measurements of CO₂, CH₄ (starting in July 2025) and N₂O (since May 2025) fluxes using static chambers and laser-based CO₂/CH₄/H₂O and N₂O/H₂O analyzers and monitored soil mineral nitrogen.

Eddy covariance data showed sustained CO₂ uptake during the spring wheat growing season with mean NEE of -8.49 ± 0.62 µmol m^-2 s^-1during the mid-season (32-102 days after sowing). The harvest, incorporation of crop residues and manure application resulted in slightly positive NEE fluxes, which then fluctuated close to zero during the oil radish period in autumn and winter. ET fluxes were also associated with crop development, with largest fluxes measured in mid-June 2025.  Carbon dioxide fluxes measured with the chambers in the ripening stage of spring wheat, July 2025, indicated moderate soil and plant respiration, while after harvest and soil management operations CO₂ efflux increased and became more variable, reaching peak values of up to 12.34 ± 2.3 µmol m^-2 s^-1. Methane fluxes were predominantly negative throughout the study, indicating that the soil acted mainly as a methane sink. The strongest uptake occurred in the limited pre-harvest measurements, reaching -61.76 ± 7.7 µg CH₄ m^-2 h^-1. After harvest and soil disturbance, CH₄ uptake weakened, with fluxes approaching zero during late autumn. Nitrous oxide fluxes exhibited clear seasonal dynamics showed generally low emissions during most of the spring wheat growing season, fluctuating around zero. In contrast, strong and short-lived emission peaks occurred after harvest and subsequent management operations, with maximum fluxes reaching 66.47± 14.14 µg N₂O-N m^-2 h^-1. During the oil radish period, fluxes rapidly declined and remained mostly low, with only occasional episodic increases.

Our results demonstrate that greenhouse-gas and water dynamics in organic cropping systems vary strongly across crop and cover-crop phases and are tightly coupled to post-harvest management. These findings improve process-based understanding of GHG fluxes in organic rotations, including cover crops, and support the development of mitigation strategies for climate-smart agriculture.