Due to the increase in anthropogenic CO2 emissions in the atmosphere, the choice of technologies for mitigating climate change is becoming an important challenge for the agricultural sector. The investigation of two farming types, i.e. organic (OF) and conventional (CF), and their environmental impact on the carbon budget in ley (grass-clover) (G) and winter wheat (W) agroecosystems was carried out in 2014 - 2015 at the Training Farm of the Aleksandras Stulginskis University. For the estimation of carbon exchange, the closed chamber method with a portable measurement system was used. Compared with CF, OF reduced the mean soil respiration by 12% (p = 0.31) and 13% (p = 0.55); however, the total respiration Ra+s (autotrophs + soil) was reduced by only 2% and 15% in the ley and wheat agroecosystems, respectively. The strong positive correlation between soil respiration and temperature (r = 0.8, p = 0.25), moisture content (r = -0.7, p = 0.04), and electrical conductivity (r = 0.3, p = 0.47) confirmed the impact of soil physical properties on CO2 emissions from soil to the atmosphere. The CO2 sequestration potential of crops or gross primary production (GPP) also correlated with air temperature (r = 0.7), precipitation (r = -0.5) and leaf area index – LAI (r = 0.7). The amount of CO2 captured from the atmosphere was higher than that emitted during respiration in both the ley and wheat agroecosystems. The net ecosystem production (NEP) of 11.48 and 11.58 μmol m-2s-1 of the OF and CF ley was higher than the 8.93 and 9.42 μmol m-2s-1 of the OF and CF wheat, respectively. Given the Rs+a and CO2 sequestered in the biomass data, the difference between the carbon exchange for the OF and CF agroecosystems was insignificant. Therefore, the crop might be a more important CO2 sequestration factor than the farming type in planned rotation. Specifically, ley is preferred over winter wheat (irrespective of the farming system) for curbing the atmospheric C in biomass in terms of ecology. Nonetheless, the preference also depends on a farm’s practical purposes.
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