Three decades of shade trees improve soil organic carbon pools but not methane uptake in coffee systems

The rapid expansion of coffee plantations in tropical area at the cost of natural forest may suppress the methane (CH₄) uptake and change the soil fertility. However, observations on soil CH₄ uptake rates and the ecological consequence studies on coffee-based plantations are sparse. The objectives of this study were to characterize the dynamics of CH₄ uptake among natural forest, coffee monoculture (CM), and coffee intercropping with shade tree (CI), and to evaluate the key drivers of soil CH₄ uptake. Results showed that the conversion of forest into 25-year and 34-year CM plantations significantly reduced the soil organic carbon (SOC) content by 57% and 76%, respectively, whereas CI plantation profoundly increased the SOC by 20%-76% compared with CM plantation. Although soils of forest, CM and CI functioned exclusively as CH₄ sinks, the CM and CI plantations significantly decreased the ambient CH₄ uptake rates by 64%-83% due to soil moisture shift and soil nitrate availability by using chemical fertilizer. Interestingly, the potential CH₄ uptake of CM and CI plantations did not decrease and in some treatments, was even higher than that of the natural forest. Potential CH₄ uptake showed a negative correlation with soil pH and SOC content, but a positive correlation with soil available phosphorus (AP). Collectively, although the SOC and soil pH were increased through intercropping with shade trees for decades, the inhibition of atmospheric CH₄ uptake was still difficult to alleviate.