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. •Three-decade forest-to-coffee conversion reduced SOC pools by 57–76%.•Coffee-shade tree intercropping significantly increased SOC pools by 20–76%.•Coffee-shade tree intercropping did not change the CH4 uptake.•Coffee plantation decreased the ambient CH4 uptake by 64–83% compared with forest.•Soil moisture and inorganic N were the controlling factors on ambient CH4 uptake.