Future climate change is predicted to have an important impact on regional precipitation patterns. Water level is an important factor influencing soil greenhouse gas emissions. However, the effect of small-scale water level fluctuations on soil greenhouse gas emissions from returning farmland to wetlands has been little studied. We collected soils of three lands from returning farmland to wetland with different restoration years and a natural wetland at the Honghe National Nature Reserve in Sanjiang Plain, China. Through indoor simulation experiments, we explored the characteristics of soil greenhouse gas (CO2, CH4, and N2O) emissions under fluctuating water levels. When the water level fluctuated between − 8 and 8 cm, the CO2 and N2O emissions decreased as the water level increased, but the CH4 emissions were highest when water level fluctuated between − 3 and 3 cm. The CH4 emissions tended to increase as laboratory time extended. Different gases react differently to water level fluctuations. The CO2 emissions contributed 78.90–96.48% of the total global warming potential of the GHG emissions. The results of this study indicate that during the process of returning farmland to wetland, more attention should be paid to the effects of CO2 emissions. An appropriately raised water level can effectively suppress the global warming potential of greenhouse gas emissions.

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