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The scientific estimation of carbon budgets induced by land use and land cover change (LUCC) can improve the accuracy of carbon budget estimates for terrestrial ecosystems and deepen our understanding of the future carbon sink potential of these ecosystems. Previous studies have typically selected one of many LUCC-induced carbon budget methods and overlooked the differences in the results between the different methods. Taking Henan Province, China, as a case study, we used the IPCC method, the bookkeeping model, and the inventory method to estimate LUCC-induced carbon budgets and compared the differences in these methods. The results showed that LUCC in Henan Province was categorized as a carbon sink from 1980 to 2015 based on the IPCC method and the inventory method. However, the estimates were significantly different, and the total estimates of the IPCC method were 40% less than those of the inventory method. At the regional ecogeographical scale, the two methods were not consistent in assessing the carbon source/sink of LUCC. The bookkeeping model categorized LUCC as a carbon source in Henan Province for the same period, and the carbon storage change trend opposed those of the other two methods. The failure of the IPCC method and the bookkeeping model to include the dynamic changes in carbon density caused by climate and land use management led to the great differences between the three methods. The inventory method is recommended to estimate the carbon budget caused by LUCC for regions where carbon density varies greatly over time. Both the IPCC method and the bookkeeping model may have great uncertainty in estimating changes in LUCC-induced carbon stocks and should be used with caution.