Soil C sequestration in croplands is deemed to be one of the most promising greenhouse gas mitigation options for agriculture. We have used crop-level yields, modeled heterotrophic respiration (Rh) and land use data to estimate spatio-temporal changes in regional scale net primary productivity (NPP), plant C inputs, and net biome productivity (NBP) in northern Japan's arable croplands and grasslands for the period of 1959–2011. We compared the changes in C stocks derived from estimated NBP and using repeated inventory datasets for each individual land use type from 2005 to 2011. For the entire study region of 2193ha, overall annual plant C inputs to the soil constituted 37% of total region NPP. Plant C inputs in upland areas (excluding bush/fallow) could be predicted by climate variables. Overall NBP for all land use types increased from −1.26MgCha−1yr−1 in 1959–0.26MgCha−1yr−1 in 2011. However, upland and paddy fields showed a decreased in NBP over the period of 1959–2011, under the current C input scenario. From 1988, an increase in agricultural abandonment (bush/fallow) and grassland cover caused a slow increase in the regional C pools. The comparison of carbon budgets using the NBP estimation method and the soil inventory method indicated no significant difference between the two methods. Our results showed C loss in upland crops, paddy fields and sites that underwent land use change from paddy field to upland sites. We also show C gain in grassland from 2005 to 2011. An underestimation of NBP or an overestimation of repeated C inventories cannot be excluded, but either method may be suitable for tracking absolute changes in soil C, considering the uncertainty associated with these methods.
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