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Allophane is a characteristic of Andisols whose presence can absorb soil organic matter. One of soil organic matter fractions called the “labile fraction” is currently an appropriate indicator in determining soil quality. However, there is limited information concerning the relationship between allophane and the labile fraction. This study assessed the content of allophane by selective dissolution methods and calculated the labile fraction of particulate organic matter and microbial activity related to the carbon (C) and nitrogen (N) soil cycles in organic and conventional vegetable farming systems of two depths (0–25 cm and 25–50 cm). The content of the labile fractions of C and N in organic farming systems is higher than in conventional farming systems, which is also higher in the upper layer compared to the lower layer. However, the availability of allophane in the upper layer and organic system tends to be low. Therefore, allophane has a strong negative correlation with the labile fractions of carbon and nitrogen. The results of this study estimate that phosphorus (P) sorption is higher in soils containing quite high allophane. Hence, an organic farming system that has low allophane content will result in higher P availability for plants.
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