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In this study, we investigated the effect of long-term integrated nutrient management (INM) involving chemical fertilizers and organic amendments viz. farmyard manure (FYM), green manure (GM), and paddy straw (PS) on the availability of micronutrients in soil, their uptake by plants, and crop yield for rice–wheat system. Soil availability of micronutrients and their plant tissue concentrations was estimated in grain and straw of both the crops. Soil recovery coefficient (SRC) and transfer coefficient (TC) were calculated to find out micronutrients availability in relation to their plant uptake and transfer of micronutrients from shoot to grain, respectively. Results revealed that integration of FYM proved significantly superior to GM and PS in improving organic carbon, micronutrients availability, and shoot to grain transfer (TC) of Fe (both the crops) and Mn (wheat). Low SRC values of Zn, Cu, Fe, and Mn indicated that long-term INM can meet their plant nutritional requirement in rice–wheat system. However, higher SRC values for B (0.49) in 100% NPK treatment as well as in the integrated ones (0.22–0.27 for rice, 0.23–0.28 for wheat) suggest that quantity of this element in soil was too low to meet plants nutritional needs which was also confirmed by its very low content in the soil (below critical levels, i.e., 0.5 mg kg−1). This study concludes that long-term integration of FYM (with NPK fertilizers) has an edge over GM and PS in regulating the supply of micronutrients in soil–plant system and correcting the micronutrient deficiencies (except B) in rice–wheat cropping system.

Rice-based cropping systems are the foundation of food security in countries of Southeast Asia, but productivity of such systems has declined with deterioration in soil quality. These systems are different from other arable systems because rice is grown under submergence, and this may require a different set of key soil attributes for maintenances of quality and productivity. A minimum dataset was screened for assessing quality of soils belonging to three Soil Orders (Inceptisols, Entisols and Alfisols) by using statistical and mathematical models and 27 physical, chemical and biological attributes. Surface soils were collected from farmers’ fields under long-term cultivation of rice–potato–sesame cropping systems. Most of the attributes varied significantly among the Soil Orders used. Four or five key attributes were screened for each Soil Order through principal component and discriminate analysis, and these explained nearly 80% and 90% of the total variation in each Soil Order dataset. The attributes were dehydrogenase activity (DHA), available K, cation exchange capacity (CEC) and pHCa for Inceptisols; organic C, pHCa, bulk density, nitrogen mineralisation (Nmin) and β-glucosidase for Entisols; and DHA, very labile C, Nmin and microbial biomass C for Alfisols. Representation of the screened attributes was validated against the equivalent rice yield of the studied system. Among the selected key soil attributes, DHA and CEC for Inceptisols, organic C for Entisols, and Nmin and very labile C for Alfisols were most strongly correlated with system yield (R2=0.45, 0.77 and 0.78). Results also showed that biological and chemical attributes were most sensitive for indicating the differences in soil quality and have a strong influence on system yield, whereas soil physical attributes largely varied but did not predict system yield.