To ensure the sustainability of crop production and ecosystem functioning, a thorough understanding of the mechanisms governing soil carbon (C) sequestration and soil health is essential. This study examined the effects of three nutrient management practices (organic, inorganic, and integrated) and two cropping systems (soybean-wheat and soybean-chickpea), on arbuscular mycorrhizal fungi (AMF) and soil C-sequestration in a long-term (12 years) field experiment. We measured the stocks of soil organic carbon, total glomalin-related soil protein, pertinent soil quality parameters such as microbial biomass carbon, and β-glucosidase activity along with AMF biomass [microscopic parameters and 16:1ω5cis phospholipid fatty acid (AM PLFA) and neutral lipid fatty acid (AM NLFA)]. It was observed that the measures of AMF biomass were positively correlated with the soil organic carbon stocks, total glomalin-related soil protein stocks, and soil quality parameters. Organic practice recorded significantly higher AMF spores, mycorrhizal colonization percentage, AM PLFA (2.58 nmol g-1 soil), AM NLFA (7.95 nmol g-1 soil), soil organic carbon stocks (15.78 Mg ha-1), total glomalin-related soil protein stocks (2.10 Mg ha-1), and soil quality parameters such as microbial biomass carbon, and β-glucosidase activity than inorganic and integrated practices. In comparison to soybean-chickpea, C-sequestration was higher in soybean-wheat. Principal component analysis validated the said results and differentiated soybean-wheat under organic practice from the rest of the treatments. In conclusion, our results suggest that organic management in conjunction with soybean-wheat crop rotation enhances AMF and can be recommended for improving soil quality and C sequestration without compromising crop yield.
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