Impact of integrated nutrient management on soil microbiome diversity and health in rice based cropping system: Insights from long-term agricultural practices

Abstract

The rhizosphere soil microbiomes, which are essential for plant development, stress adaptability, and general soil health, are greatly impacted by agricultural management practices, particularly those involving nutrient applications. This study evaluated the long-term effects of nutrient management practices on soil physicochemical properties, microbial communities, enzyme activities, and biological soil health in a rice-lentil-jute cropping system. The treatments included a control, inorganic fertilizers (recommended dose of fertilizers), and Soil Test Crop Response based integrated nutrient management (combination of inorganic fertilizer based on soil test-based fertilizer prescription equations, farmyard manure (FYM), and bioinoculants). When compared to both control and inorganic treatments, integrated nutrient management (INM) enhanced soil organic carbon, available nitrogen, phosphorus, and potassium. Microbial populations, comprising of bacteria, actinomycetes, fungi, Azotobacter, and phosphate-solubilizing microorganisms, along with soil enzymatic activities, showed marked increases under INM. Metagenomic analysis of the hypervariable V3-V4 region of 16S rRNA indicated that the bacterial community in the rice-lentil-jute cropping sequence was dominated by Proteobacteria, with 58 phyla having over 1% abundance. The INM treatment increased the Shannon diversity index by 12.6% compared to the control, reflecting improved microbial diversity, richness, and resilience, which are critical for enhancing crop productivity and stress tolerance. The Biological Soil Health Index (BSHI) was highest in the INM treatment, with average contributions from Azotobacter (22.7%), Bacteroidota (12.1%), Actinobacteriota (21.9%), very labile organic carbon (23.1%), and labile organic carbon (20.2%) to BSHI. In summary, ten years of INM enhanced soil health and bacterial community structure and composition, leading to sustainable crop yields in rice-based cropping system. These findings highlight the necessity of integrating balanced nutrient management in long-term agricultural practices.