Natural farming as a sustainable agricultural approach enhances soil health and microbial diversity in wheat cultivation: a metagenomic perspective

Natural Farming System (NFS) is an eco-friendly agricultural approach that avoids chemical inputs and promotes sustainability by utilizing locally available on-farm resources. Farmers are increasingly adopting NFS, but its scientific validation remains limited due to inadequate comparative studies with the Conventional Farming System (CFS). This study compared nine NFS treatments with a CFS control in wheat cultivation to assess impacts on soil microbial diversity, nutrient status, enzyme activities, and yield. Different NFS treatments showed significant improvements in soil health, including higher organic carbon, available nitrogen, and potassium (up to 2.47-, 1.30-, and 1.54-fold, respectively) along with enhanced microbial enzyme activities (1.35 to 2.49-fold) compared to CFS. 16S rRNA amplicon metagenomics revealed richer microbial diversity in NFS, with enrichment of beneficial bacterial genera such as Microvirga , Gp6, and Rhizobium , while ITS data indicated higher abundance of Humicola , Amesia , and Chaetomium in NFS, suggesting improved nutrient cycling and organic matter decomposition. Co-occurrence networks in NFS showed more positive correlation (bacteria: 75.3% and fungi: 72.8%) than CFS (bacteria: 59.0% and fungi: 53.6%). Moreover, NFS achieved comparable yields (grain: up to 3807 kg/ha; straw: up to 6650 kg/ha) and Benefit-Cost Ratio (up to 4.0, under condition when farmer owns a cow) compared to CFS (grain: 4088 kg/ha; straw: 4451 kg/ha; BCR: 3.5). NFS treatments with groundnut haulm mulch (>5.0 t/ha) and Ghanjeevamrit (>1.0 t/ha) performed better, highlighting their potential as sustainable alternative for wheat cultivation. In contrast, under non-livestock scenarios, NFS was economically less favorable than CFS. Further long-term evaluation of NFS treatments across soil types and agroclimatic zones will strengthen and deepen the understanding of its effects on wheat cultivation.