Abstract

Natural farming systems have gained global recognition as sustainable alternatives to conventional agriculture, yet long-term empirical evidence on their effects on soil biological processes remains limited. This review synthesizes findings from long-term field experiments and observational studies examining the impacts of natural farming practices—including Zero Budget Natural Farming (ZBNF), cow-based formulations (Jeevamrut, Beejamrut), botanical extracts, and indigenous microbial consortia—on nutrient cycling dynamics and soil enzyme activities. The 42-year DOK trial in Switzerland demonstrates that organic management practices enrich functional genes involved in organic phosphorus acquisition, nitrate transformation, and organic matter degradation, fundamentally altering soil metabolic potential. Long-term studies from Vertisols in central India reveal that organic farming practices achieve the highest soil organic carbon concentrations while significantly enhancing enzymatic indices including dehydrogenase, urease, and phosphatase activities compared to conventional systems. Research from the 19-year pearl millet-wheat experiment at Hisar, India, shows that organic amendments produce microbial biomass carbon ranging from 202–491 mg/kg and dehydrogenase activity reaching 63.7 μg TPF/g/24h, with pressmud demonstrating superior impacts on soil microbial properties. The 10-year Danish trials on perennial cropping systems document that deep-rooted perennials enhance nutrient cycling through increased hydrolytic enzyme activity while suppressing oxidative enzymes, thereby stabilizing soil organic carbon. Biodynamic and organic soils consistently exhibit higher microbial counts and enzyme activities compared to conventional soils, with spent mushroom substrate amendments further amplifying these biological indicators. This review establishes that soil enzymes—dehydrogenase, urease, phosphatase, β-glucosidase, and catalase—serve as sensitive early indicators of soil health restoration under natural farming. The geometric mean of enzyme activities and biological activity index emerge as robust integrative metrics for assessing agroecosystem sustainability. Long-term natural farming systems demonstrate enhanced nutrient cycling efficiency, improved soil microbial biomass, and greater soil resilience despite occasionally lower available nutrient concentrations compared to conventional systems. These findings have profound implications for global agroecological transitions, carbon sequestration strategies, and climate-resilient agriculture. Future research priorities include standardizing enzyme assay protocols, establishing baseline values across agroecological zones, and integrating enzyme indicators into soil health monitoring frameworks.