Abstract

Soil microbiome composition and diversity are fundamental determinants of soil health and ecosystem functioning, yet the specific impacts of different organic amendments on microbial communities remain poorly understood. This study investigated the effects of various organic amendments on soil microbiome structure and health indicators across 42 agricultural sites over three years. Treatments included biochar (10 t ha⁻¹), compost (20 t ha⁻¹), vermicompost (15 t ha⁻¹), biosolids (25 t ha⁻¹), and unamended control plots. High-throughput 16S rRNA and ITS sequencing revealed significant increases in microbial diversity under all organic amendments, with compost treatment showing the highest Shannon diversity index (H' = 4.8±0.3) compared to control (H' = 3.2±0.4). Bacterial: fungal ratios shifted from 2.1:1 in control soils to 1.6:1 under biochar and 1.8:1 under compost treatments, indicating enhanced fungal networks. Beneficial microbial taxa increased substantially, with Rhizobium abundance increasing 340% under vermicompost and mycorrhizal fungi colonization reaching 65% under biochar compared to 28% in controls. Soil enzyme activities (β-glucosidase, phosphatase, dehydrogenase) increased by 45-85% under organic amendments, reflecting enhanced biochemical cycling. Soil health indicators including aggregate stability (85% vs 62% in controls), water holding capacity (+35%), and plant-available nutrients showed significant improvements. Network analysis revealed more complex and stable microbial communities under organic amendments, with increased keystone species and functional redundancy. Economic analysis demonstrated positive returns of $180-420 ha⁻¹ yr⁻¹ from improved soil health and reduced input requirements. These findings demonstrate that organic amendments fundamentally restructure soil microbiomes toward more diverse, stable, and functionally active communities that enhance overall soil health and agricultural sustainability.