Compost-driven modulation of rhizosphere bacterial communities during red bell pepper development revealed by long-read 16S metabarcoding

Abstract Organic amendments, such as compost, are widely used to improve soil organic matter content, nutrient retention, and microbial activity; however, their effectiveness depends on multiple factors, including compost type, application rate, soil and crop characteristics, and mode of application. The spatial placement of compost can profoundly influence soil nutrient dynamics and the assembly of plant-beneficial microbial communities, such as microorganisms involved in nutrient cycling, organic matter decomposition, and plant growth promotion. Here, we investigated how two compost application strategies—surface broadcasting and deep banding of green-waste compost—affect soil physicochemical properties and the rhizosphere bacterial community of red bell pepper ( Capsicum annuum var. Fritz G740 ) across two developmental stages (maturation and ripening). To resolve microbial responses at high taxonomic resolution, we applied Oxford Nanopore long-read sequencing of the full-length 16S rRNA gene, enabling improved taxonomic assignments and more reliable functional predictions compared to short-read approaches. Deep banding resulted in significantly higher organic C, total N, and nitrate concentrations than surface broadcasting, particularly at the ripening stage. These changes were closely associated with pronounced shifts in rhizosphere bacterial community composition, with deep banding selectively enriching N-associated genera, including Azoarcus , Alcaligenes , and Ochrobactrum . Functional predictions further indicated an enhanced potential for N cycle-related pathways, such as nitrate reduction and nitrogen respiration. Overall, our results demonstrate that deep compost banding may enhances soil fertility while promoting a functionally enriched rhizosphere microbiome. By integrating temporal sampling with long-read amplicon sequencing, this study provides a comprehensive framework to evaluate how compost placement modulates soil–plant–microbe interactions in horticultural production systems.