16S Long-Read Metabarcoding in Field Conditions Uncovers Compost-Driven Modulation of Rhizosphere Bacterial Communities During Red Bell Pepper Development

Abstract Organic amendments are a sustainable alternative to mineral fertilizers, but their effectiveness depends strongly on the mode of application. The spatial placement of compost can shape soil nutrient dynamics and the assembly of beneficial microbial communities. Here, we investigated how two strategies—surface broadcasting versus deep banding of green-waste compost—affect soil physicochemical properties and the rhizosphere bacterial community of red bell pepper ( Capsicum annuum L.) across two developmental stages (maturation and ripening). To capture these dynamics with high resolution, we applied Nanopore long-read sequencing of the full-length 16S rRNA gene, enabling precise taxonomic assignments and improved functional predictions compared to short-read approaches.Deep banding consistently outperformed surface broadcasting, significantly improving organic carbon, total nitrogen, and nitrate content, particularly at ripening. These soil changes were tightly linked to shifts in rhizosphere microbiota, with deep banding inducing a distinct community composition and selectively enriching nitrogen-associated genera such as Azoarcus , Alcaligenes , and Ochrobactrum . Functional predictions revealed an enhanced potential for nitrogen cycling pathways, including nitrate reduction and nitrogen respiration.Our findings demonstrate that deep compost banding not only enhances soil fertility but also engineers a functionally enriched rhizosphere. By integrating temporal sampling with long-read sequencing, this study provides a novel framework to assess how compost placement influences soil–plant–microbe interactions, offering a promising strategy for sustainable crop production.