Significant decline in banana Fusarium wilt disease is associated with soil microbiome reconstruction under chilli pepper-banana rotation

Abstract Fusarium wilt disease of banana crops is of great economic concern because banana is the fifth most important consumed agricultural product in global trade. Crop rotation management is often used to suppress soil-borne diseases. However, little is known about the mechanisms that govern soil disease depression. A 2-year field experiment was conducted to evaluate the effects of chilli pepper-banana rotation on the suppression of banana Fusarium wilt disease. The chilli pepper-banana rotation system effectively reduced the incidence of banana wilt disease relative to that under the banana monoculture system. The abundance of Fusarium oxysporum, a causal pathogen for banana wilt disease, was significantly decreased in the chilli pepper-banana rotation system compared to the banana monoculture system, regardless of whether it was estimated after rotation or harvest. Chilli pepper-banana rotation significantly stimulated bacterial and fungal abundance and diversity, and the community structure of both bacteria and fungi showed a significant shift, with cultivated crop (chilli pepper) having the largest impact. Higher relative abundances of Gemmatimonas, Pseudomonas, Sphingobium, Sphingomonas, Penicillium, Mortierella and Chaetomium and a lower relative abundance of Fusarium were identified in the rotation soil compared to the monoculture soil. Mantel tests and redundancy analysis (RDA) indicated that soil pH best explained the overall variation in bacterial and fungal communities. Overall, chilli pepper-banana rotation changes soil physiochemical properties, thereby optimizing the niches of beneficial soil microbiome that may contribute to suppress wilt disease associated with F. oxysporum in banana monoculture systems.