Straw Submergence and Rice Rotation Suppress Banana Fusarium Wilt by Reshaping the Soil Microbiome and Metabolome

Banana Fusarium wilt, caused by Fusarium oxysporum f. sp. cubense (FOC), poses a major threat to global banana production. Straw submergence combined with rice rotation (SFR) has emerged as a promising disease-management strategy, but its underlying mechanisms remain unclear. Here, we conducted a three-year field experiment to determine how SFR alters soil physicochemical properties, microbial communities, and soil metabolites. SFR sharply decreased soil redox potential (Eh) and shifted nitrogen transformation by increasing ammonium nitrogen (AN) and reducing nitrate nitrogen (NN). Eh and NN were positively correlated with culturable Fusarium spp. counts (r = 0.36, p < 0.01), whereas AN was negatively correlated. SFR also reshaped soil microbial communities, reduced the relative abundance of Fusarium, and enriched several putatively antagonistic microbial taxa. Metabolomic profiling showed that several Fusarium-associated metabolites were downregulated and that differential metabolites were enriched in key KEGG pathways. Network analysis further identified Luteimonas as a potential keystone bacterial genus negatively associated with Fusarium-associated metabolites. Partial least squares path modeling suggested that soil physicochemical changes were linked to Fusarium wilt suppression largely through indirect bacterial–fungal–metabolite pathways. These findings indicate that SFR suppresses banana Fusarium wilt, reducing disease incidence to 16.25% at the vigorous growth stage (versus 100% in SC), an 83.8% relative reduction compared with banana monoculture, through coordinated changes in soil Eh and nitrogen status, microbial community structure, and soil metabolic profiles.