Metabarcoding reveals rhizosphere microbiome differences in healthy and basal rot-affected dragon fruit plants

Abstract

The rhizosphere microbiome plays a crucial role in plant health, yet its dynamics in Selenicereus megalanthus (yellow dragon fruit) remain poorly understood. This study employed high-throughput sequencing to characterize the bacterial and fungal communities in the rhizosphere of healthy and basal rot-affected plants across four commercial production sites in Amazonas department from Peru. Amplicon sequencing Metagenomics Sequencing (WOBI) targeting to 16S rRNA (for bacteria) and ITS (for fungi) gene regions show differences in microbial community structure associated with plant health status. Multivariate analyses revealed a clear disease-driven reassembly of the bacterial microbiome, marked by the loss of health-associated taxa (Xanthobacteraceae, Geminicoccaceae, Nocardioidaceae) and enrichment of oligotrophic and stress-tolerant groups (Nitrososphaeraceae, Acidobacteriaceae Subgroup 1). In contrast, fungal assemblages displayed structural inertia, responding primarily through pathogen-associated increases in Nectriaceae. Soil physicochemistry particularly pH, exchangeable aluminum, and nutrient levels modulated the strength of bacterial differentiation, highlighting the role of edaphic filters in microbiome resilience. Our findings provide evidence of a bacterial-centered dysbiosis associated with basal stem rot in S. megalanthus, while positioning fungal communities as structurally resilient components of the holobiont. Together, these results outline a framework in which disease is linked to altered plant microbe soil feedbacks rather than pathogen presence alone, and suggest that bacterial assemblages could inform the development of microbiome-based early-warning indicators and soil health strategies for sustainable dragon fruit management.