Differences in rhizosphere microbial communities between Fusarium wilt-resistant and susceptible watermelon cultivars

Abstract

ABSTRACT To elucidate genotype-associated differences in rhizosphere microbial community assembly, this study compared the microbiomes of three Fusarium wilt-resistant and three susceptible watermelon cultivars using amplicon sequencing. Results revealed distinct bacterial and fungal community structures between the two groups. Notably, resistant cultivars harbored a higher number of unique operational taxonomic units and displayed greater fungal richness compared to their susceptible counterparts. Beyond taxonomic composition, co-occurrence network analysis demonstrated that the fungal community within the resistant group exhibited a more highly connected network topology. Additionally, functional prediction highlighted significant divergence in potential functional profiles, including variations in Forms_Biofilms and Contains_Mobile_Elements. Collectively, these findings demonstrate that rhizosphere microbial composition, diversity, and network complexity are closely linked to watermelon resistance phenotypes. This comprehensive characterization of genotype-driven microbiome variation offers a critical basis for understanding plant–microbe interactions and their potential to enhance plant health. IMPORTANCE Fusarium wilt is one of the most destructive diseases affecting watermelon production worldwide, yet the role of soil microbes in helping plants resist this disease has remained unclear. This study shows that disease-related;resistant watermelon plants naturally recruit a richer and more cooperative community of beneficial microbes around their roots. These microbes may help protect the plant by improving nutrient use, forming biofilms that enhance microbial stability, and competing with or inhibiting harmful pathogens. In contrast, susceptible plants rely on only a few protective microbes, making their root environment less stable and more vulnerable to infection. By revealing how plant genetics shape the assembly and function of root-associated microbial communities, this work provides a scientific foundation for developing microbiome-based strategies-such as microbial inoculants or breeding for microbiome‑friendly cultivars-to improve crop resilience and reduce reliance on chemical pesticides. Fusarium wilt is one of the most destructive diseases affecting watermelon production worldwide, yet the role of soil microbes in helping plants resist this disease has remained unclear. This study shows that disease-related;resistant watermelon plants naturally recruit a richer and more cooperative community of beneficial microbes around their roots. These microbes may help protect the plant by improving nutrient use, forming biofilms that enhance microbial stability, and competing with or inhibiting harmful pathogens. In contrast, susceptible plants rely on only a few protective microbes, making their root environment less stable and more vulnerable to infection. By revealing how plant genetics shape the assembly and function of root-associated microbial communities, this work provides a scientific foundation for developing microbiome-based strategies-such as microbial inoculants or breeding for microbiome‑friendly cultivars-to improve crop resilience and reduce reliance on chemical pesticides.