Leveraging soil microbiome diversity for the management of highly virulent Fusarium wilt (FOV4) in cotton

Introduction Cotton ( Gossypium spp.) is a globally important crop increasingly threatened by Fusarium oxysporum f. sp. vasinfectum race 4 (FOV4), a soil-borne pathogen responsible for Fusarium wilt. FOV4 has negatively affected cotton production in California and was confirmed in the far west Texas region of El Paso, TX in 2017, where it has caused similar disruptions. Thus, there is an urgent need for improved disease management and the development of resistant commercial cotton cultivars to maintain agricultural productivity. Methods To understand the relationships among soil properties, fungal communities, and disease incidence, we examined the elemental composition and fungal microbiome of five cotton fields in the lower valley of El Paso, Texas region, having varying levels of Fusarium wilt incidence. Comparisons between high Fusarium wilt incidence fields (F1, F2, and F5) and low Fusarium wilt incidence fields (F3 and F4) were performed. Metabarcoding analyses identified marked differences in fungal community composition and diversity between the fields. Results Alpha diversity metrics indicated higher fungal diversity and evenness in the low Fusarium wilt incidence field F4, suggesting that high fungal diversity contributes to decreased disease incidence. In contrast, high Fusarium wilt incidence fields (F1, F2, and F5) exhibited lower diversity, indicative of a less resilient fungal ecosystem. Beta diversity analyses further confirmed the distinct fungal community composition between soils with contrasting Fusarium wilt incidence. Taxonomic profiling showed that the low Fusarium wilt incidence field F4 harbored beneficial fungal taxa, including Actinomucor, Fusarium (potentially non-pathogenic species), Penicillium, Preussia , and Pseudeurotium , generally recognized for their contributions to soil health and potential to suppress pathogenic organisms. In contrast, the high Fusarium wilt incidence fields were dominated by genera associated with plant pathogenicity, such as Alternaria , Cladosporium , and Stachybotrys , contributing to the higher disease prevalence observed. Discussion These findings underscore the crucial role of fungal diversity and soil chemical composition in influencing the incidence of Fusarium wilt in cotton. Soils with low Fusarium wilt incidence, characterized by diverse and complex fungal communities, may suppress the establishment and proliferation of pathogens. Our results provide insights for developing targeted soil management practices and enhancing cotton resilience, essential for developing sustainable disease management strategies and breeding resistant cultivars.