Reduced soil microbial diversity and altered co-occurrence networks associated with Phytophthora nicotianae infection in flue-cured tobacco fields

Background Phytophthora nicotianae is a persistent and highly destructive soilborne oomycete that causes black shank of tobacco and continues to threaten its production despite integrated management. Recent studies highlight the potential to harness microbiomes for plant disease suppression; however, it is poorly understood how soil microbial communities respond to P. nicotianae and how these responses relate to black shank severity under field conditions. Results We examined relationships among soil physicochemical properties, microbial community features, P. nicotianae DNA levels, and black shank outcomes in three flue-cured tobacco fields sampled repeatedly throughout a growing season. Phytophthora nicotianae DNA levels were correlated with soil physicochemical properties. The field with the lowest disease pressure had higher alpha diversity, the simplest bacterial network, and a moderately complex fungal network. In contrast, the field with the highest black shank mortality showed the lowest alpha diversity, the most complex bacterial network, and the least complex fungal network. Over the growing season, microbial alpha diversity decreased, and disease outcomes were associated with field-specific shifts in microbial community composition. Trichoderma , Fusarium , and Globodera were most abundant in the high-disease field, whereas multiple bacterial groups within Firmicutes, Proteobacteria, and Actinobacteriota were negatively associated with P. nicotianae in the lower-disease fields. Conclusion Our study indicates that P. nicotianae infection is associated with soil physiochemical properties and field-dependent patterns in microbial diversity, community composition, network topology, and several microbial taxa. These results provide a foundation for future research to experimentally test candidate microbe-pathogen relationships and, where supported, inform the development of microbiome-informed management approaches.