Rhizosphere microbial diversity analysis reveals enrichment of biocontrol taxa in healthy tobacco plants and yields novel antagonists against Phytophthora nicotianae

Abstract

Introduction Tobacco black shank (TBS), caused by Phytophthora nicotianae, is a devastating disease. Current control relies heavily on chemical pesticides, which pose risks of resistance and environmental pollution. Biological control using rhizosphere microorganisms offers a sustainable alternative. However, the relationship between the composition of the rhizosphere microbiome and its suppressive activity against P. nicotianae has not yet been systematically elucidated. Methods High-throughput sequencing was used to compare the differences in rhizosphere microbiota of healthy and diseased plants from multiple field sites in Yunnan, China, combined with culture-dependent isolation and screening of antagonistic microorganisms against P. nicotianae. Results No significant differences in bacterial or fungal diversity were found between healthy and diseased rhizosphere soils. Despite this overall similarity in diversity, healthy rhizosphere soil was significantly enriched in biocontrol genera, including Pseudomonas, Paenibacillus, and Massilia. A total of 204 bacterial and 95 fungal strains were isolated, among which 64 bacteria and 41 fungi exhibited antagonistic activity against P. nicotianae. Four strains (710, 733, 1088, and 1145) showed the strongest inhibitory effects and were identified as Bacillus amyloliquefaciens, Yokenella sp., Metapseudomonas resinovorans, and Bacillus subtilis, respectively. Moreover, the soluble metabolites and volatile metabolites produced by these strains also inhibited P. nicotianae. Notably, this study provides the first evidence that Y. regensburgei and M. resinovorans function as biocontrol agents against P. nicotianae, with mycelial inhibition rates reaching 72.29% and 38.96%, respectively. Discussion These results reveal the enrichment of specific biocontrol taxa in healthy tobacco rhizosphere and identify Y. regensburgei and M. resinovorans as novel antagonists against P. nicotianae. This study expands the strain library for TBS biological control and provides promising candidates for developing green management strategies.