Incidence of Crown and Root Rot in Rhododendron simsii Caused by Phytopythium vexans in China and Screening of Endophytic Bacteria for Biocontrol

<i>Azaleas (Ericaceae)</i> are among the most diverse ornamental plants, celebrated for their cultural and economic significance. <i>R. simsii</i> has been extensively utilized in horticulture as a parent species for both "pot azalea" cultivars and various cultivars grown in the warmer regions of China. From 2021 to 2023, approximately 15% of <i>R. simsii</i> in nurseries situated in the Xuanwu District, Nanjing, exhibited symptoms of wilting and chlorosis. Investigations revealed that these symptoms were caused by a pathogen responsible for crown and root rot. Strains were isolated from the roots of affected plants. The morphology of the colonies was predominantly radial to stellate, characterized by intercalary and terminal hyphal swelling. The sporangia appeared spherical, pyriform, or ovoid with a single papillae. For accurate identification, the 28S rDNA gene (Large subunit, <i>LSU</i>), cytochrome oxidase subunit I <i>(COXI</i>), and cytochrome oxidase subunit II (<i>COXII</i>) genes were amplified through PCR and then sequenced. The species was identified as <i>P. vexans</i> after completing the phylogenetic analysis. Healthy <i>R. simsii</i> plants were infected with zoospores and developed symptoms similar to those of natural infection. Furthermore, the morphological characteristics of the isolates from the experimentally infected plants were similar to those of the original inoculated strains. This study identified <i>P. vexans</i> as the pathogen causing root rot in <i>R. simsii.</i> During the sampling process, several strains were isolated from the rhizosphere soil of healthy rhododendron plants. Based on this, research was immediately initiated to explore whether there are specific bacterial species in the soil that have the potential to inhibit the occurrence of root rot. Additionally, an endophytic bacterial strain BL1 was isolated from rhizosphere soil and subjected to Whole-Genome Shotgun (WGS) sequencing, thus constructing a bacterial genome framework for this isolate. The strain BL1 was identified as <i>Bacillus licheniformis</i>. To our knowledge, this is the first report of the occurrence of <i>P. vexans</i> causing crown and root rot of <i>R. simsii</i> in China. In this study, we also focused on exploring the potential of biological control agents against <i>P. vexans</i>. The isolation and identification of the endophytic bacterial strain BL1 (<i>Bacillus licheniformis</i>) from the rhizosphere soil of healthy soil show strong in vitro antagonism, identifying it as a promising candidate for future biological control studies of root rot in <i>R. simsii</i>. The genomic component analysis and coding gene annotation of BL1 provide insights into its genetic makeup and potential mechanisms of action against pathogens. However, these findings are based on in vitro assays. Therefore, further research, including in planta experiments, is essential to confirm the efficacy of BL1 in controlling <i>P. vexans</i> infections in <i>R. simsii</i> and to evaluate its potential for practical application.