Identification, characterization and genome sequencing of Chryseobacterium indoltheticum causing stipe rot on cultivated Morchella sextelata

Morchella spp. are highly valued in global markets due to their fruiting bodies' richness in polysaccharides, amino acids, sterols, and phenolic compounds, which confer pharmacological activities including anti-tumor and immunomodulatory effects. In April 2025, a distinctive stipe rot disease was observed on cultivated Morchella sextelata 'Mel-6' in China. Approximately 40% of fruiting bodies showed severe infection, causing substantial economic losses. Literature review confirmed no prior identification of the causal pathogen. Initial symptoms appeared as brown, circular stipe lesions that expanded rapidly into dark brown discoloration. Within days, complete stipe rot developed without observable mycelia or spores. Stipes exhibited high susceptibility, whereas caps remained less affected. Basipetal symptom progression suggested soil-borne origin. The pathogen was isolated from symptomatic tissue. Representative strain SC-1 fulfilled Koch's postulates and was identified through morphological characterization and 16S rRNA gene phylogeny. Whole-genome sequencing and analysis provided confirmatory evidence. The causal bacterium was rod-shaped, Gram-negative, psychrophilic, and non-spore-forming. It infected M. sextelata stipes at 15–18°C and 70–80% RH, causing brown rot within 3–4 days post-inoculation. The circular chromosome comprised 4,390,109 bp with 34.27% GC content and encoded 4,003 protein-coding genes. Integrating morphology, phylogenetic analysis, and fulfillment of Koch's postulates, strain SC-1 was identified as Chryseobacterium indoltheticum . To the best of our knowledge, this is the first report of C. indoltheticum as a pathogen of Morchella species.