Diversity of stem endophytes communities from wild asparagus resources and the biocontrol potential on Phomopsis asparagi

BACKGROUND: Asparagus stem blight, caused by Phomopsis asparagi, is a devastating disease leading to significant yield losses in asparagus cultivation. Current control methods, such as greenhouse cultivation or extensive pesticide use, are either costly or environmentally unsustainable. Endophytes, residing within healthy plant tissues, offer a promising biocontrol alternative due to their antagonistic activities against pathogens. METHODOLOGY: This study investigated the diversity and biocontrol potential of endophytic fungi and bacteria in the stems of one cultivated variety (ATL) and three wild asparagus resources (NFY, YAY, YDL). We employed high-throughput sequencing to analyze endophytic community composition and diversity. We conducted predictive functional profiling to assess potential metabolic capabilities. Additionally, endophytic strains were isolated from stem tissues and screened for antagonistic activity against P. asparagi using dual-culture assays. RESULTS: High-throughput sequencing revealed distinct endophytic communities between cultivated (ATL) and wild (NFY, YAY, YDL) asparagus. Wild varieties exhibited significantly higher microbial diversity and more unique Operational Taxonomic Units (OTUs). Principal Coordinate Analysis (PCoA) confirmed separate clustering, with wild samples grouping apart from ATL. Community composition differed markedly: in fungi, Russula was abundant in NFY, while Incertae_sedis dominated others; in bacteria, Pseudomonadota prevailed in wild types versus Armatimonadota in ATL. Functional prediction showed wild endophytes enriched in genes for direct antagonism (e.g., chitinase), stress resistance, and competition (e.g., ABC transporters, quorum sensing). Cultivated endophytes were geared toward core metabolism. From wild stems, 14 endophytic strains were isolated. Four bacterial isolates strongly inhibited Phomopsis asparagi (> 90% inhibition), with one (YDJ119602) achieving 100% inhibition via fermentation broth. CONCLUSIONS: In conclusion, wild asparagus exhibits rich endophytic diversity and represents a promising source of biocontrol agents against stem blight, offering a sustainable disease management strategy.