Deciphering root-associated microbial communities in asymptomatic oil palm seedlings exposed to Ganoderma boninense: new insight into disease tolerance of oil palms

Understanding the microbial communities in asymptomatic oil palm seedlings is crucial for developing disease-suppressive microbiota against basal stem rot (BSR) in oil palm. In this study, we compared the microbial communities in bulk soil, rhizosphere, and endosphere of control, asymptomatic, and symptomatic seedlings following inoculation with Ganoderma boninense. Our findings revealed significant shifts in microbial structure and interactions, particularly in asymptomatic seedlings. Both Actinobacteriota and Ascomycota were notably enriched in these samples, with Actinobacteriota identified as keystone taxa. Long-read shotgun metagenomics demonstrated that 67.4% of enriched Actinobacteriota taxa were unique to asymptomatic seedlings. Similarly, Ascomycota members showed significant enrichment, suggesting their potential role in BSR suppression. The consistent identification of these phyla across various analyses underscores their importance in disease resistance. This is the first report detailing the shifts in prokaryotic and fungal communities in asymptomatic and symptomatic seedlings, offering insights into potential disease-suppressive taxa across three compartments: bulk soil, rhizosphere, and endosphere of oil palm seedlings.