Unveiling essential host genes and keystone microorganisms of the olive tree holobiont linked to Verticillium wilt...

The plant holobiont concept emphasizes the critical role of the microbiome in host plant health and resilience. Microbial communities have been shown to enhance plant resistance to abiotic stresses, such as drought and salinity, and to mitigate the impact of phytopathogens. Traditional microbiome engineering approaches face challenges due to the complexity of microbial interactions. To overcome these limitations, recent advances in transcriptomics and metataxonomics analyses enable the identification of microbiome-associated phenotypes, co-occurrence networks, and key host genes-microbiome interactions. We present a novel framework combining co-occurrence network analyses and transcriptome-microbiota correlations to identify keystone belowground microorganisms and host genes potentially involved in olive (Olea europaea L.) tolerance to Verticillium wilt, a devastating disease caused by the soil-borne, fungal vascular pathogen Verticillium dahliae Kleb. Our approach aims to identify microbiome-regulating host genes and keystone bacteria and fungi that could be instrumental as genetic and microbiological markers in olive breeding programs.

In the root endosphere, cultivars qualified as tolerant to Verticillium wilt of olive (VWO) exhibited an enrichment of the bacterial genera Actinophytocola, Kibdelosporangium and Nocardia. Keystone taxa analyses revealed clearly different profiles when comparing the microbial co-occurrence networks of the VWO-tolerant genotypes with those varieties described as susceptible to V. dahliae. Thus, tolerant cultivars harbored bacteria predominantly displaying negative interactions with the mycobiome. In contrast, VWO-susceptible cultivars displayed microbial hubs with positive fungal correlations. Transcriptomic analyses of olive roots identified 1,143 differentially expressed genes (DEGs), with 309 upregulated genes in tolerant cultivars, highlighting biological processes like defense response, carbohydrate metabolism, and amino acid transport. Key microbial taxa (Actinophytocola, Kibdelosporangium, Nocardia, Aquabispora, and Fusarium) strongly correlated with DEGs associated with plant defense.

Keystone microbial taxa, particularly Actinophytocola and Nocardia, are proposed to play an important role against V. dahliae within the indigenous olive root microbiota under natural conditions. Moreover, our findings underscore the importance of studying keystone taxa along with essential host plant genes to holistically understand plant-microbiota interactions and explore their potential in disease management. This integrative approach provides insights into the complex dialogue taking place between the host plant and its microbiota, offering potential targets for microbiome engineering to enhance olive resilience against VWO. Video Abstract.