Interconnections across microbiomes: how do plant holobionts and food fermentations relate? A focus on the Taggiasca olive tree ecosystem

Microbiomes form a continuum from the environment to the plant holobiont and the food systems, interacting with one another and influencing the plant health and ultimately the sensory traits of the fermented products. The Taggiasca olive tree (Olea europaea L.) native to Liguria, North-West Italy, exemplifies this connection, with its fruits undergoing a traditional spontaneous fermentation, where the native microorganisms shape the final product’s quality. In this study, a metabarcoding approach was used to characterize the microbial ecology of above- (brined olives, olives, leaves, barks) and below-ground (soils, rhizospheres) compartments of the Taggiasca olive tree and the final fermented products in year 2023 to detect a potential microbial transfer from the tree to the food. Alpha diversity results showed that bacterial diversity was more conserved across compartments than the fungal one, where more significant differences were observed. For beta-diversity, below-ground compartments and leaves in both bacterial and fungal datasets showed more intra-group dissimilarities than olives and brined olives, while Bray-Curtis dissimilarity matrix among samples showed a less dissimilar fungal composition across brined olives and leaves; barks and leaves; barks and rhizospheres, compared to the bacterial one. The main bacterial indicator genera across all samples were Amnibacterium, Halomonas and Sphingomonas, while the main fungal ones were Cladosporium, Zygotorulaspora and Hyphopichia. Indicator ASVs such as Cladosporium (ASV18) were shared across all compartments, while Microbacterium (ASV172) was present in all compartments except barks, suggesting that certain microorganisms are capable of transferring across plant compartments and persisting into the final fermented product. In the future, the integration of multiple -omics and the consideration of multiple harvest seasons could help investigate the connection of microbiota with the quality of the fermented food products. This study provides the first comprehensive insight into the microbiota associated with the Taggiasca olive tree, offering valuable information on its interactions with the environment and potential implications for food quality.