Plant roots support complex microbial communities that can influence nutrition, plant growth, and health. In grapevine, little is known about the impact of abiotic stresses on the belowground microbiome. In this study, we examined the drought-induced shifts in fungal composition in the root endosphere, the rhizosphere and bulk soil by internal transcribed spacer (ITS) high-throughput amplicon sequencing (HTAS). We imposed three irrigation regimes (100%, 50%, and 25% of the field capacity) to one-year old grapevine rootstock plants cv. SO₄ when plants had developed 2–3 roots. Root endosphere, rhizosphere, and bulk soil samples were collected 6- and 12-months post-plantation. Drought significantly modified the overall fungal composition of all three compartments, with the root endosphere compartment showing the greatest divergence from well-watered control (100%). The overall response of the fungal microbiota associated with black-foot disease (Dactylonectria and “Cylindrocarpon” genera) and the potential biocontrol agent Trichoderma to drought stress was consistent across compartments, namely that their relative abundances were significantly higher at 50–100% than at 25% irrigation regime. We identified a significant enrichment in several fungal genera such as the arbuscular mycorrhizal fungus Funneliformis during drought at 25% watering regime within the roots. Our results reveal that drought stress, in addition to its well-characterized effects on plant physiology, also results in the restructuring of grapevine root microbial communities, and suggest the possibility that members of the altered grapevine microbiota might contribute to plant survival under extreme environmental conditions.

Rootstocks are the link between the soil and scion in grapevines, can provide tolerance to abiotic and biotic stresses, and regulate yield and grape quality. The vascular system of grapevine rootstocks in nurseries is still an underexplored niche for research, despite its potential for hosting beneficial and pathogenic microorganisms. The purpose of this study was to investigate the changes in the composition of fungal communities in 110 Richter and 41 Berlandieri rootstocks at four stages of the grapevine propagation process. Taxonomic analysis revealed that the fungal community predominantly consisted of phylum Ascomycota in all stages of the propagation process. The alpha-diversity of fungal communities differed among sampling times for both rootstocks, with richness and fungal diversity in the vascular system decreasing through the propagation process. The core microbiome was composed of the genera Cadophora, Cladosporium, Penicillium and Alternaria in both rootstocks, while the pathogenic genus Neofusicoccum was identified as a persistent taxon throughout the propagation process. FUNguild analysis showed that the relative abundance of plant pathogens associated with trunk diseases increased towards the last stage in nurseries. Fungal communities in the vascular system of grapevine rootstocks differed between the different stages of the propagation process in nurseries. Numerous genera associated with potential biocontrol activity and grapevine trunk diseases were identified. Understanding the large diversity of fungi in the rootstock vascular tissue and the interactions between fungal microbiota and grapevine will help to develop sustainable strategies for grapevine protection.

Grapevine fungal trunk diseases (GTDs) have become a serious problem for grapevines worldwide. Nursery vines infected during the propagation process are considered one of the main ways of dissemination of GTD pathogens. In this study, we examined the status of GTDs in grapevine planting material, from rootstocks and scion mother cuttings to grafted rooted vines ready to plant, according to the local nursery propagation process. During 2018-2019, internal symptoms of GTDs were examined in 2400 propagation materials and fungal isolations were carried out from a subsample of 1026 selected materials. Our results revealed that nursery grapevine plants produced in Uruguay have a high incidence of GTDs, regardless of the scion/rootstock combination. Typical brown to black streaks and sectorial wood necrosis were observed in materials on all propagation stages, with a markedly increasing incidence throughout the nursery process, reaching almost 100% in grafted rooted vines ready to plant. Botryosphaeria dieback, Petri disease and black-foot disease were the main GTDs found. The results showed that Botryosphaeria dieback and Petri disease pathogens infect materials from the early stages of the process, with a marked increase towards the end of the plant production process, whereas black-foot disease pathogens were found exclusively in vines ready to plant. Diaporthe dieback pathogens were also detected in materials in all stages but in a low proportion (less than 10% of infected material). Based on single locus analysis, the 180 isolates selected were placed into eight genera and 89% identified within 22 fungal species associated with GTDs, with Phaeoacremonium oleae and Diaporthe terebinthifolii as new records on grapevine worldwide. Our results have concluded that locally produced vines are one of the main ways of dissemination of GTD pathogens and showed that a nursery sanitation programme is required to reduce the incidence of these diseases.

Grapevine productivity worldwide is increasingly threatened by global warming, potentially exacerbating water scarcity. This study examines drought's effects on grapevine xylem fungal communities, particularly regarding Phaeomoniella chlamydospora, linked to esca and Petri diseases. Investigating 1-year-old grafted grapevines under varied water regimes, including severe, moderate, and no water deficit, the research assessed how drought influences fungal diversity, structure, and interactions within the xylem. Utilizing internal transcribed spacer high-throughput amplicon sequencing and droplet-digital PCR, the study tracked changes in fungal composition and P. chlamydospora prevalence over two growing seasons. The induced water stress not only altered the diversity and composition of the fungal microbiome in the xylem vessels but also affected co-occurrence networks, resulting in less complex networks with fewer correlations between taxa, potentially increasing grapevine vulnerability to various biotic and abiotic stresses. Severe water deficit significantly reduced microbial diversity, leading to a shift in the abundance of pathotrophs such as P. chlamydospora in the xylem. This underscores the interconnectedness between water stress, microbiome dynamics, and plant health. The combination of compromised plant defenses, altered physiological conditions, and shifts in the surrounding microbial community may create conditions conducive to increased P. chlamydospora abundance in the xylem vessels of young vines following water stress.

Olive anthracnose, caused by Colletotrichum, is an important disease in olive-growing regions, with the most destructive symptoms being fruit rot and blossom blight. Susceptibility of fruit to Colletotrichum increases with maturity, but differences between cultivars and Colletotrichum species have been reported, still information on flower susceptibility during development is scarce. The susceptibility of the olive cultivars Arbequina, Coratina, Frantoio and Picual was evaluated during flower development and fruit maturity to Colletotrichum acutatum s.s., C. nymphaeae, C. fioriniae, C. theobromicola and C. alienum. Susceptibility to anthracnose begins in early stages during flower development and increases during blossoming. Flowers of Arbequina, Coratina and Picual were susceptible, whereas those of Frantoio were moderately susceptible. Green fruit developed less anthracnose than mature fruit. At the green fruit stage, Arbequina and Frantoio were the most susceptible, Coratina was intermediate, and Picual was moderately susceptible, while no differences were found among the cultivars at mature fruit stages. No mayor differences were found among the Colletotrichum species with exception of C. theobromicola, which caused greatest severity at the green fruit stage. Future research should focus on developing anthracnose management strategies to minimize the disease progress from early stages of flower development and fruit ripening, especially in the most susceptible olive cultivars.