Grapevine trunk diseases (GTDs) are a major threat to the wine industry, causing yield loss and dieback of grapevines. While the increasing damage caused by GTDs in recent decades have spurred several studies on grapevine-associated pathogenic fungi, key questions about the emergence and severity of GTDs remain unanswered, including possible differences in plant pathogenic fungal communities in asymptomatic and symptomatic grapevines. We generated fungal DNA metabarcoding data from soil, bark, and perennial wood samples from asymptomatic and symptomatic grapevines sampled in three terroirs. We observed larger compositional differences in plant pathogenic fungi among different plants parts within grapevine plants than among individual grapevines. This is driven by the dominance of GTD-associated fungi in perennial wood and non-GTD pathogens in soil, as well as by the lack of significant differences among asymptomatic and Esca symptomatic grapevines. These results suggest that fungi generally associated with Esca disease belong to the core grapevine microbiome and likely are commensal endophytes and/or latent saprotrophs, some of which can act as opportunistic pathogens on stressed plants. In addition, we found significant compositional differences among sampling sites, particularly in soil, which suggest a certain influence of local edaphic and mesoclimatic factors on plant pathogenic fungal communities. Furthermore, the observed differences among terroirs in plant pathogenic fungal communities in grapevine woody parts indicate that environmental factors likely are important for the development of Esca disease and further studies are needed to investigate the abiotic conditions on fungal compositional dynamics in Esca-affected plants.

Improving our knowledge on biotic and abiotic factors that influence the composition of the grapevine mycobiome is of great agricultural significance, due to potential effects on plant health, productivity, and wine characteristics. Here, we assessed the influence of scion cultivar on the diversity and composition of fungal communities in the berries and leaves of three different cultivars. We generated DNA metabarcoding data, and statistically compared the richness, relative abundance, and composition of several functional groups of fungi among cultivars, which are partly explained by measured differences in chemical composition of leaves and berries and physiological traits of leaves. Fungal communities in leaves and berries show contrasting patterns among cultivars. The richness and relative abundance of fungal functional groups statistically differ among berry and leaf samples, but less so among cultivars. Community composition of the dominant functional groups of fungi, i.e., plant pathogens in leaves and saprotrophs in berries, differs significantly among cultivars. We also detect cultivar-level differences in the macro- and microelement content of the leaves, and in acidity and sugar concentration of berries. Our findings suggest that there appears to be a relatively diverse set of fungi that make up the grapevine mycobiome at the sampled terroir that spans several cultivars, and that both berry and leaf mycobiomes are likely influenced by the chemical characteristics of berries and leaves, e.g., pH and the availability of nutrients and simple carbohydrates. Finally, the correlation between fungal community composition and physiological variables in leaves is noteworthy, and merits further research to explore causality. Our findings offer novel insights into the microbial dynamics of grapevine considering plant chemistry and physiology, with implications for viticulture.

The present study is the first observation of mycoparasitic behavior in the predominantly plant-associated fungal genus Diaporthe . Several isolates of the Phomopsis dieback pathogen Diaporthe eres s.l. were obtained from grapevine and identified by sequencing the internal transcribed spacer, translation elongation factor 1-α, and β-tubulin loci. The interactions of the isolates with Botrytis cinerea strains were examined by detailed microscopic analysis. All the tested isolates showed necrotrophic mycoparasitism against the target organism. Additional experiments with a D. eres s.l. isolate showed that mycoparasitism was also expressed against a Botryosphaeria dothidea target organism, a causal agent of Botryosphaeria dieback, another grapevine trunk disease syndrome. In addition to the first description of the mycoparasitism of D. eres , the study points out the complexity of microbial interactions established by trunk disease pathogens.

One of the major and yet unsolved threats for viticulture is the group of vascular fungal infections, the so-called grapevine trunk diseases. Besides their latent nature and the enormous number of associated pathogens, their control is also hampered by the lack of effective fungicides, directing growing attention toward the use of biocontrol agents. In the present study the isolation, identification, and characterization of a bacterial strain are presented, showing biocontrol potential against some main causal agents of grapevine trunk diseases. The strain was isolated from the wood of an asymptomatic grapevine and selected for the fungicidal activity against the pathogen Phaeomoniella chlamydospora. According to 16S rDNA, gyrA, and gyrB sequences, the isolate belongs to Bacillus velezensis species. Confrontation tests with the bacterium or with its fermentation broth further revealed growth inhibition and fungicide activity against Botryosphaeria dothidea, Eutypa lata and Diaporthe ampelina pathogens. Fractionation of the bacterial culture filtrate suggests that the antifungal agents secreted by the B. velezenzis isolate are mainly lipoproteins. Phytotoxicity tests were also carried out with the isolate, showing no harmful effects on grapevine foliar disks.

Background: Grapevines host diverse microbial communities, including fungal pathogens associated with grapevine trunk diseases (GTDs), which pose a major challenge in viticulture. Despite extensive research, the ecological drivers shaping fungal community composition across different grapevine microhabitats remain insufficiently understood. Using ITS2 metabarcoding, we characterized fungal communities in bark, wood, and soil from Esca symptomatic and asymptomatic vines, and evaluated the effects of season, year, cultivar, microhabitat, and plant health on key functional groups. Results: Seasonal variation had limited effects on fungal richness, whereas interannual differences had a strong impact on functional group diversity. Microhabitat played a key role: plant pathogens, particularly GTD-associated taxa, were most prominent in bark and wood; mycoparasites were dominant in bark; generalist saprotrophs prevailed in soil and bark; and GTD-related wood saprotrophs were most abundant in bark. Soil harbored the highest overall fungal diversity. Plant health status significantly affected only GTD pathogens, which showed higher abundance and diversity in symptomatic vines. Cultivar influenced only the richness of GTD-related wood saprotrophs. Conclusions: Year (vintage) emerged as a major driver of fungal community composition across plant tissues and soil, driving the most pronounced shifts in the mycobiome. Abiotic factors (year and season) were most strongly associated with soil fungal communities, whereas biotic factors (cultivar and plant health) exerted a greater influence on fungi associated with grapevine tissues. These findings underscore the central role of microhabitat and temporal variation in structuring the grapevine mycobiome.

The grapevine microbiome is shaped by a complex interplay of biotic and abiotic factors, affecting microbial community structure and plant health. This study investigates the diversity, composition, and dynamics of fungal communities associated with grapevine (Vitis vinifera) and neighboring cultivated plants, as well as plants from semi-natural vegetation, including pear (Pyrus communis), apricot (Prunus armeniaca), dogrose (Rosa canina), and blackthorn (Prunus spinosa), in a landscape-level habitat matrix. Using metabarcoding techniques, fungal communities from leaves and woody tissues of grapevine and neighboring plants were analyzed over a growing season. Fungal richness and abundance differed significantly among host plants, with woody tissues exhibiting higher diversity. Host plant identity was the primary factor shaping wood-associated fungal communities (15.7% of explained variance), whereas sampling time dominated in leaves (16.3%), with sampling site having a weaker effect in both cases. Pathogenic fungi associated with grapevine trunk diseases, such as Diaporthe, Eutypa, and Phaeomoniella, were identified across grapevine and neighboring plants, suggesting that multiple hosts may act as reservoirs for fungal inoculum. These findings highlight the complex interactions between fungal communities, host plants, and environmental factors, underscoring the need for landscape-level approaches to plant protection that account for both cultivated and surrounding ecosystems.