Grapevine wood microbiome analysis identifies key fungal pathogens and potential interactions with the bacterial community implicated in grapevine trunk disease appearance

Abstract

Background Grapevine trunk diseases (GTDs) is a disease complex caused by wood pathogenic fungi belonging to genera like Phaeomoniella, Phaeoacremonium, Fomitiporia, Eutypa and members of the family Botryosphaeriaceae. However, the co-occurrence of these fungi in symptomatic and asymptomatic vines at equivalent abundances has questioned their role in GTDs. Hence, we still lack a good understanding of the fungi involved in GTDs, their interactions and the factors controlling their assemblage in vines. We determined the fungal and bacterial microbiome in wood tissues of asymptomatic and symptomatic vines of three main Greek cultivars (Agiorgitiko, Xinomavro, Vidiano), each cultivated in geographically distinct viticultural zones, using amplicon sequencing. Results We noted that cultivar/biogeography (lumped factor) was the strongest determinant of the wood fungal microbiome (p < 0.001, 22.7%), while GTD symptoms condition had a weaker but still significant effect (p < 0.001, 3.5%), being prominent only in the cultivar Xinomavro. Several fungal Amplicon Sequence Variants (ASVs), reported as GTD-associated pathogens like Kalmusia variispora, Fomitiporia spp., and Phaemoniella chlamydosporα (most dominant in our study), were positively correlated with symptomatic vines in a cultivar/viticultural zone dependent manner. Random Forest analysis pointed to P. chlamydosporα, K. variispora, A. alternata and Cladosporium sp., as highly accurate predictors of symptomatic vines (0% error rate). The wood bacterial microbiome showed similar patterns, with biogeography/cultivar being the main determinant (p < 0.001, 25.5%) of its composition, followed by the GTD status of vines (p < 0.001, 5.2%). Differential abundance analysis revealed a universal positive correlation (p < 0.001) of Bacillus and Streptomyces ASVs with asymptomatic vines. Network analysis identified a significant negative co-occurrence network between these bacterial genera and Phaemoniella, Phaeoacrominum and Seimatosporium. These results point to a plant beneficial interaction between Bacillus/Streptomyces and GTD pathogens. Conclusions Our study (a) provides evidence that GTD symptomatic plants support a wood fungal microbiome, showing cultivar and biogeography-dependent patterns, that could be used as a proxy to distinguish between healthy and diseased vines, (b) points to strong interactions between the bacterial and fungal wood microbiome in asymptomatic vines that should be further pursued in the quest for discovery of novel biocontrol agents.

Variation in Fungal Community in Grapevine (Vitis vinifera) Nursery Stock Depends on Nursery, Variety and Rootstock

“…In our work, Lophiostoma sp. appeared accompanied by the GTD-related fungus Truncatella sp., a species that has repeatedly been associated with esca complex fungi [150], as well as Acremonium sp., which is a non-pathogenic fungus that has recently been found to be an indicator of symptoms (necrosis) in non-GTD infected vines [151]. Considering the co-occurrence of these indicators in the context of previous work emphasizes the plasticity of their presence and relationships to other indicator species, which can differ depending on the situation in which they are detected (variety, rootstock, environment, etc.…”

Evaluation of the Antifungal Activity of Endophytic and Rhizospheric Bacteria against Grapevine Trunk Pathogens

“…Bacterial isolates ( n = 1344) were initially screened in vitro against the mycelium of N. parvum and D. seriata through antagonism assays described previously [ 17 ]. Both fungal isolates ( N. parvum UCD7395 and D. seriata UCD7767) were obtained from the fungal collection of the Eskalen laboratory at the Department of Plant Pathology, University of California, Davis, that were originally isolated from GTD-symptomatic grapevine samples.…”

“…Therefore, the concept of a “balanced microbiome” has recently gained notorious attention due to recent work on grapevine microbial communities and their impact in disease expression [ 15 , 16 ]. In this context, it has been shown that grapevines with a higher abundance of endophytic beneficial bacteria display less or no symptoms in vineyards with known history of GTDs [ 17 ]. On the other hand, the endophytic nature of latent infections caused by trunk pathogens pose an advantage for biocontrol treatments, allowing grapevines to strengthen their tolerance to biotic and abiotic stress before the switch from endophytic to pathogenic behavior [ 18 , 19 ].…”

The road to molecular identification and detection of fungal grapevine trunk diseases

“…These methodologies also allow to identify and relatively quantify the presence of each microbial agent (Eichmeier et al, 2018;Morales-Cruz et al, 2018b;Nerva et al, 2022). Additionally, distinct NGS approaches can have several outcomes, such as the perception of the role of the genes in the infectious process by RNA sequencing (Morales-Cruz et al, 2015, 2018aPaolinelli et al, 2022), the prevalence of certain pathogens in distinct environments and grapevine cultivars by environmental microbiome metasequencing (Maree et al, 2012;Eichmeier et al, 2018;del Frari et al, 2019;Azevedo-Silva et al, 2021), and the role of other microbial agents toward GTD-causing fungal pathogens (Berlanas et al, 2019;Saccà et al, 2019;Niem et al, 2020;Bekris et al, 2021;Cobos et al, 2022).…”