The Grapevine Microbiome to the Rescue: Implications for the Biocontrol of Trunk Diseases

Abstract

Grapevine trunk diseases (GTDs) are one of the most devastating pathologies that threaten the survival and profitability of vineyards around the world. Progressive banning of chemical pesticides and their withdrawal from the market has increased interest in the development of effective biocontrol agents (BCAs) for GTD treatment. In recent years, considerable progress has been made regarding the characterization of the grapevine microbiome, including the aerial part microbiome (flowers, berries and leaves), the wood microbiome, the root environment and vineyard soil microbiomes. In this work, we review these advances especially in relation to the etiology and the understanding of the composition of microbial populations in plants affected by GTDs. We also discuss how the grapevine microbiome is becoming a source for the isolation and characterization of new, more promising BCAs that, in the near future, could become effective tools for controlling these pathologies.

Fungal trunk diseases of fruit trees in Europe: pathogens, spread and future directions

“…Meta barcoding studies of grapevines in Portugal (Del Frari et al, 2019) and Greece (Bekris et al, 2021) have assessed the mycobiomes of grapevine trunks with esca, and cultivar and biogeography-dependent patterns were identified that could be used as to distinguish between healthy and diseased grapevines. By analyzing the microbiomes of healthy and diseased grapevines, strong interactions between the bacterial and fungal wood microbiomes in asymptomatic grapevines could be used for discovery of novel biocontrol agents (Cobos et al, 2022). However, specific bacteria isolated from healthy or diseased host tissues have been described as potentially increasing wood degradation by esca pathogens.…”

The functional microbiome of grapevine throughout plant evolutionary history and lifetime

“…GTDs include Botryosphaeria dieback, Diaporthe dieback, Eutypa dieback, Phomopsis dieback, Petri disease, black-foot disease and Esca complex diseases. Pathogenic fungi associated with GTDs belong to several genera, including Phaeomoniella, Phaeoacremonium, Fomitiporia, Eutypa, and to the Botryosphaeriaceae family (Cobos et al, 2022;Fig. 3).…”

Belowground microbiota analysis indicates that Fusarium spp. exacerbate grapevine trunk disease

“…Advances in sequencing and meta-omics tools have led to the gradual widespread use of high-throughput sequencing approaches to characterize the microbial communities inhabiting grapevines and gain insights into the factors that contribute to GTD development from an ecological perspective. Because GTDs primarily occur in perennial woods, greater attention has been paid to the bacterial and fungal communities inhabiting aboveground wood associated with symptomatic and asymptomatic plants [ 10 ]. Several potential antagonist microorganisms against GTDs have been found to be abundant in asymptomatic vines compared to symptomatic vines, including Pseudomonas, Bacillus, and Streptomyces [ 11 , 12 ] .…”

“…Furthermore, diverse GTD pathogens have been detected in both asymptomatic and symptomatic grapevines using culture-independent approaches, suggesting high GTD complexity [ 13 – 16 ]. However, several studies have shown that more severe necrosis is associated with lower relative abundances of GTD pathogens, suggesting that other, yet-to-be identified factors may be involved in GTD development [ 10 , 13 , 16 ]. Thus, additional research is needed to generate insights into the microbial populations associated with GTDs.…”

“…Soil microbiomes can influence grapevine-associated microbiota and may serve as a bacterial reservoir for aboveground plant components [ 21 ]. Grapevine root and rhizosphere microbiomes are also promising potential sources of more efficient and effective GTD biocontrol agents [ 10 ]. For example, Pythium oligandrum [ 22 – 24 ], Streptomyces spp.…”