Diversity Profiling of Grapevine Microbial Endosphere and Antagonistic Potential of Endophytic Pseudomonas Against Grapevine Trunk Diseases

Abstract

Grapevine trunk diseases (GTDs) are a serious problem of grapevines worldwide. The microbiota of the grapevine endosphere comprises prokaryotic and eukaryotic endophytes, which may form varied relationships with the host plant from symbiotic to pathogenic. To explore the interaction between grapevine endophytic bacteria and GTDs, the endomicrobiome associated with grapevine wood was characterized using next-generation Illumina sequencing. Wood samples were collected from grapevine trunks with and without external symptoms of GTD (cankers) from two vineyards in the Hunter Valley and Hilltops, NSW, Australia and metagenomic characterization of the endophytic community was conducted using the 16S rRNA gene (341F/806R) and ITS (1F/2R) sequences. Among the important GTD pathogens, Phaeomoniella, Phaeoacremonium, Diplodia and Cryptovalsa species were found to be abundant in both symptomatic and asymptomatic grapevines from both vineyards. Eutypa lata and Neofusicoccum parvum, two important GTD pathogens, were detected in low numbers in Hilltops and the Hunter Valley, respectively. Interestingly, Pseudomonas dominated the bacterial community in canker-free grapevine tissues in both locations, comprising 56-74% of the total bacterial population. In contrast, the Pseudomonas population in grapevines with cankers was significantly lower, representing 29 and 2% of the bacterial community in Hilltops and the Hunter Valley, respectively. The presence of Pseudomonas in healthy grapevine tissues indicates its ability to colonize and survive in the grapevine. The potential of Pseudomonas spp. as biocontrol agents against GTD pathogens was also explored. Dual culture tests with isolated fluorescent Pseudomonas against mycelial discs of nine Botryosphaeria dieback, three Eutypa dieback, and two Esca/Petri disease pathogens, revealed antagonistic activity for 10 Pseudomonas strains. These results suggest the potential of Pseudomonas species from grapevine wood to be used as biocontrol agents to manage certain GTD pathogens.

Major changes in grapevine wood microbiota are associated with the onset of esca, a devastating trunk disease

“…Green dots = non-specific detection of all bacterial taxa. Niem et al (2020), meta-barcoding analysis of bacterial microbiota from woody tissues was performed, using old grapevines from Australia that displayed BDA, but not esca disease. In trunks from healthy plants, these authors identified mostly Pseudomonas (50%-75%), Roseococcus (16%) and Chitinophagaceae (13%).…”

“…Comparison of fungal microbiota of woody tissues from young grapevines to those reported for old grapevines Two other meta-barcoding studies of fungal microbiota from woody tissues were performed, using old grapevines from Portugal (Del Frari et al, 2019), or Australia (Niem et al, 2020). These authors studied old grapevines that were either healthy or displaying esca (Portugal) or BDA (Australia).…”

“…This strategy allows an in‐depth characterization of microbiota, including the detection of species difficult to cultivate, or only present at low abundance (Cuadros‐Orellana et al ., 2013). These techniques have been successfully applied to the analysis of fungal microbiota from grapevine woody tissues (Del Frari et al ., 2019; Niem et al ., 2020). In addition, we used in situ hybridization to localize fungi and bacteria in grapevine woody tissues.…”

Paenibacillus alvei K165 and Fusarium oxysporum F2: Potential Biocontrol Agents against Phaeomoniella chlamydospora in Grapevines

“…In addition, Alfonzo et al [21] reported the efficacy of Bacillus subtilis strain AG1 to inhibit mycelial growth of Pch and P. aleophilum due to antibiosis. More recently, Andreolli et al [22] reported the isolation of soil inhabiting Pseudomonas strains antagonistic to Pch; as it was also observed by Niem et al [23], in the case of grapevine-endophytic Pseudomonas strains.…”

Protection of grapevine pruning wounds against Phaeomoniella chlamydospora and Diplodia seriata by commercial biological and chemical methods

“…The high restrictions that most effective chemical active ingredients are currently facing in Europe because of environmental and human health risks (Larignon et al, 2008;Spinosi et al, 2009), make indispensable address new alternatives for controlling GTDs. Over the last years, research on biological control of GTD fungi with antagonistic microorganisms has shown promising results primarily under controlled conditions (Alfonzo et al, 2009;Mutawila et al, 2011a;Haidar et al, 2016;Rezgui et al, 2016;Álvarez-Pérez et al, 2017;Daraignes et al, 2018;Mondello et al, 2018;Andreolli et al, 2019;Del Frari et al, 2019;Mondello et al, 2019;Trotel-Aziz et al, 2019;Niem et al, 2020). Field trials with biological control agents (BCAs) have shown variable results for preventing infection by Botryosphaeriaceae and esca fungi (Kotze et al, 2011;Mutawila et al, 2011bMutawila et al, , 2015Mutawila et al, , 2016Mounier et al, 2014;Reis et al, 2017;Martínez-Diz et al, 2020a).…”