The microbiome associated with grapevines escaping trunk disease: A potential source of beneficial microorganisms for disease control

Abstract

Grapevine trunk diseases (GTD) represent a major challenge to viticulture in New Zealand and globally. Due to the limited availability of effective control strategies for these intractable diseases, identifying alternatives, including biological control is an increasing focus. Vines that remain healthy in a background of heavy GTD pressure have been observed in some New Zealand vineyards. This study surveyed vineyards for the presence of grapevines escaping GTD, referred to as disease escape vines. Wood tissue samples were collected from these putative disease escape vines and the surrounding diseased vines. The fungal and bacterial communities were characterised using DNA metabarcoding of the ribosomal internal transcribed spacer 1 (ITS1) and 16S ribosomal RNA gene. The results showed that the status of the vine as either GTD escape or diseased was a significant determinant of the bacterial and fungal microbiome structure of the grapevine trunk. The bacterial taxa Pseudomonas and Hymenobacter and the fungal taxa Aureobasidium, Seimatosporium, Cladosporium, and Rhodotorula were differentially associated with GTD escape vines. In contrast, the GTD pathogen Eutypa lata was associated with diseased vines. Based on the DNA metabarcoding results and functionality testing, Aureobasidium pullulans, Seimatosporium vitis, and seven Pseudomonas isolates were selected from the cultures retrieved from the disease escape vines for inclusion in a synthetic community (SynCom). Separate and combined fungal and bacterial consortia were assessed in planta against the GTD pathogens E. lata and Neofusicoccum luteum. After 3 months, the bacteria successfully established within the grapevines, with the combined bacterial and fungal consortia treatment resulting in significantly shorter lesions than the pathogen controls. These results highlight the potential for using selected microbial consortia as a promising strategy for controlling GTD pathogens in planta.