Investigation of the microbiome structure and function in grapevines escaping trunk diseases

Abstract

Grapevine trunk diseases (GTD) represent a major challenge to the viticulture industry in New Zealand and other winegrowing regions worldwide. Due to the limited availability of effective control strategies for these intractable diseases there is increased interest in identifying alternative control strategies, including biological control. In some New Zealand vineyards, vines that remain healthy in a background of heavy GTD pressure have been observed. In this study, vineyards in two grape growing regions, Hawke's Bay and Canterbury, were surveyed for the presence of grapevines escaping GTD, referred to as disease escape vines. Woody trunk tissue samples were collected from these putative disease escape vines and the surrounding diseased vines. DNA metabarcoding of the ribosomal internal transcribed spacer 1 (ITS1) and 16S ribosomal RNA gene was used to characterise their fungal and bacterial communities. 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 were consistently at higher relative abundance in GTD escape vines, whilst 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. Bacterial and fungal isolates matching the key taxa identified by DNA metabarcoding from GTD escape vines were retrieved from the cultures recovered from the vines and tested for inclusion in a synthetic microbial community (SynCom). Additional selection criteria for inclusion were the microorganism's functional properties, such as not being a known plant pathogen, not causing lesions on grapevine shoots, and demonstrating inhibitory activities against the GTD pathogens E. lata and Neofusicoccum luteum in dual culture plate assays. Using these criteria, Aureobasidium pullulans, Seimatosporium vitis, and seven Pseudomonas isolates were selected as consortium members. Combined and separate fungal and bacterial consortia were tested in plant assays against the GTD pathogens E. lata and N. luteum. After 3 months, the bacteria successfully established and persisted within the grapevines, significantly altering the grapevines' microbiome structure. Treatment with combined bacterial and fungal consortia resulted 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.