Adejoro, Damola2024-02-012024-02-012023https://hdl.handle.net/10182/16837Grapevine trunk diseases (GTD) represent a substantial challenge to viticulture in New Zealand and other winegrowing regions worldwide. With no approved fungicides for their eradication, alternative methods, such as biological control, are of significant interest. Key international studies have identified plants, called disease escape plants, that remain healthy under a high disease pressure, and this trait has been linked to microbiome function. In some New Zealand vineyards, such disease escape vines have been observed in backgrounds of heavy GTD pressure. This study aimed to investigate a microbiome approach to GTD management by surveying New Zealand vineyards for the occurrence of GTD escape vines and characterising the trunk microbiome of such vines. Based on preliminary assessments of nine vineyards across Hawke's Bay and Canterbury, New Zealand, a detailed visual survey was conducted in four vineyards, two each in Hawke's Bay and Canterbury. Candidate GTD escape vines were identified based on the absence of GTD symptoms, chlorophyll content of leaves, and high GTD pressure in the vineyard block. Woody trunk tissue samples were collected from these vines and the diseased vines nearby. The fungal and bacterial communities in the samples were characterised using a combination of DNA metabarcoding of the ribosomal internal transcribed spacer 1 (ITS1) and 16S ribosomal RNA gene and microbial isolations. The results showed that the status of the vine as either GTD escape or diseased was a strong determinant of the structure of the bacterial and fungal microbiomes of the grapevine trunk. For bacteria, the GTD escape vines consistently harboured Pseudomonas and Hymenobacter in higher relative abundance. Aureobasidium, Seimatosporium, Cladosporium, and Rhodotorula were fungal genera differentially associated with GTD escape vines. On the other hand, the GTD pathogen, Eutypa lata, was differentially associated with diseased vines. Bacterial and fungal isolates matching the key taxa identified by DNA metabarcoding from GTD escape vines were retrieved and tested for inclusion in microbial consortia. 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 exhibiting desirable inhibitory activities against E. lata and Neofusicoccum luteum in dual culture plate assays. Using these criteria, consortium members Aureobasidium pullulans, Seimatosporium vitis, and seven Pseudomonas isolates were selected. Combined and separate fungal and bacterial consortia were tested in plant assays against the GTD pathogens E. lata and N. luteum. Over 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 (71% reduction, p = 0.002) than the pathogen controls. The relative abundance of E. lata was reduced by 85% in the presence of the bacteria-only consortium. This research enhanced knowledge of the grapevine trunk microbiome structure within the context of the GTD escape phenotype. In addition, it expanded the understanding of grapevine microbiome manipulation by developing and delivering microbial consortia into grapevines, which resulted in changes in the grapevine microbiome structure. These results highlight the potential of using selected microbial consortia as a promising strategy for controlling GTD pathogens in planta. Given the perennial nature of grapevines and the extended development periods associated with GTD, future research could investigate the potential long-term impact of grapevine microbiome manipulation on the protection of grapevines against GTD pathogens.enhttps://researcharchive.lincoln.ac.nz/pages/rightsAureobasidium pullulansbiocontrolconsortiumdisease escapeDNA metabarcodingendophytesEutypa latagrapevinegrapevine trunk diseaseHymenobactermicrobiomemicrobiome manipulationmicrobiotaNeofusicoccum luteumPseudomonasSeimatosporium vitisvineyardstrunk diseaseThesisANZSRC::310703 Microbial ecologyANZSRC::310805 Plant pathologyANZSRC::300804 Horticultural crop protection (incl. pests, diseases and weeds)ANZSRC::310803 Plant cell and molecular biology