New strategies to study and control plant diseases and their application to Kiwifruit Decline

In 2012, leaf scorches, wilting, sudden defoliation and dieback symptoms were observed for the first time on several kiwifruit plants in orchards located in Veneto (Northeast of Italy). Diseased plants were also characterised by a heavily compromised root system with none or very few feeding roots, rotting tissues on smaller roots and lack of cohesion between the external cylinder and the core. In relation to these symptoms the new disease was named Kiwifruit Decline (KD). KD rapidly spread in all the most important Italian growing areas and probably up to date is the most concerning phyto-pathological issue for kiwifruit growers. With the main aim to determine KD aetiology and to identify the epidemiological pattern of this disease outbreaks, canonical strategies and new technologies were integrated in an interdisciplinary approach. The work started with the definition of a conceptual framework on the symptoms observed in the field and with the reconstruction of the history of the disease based on the farmers’ experiences. These evidences were used as first-hand source of information and integrated with the experiences gathered by other Italian research groups to hypothesize the etiological causes most probably involved in the disease. From this analysis waterlogging and soil-borne pathogens emerged as the two most probable factors involved in the disease, although their role in the disease was still unknown. Therefore, the following step was the setup of a canonical experimental trial, where the effect of the two most probable etiological causes were compared under controlled conditions. The trial gave unequivocal results clearly stating the necessary interaction between waterlogging and soil borne pathogens to incite the disease. Furthermore, axenic isolation starting from plants that became diseased during this trial, allowed to have a first insight on soil-borne microorganisms potentially involved in the disease, suggesting that one or more pathogens (most probably Oomycetes) might be involved in the disease. Given these results a pathogenicity test was set up and confirmed that Phytopythium vexans was able to induce KD symptoms in both canopy and roots of kiwifruit plants. Once the role of a biotic factor was demonstrated, the studies moved back to the field focusing mostly on remote sensing technologies able to infer the physiological traits of the plants. Thermal and multispectral imagery acquired over a diseased field and classified with unsupervised clustering algorithms allowed to efficiently distinguish asymptomatic from symptomatic plants and to predict, one year in advance, the disease outbreak. Since the involvement of one or more potential soil-borne pathogens was proposed, a metabarcoding study was performed to have a first insight on fungal and oomycete communities associated with KD. Interestingly, Phytopythium vexans not only was found with a low relative abundance within diseased samples, but it was also recorded in healthy samples suggesting that the asymptomatic state of the plants is most probably linked to the environmental conditions averse to the development of the pathogens. Metabarcoding analysis also suggested Phytophthora sojae and Ilyonectria macrodidyma as new potential pathogen candidates. Results from this thesis provided several breakthroughs regarding the KD syndrome and defined the starting point for future studies. Indeed, not only the disease is now clearly associated to a combination of waterlogging conditions and soil-borne pathogens, but also a standardized protocol was setup to reproduce the disease. Moreover, new tools for in-field early disease detection are proposed and the first overview of fungal and oomycete community associated to KD is given for both root endosphere and rhizosphere compartments.