Technologies for early detection and monitoring of new and emerging pathogens: safeguarding urban and forest trees

Forests and urban trees face growing threats from pathogens, both alien and native, and historical examples have proven invasive forest pathogens capable of reshaping entire ecosystems. Climate change exacerbates the problem by favoring pathogen growth and predisposing trees to infection. The galloping rates at which forest pathogen outbreaks are occurring needs to be addressed, but there is a lack of appropriate detection tools that can be implemented into biosurveillance infrastructures to mitigate these issues. This thesis aimed to acquire new knowledge and improve the applicability of a new generation of detection tools, focusing on analysis of volatile organic compounds for pathogens relevant for Sweden (Fusarium circinatum and Phytophthora), and high-throughput DNA sequencing of pine needle fungi. In this thesis, volatile analysis could distinguish between species of Fusarium and Phytophthora in vitro. In vivo studies showed that quantitative volatile comparisons can distinguish between Fusarium circinatum-inoculated pine trees and mock-inoculated controls, and that beech and oak trees infected with Phytophthora cinnamomi or Phytophthora plurivora produced volatiles that were qualitatively distinct from controls, though volatiles emitted by the pathogens grown in vitro were not detected in vivo. Pine needle associated mycobiomes were compared using Illumina and nanopore sequencing technologies which revealed that nanopore identified a larger proportion of the taxa to the species level, while Illumina captured higher species diversity. Both platforms successfully identified pathogenic species in asymptomatic needles, illustrating their capacity for early detection. This work underscores the potential of implementing already available technologies for improving the biosecurity infrastructures for safeguarding future forest health.