Examining effector requirements, redundancies, and repertoire refinement in the emergent kiwifruit pathogen Pseudomonas syringae pv. actinidiae

Abstract

Pseudomonas syringae pv. actinidiae (Psa) is a bacterial pathogen which causes canker disease on susceptible kiwifruit (Actinidia spp.) hosts. A global pandemic of Psa biovar 3 (Psa3) devastated susceptible kiwifruit orchards. The kiwifruit industry has since recovered following the deployment of more tolerant cultivars. However, little is known about the extent to which the Psa3 population is evolving in orchards and further adapting to its kiwifruit hosts. Effector proteins help pathogens invade their host, extract nutrients, and suppress immunity. Psa3 is an emergent kiwifruit pathogen with over thirty functional effectors, providing a unique opportunity to understand how host selection shapes pathogen evolution. In particular, this thesis sought to understand whether Psa3 requires all of its effectors to cause disease. Recent research suggests that only a few Psa effectors are required for virulence on susceptible kiwifruit hosts. Further still, resistant kiwifruit hosts such as Actinidia arguta can recognise several Psa effectors. Why, then, does Psa retain so many effectors in its repertoire? Using complementary approaches of orchard-based genome biosurveillance and effector knockout strain competition, this work examined effector requirements, redundancies, and repertoire refinement across different kiwifruit hosts. The selective pressure exerted by serially passaging a competitive pool of effector knockout strains in planta has allowed the detection of the subtle contributions many effectors make to virulence. While the majority of Psa’s effectors previously appeared to be non-essential, competition results suggest they may be collectively required for successful virulence, with host-specific effector requirements. The methodologies developed in this work present a far more nuanced way to assess subtle effector requirements, informing our understanding of why pathogens may retain expansive effector repertoires. Examination of effector repertoire dynamics, combined with divergence dating, suggests that Psa emerged before the commercial cultivation of kiwifruit, with the contemporary pandemic lineage of Psa3 representing a highly adapted pathogen at the peak of its fitness landscape. Ultimately, this research has provided important insights into the evolution of emergent pathogens and advances our understanding of effector requirements and repertoire refinement across natural and experimental settings.