The genomic diversity, taxonomy, and molecular diagnostics of the Xanthomonas hortorum – Xanthomonas hydrangeae species complex

Abstract

The bacterial genus Xanthomonas mainly contains phytopathogenic members that cause devastating diseases on over 400 plant species, including grasses, citrus, and fruit trees. Some Xanthomonas species, such as Xanthomonas hortorum, are mostly known to affect ornamental plants (Latin etymology: hortorum - “garden”). At the start of this thesis, and even though X. hortorum was reported on new hosts and in new countries with an increased frequency, knowledge regarding this species was scarce. Therefore, the general aim of this thesis was to use genomics tools to fill the knowledge gap regarding X. hortorum in terms of genomic diversity, taxonomy, and molecular diagnostics. This thesis revisited the phylogeny of the species, first by formally and validly describing Xanthomonas hydrangeae, the closest phylogenetic relative of X. hortorum, thereby defining the X. hortorum – X. hydrangeae species complex. The phylogeny was updated during the course of the thesis, reflecting the very dynamic nature of bacterial taxonomy and the wide host range of members within this species complex. The genomics information was used to develop seven isothermal diagnostic assays, detecting multilevel taxa within the species complex. The dual applicability of the assays as diagnostics and differentiation tools was also demonstrated. These assays can 1) be used directly on symptomatic plant material for diagnostics and 2) assign the causal agents to the species complex and, if possible, to lower taxonomic levels. The results of the assays revealed that the host range of X. hortorum may be more diverse than described to date. A comparative genomics analysis showed conserved genomic features including the type III secretion system as one of the potentially major pathogenicity factors. The study further suggested that the diversity of members within the species complex is mostly related to their type III effectome and their plasmid content. This thesis also gathered evidence related to the expansive host range of X. hortorum, suggesting that the pathovar concept may not be applicable to the species anymore given the many disadvantages of this infraspecific classification. A move towards a relational genomic classification (e.g., not related to the host) is discussed, and the drawbacks of such classification are put into perspective, notably within the scope of plant health regulation.