Several species of Xanthomonas cause bacterial leaf spot, a disease that affects solanaceous crops worldwide. The diversity of 64 Australian isolates of Xanthomonas spp. associated with bacterial leaf spot in tomato, capsicum and chilli crops in eastern Australia was determined using multi-locus sequence analysis of atpD, dnaK, efp and gyrB genes, species-specific PCR assays and biochemical analyses. At least five species of Xanthomonas associated with bacterial leaf spot were identified in Australian tomato, capsicum and chilli crops and their pathogenicity assessed. Phylogenetic and biochemical analyses identified X. euvesicatoria, X. perforans and X. vesicatoria as the most frequently recovered pathogenic species. Non-pathogenic and weakly pathogenic species were also identified. The suitability of the identification methods used and the implications of the detection of these species will be discussed.Keywords amylolytic . pectolytic . Solanaceae . disease management IntroductionBacterial leaf spot (BLS) is a disease of solanaceous crops that occurs worldwide, especially in warm and humid climates (Jones et al. 2014). Several species of Xanthomonas are reported to cause BLS of tomato (Solanum lycopersicum), capsicum and chilli (Capsicum annuum) . The symptoms of BLS are small, brown, angular, water-soaked lesions on leaves, stems and fruit, and result in defoliation and direct fruit damage. Severe infection may result in extensive damage to crops with significant yield losses (Pernezny et al. 2003). Species reported to cause BLS all produce similar symptoms on their hosts, making precise diagnosis difficult from visual symptoms alone. The impact of pathological convergence and importance of phylogenetic testing in the case of BLS are further highlighted by Hajri et al. (2009). The causal bacteria are spread by wind and water, and may survive in crop residues, weeds and volunteer plants (Jones et al. 1986). A link between field disease and seed contamination has Eur J Plant Pathol (2018) 150:595-608

Contamination of the root canal system by persistent, enteric bacteria via leakage through interim restorations has been well documented. This in vitro study evaluated the ability of interappointment medications to prevent contamination of the root canal system by Enterococcus faecalis. Coronally unsealed, medicated tooth roots fixed in a closed system were contaminated daily with a standardized, aerobic, broth culture of E. faecalis. Four medications were evaluated (n = 15): group A, calcium hydroxide/methylcellulose paste; group B, camphorated parachlorophenol/calcium hydroxide paste; group C, 1% chlorhexidine/methylcellulose gel; and group D, calcium hydroxide points. The mean number of days to contamination as indicated by turbidity in the closed system was the following: group A, 37; group B, 46; group C, 16; group D, 5; and a positive control (no medication), 3. A one-way analysis of variance with a Scheffe post hoc test (p = 0.05) detected significant differences in effectiveness with A and B superior to C and D, and C superior to D.

Zucchini plants, with symptoms including twisted petioles, necrotic leaves, crown-rot and internal fruit-rot, were found in Bundaberg, Australia at a commercial field for the first time during late autumn 2016, resulting in direct yield losses of 70 to 80%. Three Pseudomonas syringae strains that isolated from symptomatic leaf (KL004-k1), crown (77-4C) and fruit (KFR003-1) were characterised and their pathogenicity evaluated on pumpkin, rockmelon, squash and zucchini. Biochemical assays showed typical results for P. syringae. The three isolates differed, however, in that two produced fluorescent pigment (KFR003-1 and 77-4C) whilst the third, KL004-k1, was non-florescent. Multi-locus sequence analysis classified the isolates to phylogroup 2b. The SNP analysis of core genome from the Australian and closely related international isolates of P. syringae showed two separate clusters. The Australian isolates were clustered based on fluorescent phenotype. Pathogenicity tests demonstrated all three isolates moved systemically within the inoculated plants and induced necrotic leaf symptoms in zucchini plants. Their identities were confirmed with specific PCR assays for P. syringae and phylogroup 2. Pathogenicity experiments also showed the Eva variety of zucchini was more susceptible than Rosa for all three isolates. Isolate KL004-k1 was more virulent than 77-4C on pumpkin, rockmelon, squash and zucchini. This study expands the knowledge of P. syringae isolates that infect cucurbits and provides useful information for growers about the relative susceptibility of a range of cucurbit species.

Background The genetic diversity in Australian populations of Xanthomonas species associated with bacterial leaf spot in tomato, capsicum and chilli were compared to worldwide bacterial populations. The aim of this study was to confirm the identities of these Australian Xanthomonas species and classify them in comparison to overseas isolates. Analysis of whole genome sequence allows for the investigation of bacterial population structure, pathogenicity and gene exchange, resulting in better management strategies and biosecurity. Results Phylogenetic analysis of the core genome alignments and SNP data grouped strains in distinct clades. Patterns observed in average nucleotide identity, pan genome structure, effector and carbohydrate active enzyme profiles reflected the whole genome phylogeny and highlight taxonomic issues in X. perforans and X. euvesicatoria . Circular sequences with similarity to previously characterised plasmids were identified, and plasmids of similar sizes were isolated. Potential false positive and false negative plasmid assemblies were discussed. Effector patterns that may influence virulence on host plant species were analysed in pathogenic and non-pathogenic xanthomonads. Conclusions The phylogeny presented here confirmed X. vesicatoria , X. arboricola , X. euvesicatoria and X. perforans and a clade of an uncharacterised Xanthomonas species shown to be genetically distinct from all other strains of this study. The taxonomic status of X. perforans and X. euvesicatoria as one species is discussed in relation to whole genome phylogeny and phenotypic traits. The patterns evident in enzyme and plasmid profiles indicate worldwide exchange of genetic material with the potential to introduce new virulence elements into local bacterial populations. Electronic supplementary material The online version of this article (10.1186/s12864-019-5600-x) contains supplementary material, which is available to authorized users.