Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

A dramatic outbreak of Xylella fastidiosa decimating olive was discovered in 2013 in Apulia, Southern Italy. This pathogen is a quarantine bacterium in the European Union (EU) and created unprecede...

https://apsjournals.apsnet.org/doi/pdf/10.1094/PHYTO-08-18-0319-FI

Xylella fastidiosa in Olive in Apulia: Where We Stand.

Xylella fastidiosa is a plant pathogenic bacterium emerging in Europe. In France its emergence has been demonstrated through interceptions of contaminated coffee plants and, in 2015, by a survey of natural settings. The first French focus of contamination was detected in 2015 in Corsica; since then, almost 300 foci have been found and nearly 30 plant species have been declared contaminated, with Polygala myrtifolia remaining the principal host, suffering from severe leaf scorch. This study reports on the diversity of X. fastidiosa identified in France in 2015. Multilocus sequence analysis/typing revealed the presence of mainly X. fastidiosa subsp. multiplex sequence types (STs) ST6 and ST7. A focus of X. fastidiosa subsp. pauca ST53 was identified in mainland France; one sample contaminated by X. fastidiosa subsp. sandyi ST76, one novel recombinant, and coinfections of different isolates in individual samples were also identified, but could not be confirmed by successive samplings, indicating limited or transient contamination. Koch's postulates were fulfilled for two isolates of X. fastidiosa subsp. multiplex on P. myrtifolia, one being ST6 and the other ST7. Comparative genomics of the genome sequences of three French isolates (one ST6 and two ST7) with available sequences revealed that, unlike the American Dixon strain, the French ST6 and ST7 strains are devoid of a plasmid encoding a complete type IV secretion system. Other differences regarding phage sequences were highlighted. Altogether, the results suggest that the emergence of X. fastidiosa in France is linked to several introduction events of diverse strains from different subspecies.

https://bsppjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/ppa.12695

Several subspecies and sequence types are associated with the emergence of Xylella fastidiosa in natural settings in France

After the first confirmed outbreak of Xylella fastidiosa in the European Union (EU), associated with an olive disease denoted olive quick decline syndrome, mandatory surveys are now carried out in the member States and inspections increased at EU entry points such as ports. Such activities led to the interception of X. fastidiosa-infected coffee plants in consignments originating from Central America. Similarly, the geographic expansion of the olive decline epidemic area of the Apulia region (southern Italy) prompted investigations to identify new host plants. Here we report the interception of three novel bacterial sequence types in Italy, based on multi-locus sequence typing, that cluster with different X. fastidiosa subspecies, illustrating the risk of the introduction of additional pathogen genetic diversity into Europe. In the epidemic area of Apulia, new foci as well as host plant species positive with X. fastidiosa, including cherry, myrtleleaf and rosemary, were found to be all infected with the same sequence type of this bacterium (ST53, or CoDiRO strain). This work highlights the limited knowledge of X. fastidiosa phylogenetic and phenotypic diversity, the risk of novel X. fastidiosa introductions via contaminated plant material, and corroborates other studies indicating that the Apulia epidemic emerged from a single introduction of this pathogen into the region.

/pdf/intercepted-isolates-of-xylella-fastidiosa-in-europe-reveal-3xsl6ytx5p.pdf

Intercepted isolates of Xylella fastidiosa in Europe reveal novel genetic diversity.

The quick decline syndrome of olive (OQDS) is a disease that appeared all of a sudden some years ago in a restricted area near the city of Gallipoli (Ionian coast of the Salento peninsula, southern-east Italy) and began spreading through the heavily olive-grown countryside of lower Salento. Xylella fastidiosa, a quarantine pathogen of American origin previously undetected in the European Union territory, except for two unconfirmed records from Kosovo and Turkey, proved to be consistently associated with symptomatic trees. X. fastidiosa is a Gram-negative bacterium that invades and multiplies in the xylem vessels of infected hosts, from which it is acquired by xylem-feeding insect vectors (belonging to Auchenorrhyncha, including cicadellids sharpshooter leafhoppers group, Cicadellidae, Cicadellinae), and aphrophorids (cercopids and spittlebugs, Cercopidae) and transferred to other plants. The Salentian strain of X. fastidiosa, denoted CoDiRO, was obtained in axenic culture. Its genome, a DNA molecule ca. 2.5 million base-pairs in size, was sequenced and identified as a genotype of X. fastidiosa subsp. pauca molecularly identical to an isolate of the same subspecies from Costa Rica. In nature, strain CoDiRO infects a number of woody and shrubby hosts but not grapevines and citrus and is mainly transmitted by Philaenus spumarius (meadow spittlebug), a froghopper quite common in the Salento area where it thrives primarily on olive. Since OQDS eradication and sanitation of infected olives are unfeasible, strategies have been envisaged for restraining the spread of the pathogen and its vector within the boundaries of the currently infected zone.

The current status of the quick decline syndrome of olive in southern Italy

The recent finding of Xylella fastidiosa ( Xf ) in olive trees in southern Italy, the scanty molecular information on this bacterium and its association with the olive quick decline syndrome (OQDS) prompted the necessity to isolate and acquire more genetic data on the type of strain present in that region. For the first time, the bacterium was isolated from infected olive on culture media. Genetic information were obtained through genomic comparison with other subspecies or strains. The sequences of thirteen genes from its genome, comprising seven housekeeping genes ( leuA, petC, lacF , cysG, holC, nuoL and gltT ) usually used in multilocus sequence typing (MLST) systems, and six genes involved in different biochemical functions ( RNA Pol sigma-70 factor, hypothetical protein HL, 16S rRNA, rfbD, nuoN, and pilU ), were analyzed. The sequences of the biochemical function genes were explored  individually to study the genetic structure of this bacterium, while the MLST genes were linked together into one concatameric sequence (4161 bp long) to increase the resolution of the phylogenetic analysis when compared with Xf strains previously reported. Sequence analyses of single genes showed that the Xf olive strain is distinct from the four previously defined taxons ( Xf subsp. fastidiosa , Xf subsp. multiplex , Xf subsp. sandyi and Xf subsp. pauca ) with a dissimilarity rate that reached 4%. In particular, Xf from olive shared the greatest identity with the strain “9a5c” (subsp. pauca ), but was nevertheless distinct from it. Similarly, the MLST based on concatameric sequences confirmed the genetic variance of Xf from olive by generating a novel sequence type profile (ST53). Phylogenetic tree analyses showed that Xf from olive clustered in one clade close to subspecies pauca (strains “9a5c” and “CVC0018”), but was nevertheless distinct from them. These results indicate molecular divergence of this olive bacterium with all other strains yet reported.

Multilocus sequence typing of Xylella fastidiosa isolated from olive affected by “olive quick decline syndrome” in Italy

Bacterial canker of stone fruit is a destructive disease of Prunus species. Here we characterized five Pseudomonas syringae (Ps) strains isolated from bacterial cankers of stone fruits in East Azerbaijan province, Iran. Koch’s postulates were performed demonstrating pathogenicity on apricot cuttings. Ice-nucleation activity and syringomycin synthesis were determined phenotypically and confirmed molecularly in all five strains. Strains were variably resistant to copper. The strains were then compared to a sample of 227 strains of the Ps species complex using multilocus sequence analysis (MLSA) of the four housekeeping genes gap1, gltA, gyrB, and rpoD. The concatenated sequences of the four genes provided a deeply-resolved phylogeny. Iranian strains all belonged to Ps phylogroup 2 but clustered into three separate sub-groups. They had the greatest similarity to strains isolated from stone fruit trees in the USA, UK, and Lebanon but also to strains isolated from other plant species and the water cycle. We conclude that canker of stone fruit is caused by a diverse group of Ps phylogroup 2 strains with global distribution. Further sampling, host range testing, and genome sequencing will be needed to get further insight into the relative role of the water cycle and other modes of long distance movement in the dissemination of Ps strains that cause bacterial canker of stone fruit.

Phenotypic characterization and phylogenetic analysis of Pseudomonas syringae strains associated with canker disease on apricot in Iran within the context of the global genetic diversity of the P. syringae complex

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Multilocus sequence typing of Xylella fastidiosa isolated from olive affected by “olive quick decline syndrome” in Italy

Phenotypic characterization and phylogenetic analysis of Pseudomonas syringae strains associated with canker disease on apricot in Iran within the context of the global genetic diversity of the P. syringae complex