The Complex Biogeography of the Plant Pathogen Xylella fastidiosa: Genetic Evidence of Introductions and Subspecific Introgression in Central America

Abstract

The bacterium Xylella fastidiosa is a plant pathogen with a history of economically damaging introductions of subspecies to regions where its other subspecies are native. Genetic evidence is presented demonstrating the introduction of two new taxa into Central America and their introgression into the native subspecies, X. fastidiosa subsp. fastidiosa. The data are from 10 genetic outliers detected by multilocus sequence typing (MLST) of isolates from Costa Rica. Six (five from oleander, one from coffee) defined a new sequence type (ST53) that carried alleles at six of the eight loci sequenced (five of the seven MLST loci) diagnostic of the South American subspecies Xylella fastidiosa subsp. pauca which causes two economically damaging plant diseases, citrus variegated chlorosis and coffee leaf scorch. The two remaining loci of ST53 carried alleles from what appears to be a new South American form of X. fastidiosa. Four isolates, classified as X. fastidiosa subsp. fastidiosa, showed a low level of introgression of non-native DNA. One grapevine isolate showed introgression of an allele from X. fastidiosa subsp. pauca while the other three (from citrus and coffee) showed introgression of an allele with similar ancestry to the alleles of unknown origin in ST53. The presence of X. fastidiosa subsp. pauca in Central America is troubling given its disease potential, and establishes another route for the introduction of this economically damaging subspecies into the US or elsewhere, a threat potentially compounded by the presence of a previously unknown form of X. fastidiosa.

Intercepted isolates of Xylella fastidiosa in Europe reveal novel genetic diversity

“…Our results indicate that three of these isolates represent novel STs, with loci originating from different X. fastidiosa subspecies; these isolates were all intercepted in northern Italy. A fourth ST, ST53, has already been described in Italy and Costa Rica (Nunney et al 2014a;Loconsole et al 2014). These findings corroborate previous analyses that X. fastidiosa-colonized plant material represents a major pathway for the long-distance dispersal of this bacterium.…”

“…All isolates collected from the Apulia region belonged to ST53; details of the allelic profile of ST53 have been analyzed in detail elsewhere (Nunney et al 2014a). Four Fig.…”

“…Examples include a North American genotype causing plum leaf scald in South America (Nunes et al 2003), a Pierce's disease of grapevines genotype from the United States in Taiwan (Su et al 2013), with the United States Pierce's disease clade itself having been introduced from Central America . The recent introduction of a genotype of X. fastidiosa subspecies pauca, previously limited to South America, to Central America (Nunney et al 2014a) and Italy Elbeaino et al 2014), represents another example. Therefore, long-distance dispersal followed by establishment has occurred multiple times, occasionally having devastating consequences.…”

“…Furthermore, X. fastidiosa taxonomy has had a convoluted story, which now is understood to be a consequence of homologous recombination as this bacterium is naturally competent (Kung and Almeida 2011). The emergence of a previously unknown genotype in Italy Elbeaino et al 2014), coupled with its first report from Costa Rica during the same year (Nunney et al 2014a), highlights the risk as well as threat of such knowledge gap, as no information was previously available about the host plant range or biology of this specific genotype (known as ST53). The introduction of multilocus sequence typing (MLST, Yuan et al 2010) revolutionized X. fastidiosa taxonomy and organized phylogenetic clades in a meaningful manner in the face of frequent homologous recombination.…”

Scientific Opinion on the risks to plant health posed byXylella fastidiosain the EU territory, with the identification and evaluation of risk reduction options

“…More recently, another subspecies has been proposed, subspecies morus, associated with isolates in the USA colonising mulberry (Nunney et al 2014b). This subspecies, proposed based on multilocus sequence typing (MLST) data, is recombinogenic with alleles from subspecies fastidiosa and multiplex (Nunney et al, 2014a). A report from Taiwan (Leu and Su, 1993;Su et al, 2012) describing a genotype of X. fastidiosa causing a disease in pear classifies the agent as X. fastidiosa based on its 16S rDNA sequence.…”