Homologous Recombination and Xylella fastidiosa Host–Pathogen Associations in South America

Abstract

Homologous recombination affects the evolution of bacteria such as Xylella fastidiosa, a naturally competent plant pathogen that requires insect vectors for dispersal. This bacterial species is taxonomically divided into subspecies, with phylogenetic clusters within subspecies that are host specific. One subspecies, pauca, is primarily limited to South America, with the exception of recently reported strains in Europe and Costa Rica. Despite the economic importance of X. fastidiosa subsp. pauca in South America, little is known about its genetic diversity. Multilocus sequence typing (MLST) has previously identified six sequence types (ST) among plant samples collected in Brazil (both subsp. pauca and multiplex). Here, we report on a survey of X. fastidiosa genetic diversity (MLST based) performed in six regions in Brazil and two in Argentina, by sampling five different plant species. In addition to the six previously reported ST, seven new subsp. pauca and two new subsp. multiplex ST were identified. The presence of subsp. multiplex in South America is considered to be the consequence of a single introduction from its native range in North America more than 80 years ago. Different phylogenetic approaches clustered the South American ST into four groups, with strains infecting citrus (subsp. pauca); coffee and olive (subsp. pauca); coffee, hibiscus, and plum (subsp. pauca); and plum (subsp. multiplex). In areas where these different genetic clusters occurred sympatrically, we found evidence of homologous recombination in the form of bidirectional allelic exchange between subspp. pauca and multiplex. In fact, the only strain of subsp. pauca isolated from a plum host had an allele that originated from subsp. multiplex. These signatures of bidirectional homologous recombination between endemic and introduced ST indicate that gene flow occurs in short evolutionary time frames in X. fastidiosa, despite the ecological isolation (i.e., host plant species) of genotypes.

Natural Competence Rates Are Variable Among Xylella fastidiosa Strains and Homologous Recombination Occurs In Vitro Between Subspecies fastidiosa and multiplex

“…multiplex and subsp. pauca strains was also reported in a recent study (Coletta-Filho et al 2017). Results of this and previous studies (Oliver et al 2014(Oliver et al , 2015 demonstrated that certain plants serve as hosts for strains from multiple subspecies.…”

“…Both WM1-1 and AlmaEM3 and their recombinants produced symptoms in tobacco, while only AlmaEM3 and their recombinants produced symptoms in blueberry. (Coletta-Filho et al 2017) and from confirmation of natural competence in habitats mimicking natural environments (Kandel et al 2016) to the experimental validation of IHR (this study) suggests that IHR is occurring in nature and may have broader evolutionary implications in X. fastidiosa disease dynamics. In conclusion, X. fastidiosa strains showed extensive natural competence abilities and the recombination potential differed among strains.…”

“…fastidiosa), although recombination among strains of other subspecies has been described (Coletta-Filho et al 2017;Nunes et al 2003;Nunney et al 2012;2014a and c). On testing natural competence in 13 different strains, almost ubiquitous natural competence ability was detected.…”

“…For instance, strains collected from a single host and geographic location formed different haplotypes when they were analyzed by MLSA of environmentally mediated genes (Parker et al 2012). Interestingly, studies that detected genetic diversity among X. fastidiosa strains have also reported the presence of homologous recombination (HR) Coletta-Filho et al 2017;Marcelletti and Scortichini 2016;Nunney et al 2010Nunney et al , 20122013, 2014a andScally et al 2005). In fact, HR was predicted to have a greater effect in creating genetic diversity in X. fastidiosa than point mutation (Kung et al 2013; Nucleotide sequence data is available in the GenBank database under accession numbers KY616728 to KY616749.…”

“…One key knowledge gap is related to the variability of natural competence among strains, as previous studies were based on a few closely related strains belonging to the same subsp., namely, fastidiosa (Kandel et al 2016;Almeida 2011, 2014;Kung et al 2013). Since both genotypic and phenotypic differences have been described in X. fastidiosa strains (Antonova and Hammer 2015;Coletta-Filho et al 2017;Oliver et al 2014Oliver et al , 2015Parker et al 2012;Scally et al 2005), their natural competence abilities could differ, as is the case reported in other naturally competent bacteria (Bossé et al 2009;Coupat et al 2008;Evans and Rozen 2013;Fujise et al 2004;Gromkova et al 1998;Maughan and Redfield 2009;Sikorski et al 2002). Moreover, although IHR has been detected by MLST studies and was hypothesized to lead to plant host shift (Nunney et al 2012;2014a and2014c), there is still no experimental evidence demonstrating the generation of recombinants by mixing two different subspecies.…”