Phylogenetic relationships of Xylella fastidiosa strains from different hosts, based on 16S rDNA and 16S-23S intergenic spacer sequences

TaqMan Quantitative PCR Detection of Xylella taiwanensis in Taiwan

Xylella taiwanensis (Xt) is a nutritionally fastidious bacterial pathogen causing pear leaf scorch disease (PLSD) in Taiwan. The disease causes early defoliation, loss of tree vigor, and reduction in fruit yield and quality. No cure for PLSD is available. The only option for growers to control the disease is to use pathogen-free propagation material, which requires early and accurate detection of Xt. Currently, only one simplex PCR method is available for the diagnosis of PLSD. We developed five Xt-specific TaqMan quantitative PCR (TaqMan qPCR) systems (primers-probe sets) for the detection of Xt. The PCR systems target three conserved genomic loci commonly used in bacterial pathogen detection: the 16S rRNA gene (rrs), the 16S-23S rRNA intergenic transcribed sequence (16S-23S rRNA ITS), and the DNA gyrase gene (gyrB). BLAST analysis using the GenBank nr sequence database, including whole genome sequences of 88 Xanthomonas campestris pv. campestris (Xcc) strains, 147 X. fastidiosa (Xf) strains, and 32 Xt strains, showed that all primer and probe sequences were specific only to Xt. Single nucleotide polymorphisms (SNPs) provided the primer/probe specificity to Xt. The PCR systems were evaluated by using DNA samples from pure cultures of two Xt strains, one Xf strain, one Xcc strain, and 140 plant samples collected from 23 pear orchards in four counties in Taiwan. The two-copy rrs and 16S-23S rRNA ITS-based PCR systems (Xt803-F/R, Xt731-F/R, and Xt16S-F/R) showed higher detection sensitivity than the two single-copy gyrB-based systems (XtgB1-F/R and XtgB2-F/R). A metagenomic analysis of a representative PLSD leaf sample detected the presence of non-Xt proteobacteria and fungal pathogens that should be taken into consideration in PLSD, as they might interfere with diagnosis.

Pest categorisation of Xylella taiwanensis

The EFSA Plant Health Panel performed a pest categorisation of Xylella taiwanensis, a Gram-negative bacterium belonging to the Xanthomonadaceae. The pathogen is a well-defined taxonomic entity, and it is the causal agent of the pear leaf scorch. X. taiwanensis is present in subtropical and temperate areas of the island of Taiwan, where it affects low chilling pear cultivars of the species Pyrus pyrifolia (Asian pear). No other plant species are reported to be affected by the pathogen. The pathogen is not known to be present in the EU territory and it is not included in the Commission Implementing Regulation (EU) 2019/2072. The main pathway for the entry of the pathogen into the EU territory is host plants for planting (except seeds); another possible pathway might be represented by putative insect vectors, though their identity remains unknown. The cultivated area of P. pyrifolia in the EU territory is very limited. Conversely, the genetically related P. communis is widely cultivated in most EU Member States and there is no information so far on the susceptibility of its several cultivars. Should the pest establish in the EU, economic impact is expected, provided that suitable insect vectors are present and P. communis is as susceptible to infection as P. pyrifolia. Phytosanitary measures are available to prevent the introduction and spread of the pathogen into the EU, since plants for planting from Taiwan is a closed pathway; nonetheless, putative vectors, if confirmed and identified, may represent an additional risk of the pathogen's introduction and spread. The lack of knowledge on whether X. taiwanensis can infect P. communis, the identity and presence of suitable vectors in the EU lead to key uncertainties on entry, establishment, spread and impact. X. taiwanensis satisfies the criteria that are within the remit of EFSA to assess for this species to be regarded as a potential Union quarantine pest.

Xylella fastidiosa: Host Range and Advance in Molecular Identification Techniques

In the never ending struggle against plant pathogenic bacteria, a major goal is the early identification and classification of infecting microorganisms. Xylella fastidiosa, a Gram-negative bacterium belonging to the family Xanthmonadaceae, is no exception as this pathogen showed a broad range of vectors and host plants, many of which may carry the pathogen for a long time without showing any symptom. Till the last years, most of the diseases caused by X. fastidiosa have been reported from North and South America, but recently a widespread infection of olive quick decline syndrome caused by this fastidious pathogen appeared in Apulia (south-eastern Italy), and several cases of X. fastidiosa infection have been reported in other European Countries. At least five different subspecies of X. fastidiosa have been reported and classified: fastidiosa, multiplex, pauca, sandyi, and tashke. A sixth subspecies (morus) has been recently proposed. Therefore, it is vital to develop fast and reliable methods that allow the pathogen detection during the very early stages of infection, in order to prevent further spreading of this dangerous bacterium. To this purpose, the classical immunological methods such as ELISA and immunofluorescence are not always sensitive enough. However, PCR-based methods exploiting specific primers for the amplification of target regions of genomic DNA have been developed and are becoming a powerful tool for the detection and identification of many species of bacteria. The aim of this review is to illustrate the application of the most commonly used PCR approaches to X. fastidiosa study, ranging from classical PCR, to several PCR-based detection methods: random amplified polymorphic DNA (RAPD), quantitative real-time PCR (qRT-PCR), nested-PCR (N-PCR), immunocapture PCR (IC-PCR), short sequence repeats (SSRs, also called VNTR), single nucleotide polymorphisms (SNPs) and multilocus sequence typing (MLST). Amplification and sequence analysis of specific targets is also mentioned. The fast progresses achieved during the last years in the DNA-based classification of this pathogen are described and discussed and specific primers designed for the different methods are listed, in order to provide a concise and useful tool to all the researchers working in the field.

Xylella taiwanensis sp. nov., causing pear leaf scorch disease

A Gram-stain-negative, nutritionally fastidious bacterium (PLS229T) causing pear leaf scorch was identified in Taiwan and previously grouped into Xylella fastidiosa. Yet, significant variations between PLS229T and Xylellafastidiosa were noted. In this study, PLS229T was evaluated phenotypically and genotypically against representative strains of Xylellafastidiosa, including strains of the currently known subspecies of Xylellafastidiosa, Xylella fastidiosa subsp. multiplex and 'Xylella fastidiosasubsp.pauca'. Because of the difficulty of in vitro culture characterization, emphases were made to utilize the available whole-genome sequence information. The average nucleotide identity (ANI) values, an alternative for DNA-DNA hybridization relatedness, between PLS229T and Xylellafastidiosa were 83.4-83.9 %, significantly lower than the bacterial species threshold of 95 %. In contrast, sequence similarity of 16S rRNA genes was greater than 98 %, higher than the 97 % threshold to justify if two bacterial strains belong to different species. The uniqueness of PLS229T was also evident by observing only about 87 % similarity in the sequence of the 16S-23S internal transcribed spacer (ITS) between PLS229T and strains of Xylellafastidiosa, discovering significant single nucleotide polymorphisms at 18 randomly selected housekeeping gene loci, observing a distinct fatty acid profile for PLS229T compared with Xylellafastidiosa, and PLS229T having different observable phenotypes, such as different susceptibility to antibiotics. A phylogenetic tree derived from 16S rRNA gene sequences showed a distinct PLS229T phyletic lineage positioning it between Xylellafastidiosa and members of the genus Xanthomonas. On the basis of these data, a novel species, Xylella taiwanensis sp. nov. is proposed. The type strain is PLS229T (=BCRC 80915T=JCM 31187T).

Diversity Evaluation of Xylella fastidiosa from Infected Olive Trees in Apulia (Southern Italy)

Olive culture is very important in the Mediterranean Basin. A severe outbreak of Olive Quick Decline Syndrome (OQDS) caused by Xylella fastidiosa infection was first noticed in 2013 on olive trees in the southern part of Apulia region (Lecce province, southern Italy). Studies were carried out for detection and diversity evaluation of the Apulian strain of Xylella fastidiosa. The presence of the pathogen in olive samples was detected by PCR amplifying the 16S rDNA, gyrase B subunit (gyrB) and HL hypothetical protein genes and single nucleotide polymorphisms (SNPs) assessment was performed to genotype X. fastidiosa. Twelve SNPs were recorded over gyrB and six SNPs were found for HL gene. Less variations were detected on 16S rDNA gene. Only gyrB and HL provided sufficient information for dividing the Apulian X. fastidiosa olive strains into subspecies. Using HL nucleotide sequences was possible to separate X. fastidiosa into subspecies pauca and fastidiosa. Whereas, nucleotide variation present on gyrB gene allowed separation of X. fastidiosa subsp. pauca from the other subspecies multiplex and fastidiosa. The X. fastidiosa strain from Apulia region was included into the subspecies pauca based on three genes phylogenetic analyses.

Draft Genome Sequence of Xylella fastidiosa Pear Leaf Scorch Strain in Taiwan

The draft genome sequence of Xylella fastidiosa pear leaf scorch strain PLS229, isolated from the pear cultivar Hengshan (Pyrus pyrifolia) in Taiwan, is reported here. The bacterium has a genome size of 2,733,013 bp, with a G+C content of 53.1%. The PLS229 genome was annotated and has 3,259 open reading frames and 50 RNA genes.

A Systematic Study Reveals that Xylella fastidiosa Strains from Pecan Are Part of X. fastidiosa subsp. multiplex

Xylella fastidiosa causes disease in a number of economically important crops, ornamental plants, and shade trees, including grapevine, citrus, oleander, and sycamore. In pecan, X. fastidiosa causes pecan bacterial leaf scorch (PBLS), which leads to defoliation and reduces nut yield. No economically effective treatments are available for PBLS. In order to improve PBLS management practices, it is necessary to determine the subspecies of X. fastidiosa strains that infect pecan so that potential sources of inoculum may be identified. Multiprimer polymerase chain reaction (PCR) and phylogenetic analyses using nucleotide sequence data from the 16S-23S rRNA intergenic transcribed spacer (ITS) region and pglA consistently identified strains of X. fastidiosa isolated from pecan as X. fastidiosa subsp. multiplex. Enterobacterial repetitive intergenic consensus PCR and repetitive extragenic palindromic (REP)-PCR analyses were congruent with phylogenetic analyses. REP-PCR analyses indicated genetic variation within strains of X. fastidiosa from pecan. From these same analyses, X. fastidiosa strains from sycamore, grapevine, and oleander from Louisiana were identified as subsp. multiplex, subsp. fastidiosa, and subsp. sandyi, respectively. This study provides additional information about the host ranges of X. fastidiosa subspecies.

Differentiation of Xylella fastidiosa strains via multilocus sequence analysis of environmentally mediated genes (MLSA-E)

Isolates of the plant pathogen Xylella fastidiosa are genetically very similar, but studies on their biological traits have indicated differences in virulence and infection symptomatology. Taxonomic analyses have identified several subspecies, and phylogenetic analyses of housekeeping genes have shown broad host-based genetic differences; however, results are still inconclusive for genetic differentiation of isolates within subspecies. This study employs multilocus sequence analysis of environmentally mediated genes (MLSA-E; genes influenced by environmental factors) to investigate X. fastidiosa relationships and differentiate isolates with low genetic variability. Potential environmentally mediated genes, including host colonization and survival genes related to infection establishment, were identified a priori. The ratio of the rate of nonsynonymous substitutions to the rate of synonymous substitutions (dN/dS) was calculated to select genes that may be under increased positive selection compared to previously studied housekeeping genes. Nine genes were sequenced from 54 X. fastidiosa isolates infecting different host plants across the United States. Results of maximum likelihood (ML) and Bayesian phylogenetic (BP) analyses are in agreement with known X. fastidiosa subspecies clades but show novel within-subspecies differentiation, including geographic differentiation, and provide additional information regarding host-based isolate variation and specificity. dN/dS ratios of environmentally mediated genes, though <1 due to high sequence similarity, are significantly greater than housekeeping gene dN/dS ratios and correlate with increased sequence variability. MLSA-E can more precisely resolve relationships between closely related bacterial strains with low genetic variability, such as X. fastidiosa isolates. Discovering the genetic relationships between X. fastidiosa isolates will provide new insights into the epidemiology of populations of X. fastidiosa, allowing improved disease management in economically important crops.

Cicadomorpha insects associated with bacterial leaf scorch infected oak in central New Jersey

Potential insect vectors for transmission of oak leaf scorch caused by Xylella fastidiosa Wells et al., in pin and red oaks in New Jersey were surveyed by placing yellow sticky card traps in tree canopies and fogging with pyrethrin insecticide during 2002-2006. Thirty-seven Cicadomorpha species were collected from 20 genera in Membracidae, Cicadellidae, Aphrophoridae, and Clastopteridae. Of the 12,880 potential vectors collected, 91.4% were Membracidae, 6.9% were Cicadellidae, and 1.7% were Aphrophoridae and Clastopteridae. Fogging collected more insect species and individuals than sticky card collections. Sticky card sampling, done more frequently and at a larger number of locations provided similar community structure information as fogging. Sticky card collections of the dominant treehopper species, Ophiderma definita Woodruff were male biased when females were gravid. O. definita populations peaked in early June, comprised 68.2% of the total collection, and were more abundant in pin oaks than red oaks. Graphocephala versuta (Say) peaked in mid-July, comprising 6.2% of the total collection. Higher Cicadomorpha populations were observed in asymptomatic oak canopies than in neighboring X. fastidiosa infected oaks. Individual insect specimens collected from oaks were subjected to a X. fastidiosa DNA assay by polymerase chain reaction amplification. The average X. fastidiosa positive rate was 13.89% for all specimens tested. Eleven treehopper species, six leafhopper species, and four spittlebug species tested DNA positive for X. fastidiosa.

Development of LAMP and real-time PCR methods for the rapid detection of Xylella fastidiosa for quarantine and field applications

Xylella fastidiosa is a regulated plant pathogen in many parts of the world. To increase diagnostic capability of X. fastidiosa in the field, a loop-mediated isothermal amplification (LAMP) and real-time polymerase chain reaction (PCR) assay were developed to the rimM gene of X. fastidiosa and evaluated for specificity and sensitivity. Both assays were more robust than existing published assays for detection of X. fastidiosa when screened against 20 isolates representing the four major subgroups of the bacterium from a range of host species. No cross-reaction was observed with DNA from healthy hosts or other bacterial species. The LAMP and real-time assays could detect 250 and 10 copies of the rimM gene, respectively, and real-time sensitivity was comparable with an existing published real-time PCR assay. Hydroxynapthol blue was evaluated as an endpoint detection method for LAMP. When at least 500 copies of target template were present, there was a noticeable color change indicating the presence of the bacterium. Techniques suitable for DNA extraction from plant tissue in situ were compared with a standard silica-column-based laboratory extraction method. A portable PickPen and magnetic bead system could be used to successfully extract DNA from infected tissue and could be used in conjunction with LAMP in the field.

Multilocus sequence typing of Xylella fastidiosa causing Pierce's disease and oleander leaf scorch in the United States

Using a modified multilocus sequence typing (MLST) scheme for the bacterial plant pathogen Xylella fastidiosa based on the same seven housekeeping genes employed in a previously published MLST, we studied the genetic diversity of two subspecies, X. fastidiosa subsp. fastidiosa and X. fastidiosa subsp. sandyi, which cause Pierce's disease and oleander leaf scorch, respectively. Typing of 85 U.S. isolates (plus one from northern Mexico) of X. fastidiosa subsp. fastidiosa from 15 different plant hosts and 21 isolates of X. fastidiosa subsp. sandyi from 4 different hosts in California and Texas supported their subspecific status. Analysis using the MLST genes plus one cell-surface gene showed no significant genetic differentiation based on geography or host plant within either subspecies. Two cases of homologous recombination (with X. fastidiosa subsp. multiplex, the third U.S. subspecies) were detected in X. fastidiosa subsp. fastidiosa. Excluding recombination, MLST site polymorphism in X. fastidiosa subsp. fastidiosa (0.048%) and X. fastidiosa subsp. sandyi (0.000%) was substantially lower than in X. fastidiosa subsp. multiplex (0.240%), consistent with the hypothesis that X. fastidiosa subspp. fastidiosa and sandyi were introduced into the United States (probably just prior to 1880 and 1980, respectively). Using whole-genome analysis, we showed that MLST is more effective at genetic discrimination at the specific and subspecific level than other typing methods applied to X. fastidiosa. Moreover, MLST is the only technique effective in detecting recombination.

Specific detection and identification of Xylella fastidiosa strains causing oleander leaf scorch using polymerase chain reaction

A pair of PCR primers, QH-OLS05/QH-OLS08 specific for strains of Xylella fastidiosa causing oleander leaf scorch was developed. The primers were designed according to a DNA sequence of a randomly amplified polymorphic DNA (RAPD)-polymerase chain reaction (PCR) product unique to oleander strains. The PCR assay using primer pair QH-OLS05/QH-OLS08 allowed quick and simple detection and identification of oleander strains in cultured bacterium and infected plant samples. The assay also can be applied to insect samples. Specific detection and identification of oleander strains of X. fastidiosa by PCR is useful for epidemiologic and etiologic studies of oleander leaf scorch by identifying what plants and insect vectors harbor or carry this particular strain of X. fastidiosa, especially in locations where mixed natural infections by oleander and other strains of X. fastidiosa occur.

Isolation and molecular characterization of Xylella fastidiosa from coffee plants in Costa Rica

Coffee plants exhibiting a range of symptoms including mild to severe curling of leaf margins, chlorosis and deformation of leaves, stunting of plants, shortening of internodes, and dieback of branches have been reported since 1995 in several regions of Costa Rica's Central Valley. The symptoms are referred to by coffee producers in Costa Rica as "crespera" disease and have been associated with the presence of the bacterium Xylella fastidiosa. Coffee plants determined to be infected by the bacterium by enzyme linked immunosorbent assay (ELISA), were used for both transmission electron microscopy (TEM) and for isolation of the bacterium in PW broth or agar. Petioles examined by TEM contained rod-shaped bacteria inside the xylem vessels. The bacteria measured 0.3 to 0.5 microm in width and 1.5 to 3.0 microm in length, and had rippled cell walls 10 to 40 nm in thickness, typical of X. fastidiosa. Small, circular, dome-shaped colonies were observed 7 to 26 days after plating of plant extracts on PW agar. The colonies were comprised of Gram-negative rods of variable length and a characteristic slight longitudinal bending. TEM of the isolated bacteria showed characteristic rippled cell walls, similar to those observed in plant tissue. ELISA and PCR with specific primer pairs 272-l-int/272-2-int and RST31/RST33 confirmed the identity of the isolated bacteria as X. fastidiosa. RFLP analysis of the amplification products revealed diversity within X. fastidiosa strains from Costa Rica and suggest closer genetic proximity to strains from the United States of America than to other coffee or citrus strains from Brazil.

Identification of Lactobacillus UFV H2B20 (probiotic strain) using DNA-DNA hybridization

Sequence analyses of the 16S rDNA gene and DNA-DNA hybridization tests were performed for identification of the species of the probiotic Lactobacillus UFV H2b20 strain. Using these two tests, we concluded that this strain, originally considered Lact. acidophilus, should be classified as Lact. delbrueckii.

Genetic structure and biology of Xylella fastidiosa strains causing disease in citrus and coffee in Brazil

Xylella fastidiosa is a vector-borne, plant-pathogenic bacterium that causes disease in citrus (citrus variegated chlorosis [CVC]) and coffee (coffee leaf scorch [CLS]) plants in Brazil. CVC and CLS occur sympatrically and share leafhopper vectors; thus, determining whether X. fastidiosa isolates can be dispersed from one crop to another and cause disease is of epidemiological importance. We sought to clarify the genetic and biological relationships between CVC- and CLS-causing X. fastidiosa isolates. We used cross-inoculation bioassays and microsatellite and multilocus sequence typing (MLST) approaches to determine the host range and genetic structure of 26 CVC and 20 CLS isolates collected from different regions in Brazil. Our results show that citrus and coffee X. fastidiosa isolates are biologically distinct. Cross-inoculation tests showed that isolates causing CVC and CLS in the field were able to colonize citrus and coffee plants, respectively, but not the other host, indicating biological isolation between the strains. The microsatellite analysis separated most X. fastidiosa populations tested on the basis of the host plant from which they were isolated. However, recombination among isolates was detected and a lack of congruency among phylogenetic trees was observed for the loci used in the MLST scheme. Altogether, our study indicates that CVC and CLS are caused by two biologically distinct strains of X. fastidiosa that have diverged but are genetically homogenized by frequent recombination.

Initial genetic analysis of Xylella fastidiosa in Texas

Xylella fastidiosa is the causative agent of Pierce's Disease of grape. No published record of X. fastidiosa genetics in Texas exists despite growing financial risk to the U.S. grape industry, a Texas population of the glassy-winged sharpshooter insect vector (Homalodisca vitripennis) now spreading in California, and evidence that the bacterium is ubiquitous to southern states. Using sequences of conserved gyrB and mopB genes, we have established at least two strains in Texas, grape strain and ragweed strain, corresponding genetically with subsp. piercei and multiplex, respectively. The grape strain in Texas is found in Vitis vinifera varieties, hybrid vines, and wild Vitis near vineyards, whereas the ragweed strain in Texas is found in annuals, shrubs, and trees near vineyards or other areas. RFLP and QRT PCR techniques were used to differentiate grape and ragweed strains with greater efficiency than sequencing and are practical for screening numerous X. fastidiosa isolates for clade identity.

Comparative genomic characterization of citrus-associated Xylella fastidiosa strains

Background

The xylem-inhabiting bacterium Xylella fastidiosa (Xf) is the causal agent of Pierce's disease (PD) in vineyards and citrus variegated chlorosis (CVC) in orange trees. Both of these economically-devastating diseases are caused by distinct strains of this complex group of microorganisms, which has motivated researchers to conduct extensive genomic sequencing projects with Xf strains. This sequence information, along with other molecular tools, have been used to estimate the evolutionary history of the group and provide clues to understand the capacity of Xf to infect different hosts, causing a variety of symptoms. Nonetheless, although significant amounts of information have been generated from Xf strains, a large proportion of these efforts has concentrated on the study of North American strains, limiting our understanding about the genomic composition of South American strains – which is particularly important for CVC-associated strains.

Results

This paper describes the first genome-wide comparison among South American Xf strains, involving 6 distinct citrus-associated bacteria. Comparative analyses performed through a microarray-based approach allowed identification and characterization of large mobile genetic elements that seem to be exclusive to South American strains. Moreover, a large-scale sequencing effort, based on Suppressive Subtraction Hybridization (SSH), identified 290 new ORFs, distributed in 135 Groups of Orthologous Elements, throughout the genomes of these bacteria.

Conclusion

Results from microarray-based comparisons provide further evidence concerning activity of horizontally transferred elements, reinforcing their importance as major mediators in the evolution of Xf. Moreover, the microarray-based genomic profiles showed similarity between Xf strains 9a5c and Fb7, which is unexpected, given the geographical and chronological differences associated with the isolation of these microorganisms. The newly identified ORFs, obtained by SSH, represent an approximately 10% increase in our current knowledge of the South American Xf gene pool and include new putative virulence factors, as well as novel potential markers for strain identification. Surprisingly, this list of novel elements include sequences previously believed to be unique to North American strains, pointing to the necessity of revising the list of specific markers that may be used for identification of distinct Xf strains.

Genetic Diversity of Xylella fastidiosa Strains from Costa Rica, São Paulo, Brazil, and United States

ABSTRACT The diversity of 42 Xylella fastidiosa strains from Costa Rica, São Paulo, Brazil, and the United States were analyzed using the sequence of the 16S rRNA gene by variable number of tandem repeat (VNTR) fragment analysis and by restriction fragment length polymorphisms (RFLP) of a specific polymerase chain reaction (PCR)-amplification product using enzyme CfoI. Limited variability in the sequence of the 16S rRNA gene was observed and, although the separation was not absolute, most strains from Costa Rica clustered with strains from the United States and not with strains from São Paulo. The PCR-RFLP produced different patterns of DNA bands. The same pattern was shared by strains from Costa Rica, the United States, and two coffee strains from São Paulo, but a different pattern was observed in six coffee and orange strains from Brazil. In all, 32 amplification products were scored in the VNTR fragment analysis. The total variation observed among the X. fastidiosa strains had significant (P < 0.001) contributions from both geography and host origin as inferred by Nei's values of genetic diversity and WINAMOVA statistics. The strains from Costa Rica were isolated from diseased grapevines, coffee, and sweet orange and these strains grouped together and could be distinguished from strains from grapevine from the United States or from either coffee or sweet orange from São Paulo. The strains tested from Costa Rica are most likely of local origin, although the possibility that they have been introduced along with horticultural crops cannot be excluded. In either case, they are examples of independent selection of strains of X. fastidiosa affecting coffee and sweet orange. Greater genetic similarity was observed between strains from Costa Rica and the United States than with those from São Paulo.

Phylogenetic Relationships of Xylella fastidiosa Strains Isolated from Landscape Ornamentals in Southern California

ABSTRACT Xylella fastidiosa is an insect-borne, xylem-limited pathogenic bacterium that has been associated with a rise in incidence of diseased landscape ornamentals in southern California. The objective of this study was to genetically characterize strains isolated from ornamental hosts to understand their distribution and identity. Strains of X. fastidiosa isolated from ornamentals were characterized using a multiprimer polymerase chain reaction (PCR) system, random amplified polymorphic DNA (RAPD)-PCR, and sequence analysis of the 16S-23S rDNA intergenic spacer region (ISR). Based on RAPD-PCR and 16S-23S rDNA ISR, strains isolated from daylily, jacaranda, and magnolia clustered with members of X. fastidiosa subsp. sandyi and caused oleander leaf scorch but not Pierce's disease symptoms in glasshouse assays on oleander and grape, respectively. This demonstrated both that our groupings based on genetic characterization were valid and that strains of X. fastidiosa subsp. sandyi are present in hosts other than oleander. Strains isolated from Spanish broom, cherry, and one strain isolated from western redbud clustered with X. fastidiosa subsp. fastidiosa members. Strains isolated from purple-leafed plum, olive, peach, plum, sweetgum, maidenhair tree, crape myrtle, and another western redbud strain clustered with members of X. fastidiosa subsp. multiplex. All strains isolated from mulberry and one from heavenly bamboo formed a separate cluster that has not yet been defined as a subspecies.

Differentiation of Strains of Xylella fastidiosa Infecting Grape, Almonds, and Oleander Using a Multiprimer PCR Assay

Xylella fastidiosa is a xylem-limited, nutritionally fastidious bacterium that causes several plant diseases including Pierce's disease (PD) in grape and leaf scorch in almond (ALS) and oleander (OLS). OLS strains belong to X. fastidiosa subsp. sandyi, PD strains belong to X. fastidiosa subsp. fastidiosa, and strains from almond designated as ALS strains are of two general types belonging either to X. fastidiosa subsp. multiplex or X. fastidiosa subsp. fastidiosa. The ALS strains assigned to X. fastidiosa subsp. multiplex belong to two different genotypes (ALSI and ALSII) below the subspecies level. The OLS strains do not infect grape or almond. PD strains produce diseases in grape, alfalfa, almond, and some weeds, but they do not infect oleander, oak, peach, or citrus. ALS strains that belong to X. fastidiosa subsp. multiplex do not produce disease on grape. In this study, a relatively simple polymerase chain reaction (PCR) based method was developed to distinguish among PD, OLS, and ALS strains. PCR performed with primers XF1968-L and XF1968-R amplified a 638-bp fragment from OLS strains but not from PD strains or ALS strains that belong to X. fastidiosa subsp. fastidiosa. PCR with primers XF2542-L and XF2542-R amplified a 412-bp fragment from PD strains, but not from OLS strains. PCR with primers ALM1 and ALM2 produced a fragment of 521 bp from strains isolated from almond that belong to X. fastidiosa subsp. multiplex. The combination of the three primer sets allowed the distinction of the two ALS genotypes of X. fastidiosa subsp. multiplex. These results are in agreement with those obtained from analysis of sequences of 16S-23S rDNA intergenic spacer regions sequence analysis and with previous results based on randomly amplified polymorphic DNA analysis.

A multigene phylogenetic study of clonal diversity and divergence in North American strains of the plant pathogen Xylella fastidiosa

Xylella fastidiosa is a pathogen that causes leaf scorch and related diseases in over 100 plant species, including Pierce's disease in grapevines (PD), phony peach disease (PP), plum leaf scald (PLS), and leaf scorch in almond (ALS), oak (OAK), and oleander (OLS). We used a high-resolution DNA sequence approach to investigate the evolutionary relationships, geographic variation, and divergence times among the X. fastidiosa isolates causing these diseases in North America. Using a large data set of 10 coding loci and 26 isolates, the phylogeny of X. fastidiosa defined three major clades. Two of these clades correspond to the recently identified X. fastidiosa subspecies piercei (PD and some ALS isolates) and X. fastidiosa subsp. multiplex (OAK, PP, PLS, and some ALS isolates). The third clade grouped all of the OLS isolates into a genetically distinct group, named X. fastidiosa subsp. sandyi. These well-differentiated clades indicate that, historically, X. fastidiosa has been a clonal organism. Based on their synonymous-site divergence ( approximately 3%), these three clades probably originated more than 15,000 years ago, long before the introduction of the nonnative plants that characterize most infections. The sister clades of X. fastidiosa subsp. sandyi and X. fastidiosa subsp. piercei have synonymous-site evolutionary rates 2.9 times faster than X. fastidiosa subsp. multiplex, possibly due to generation time differences. Within X. fastidiosa subsp. multiplex, a low level ( approximately 0.1%) of genetic differentiation indicates the recent divergence of ALS isolates from the PP, PLS, and OAK isolates due to host plant adaptation and/or allopatry. The low level of variation within the X. fastidiosa subsp. piercei and X. fastidiosa subsp. sandyi clades, despite their antiquity, suggests strong selection, possibly driven by host plant adaptation.

Two Xylella fastidiosa Genotypes Associated with Almond Leaf Scorch Disease on the Same Location in California

ABSTRACT Almond leaf scorch disease (ALSD) has recently reemerged in the San Joaquin Valley of California threatening almond production. ALSD is caused by Xylella fastidiosa, a nutritionally fastidious bacterium. Single nucleotide polymorphisms (SNPs) in the 16S rRNA gene (16S rDNA) of X. fastidiosa strains were identified to characterize the bacterial population in infected trees. Genotype-specific SNPs were used to design primers for multiplex polymerase chain reaction assays of early passage cultures. Two genotypically distinct types of X. fastidiosa strains, G-type and A-type, coexist simultaneously in the same infected almond orchard. This was substantiated by restriction fragment length polymorphism analysis of a different genetic locus, RST31-RST33, which has previously been used to identify and differentiate X. fastidiosa strains. Furthermore, unique bacterial colony morphology was consistently associated with the A-type X. fastidiosa strains. To our knowledge, this is the first report of a mixed genotype infection of X. fastidiosa disease on the same location under natural environmental conditions. The concept of mixed genotype infection could affect the current epidemiological study based on the assumption that one genotype causes ALSD on one location and, therefore, the disease management strategy.

Spatial Analysis of Almond Leaf Scorch Disease in the San Joaquin Valley of California: Factors Affecting Pathogen Distribution and Spread

Almond leaf scorch (ALS) disease has emerged as a serious threat to almond (Prunus amygdalus) production areas throughout California's San Joaquin Valley. This disease is caused by the xylem-limited bacterium Xylella fastidiosa, and this pathogen is transmitted by xylophagous insects including sharpshooter leafhoppers (Hemiptera: Cicadellidae) and spittlebugs (Hemiptera: Cercopidae). Among four orchards surveyed, enzyme-linked immunosorbent assay (ELISA) and bacterial isolation followed by polymerase chain reaction (PCR) were equally effective in detecting X. fastidiosa from ALS-symptomatic trees. Disease incidence varied among almond cultivars in each orchard, with the highest mean incidence and most severe symptoms frequently encountered in 'Sonora'. X. fastidiosa isolates consisted of mixtures of grape or "G-genotype" and almond or "A-genotype" strains present in surveyed orchards. The X. fastidiosa G-genotypes characterized from each orchard were associated with the most severely affected 'Sonora' trees in three of the four orchards. Both ordinary runs and simple randomization analyses revealed aggregations of ALS in three of the four orchards. Clusters of ALSaffected trees frequently occurred in the outermost orchard rows. Plots of semivariance in ALS incidence over distance varied in shape and magnitude among cultivars. Semivariance increased over distance in 'Sonora' and 'Carmel', indicating spatial dependence or aggregations of incidence best fit by a combination of spherical and linear models. These results document both random and aggregate patterns of ALS spatial distribution in selected orchards and further illustrate how cultivar susceptibility influences the distribution patterns of ALS incidence. Following the recent introduction and establishment of the glassy-winged sharpshooter, Homalodisca coagulata, the impact upon the epidemiology and spread of ALS is unknown.

Characterization of Paenibacillus popilliae rRNA operons

The terminal 39 nucleotides on the 3' end of the 16S rRNA gene, along with the complete DNA sequences of the 5S rRNA, 23S rRNA, tRNA(Ile), and tRNA(Ala) genes were determined for Paenibacillus popilliae using strains NRRL B-2309 and Dutky 1. Southern hybridization analysis with a 16S rDNA hybridization probe and restriction-digested genomic DNA demonstrated 8 copies of the 16S rRNA gene in P. popilliae strains KLN 3 and Dutky 1. Additionally, the 23S rRNA gene in P. popilliae strains NRRL B-2309, KLN 3, and Dutky 1 was shown by I-CeuI digestion and pulsed-field gel electrophoresis of genomic DNA to occur as 8 copies. It was concluded that these 3 P. popilliae strains contained 8 rrn operons. The 8 operon copies were preferentially located on approximately one-half of the chromosome and were organized into 3 different patterns of genes, as follows: 16S-23S-5S, 16S-ala-23S-5S, and 16S-5S-ile-ala-23S-5S. This is the first report to identify a 5S rRNA gene between the 16S and 23S rRNA genes of a bacterial rrn operon. Comparative analysis of the nucleotides on the 3' end of the 16S rRNA gene suggests that translation of P. popilliae mRNA may occur in Bacillus subtilis and Escherichia coli.

Phylogenetic relationships of Xylella fastidiosa strains based on 16S-23S rDNA sequences

In spite of the lack of resolution of Xylella fastidiosa phylogenetic relationships, parsimony analysis of the 16S-23S rDNA sequence from a wide range of hosts has been evaluated in this research. In order to establish an easier method for sequencing the spacer region completely, a new primer pair was designed. The sequences obtained revealed a higher level of variation than that found in 16S gene sequences, with similarity values ranging from 0.80 to 1.00. The cladogram constructed allowed the clustering of two major clades. From these results it has been possible to recognize the monophyletic grouping of some strains belonging to the same host, possibly representing only one infection process. However, for other hosts there is paraphyletic and polyphyletic grouping. This methodology followed from promising results regarding strain-host clustering. With the parsimony approach, hypothetical genealogical relationship among Xylella strains may be inferred.

Analysis of 16S-23S intergenic spacer regions and rrn operon copy number of Aeromonas culicicola MTCC 3249T

The 16S-23S intergenic spacer and 23S rRNA gene sequence were determined for A. culicicola MTCC 3249T. Ten different ISR, indicative of ten rrn operons, were found in the strain that were grouped in three major types. Of the three types, ISR I was non-coding while ISR II and III coded for tRNA(Glu)(UUC). The tRNA(Glu)(UUC) sequence was identical to that of E. coli. Both ISR I and II were represented by three clones whereas four clones represented ISR III. The number of nucleotide differences between all these ISR ranged from 4 to 157. There were ten rrn operons present in A. culicicola MTCC 3249T as confirmed by Southern hybridization analysis. The 23S rRNA gene sequence analysis of A. culicicloa showed 89.6% homology to that from E. coli with differences of 292 bases, whereas it was 98.6% similar to A. hydrophila 23S rRNA gene with 38 nucleotide differences. The sequences of the helix 21 region were identical in both A. culicicola MTCC 3249T and A. hydrophila and showed two nucleotides different at 389 and 390th positions as compared to E. coli. The upstream and downstream regions of 23S rRNA gene in the strain showed high sequence similarity with A. hydrophila and E. coli indicating their importance in processing of rRNA molecules.

Comparative genomics analyses of citrus-associated bacteria

Xylella fastidiosa 9a5c (XF-9a5c) and Xanthomonas axonopodis pv. citri (XAC) are bacteria that infect citrus plants. Sequencing of the genomes of these strains is complete and comparative analyses are now under way with the genomes of other bacteria of the same genera. In this review, we present an overview of this comparative genomic work. We also present a detailed genomic comparison between XF-9a5a and XAC. Based on this analysis, genes and operons were identified that might be relevant for adaptation to citrus. XAC has two copies of a type II secretion system, a large number of cell wall-degrading enzymes and sugar transporters, a complete energy metabolism, a whole set of avirulence genes associated with a type III secretion system, and a complete flagellar and chemotatic system. By contrast, XF-9a5c possesses more genes involved with type IV pili biosynthesis than does XAC, contains genes encoding for production of colicins, and has 4 copies of Type I restriction/modification system while XAC has only one.

Biological traits of Xylella fastidiosa strains from grapes and almonds

Xylella fastidiosa is a xylem-limited bacterium that causes various diseases, among them Pierce's disease of grapevine (PD) and almond leaf scorch (ALS). PD and ALS have long been considered to be caused by the same strain of this pathogen, but recent genetic studies have revealed differences among X. fastidiosa isolated from these host plants. We tested the hypothesis that ALS is caused by PD and ALS strains in the field and found that both groups of X. fastidiosa caused ALS and overwintered within almonds after mechanical inoculation. Under greenhouse conditions, all isolates caused ALS and all isolates from grapes caused PD. However, isolates belonging to almond genetic groupings did not cause PD in inoculated grapes but systemically infected grapes with lower frequency and populations than those belonging to grape strains. Isolates able to cause both PD and ALS developed 10-fold-higher concentrations of X. fastidiosa in grapes than in almonds. In the laboratory, isolates from grapes overwintered with higher efficiency in grapes than in almonds and isolates from almonds overwintered better in almonds than in grapes. We assigned strains from almonds into groups I and II on the basis of their genetic characteristics, growth on PD3 solid medium, and bacterial populations within inoculated grapevines. Our results show that genetically distinct strains from grapes and almonds differ in population behavior and pathogenicity in grapes and in the ability to grow on two different media.

Genotypic analysis of Xylella fastidiosa isolates from different hosts using sequences homologous to the Xanthomonas rpf genes

SUMMARY This is the first report of a genotypic analysis of the phytopathogenic bacteria Xylella fastidiosa (Xf) using differences within intra- and intergenic regions of pathogenic genes. Orthologous sequences from the genome of Xf were identified for genes involved in the regulation of pathogenicity factors (rpf) from Xanthomonas campestris pv. campestris (Xcc). While the rpf genes were conserved, the chromosomal region revealed differences in gene sizes and intergenic spacings and a major translocational event when compared to Xcc. Primers were designed to amplify three regions: the intragenic region of rpfA (2354 bp), the intergenic region between rpfA and rpfB (5772 bp), and the intergenic region between rpfC and rpfF (2314 bp). Amplicons were obtained for all three regions from 32 of the 33 Xf isolates tested from citrus, grape, coffee, plum, hibiscus and periwinkle. Three Xcc isolates from cruciferous plants only generated PCR products for the rpfC-F region. Cleaved amplified polymorphic sequences (CAPS) (Taq(alpha)I) revealed differential banding profiles for the rpfA-B and rpfC-F regions. Xylella isolates were separated into seven groups via rpfA-B, of which five contained only citrus, while the other two had citrus, grape and coffee, and citrus, coffee, plum and hibiscus isolates. rpfC-F separated the isolates into three host-related groups. Citrus, coffee and hibiscus isolates formed one group, while the other two groups were comprised solely of grape and plum isolates. Xcc isolates formed an out-group. In silico analysis supports these results, which reveal the potential of the rpf genes for genotypic analysis of Xylella fastidiosa.

Detection and diversity assessment of Xylella fastidiosa in field-collected plant and insect samples by using 16S rRNA and gyrB sequences

The causal agent of diseases in many economically important plants is attributed to the xylem-limited bacterium Xylella fastidiosa. The detection of this plant pathogen has been hampered due to its difficult isolation and slow growth on plates. Nearly complete nucleotide sequences of the 16S rRNA gene and partial sequences of the gyrB gene were determined for 18 strains of X. fastidiosa isolated from different plant hosts. A phylogenetic analysis, based on gyrB, grouped strains in three clusters; grape-isolated strains formed one cluster, citrus-coffee strains formed another cluster, and a third cluster resulted from all other strains. Primer pairs designed for the 16S rRNA and gyrB genes were extensively searched in databases to verify their in silico specificity. Primer pairs were certified with 30 target and 36 nontarget pure cultures of microorganisms, confirming 100% specificity. A multiplex PCR protocol was developed and its sensitivity tested. Sequencing of PCR products confirmed the validity of the multiplex PCR. Xylella fastidiosa was detected in field-collected plants, disease vector insects, and nonsymptomatic but infected plants. Specific detection of X. fastidiosa may facilitate the understanding of its ecological significance and prevention of spread of the disease.

Weeds as Alternative Hosts of the Citrus, Coffee, and Plum Strains of Xylella fastidiosa in Brazil

In Brazil, Xylella fastidiosa is present in citrus (Citrus sinensis), coffee (Coffea arabica), and plum (Prunus sp.) crops, causing the citrus variegated chlorosis (CVC), coffee leaf scorch (CLS), and plum leaf scald (PLS). Also present in these crops and infesting weeds, which ultimately could serve as sources of inoculum for the cultivated trees, are diverse populations of xylem-feeding leafhopper vectors. In order to assess host range of X. fastidiosa among weeds and to better understand their role in epidemics, field surveys, mechanical inoculations, and insect transmission tests were conducted. Polymerase chain reaction (PCR) and culture plating were used to detect the pathogen from plant tissues. X. fastidiosa was detected in 10 out of 23 species of the weed plants sampled in two citrus groves affected by CVC. None of the weed plants showed external symptoms. In the greenhouse, the average percentages of infection on plants mechanically inoculated with the CVC, CLS, and PLS strains of X. fastidiosa were, respectively, 25, 10, 0 in Medicago sativa; 70, 45, 20 in Echinochloa crus-galli; 45, 30, 0 in Brachiaria decumbens; 72, 70, 40 in Brachiaria plantaginea; 13, 10, 0 in Digitaria horizontalis; 31, 30, 0 in Solanum americanum; and 17, 0, 0 in Bidens pilosa. Symptoms were observed only in S. americanum and citrus and only when inoculated with the CVC strain. In insect transmission tests, the grass leafhopper Ferrariana trivittata was first caged on citrus plants showing CVC symptoms and then on healthy citrus and on the four most common weeds. No plants tested positive by PCR or culture, or showed symptoms for at least 4 months after inoculation. The amount of X. fastidiosa cells that may accumulate in weeds inoculated by leafhoppers is probably under insect acquisition thresholds, a factor that would limit their importance to the CVC epidemics, as studies on spatial distribution of diseased citrus trees over time indicate.

Microarray analyses of Xylella fastidiosa provide evidence of coordinated transcription control of laterally transferred elements

Genetically distinct strains of the plant bacterium Xylella fastidiosa (Xf) are responsible for a variety of plant diseases, accounting for severe economic damage throughout the world. Using as a reference the genome of Xf 9a5c strain, associated with citrus variegated chlorosis (CVC), we developed a microarray-based comparison involving 12 Xf isolates, providing a thorough assessment of the variation in genomic composition across the group. Our results demonstrate that Xf displays one of the largest flexible gene pools characterized to date, with several horizontally acquired elements, such as prophages, plasmids, and genomic islands (GIs), which contribute up to 18% of the final genome. Transcriptome analysis of bacteria grown under different conditions shows that most of these elements are transcriptionally active, and their expression can be influenced in a coordinated manner by environmental stimuli. Finally, evaluation of the genetic composition of these laterally transferred elements identified differences that may help to explain the adaptability of Xf strains to infect such a wide range of plant species.

Comparative analyses of the complete genome sequences of Pierce's disease and citrus variegated chlorosis strains of Xylella fastidiosa

Xylella fastidiosa is a xylem-dwelling, insect-transmitted, gamma-proteobacterium that causes diseases in many plants, including grapevine, citrus, periwinkle, almond, oleander, and coffee. X. fastidiosa has an unusually broad host range, has an extensive geographical distribution throughout the American continent, and induces diverse disease phenotypes. Previous molecular analyses indicated three distinct groups of X. fastidiosa isolates that were expected to be genetically divergent. Here we report the genome sequence of X. fastidiosa (Temecula strain), isolated from a naturally infected grapevine with Pierce's disease (PD) in a wine-grape-growing region of California. Comparative analyses with a previously sequenced X. fastidiosa strain responsible for citrus variegated chlorosis (CVC) revealed that 98% of the PD X. fastidiosa Temecula genes are shared with the CVC X. fastidiosa strain 9a5c genes. Furthermore, the average amino acid identity of the open reading frames in the strains is 95.7%. Genomic differences are limited to phage-associated chromosomal rearrangements and deletions that also account for the strain-specific genes present in each genome. Genomic islands, one in each genome, were identified, and their presence in other X. fastidiosa strains was analyzed. We conclude that these two organisms have identical metabolic functions and are likely to use a common set of genes in plant colonization and pathogenesis, permitting convergence of functional genomic strategies.

Competitive hybridization on spotted microarrays as a tool to conduct comparative genomic analyses of Xylella fastidiosa strains

Xylella fastidiosa strains are responsible for several plant diseases and since such isolates display a broad host range and complex biological behavior, genomic comparisons employing microarray hybridizations may provide an effective method to compare them. Thus, we performed a thorough validation of this type of approach using two recently sequenced strains of this phytopathogen. By matching microarray hybridization results to direct sequence comparisons, we were able to establish precise cutoff ratios for common and exclusive sequences, allowing the identification of exclusive genes involved in important biological traits. This validation will enable the use of microarray-based comparisons across a wide variety of microorganisms

Characterization of Biofilm Formation by Xylella fastidiosa In Vitro

Xylella fastidiosa colonizes the xylem of various host plants, causing economically important diseases such as Pierce's disease in grapevine and citrus variegated chlorosis (CVC) in sweet oranges. The aggregative nature of this bacterium has been extensively documented in the plant xylem and the insect's foregut. Structured communities of microbial aggregates enclosed in a self-produced polymeric matrix and attached to a surface are defined as biofilms. In this study, we characterized biofilm formation by X. fastidiosa through the use of a novel in vitro assay for studying biofilm growth in a potential mimic system of what might occur in planta. We used wood, a xylem rich material, as a surface for bacterial attachment and biofilm formation, under shear force. We demonstrated that X. fastidiosa strains isolated from various hosts formed biofilm on wood in this in vitro assay. Different biofilm morphology was detected, which seems to vary according to the strain tested and microenvironmental conditions analyzed. We observed that strains from different hosts could be grouped according to three parameters: biofilm morphology, the ability to form clumps in liquid culture, and the ability to attach to glass surfaces. We hypothesize that biofilm formation is likely a major virulence factor in diseases related to X. fastidiosa, bringing a new perspective for disease treatment.

Intraspecific diversity of Brevibacterium linens, Corynebacterium glutamicum and Rhodococcus erythropolis based on partial 16S rDNA sequence analysis and Fourier-transform infrared (FT-IR) spectroscopy

The intraspecific diversity of 31 strains of Brevibacterium linens, 27 strains of Corynebacterium glutamicum and 29 strains of Rhodococcus erythropolis was determined by partial 16S rDNA sequence analysis and Fourier-transform infrared (FT-IR) spectroscopy. As a prerequisite for the analyses, 27 strains derived from culture collections which had carried invalid or wrong species designations were reclassified in accordance with polyphasic taxonomical data. FT-IR spectroscopy proved to be a rapid and reliable method for screening for similar isolates and for identifying these actinomycetes at the species level. Two main conclusions emerged from the analyses. (1) Comparison of intraspecific 16S rDNA similarities suggested that R. erythropolis strains have a very low diversity, B. linens displays high diversity and C. glutamicum occupies an intermediate position. (2) No correlation of FT-IR spectral similarity and 16S rDNA sequence similarity below the species level (i.e. between strains of one species) was observed. Therefore, diversification of 16S rDNA sequences and microevolutionary change of the cellular components detected by FT-IR spectroscopy appear to be de-coupled.