1887

Abstract

A Gram-stain-negative, nutritionally fastidious bacterium (PLS229) causing pear leaf scorch was identified in Taiwan and previously grouped into . Yet, significant variations between PLS229 and were noted. In this study, PLS229 was evaluated phenotypically and genotypically against representative strains of , including strains of the currently known subspecies of , subsp. and ‘ ’. Because of the difficulty of 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 PLS229 and 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 PLS229 was also evident by observing only about 87 % similarity in the sequence of the 16S-23S internal transcribed spacer (ITS) between PLS229 and strains of , discovering significant single nucleotide polymorphisms at 18 randomly selected housekeeping gene loci, observing a distinct fatty acid profile for PLS229 compared with , and PLS229 having different observable phenotypes, such as different susceptibility to antibiotics. A phylogenetic tree derived from 16S rRNA gene sequences showed a distinct PLS229 phyletic lineage positioning it between and members of the genus . On the basis of these data, a novel species, sp. nov. is proposed. The type strain is PLS229 (=BCRC 80915=JCM 31187).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.001426
2016-11-01
2021-07-25
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/66/11/4766.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.001426&mimeType=html&fmt=ahah

References

  1. Alencar V. C., Barbosa D., Santos D. S., Oliveira A. C. F., de Oliveira R. C., Nunes L. R. 2014; Genomic sequencing of two coffee-infecting strains of Xylella fastidiosa isolated from Brazil. Genome Announc 2:e01190-13 [View Article][PubMed]
    [Google Scholar]
  2. Ash C., Farrow J. A. E., Dorsch M., Stackebrandt E., Collins M. D. 1991; Comparative analysis of Bacillus anthracis, Bacillus cereus, and related species on the basis of reverse transcriptase sequencing of 16S rRNA. Int J Syst Bacteriol 41:343–346 [View Article][PubMed]
    [Google Scholar]
  3. Chang C. J., Walker J. T. 1988; Bacterial leaf scorch of northern red oak: isolation, cultivation, and pathogenicity of a xylem-limited bacterium. Plant Dis 72:730–733 [View Article]
    [Google Scholar]
  4. Chen J., Jarret R. L., Qin X., Hartung J. S., Banks D., Chang C. J., Hopkins D. L. 2000; 16S rDNA sequence analysis of Xylella fastidiosa strains. Syst Appl Microbiol 23:349–354 [View Article][PubMed]
    [Google Scholar]
  5. Chen J., Xie G., Han S., Chertkov O., Sims D., Civerolo E. L. 2010; Whole genome sequences of two Xylella fastidiosa strains (M12 and M23) causing almond leaf scorch disease in California. J Bacteriol 192:4534 [View Article][PubMed]
    [Google Scholar]
  6. Chen J., Huang H., Chang C.-J., Stenger D. C. 2013; Draft genome sequence of Xylella fastidiosa subsp. multiplex strain griffin-1 from Quercus rubra in Georgia. Genome Announc 1:e00756-13 [View Article][PubMed]
    [Google Scholar]
  7. da Silva A. C., Ferro J. A., Reinach F. C., Farah C. S., Furlan L. R., Quaggio R. B., Monteiro-Vitorello C. B., Van Sluys M. A., Almeida N. F. et al. 2002; Comparison of the genomes of two Xanthomonas pathogens with differing host specificities. Nature 417:459–463 [View Article][PubMed]
    [Google Scholar]
  8. Davis M. J., Purcell A. H., Thomson S. V. 1980; Isolation medium for Pierce’s disease bacterium. Phytopathology 70:425–429 [CrossRef]
    [Google Scholar]
  9. Davis M. J., French W. J., Schaad N. W. 1981a; Axenic culture of the bacteria associated with phony disease of peach and plum leaf scald. Curr Microbiol 6:309–314 [View Article]
    [Google Scholar]
  10. Davis M. J., Whitcomb R. F., Gillaspie A. G. J. 1981b; Fastidious bacteria of plant vascular tissue and invertebrates (including so-called rickettsia-like bacteria). In The Prokaryotes: A Handbook on Habits, Isolation, and Identification of Bacteria pp. 2172–2188 Edited by Starr M. P., Stolp H., Truper H. G., Balows A., Schlegel H. G. Berlin, Heidelberg: Springer-Verlag;
    [Google Scholar]
  11. Giampetruzzi A., Chiumenti M., Saponari M., Donvito G., Italiano A., Loconsole G., Boscia D., Cariddi C., Martelli G. P., Saldarelli P. 2015; Draft genome sequence of the Xylella fastidiosa CoDiRO strain. Genome Announc 3:e01538-14 [View Article][PubMed]
    [Google Scholar]
  12. Goris J., Konstantinidis K. T., Klappenbach J. A., Coenye T., Vandamme P., Tiedje J. M. 2007; DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57:81–91 [View Article][PubMed]
    [Google Scholar]
  13. Guan W., Shao J., Zhao T., Huang Q. 2014a; Genome sequence of a Xylella fastidiosa strain causing mulberry leaf scorch disease in Maryland. Genome Announc 2:e00916-13 [View Article][PubMed]
    [Google Scholar]
  14. Guan W., Shao J., Davis R. E., Zhao T., Huang Q. 2014b; Genome sequence of a Xylella fastidiosa strain causing sycamore leaf scorch disease in Virginia. Genome Announc 2:e00773-14 [View Article][PubMed]
    [Google Scholar]
  15. Hauben L., Vauterin L., Swings J., Moore E. R. 1997; Comparison of 16S ribosomal DNA sequences of all Xanthomonas species. Int J Syst Bacteriol 47:328–335 [View Article][PubMed]
    [Google Scholar]
  16. Hopkins D. 2001 Xylella fastidiosa In Laboratory Guide for Identification of Plant Pathogenic Bacteria pp. 201–213 Edited by Schaad N. W., Jones J. B., Chun W. St. Paul, MN: APS Press;
    [Google Scholar]
  17. Kamper S. M., French W. J., deKloet S. R. 1985; Genetic relationships of some fastidious xylem-limited bacteria. Int J Syst Bacteriol 35:185–188 [View Article]
    [Google Scholar]
  18. Kim M., Oh H. S., Park S. C., Chun J. 2014; Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 64:346–351 [View Article][PubMed]
    [Google Scholar]
  19. Konstantinidis K. T., Tiedje J. M. 2005; Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci U S A 102:2567–2572 [View Article]
    [Google Scholar]
  20. Koressaar T., Remm M. 2007; Enhancements and modifications of primer design program Primer3. Bioinformatics 23:1289–1291 [View Article]
    [Google Scholar]
  21. Leu L. S., Su C. C. 1993; Isolation, cultivation, and pathogenicity of Xylella fastidiosa, the causal bacterium of pear leaf scorch disease in Taiwan. Plant Dis 77:642–646 [View Article]
    [Google Scholar]
  22. MacFaddin J. 1976 Biochemical Tests for Identification of Medical Bacteria pp. 80–82 Baltimore: The Williams & Wilkins Co;
    [Google Scholar]
  23. Marcelletti S., Scortichini M. 2016; Genome-wide comparison and taxonomic relatedness of multiple Xylella fastidiosa strains reveal the occurrence of three subspecies and a new Xylella species. Arch Microbiol 198:803–812 [View Article][PubMed]
    [Google Scholar]
  24. Mehta A., Rosato Y. B. 2001; Phylogenetic relationships of Xylella fastidiosa strains from different hosts, based on 16S rDNA and 16S-23S intergenic spacer sequences. Int J Syst Evol Microbiol 51:311–318 [View Article][PubMed]
    [Google Scholar]
  25. Nunney L., Schuenzel E. L., Scally M., Bromley R. E., Stouthamer R. 2014; Large-scale intersubspecific recombination in the plant-pathogenic bacterium Xylella fastidiosa is associated with the host shift to mulberry. Appl Environ Microbiol 80:3025–3033 [View Article][PubMed]
    [Google Scholar]
  26. Oberhofer T. R., Towle D. W. 1982; Evaluation of the rapid penicillinase paper strip test for detection of betalactamase. J Clin Microbiol 15:196–199[PubMed]
    [Google Scholar]
  27. Richter M., Rossello-Mora R. 2009; Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 106:19126–19131 [View Article]
    [Google Scholar]
  28. Rossello-Mora R., Amann R. 2001; The species concept for prokaryotes. FEMS Microbiol Rev 25:39–67 [View Article][PubMed]
    [Google Scholar]
  29. Saddler G. S., Bradbury J. F. 2005; Genus XI. Xylella Wells, Raju, Hung, Weisburg, Mandelco-Paul and Brenner 1987, 141vp. In Bergery’s Manual of Systematic Bacteriology vol. 2 pp. 119–122 Edited by Brenner D. J., Krieg N. R., Staley J. T., Garrity G. M. New York, NY: Springer;
    [Google Scholar]
  30. Schaad N. W., Postnikova E., Lacy G., Fatmi M., Chang C. J. 2004; Xylella fastidiosa subspecies: X. fastidiosa subsp. [correction] fastidiosa [correction] subsp. nov., X. fastidiosa subsp. multiplex subsp. nov., and X. fastidiosa subsp. pauca subsp. nov. Syst Appl Microbiol 27:290–300 [View Article][PubMed]
    [Google Scholar]
  31. Schreiber H. L., Koirala M., Lara A., Ojeda M., Dowd S. E., Bextine B., Morano L. 2010; Unraveling the first Xylella fastidiosa subsp. fastidiosa genome from Texas. Southwest Entomol 35:479–483 [View Article]
    [Google Scholar]
  32. Schuenzel E. L., Scally M., Stouthamer R., Nunney L. 2005; A multigene phylogenetic study of clonal diversity and divergence in North American strains of the plant pathogen Xylella fastidiosa. Appl Environ Microbiol 71:3832–3839 [View Article][PubMed]
    [Google Scholar]
  33. Simpson A. J., Reinach F. C., Arruda P., Abreu F. A., Acencio M., Alvarenga R., Alves L. M., Araya J. E., Baia G. S. et al. 2000; The genome sequence of the plant pathogen Xylella fastidiosa. Nature 406:151–159 [View Article][PubMed]
    [Google Scholar]
  34. Smibert R. M., Krieg N. R. 1981; General characterization. In Manual of Methods for General Bacteriology pp. 409–443 Edited by Gerhardt R. G. E., Murray R. N., Costilow E. W., Nester W. A., Wood N. R., Krieg N. R., Phillips G. B. Washington, DC: American Society for Microbiology;
    [Google Scholar]
  35. Stackebrandt E., Goebel B. M. 1994; Taxonomic note: a place for DNA–DNA reassociation and 16s rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Evol Microbiol. 44:846–849 [View Article]
    [Google Scholar]
  36. Su C. C., Yang W. J., Feng C. Y., Hsu S. T., Tzeng K. C. 2008; The application of DNA fingerprintings amplified by arbitrary primers in differentiating pear leaf scorch bacterium from other Xylella fastidiosa strains. Plant Pathol Bulletin 17:261–269
    [Google Scholar]
  37. Su C. C., Chang C. J., Yang W. J., Hsu S. T., Tzeng K. C., Jan F. J., Deng W. L. 2012; Specific characters of 16S rRNA gene and 16S–23S rRNA internal transcribed spacer sequences of Xylella fastidiosa pear leaf scorch strains. Eur J Plant Pathol 132:203–216 [View Article]
    [Google Scholar]
  38. Su C.-C., Chang C.-J., Chang C.-M., Shih H.-T., Tzeng K.-C., Jan F.-J., Kao C.-W., Deng W.-L. 2013; Pierce's disease of grapevines in Taiwan: isolation, cultivation and pathogenicity of Xylella fastidiosa. J Phytopathol 161:389–396 [View Article]
    [Google Scholar]
  39. Su C.-C., Deng W.-L., Jan F.-J., Chang C.-J., Huang H., Chen J. 2014; Draft genome sequence of Xylella fastidiosa pear leaf scorch strain in Taiwan. Genome Announc 2:e00166-14 [View Article][PubMed]
    [Google Scholar]
  40. Tamura K., Stecher G., Peterson D., Filipski A., Kumar S. 2013; mega6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729 [View Article][PubMed]
    [Google Scholar]
  41. Thompson J. D., Higgins D. G., Gibson T. J. 1994; clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680 [View Article][PubMed]
    [Google Scholar]
  42. Van Sluys M. A., de Oliveira M. C., Monteiro-Vitorello C. B., Miyaki C. Y., Furlan L. R., Camargo L. E., da Silva A. C., Moon D. H., Takita M. A. et al. 2003; Comparative analyses of the complete genome sequences of Pierce's disease and citrus variegated chlorosis strains of Xylella fastidiosa. J Bacteriol 185:1018–1026 [View Article][PubMed]
    [Google Scholar]
  43. Wayne L. G., Brenner D. J., Colwell R. R., Grimont P. A. D., Kandler O., Krichevsky M. I., Moore L. H., Moore W. E. C., Murray R. G. E. et al. 1987; Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464 [View Article]
    [Google Scholar]
  44. Wells J. M., Raju B. C., Nyland G., Lowe S. K. 1981; Medium for isolation and growth of bacteria associated with plum leaf scald and phony peach diseases. Appl Environ Microbiol 42:357–363
    [Google Scholar]
  45. Wells J. M., Raju B. C., Hung H.-Y., Weisburg W. G., Mandelco-Paul L., Brenner B. J. 1987; Xylella fastidiosa new-genus new-species gram-negative xylem-limited fastidious plant bacteria related to Xanthomonas spp. Int J Syst Bacteriol 37:136–143 [CrossRef]
    [Google Scholar]
  46. Zhang S., Flores-Cruz Z., Kumar D., Chakrabarty P., Hopkins D. L., Gabriel D. W. 2011; The Xylella fastidiosa biocontrol strain EB92-1 genome is very similar and syntenic to Pierce's disease strains. J Bacteriol 193:5576–5577 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.001426
Loading
/content/journal/ijsem/10.1099/ijsem.0.001426
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most cited this month Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error