1887
  1. Home
  2. Publications
  3. International Journal of Systematic and Evolutionary Microbiology
  4. Volume 66, Issue 11
  5. Article

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

PDF
418.89 Kb
HTML
79.83 Kb
  • Authors: C.-C. Su1​ ,  W.-L. Deng2​ ,  F.-J. Jan2​ ,  C.-J. Chang2​,3​ ,  H. Huang4​ ,  H.-T. Shih5​ , J. Chen6​
    • VIEW AFFILIATIONS
    • 1​ 1​Division of Pesticide Application, Taiwan Agricultural Chemicals and Toxic Substances Research Institute, Wufeng, Taichung 41358, Taiwan, ROC 2​ 2​Department of Plant Pathology, National Chung Hsing University, Taichung 40227, Taiwan, ROC 3​ 3​Department of Plant Pathology, University of Georgia, Griffin, Georgia 30223, USA 4​ 4​School of Information, University of South Florida, Tampa, FL 33620, USA 5​ 5​Applied Zoology Division, Taiwan Agricultural Research Institute, Council of Agriculture, 189 Chung-Cheng Road, Wufeng, 413 Taichung, Taiwan, ROC 6​ 6​USDA-ARS San Joaquin Valley Agricultural Sciences Center, Parlier, California 93648, USA
  • Correspondence J. Chen [email protected]
  • First Published Online: 01 November 2016, International Journal of Systematic and Evolutionary Microbiology 66: 4766-4771, doi: 10.1099/ijsem.0.001426
  • Subject: New taxa - Proteobacteria
  • Received:
  • Accepted:
  • Cover date:
Preview this:
Free Preview thumbnail Magnify
Zoom in
Zoomout

Xylella taiwanensis sp. nov., causing pear leaf scorch disease, Page 1 of 1

| /docserver/preview/fulltext/ijsem/66/11/4766_ijsem001426-1.gif

  • A Gram-stain-negative, nutritionally fastidious bacterium (PLS229) causing pear leaf scorch was identified in Taiwan and previously grouped into Xylella fastidiosa . Yet, significant variations between PLS229 and Xylella fastidiosa were noted. In this study, PLS229 was evaluated phenotypically and genotypically against representative strains of Xylella fastidiosa , including strains of the currently known subspecies of Xylella fastidiosa , Xylella fastidiosa subsp. multiplex and ‘ Xylella fastidiosa subsp. 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 PLS229 and Xylella fastidiosa 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 Xylella fastidiosa , discovering significant single nucleotide polymorphisms at 18 randomly selected housekeeping gene loci, observing a distinct fatty acid profile for PLS229 compared with Xylella fastidiosa , 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 Xylella fastidiosa 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 PLS229 (=BCRC 80915=JCM 31187).

  • Four supplementary tables are available with the online Supplementary Material.

  • Abbreviations:
    ANI average nucleotide identity
    DDH DNA-DNA hybridization
    ITS internal transcribed spacer
    PD Pierce's disease
    PLS pear leaf scorch
  • 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 Announc2:e01190-13. [CrossRef][PubMed]
     [Google Scholar]
  • 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 Bacteriol41:343––346. [CrossRef][PubMed]
     [Google Scholar]
  • Chang C. J., Walker J. T..( 1988;). Bacterial leaf scorch of northern red oak: isolation, cultivation, and pathogenicity of a xylem-limited bacterium. . Plant Dis72:730––733. [CrossRef]
     [Google Scholar]
  • 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 Microbiol23:349––354. [CrossRef][PubMed]
     [Google Scholar]
  • 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 Bacteriol192:4534. [CrossRef][PubMed]
     [Google Scholar]
  • 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 Announc1:e00756-13. [CrossRef][PubMed]
     [Google Scholar]
  • 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. . Nature417:459––463. [CrossRef][PubMed]
     [Google Scholar]
  • Davis M. J., Purcell A. H., Thomson S. V..( 1980;). Isolation medium for Pierce’s disease bacterium. . Phytopathology70:425––429.[CrossRef]
     [Google Scholar]
  • 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 Microbiol6:309––314. [CrossRef]
     [Google Scholar]
  • 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]
  • 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 Announc3:e01538-14. [CrossRef][PubMed]
     [Google Scholar]
  • 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 Microbiol57:81––91. [CrossRef][PubMed]
     [Google Scholar]
  • Guan W., Shao J., Zhao T., Huang Q..( 2014a;). Genome sequence of a Xylella fastidiosa strain causing mulberry leaf scorch disease in Maryland. . Genome Announc2:e00916-13. [CrossRef][PubMed]
     [Google Scholar]
  • 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 Announc2:e00773-14. [CrossRef][PubMed]
     [Google Scholar]
  • Hauben L., Vauterin L., Swings J., Moore E. R..( 1997;). Comparison of 16S ribosomal DNA sequences of all Xanthomonas species. . Int J Syst Bacteriol47:328––335. [CrossRef][PubMed]
     [Google Scholar]
  • 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]
  • Kamper S. M., French W. J., deKloet S. R..( 1985;). Genetic relationships of some fastidious xylem-limited bacteria. . Int J Syst Bacteriol35:185––188. [CrossRef]
     [Google Scholar]
  • 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 Microbiol64:346––351. [CrossRef][PubMed]
     [Google Scholar]
  • Konstantinidis K. T., Tiedje J. M..( 2005;). Genomic insights that advance the species definition for prokaryotes. . Proc Natl Acad Sci U S A102:2567––2572. [CrossRef]
     [Google Scholar]
  • Koressaar T., Remm M..( 2007;). Enhancements and modifications of primer design program Primer3. . Bioinformatics23:1289––1291. [CrossRef]
     [Google Scholar]
  • 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 Dis77:642––646. [CrossRef]
     [Google Scholar]
  • MacFaddin J..( 1976;). Biochemical Tests for Identification of Medical Bacteria, pp. 80––82. Baltimore:: The Williams & Wilkins Co;.
     [Google Scholar]
  • 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 Microbiol198:803––812. [CrossRef][PubMed]
     [Google Scholar]
  • 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 Microbiol51:311––318. [CrossRef][PubMed]
     [Google Scholar]
  • 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 Microbiol80:3025––3033. [CrossRef][PubMed]
     [Google Scholar]
  • Oberhofer T. R., Towle D. W..( 1982;). Evaluation of the rapid penicillinase paper strip test for detection of betalactamase. . J Clin Microbiol15:196––199.[PubMed]
     [Google Scholar]
  • Richter M., Rossello-Mora R..( 2009;). Shifting the genomic gold standard for the prokaryotic species definition. . Proc Natl Acad Sci U S A106:19126––19131. [CrossRef]
     [Google Scholar]
  • Rossello-Mora R., Amann R..( 2001;). The species concept for prokaryotes. . FEMS Microbiol Rev25:39––67. [CrossRef][PubMed]
     [Google Scholar]
  • 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]
  • 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 Microbiol27:290––300. [CrossRef][PubMed]
     [Google Scholar]
  • 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 Entomol35:479––483. [CrossRef]
     [Google Scholar]
  • 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 Microbiol71:3832––3839. [CrossRef][PubMed]
     [Google Scholar]
  • 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. . Nature406:151––159. [CrossRef][PubMed]
     [Google Scholar]
  • 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]
  • 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. [CrossRef]
     [Google Scholar]
  • 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 Bulletin17:261––269.
     [Google Scholar]
  • 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 Pathol132:203––216. [CrossRef]
     [Google Scholar]
  • 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 Phytopathol161:389––396. [CrossRef]
     [Google Scholar]
  • 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 Announc2:e00166-14. [CrossRef][PubMed]
     [Google Scholar]
  • Tamura K., Stecher G., Peterson D., Filipski A., Kumar S..( 2013;). mega6: molecular evolutionary genetics analysis version 6.0. . Mol Biol Evol30:2725––2729. [CrossRef][PubMed]
     [Google Scholar]
  • 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 Res22:4673––4680. [CrossRef][PubMed]
     [Google Scholar]
  • 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 Bacteriol185:1018––1026. [CrossRef][PubMed]
     [Google Scholar]
  • 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 Bacteriol37:463––464. [CrossRef]
     [Google Scholar]
  • 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 Microbiol42:357––363.
     [Google Scholar]
  • 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 Bacteriol37:136––143.[CrossRef]
     [Google Scholar]
  • 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 Bacteriol193:5576––5577. [CrossRef][PubMed]
     [Google Scholar]
http://sgm.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.001426
Loading

Supplementary Data

 Data loading....

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.001426
2016-11-01
2019-02-15
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

Author and Article Information

 Figure data loading....

Footnotes:

Validated antibodies in this article

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error