1887

Abstract

Although the genus was originally proposed to accommodate all phytopathogenic coryneform bacteria containing B2γ diaminobutyrate in the peptidoglycan, reclassification of all but one species into other genera has resulted in the current monospecific status of the genus. The single species in the genus, , has multiple subspecies, which are all highly host-specific plant pathogens. Whole genome analysis based on average nucleotide identity and digital DNA–DNA hybridization as well as multi-locus sequence analysis (MLSA) of seven housekeeping genes support raising each of the subspecies to species status. On the basis of whole genome and MLSA data, we propose the establishment of two new species and three new combinations: sp. nov., comb. nov. and sp. nov., comb. nov., and comb. nov., comb. nov. and comb. nov.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.002492
2018-01-01
2020-01-22
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/68/1/234.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.002492&mimeType=html&fmt=ahah

References

  1. Davis MJ, Gillaspie AG, Vidaver AK, Harris RW. Clavibacter: a new genus containing some phytopathogenic coryneform bacteria, including Clavibacter xyli subsp. xyli sp. nov., subsp. nov. and Clavibacter xyli subsp. cynodontis subsp. nov., pathogens that cause ratoon stunting disease of sugarcane and bermudagrass stunting disease. Int J Syst Bacteriol 1984;34:107–117 [CrossRef]
    [Google Scholar]
  2. Zgurskaya HI, Evtushenko LI, Akimov VN, Kalakoutskii LV. Rathayibacter gen. nov., Including the species Rathayibacter rathayi comb. nov., Rathayibacter tritici comb. nov., Rathayibacter iranicus comb. nov., and six strains from annual grasses. Int J Syst Bacteriol 1993;43:143–149 [CrossRef]
    [Google Scholar]
  3. Evtushenko LI, Dorofeeva LV, Subbotin SA, Cole JR, Tiedje JM. Leifsonia poae gen. nov., sp. nov., isolated from nematode galls on Poa annua, and reclassification of 'Corynebacterium aquaticum' Leifson 1962 as Leifsonia aquatica (ex Leifson 1962) gen. nov., nom. rev., comb. nov. and Clavibacter xyli Davis et al. 1984 with two subspecies as Leifsonia xyli (Davis et al. 1984) gen. nov., comb. nov. Int J Syst Evol Microbiol 2000;50:371–380 [CrossRef][PubMed]
    [Google Scholar]
  4. Suzuki KI, Suzuki M, Sasaki J, Park YH, Komagata KK. Leifsonia gen. nov., a genus for 2,4-diaminobutyric acid-containing actinomycetes to accommodate "Corynebacterium aquaticum" Leifson 1962 and Clavibacter xyli subsp. cynodontis Davis et al. 1984. J Gen Appl Microbiol 1999;45:253–262 [CrossRef][PubMed]
    [Google Scholar]
  5. González AJ, Trapiello E. Clavibacter michiganensis subsp. phaseoli subsp. nov., pathogenic in bean. Int J Syst Evol Microbiol 2014;64:1752–1755 [CrossRef][PubMed]
    [Google Scholar]
  6. Oh EJ, Bae C, Lee HB, Hwang IS, Lee HI et al. Clavibacter michiganensis subsp. capsici subsp. nov., causing bacterial canker disease in pepper. Int J Syst Evol Microbiol 2016;66:4065–4070 [CrossRef][PubMed]
    [Google Scholar]
  7. Yasuhara-Bell J, Alvarez AM. Seed-associated subspecies of the genus Clavibacter are clearly distinguishable from Clavibacter michiganensis subsp. michiganensis. Int J Syst Evol Microbiol 2015;65:811–826 [CrossRef][PubMed]
    [Google Scholar]
  8. Kim M, Oh HS, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014;64:346–351 [CrossRef][PubMed]
    [Google Scholar]
  9. Konstantinidis KT, Tiedje JM. Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci USA 2005;102:2567–2572 [CrossRef][PubMed]
    [Google Scholar]
  10. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009;106:19126–19131 [CrossRef][PubMed]
    [Google Scholar]
  11. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007;57:81–91 [CrossRef][PubMed]
    [Google Scholar]
  12. Załuga J, Stragier P, Baeyen S, Haegeman A, van Vaerenbergh J et al. Comparative genome analysis of pathogenic and non-pathogenic Clavibacter strains reveals adaptations to their lifestyle. BMC Genomics 2014;15:392 [CrossRef][PubMed]
    [Google Scholar]
  13. Auch AF, von Jan M, Klenk HP, Göker M. Digital DNA–DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010;2:117–134 [CrossRef][PubMed]
    [Google Scholar]
  14. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013;14:60 [CrossRef][PubMed]
    [Google Scholar]
  15. Mulet M, Lalucat J, García-Valdés E. DNA sequence-based analysis of the Pseudomonas species. Environ Microbiol 2010;12:1513–1530 [CrossRef][PubMed]
    [Google Scholar]
  16. González AJ, Cleenwerck I, de Vos P, Fernández-Sanz AM. Pseudomonas asturiensis sp. nov., isolated from soybean and weeds. Syst Appl Microbiol 2013;36:320–324 [CrossRef][PubMed]
    [Google Scholar]
  17. Tambong JT, Xu R, Bromfield ESP. Pseudomonas canadensis sp. nov., a biological control agent isolated from a field plot under long-term mineral fertilization. Int J Syst Evol Microbiol 2017;67:889–895 [CrossRef][PubMed]
    [Google Scholar]
  18. Davis MJ, Vidaver AK. Coryneform plant pathogens. In Schaad NW, Jones JB, Chun W. (editors) Laboratory Guide for Identification of Plant Pathogenic Bacteria, 3rd ed. St Paul, MN: APS Press; 2001; pp.218–234
    [Google Scholar]
  19. Eichenlaub R, Gartemann K-H, Burger A. Clavibacter michiganensis, a group of Gram-positive phytopathogenic bacteria. In Gnanamanickam SS. (editor) Plant-Associated Bacteria Dordrecht: Springer; 2006; pp.385–422[Crossref]
    [Google Scholar]
  20. Carlson RR, Vidaver AK. Taxonomy of Corynebacterium plant pathogens, including a new pathogen of wheat, based on polyacrylamide gel electrophoresis of cellular proteins. Int J Syst Bacteriol 1982;32:315–326 [CrossRef]
    [Google Scholar]
  21. Tambong JT. Comparative genomics of Clavibacter michiganensis subspecies, pathogens of important agricultural crops. PLoS One 2017;12:e0172295 [CrossRef][PubMed]
    [Google Scholar]
  22. du Y, Yuan B, Zeng Y, Meng J, Li H et al. Draft genome sequence of the cellulolytic bacterium Clavibacter sp. CF11, a strain producing cold-active cellulase. Genome Announc 2015;3:e01304-14 [CrossRef][PubMed]
    [Google Scholar]
  23. Lu Y, Samac DA, Glazebrook J, Ishimaru CA. Complete genome sequence of Clavibacter michiganensis subsp. insidiosus R1-1 using pacbio single-molecule real-time technology. Genome Announc 2015;3:e00396-15 [CrossRef][PubMed]
    [Google Scholar]
  24. Gartemann KH, Abt B, Bekel T, Burger A, Engemann J et al. The genome sequence of the tomato-pathogenic actinomycete Clavibacter michiganensis subsp. michiganensis NCPPB382 reveals a large island involved in pathogenicity. J Bacteriol 2008;190:2138–2149 [CrossRef][PubMed]
    [Google Scholar]
  25. Tambong JT, Xu R, Adam Z, Cott M, Rose K et al. Draft genome sequence of Clavibacter michiganensis subsp. nebraskensis Strain DOAB 397, isolated from an infected field corn plant in Manitoba, Canada. Genome Announc 2015;3:e00768-15 [CrossRef][PubMed]
    [Google Scholar]
  26. Bentley SD, Corton C, Brown SE, Barron A, Clark L et al. Genome of the actinomycete plant pathogen Clavibacter michiganensis subsp. sepedonicus suggests recent niche adaptation. J Bacteriol 2008;190:2150–2160 [CrossRef][PubMed]
    [Google Scholar]
  27. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013;30:2725–2729 [CrossRef][PubMed]
    [Google Scholar]
  28. Gross DC. A selective medium for isolation of Corynebacterium nebraskense from soil and plant parts. Phytopathology 1979;69:82–87 [CrossRef]
    [Google Scholar]
  29. Kelman A. The relationship of pathogenicity in Pseudomonas solanacearum to colony appearance on tetrazolium medium. Phytopathol 1954;44:693–695
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.002492
Loading
/content/journal/ijsem/10.1099/ijsem.0.002492
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most cited articles

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