Advertisement

Journal of General Plant Pathology

, Volume 80, Issue 3, pp 237–254 | Cite as

Phylogenetic study of Japanese Dickeya spp. and development of new rapid identification methods using PCR–RFLP

  • Radix Suharjo
  • Hiroyuki Sawada
  • Yuichi TakikawaEmail author
Bacterial and Phytoplasma Diseases

Abstract

Forty-one representative Japanese Dickeya spp. (Erwinia chrysanthemi) strains isolated from 24 plants in Japan were investigated using multilocus sequence analysis of recA, dnaX, rpoD, gyrB and 16S rDNA; PCR–RFLP (restriction fragment length polymorphism) of recA, rpoD and gyrB genes; PCR genomic fingerprinting; and biochemical tests. Based on the recA, dnaX, rpoD, gyrB and 16S rDNA sequences and PCR genomic fingerprinting, the strains were essentially divided into six groups (I–VI). Group I corresponded to D. chrysanthemi, group II corresponded to D. dadantii, group III to D. dianthicola and group IV to D. zeae. Meanwhile, group V and group VI could not be assigned to any existing Dickeya species, and they were deduced to be two putative new species. The PCR–RFLP analysis of gyrB, rpoD and recA clearly differentiated the six groups of Dickeya strains. From the results of the biochemical tests, the strains were assigned to biovars 1, 3, 5, 8 and 9; only one strain (SUPP 2525) was not assignable to the existing biovars. We also showed that the PCR–RFLP analysis of rpoD, gyrB and recA can be used as a rapid technique to identify Japanese Dickeya strains.

Keywords

Biochemical assays Dickeya strains Genomic fingerprinting MLSA (multilocus sequence analysis) PCR–RFLP 

Notes

Acknowledgments

This study was supported in part by grants provided by a research project of the NIAS Genebank.

Supplementary material

10327_2014_511_MOESM1_ESM.doc (379 kb)
Supplementary material 1 (DOC 379 kb)
10327_2014_511_MOESM2_ESM.doc (399 kb)
Supplementary material 2 (DOC 399 kb)

References

  1. Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K (eds) (1987) Current protocols in molecular biology, vol 1. Wiley, New YorkGoogle Scholar
  2. Brady CL, Cleenwerck I, Denman S, Venter SN, Rodríguez-Palenzuela P, Coutinho TA, Vos PD (2012) Proposal to reclassify Brenneria quercina (Hildebrand and Schroth 1967) Hauben et al. 1999 into a new genus, Lonsdalea gen. nov., as Lonsdalea quercina comb. nov., description of Lonsdalea quercina subsp. quercina comb. nov., Lonsdalea quercina subsp. iberica subsp. nov and Lonsdalea quercina subsp. britannica subsp. nov., emendation of the description of the genus Brenneria, reclassification of Dickeya dieffenbachiae as Dickeya dadantii subsp. dieffenbachiae comb. nov., and emendation of the description of Dickeya dadantii. Int J Syst Evol Microbiol 62:1592–1602PubMedCrossRefGoogle Scholar
  3. Cother EJ, Bradley JK, Gillings MR, Fahy PC (1992) Characterization of Erwinia chrysanthemi biovars in alpine water sources by biochemical properties, GLC fatty acid analysis and genomic DNA fingerprinting. J Appl Bacteriol 73:99–107CrossRefGoogle Scholar
  4. Dickey RS (1979) Erwinia chrysanthemi: a comparative study of phenotypic properties of strains from several hosts and other Erwinia species. Phytopathology 69:324–329CrossRefGoogle Scholar
  5. Dickey RS, Victoria JI (1980) Taxonomy and emended description of strains of Erwinia isolated from Musa paradisiaca Linnaeus. Int J Syst Bacteriol 30:129–134CrossRefGoogle Scholar
  6. Duarte V, De Boer SH, Ward LJ, de Oliveira AMR (2004) Characterization of atypical Erwinia carotovora strains causing blackleg of potato in Brazil. J Appl Microbiol 96:535–545PubMedCrossRefGoogle Scholar
  7. Dye DW (1968) A taxonomic study of the genus Erwinia. I. The, “amylovora” group. New Zeal J Sci 11:590–607Google Scholar
  8. Dye DW (1969a) A taxonomic study of the genus Erwinia. II. The “carotovora” group. New Zeal J Sci 12:81–97Google Scholar
  9. Dye DW (1969b) A taxonomic study of the genus Erwinia. III. The “herbicola” group. New Zeal J Sci 12:223–236Google Scholar
  10. Dye DW (1969c) A taxonomic study of the genus Erwinia. IV. “Atypical” erwinias. New Zeal J Sci 12:833–839Google Scholar
  11. Dye DW (1978) Genus V Erwinia Winslow, Broadhurst, Buchanan, Krumwiede, Rogers and Smith, 1920. In: Young JM, Dye DW, Bradbury JF, Panagopoulos CG, Robbs CF (eds) A proposed nomenclature and classification for plant pathogenic bacteria. New Zeal J Agric Res 21:153–177Google Scholar
  12. Elphinstone JG (1987) Soft rot and black leg of potato: Erwinia spp. Technical Information Bulletin 21 International Potato Center, Lima p 18Google Scholar
  13. Funakubo T, Watauchi K, Murakami Y, Takikawa Y (2010) Erwinia chrysanthemi isolated from sudden death syndrome (in Japanese). Proc Kanto-Tosan Plant Prot Soc 57:41–43Google Scholar
  14. Goto M (1979) Bacterial foot rot of rice caused by strain of Erwinia chrysanthemi. Phytopathology 69:213–216CrossRefGoogle Scholar
  15. Goto M (1983) Nomenclature of the rice strain of Erwinia chrysanthemi, the causal agent of bacterial foot rot of rice. Ann Phytopath Soc Jpn 49:576–579CrossRefGoogle Scholar
  16. Hauben L, Moore ERB, Vauterin L, Steenackers M, Mergaert J, Verdonck L, Swings J (1998) Phylogenetic position of phytopathogens within the Enterobacteriaceae. Syst Appl Microbiol 21:384–397PubMedCrossRefGoogle Scholar
  17. Hugh R, Leifson E (1953) The taxonomic significance of fermentative versus oxidative metabolism of carbohydrates by various gram negative bacteria. J Bacteriol 66:24–26PubMedCentralPubMedGoogle Scholar
  18. Ito Y, Takikawa Y, Tsuyumu S, Goto M (1990a) Erwinia chrysanthemi isolated from soft rotted Phalaenopsis (in Japanese). Ann Phytopath Soc Jpn 56:98–99Google Scholar
  19. Ito Y, Takikawa Y, Akayama K, Uematsu S, Tsuyumu S, Goto M (1990b) Bacterial soft rot of Oncidium and Vanda (abstract in Japanese). Ann Phytopath Soc Jpn 56:394Google Scholar
  20. Jiménez-Hidalgo I, Virgen-Calleros G, Martínez-de la Vega O, Vandemark G, Olalde-Portugal V (2004) Identification and characterisation of bacteria causing soft-rot in Agave tequilana. Eur J Plant Pathol 110:317–331CrossRefGoogle Scholar
  21. Kanno E, Ito K, Shinohara H, Sasaki M (2002) Occurrence of peach sudden death syndrome in Fukushima Prefecture and a study of causal pathogenic bacteria (in Japanese). Annu Rept Plant Prot North Jpn 53:137–140Google Scholar
  22. Kijima T, Yamashita S, Doi Y (1985) Bacterial foot rot of foxtail millet, stem gall of Gypsophila paniculata and leaf rot of Spathiphyllum spp. caused by Erwinia spp. (abstract in Japanese). Ann Phytopath Soc Jpn 51:344Google Scholar
  23. Kim WK, Gardan L, Rhim SL, Geiderl K (1999) Erwinia pyrifoliae sp. nov., a novel pathogen that affects Asian pear trees (Pyrus pyrifolia Nakai). Int J Syst Bacteriol 49:899–906PubMedCrossRefGoogle Scholar
  24. King EO, Ward MK, Raney DE (1954) Two simple media for the demonstration of pyocyanin and fluorescin. J Lab Clin Med 44:301–307PubMedGoogle Scholar
  25. Kwon SW, Go SJ, Kang HW, Ryu JC, Jo JK (1997) Phylogenetic analysis of Erwinia species based on 16S rRNA gene sequences. Int J Syst Bacteriol 47:1061–1067PubMedCrossRefGoogle Scholar
  26. Laurila J, Ahola V, Lehtinen A, Joutsjoki T, Hannukkala A, Rahkonen A, Pirhonen M (2008) Characterization of Dickeya strains isolated from potato and river water samples in Finland. Eur J Plant Pathol 122:213–225CrossRefGoogle Scholar
  27. Lelliot RA (1974) Genus XII Erwinia. In: Buchanan RE, Gibbons NE (eds) Bergey’s manual of determinative bacteriology, 8th edn. Williams & Wilkins Co., Baltimore, pp 332–339Google Scholar
  28. Lelliot RA, Billing E, Hayward AC (1966) A determinative scheme for the fluorescent plant pathogenic pseudomonads. J App Bacteriol 29:470–489CrossRefGoogle Scholar
  29. Ma B, Hibbing ME, Kim HS, Reedy RM, Yedidia I, Breuer J, Breuer J, Glasner JD, Perna NT, Kelman A, Charkowski O (2007) Host range and molecular phylogenies of the soft rot enterobacterial genera Pectobacterium and Dickeya. Phytopathology 97:1150–1163PubMedCrossRefGoogle Scholar
  30. Maeda Y, Shinohara H, Kiba A, Ohnishi K, Furuya N, Kawamura Y, Ezaki T, Vandamme P, Tsushima S, Hikichi Y (2006) Phylogenetic study and multiplex PCR-based detection of Burkholderia plantarii, Burkholderia glumae and Burkholderia gladioli using gyrB and rpoD sequences. Int J Syst Evol Microbiol 56:1031–1038PubMedCrossRefGoogle Scholar
  31. Matsuda I, Shirota A, Tsuchiya Y, Ikeda H (1984) Bacterial soft rot on eggplant caused by Erwinia chrysanthemi (abstract in Japanese). Ann Phytopathol Soc Jpn 50:420Google Scholar
  32. Matsuura T, Shinohara H, Inoue Y, Azegami K, Tsushima S, Tsukamoto T, Mizuno A (2007) Erwinia isolates from the bacterial shoot blight of pear in Japan are closely related to Erwinia pyrifoliae based on phylogenetic analyses of gyrB and rpoD genes. J Gen Plant Pathol 73:53–58CrossRefGoogle Scholar
  33. Miyahira N, Takushi T, Furuya N, Kawano S, Takeshita M, Tsuchiya K (2008) Bacterial shoot blight of mango (Mangifera indica L.) caused by Erwinia chrysanthemi (abstract in Japanese). Ann Phytopathol Soc Jpn 74:253–254Google Scholar
  34. Mizuno A, Nakanishi T, Nishiyama K (1993) Bacterial wilt of yacon strawberry caused by Erwinia chrysanthemi (in Japanese). Ann Phytopath Soc Jpn 59:702–708CrossRefGoogle Scholar
  35. Ngwira N, Samson R (1990) Erwinia chrysanthemi: description of two new biovars (bv 8 and bv 9) isolated from kalanchoe and maize host plants. Agronomie 10:341–345CrossRefGoogle Scholar
  36. Nishiyama K (1978) The tentative plan of simple identification method of plant pathogenic bacteria (in Japanese). Plant Prot (Shokubutsu Boeki) 32:283–288Google Scholar
  37. Olive DM, Bean P (1999) Principles and applications of methods for DNA-based typing of microbial organisms. J Clin Microbiol 37:1661–1669PubMedCentralPubMedGoogle Scholar
  38. Parkinson N, Stead D, Bew J, Heeney J, Tsror (Lahkim) L, Elphinstone J (2009) Dickeya species relatedness and clade structure determined by comparison of recA sequences. Int J Syst Evol Microbiol 59:2388–2393PubMedCrossRefGoogle Scholar
  39. Perombelon MCM, Kelman A (1980) Ecology of the soft rot erwinias. Annu Rev Phytopathol 18:361–387CrossRefGoogle Scholar
  40. Rademaker JLW, Louws FJ, de Bruijn FJ (1998) Characterization of the diversity of ecologically important microbes by rep-PCR genomic fingerprinting. In: Akkermans ADL, van Elsas JD, de Bruijin FL (eds) Molecular microbial ecology manual, suppl 3, chapter 3.4.3. Kluwer, Dordrecht pp 1–27Google Scholar
  41. Ryu E (1940) A simple method of differentiation between gram-positive and gram-negative organism without staining. Kitasato Arch Exp Med 17:58–63Google Scholar
  42. Saito T (1985) Bacterial stunt of carnation caused by Erwinia chrysanthemi pv dianthicola. Ann Phytopath Soc Jpn 51:145–151CrossRefGoogle Scholar
  43. Sakai K (1995) Occurrence of bacterial wilt disease of chicory, Cichorium intybus L., and control experiments by chemicals (in Japanese). Proc Kanto-Tosan Plant Prot Soc 42:55–57Google Scholar
  44. Sakai K (1997) Occurrence of bacterial wilt of Kalanchoe blossfeldiana caused by Erwinia chrysanthemi (in Japanese). Proc Kanto-Tosan Plant Prot Soc 44:155–159Google Scholar
  45. Sakamoto M, Huang Y, Ohnishi M, Umeda M, Ishikawa I, Benno Y (2004) Changes in oral microbial profiles after periodontal treatment as determined by molecular analysis of 16S rRNA genes. J Med Microbiol 53:563–571PubMedCrossRefGoogle Scholar
  46. Samson R, Legendre JB, Christen R, Fischer-Le Saux M, Achouak W, Gardan L et al (2005) Transfer of Pectobacterium chrysanthemi (Burkholder et al. 1953) Brenner et al. 1973 and Brenneria paradisiaca to the genus Dickeya gen. nov. as Dickeya chrysanthemi comb. nov. and Dickeya paradisiaca comb. nov. and delineation of four novel species, Dickeya dadantii sp. nov., Dickeya dianthicola sp. nov., Dickeya dieffenbachiae sp. nov. and Dickeya zeae sp. nov. Int J Syst Evol Microbiol 55:1415–1427PubMedCrossRefGoogle Scholar
  47. Slawiak M, van Beckhoven JRCM, Speksnijder AGCL, Czajkowski R, Grabe G, van der Wolf JM (2009) Biochemical and genetical analysis reveal a new clade of biovar 3 Dickeya spp. strains isolated from potato in Europe. Eur J Plant Pathol 125:245–261CrossRefGoogle Scholar
  48. Society of American Bacteriologists (1957) Manual of microbiological methods. McGraw-Hill, New York, p 54Google Scholar
  49. Starr MP, Chatterjee AK (1972) The genus Erwinia: enterobacteria pathogenic to plants and animals. Annu Rev Microbiol 26:389–426PubMedCrossRefGoogle Scholar
  50. Sugama E, Tsuchiya K, Tamori M, Wakimoto S (1986) Bacterial corm and root of taro (Colocasia esculenta (L) Schott) (abstract in Japanese). Ann Phytopath Soc Jpn 52:505Google Scholar
  51. Suyama K, Nashu Y, Fuji H, Fumemoto K, Aono N (1987) Pathogen on Erwinia rusty canker of Japanese pear (abstract in Japanese). Ann Phytopath Soc Jpn 53:71Google Scholar
  52. Takeuchi T, Kodama F (1992) Bacterial stalk rot of corn caused by Erwinia chrysanthemi pv. zeae (Sabet) Victoria, Arboleda et Munoz occurred in Hokkaido, Japan (in Japanese). Soc Plant Prot North Jpn 43:42–44Google Scholar
  53. Takikawa Y, Yamashita S, Doi Y, Koshira K (1982) Bacterial stalk rot of corn, bacterial streak of bromus grass and bacterial gall of Myrica rubra (abstract in Japanese). Ann Phytopath Soc Jpn 48:76CrossRefGoogle Scholar
  54. Takikawa Y, Yoshino M, Yamashita S, Doi Y (1983) Erwinia chrysanthemi isolated from rotted Welsh onion (abstract in Japanese). Ann Phytopath Soc Jpn 49:415Google Scholar
  55. Tamura I, Azegami K, Miura T, Nishi K (1998) Bacterial stem and root rot of sweet potato caused by Erwinia chrysanthemi (abstract in Japanese). Ann Phytopathol Soc Jpn 64:376CrossRefGoogle Scholar
  56. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599PubMedCrossRefGoogle Scholar
  57. Tanii A, Baba T et al (1971) Bacterial plant diseases in Hokkaido. II. Bacterial stem rot of potato plant caused by Erwinia chrysanthemi Burkholder et al. (Pectobacterium carotovorum var. chrysanthemi) (in Japanese). Bull Hokkaido Agric Exp Stn 24:1–9Google Scholar
  58. Tominaga T, Ogasawara K (1979) Bacterial stem rot of potato caused by Erwinia chrysanthemi (in Japanese). Ann Phytopath Soc Jpn 45:474–477CrossRefGoogle Scholar
  59. Toth IK, Avrova AO, Hyman LJ (2001) Rapid identification and differentiation of the soft rot erwinias by 16S–23S intergenic transcribed spacer-PCR and restriction fragment length polymorphism analyses. App Environ Microbiol 67:4070–4076CrossRefGoogle Scholar
  60. Toth IK, van der Wolf JM, Saddler G, Lojkowska E, Helias V, Pirhonen M, Tsor (Lahkim) L, Elphinstone JG (2011) Dickeya species: an emerging problem for potato production in Europe. Plant Pathol 60:385–399CrossRefGoogle Scholar
  61. Uematsu T, Tagami M, Tekeuchi T, Kato H (1985) Characterization of the bacterium inciting rice foot rot in Mie and Chiba Prefectures (in Japanese). Proc Kanto-Tosan Plant Prot Soc 32:30–32Google Scholar
  62. Umemoto K, Nagai Y (1984) Occurrence of erwinia rusty canker on Japanese pear (abstract in Japanese). Ann Phytopath Soc Jpn 50:83Google Scholar
  63. van der Merwe JJ, Coutinho TA, Korsten L, van der Waals JE (2010) Pectobacterium carotovorum subsp. brasiliensis causing blackleg on potatoes in South Africa. Eur J Plant Pathol 126:175–185CrossRefGoogle Scholar
  64. Waldee EL (1945) Comparative studies of some peritrichous phytopathogenic bacteria. Iowa State J Sci 19:435–484Google Scholar
  65. Waleron M, Waleron K, Podhajska AJ, Łojkowska E (2002) Genotyping of bacteria belonging to the former Erwinia genus by PCR-RFLP analysis of a recA gene fragment. Microbiology 148:583–595PubMedGoogle Scholar
  66. Waleron M, Waleron K, Geider K, Lojkowska E (2008) Application of RFLP analysis of recA, gyrA and rpoS gene fragments for rapid differentiation of Erwinia amylovora from Erwinia strains isolated in Korea and Japan. Eur J Plant Pathol 121:161–172CrossRefGoogle Scholar
  67. Weisburg WG, Barns SM, Pelletier DA, Lane DJ (1991) 16S Ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697–703PubMedCentralPubMedGoogle Scholar
  68. Winslow C-EA, Broadhurst J, Buchanan RE, Krumwiede C Jr, Rogers LA, Smith GH (1917) The families and genera of the bacteria. Preliminary report of the committee of the Society of American Bacteriologists on characterization and classification of bacterial types. J Bacteriol 2:505–566PubMedCentralPubMedGoogle Scholar
  69. Yamamoto S, Bouvet PJM, Harayama S (1999) Phylogenetic structures of the genus Acinetobacter based on gyrB sequences: comparison with the grouping by DNA–DNA hybridization. Int J Syst Bacteriol 49:87–95PubMedCrossRefGoogle Scholar
  70. Yanagiya Y, Furuya N, Kurose D, Inada M, Yamaguchi J, Takesita M, Tsuchiya K (2013) On the Erwinia spp. isolated from Chinese lantern plant (Physalis alkekengi L.) showing soft rot (abstract in Japanese). Jpn J Phytopathol 79:71–72Google Scholar
  71. Yoshimatsu H, Hasama W (1997) Bacterial stem rot of strawberry (Fragaria × ananassa, Duch) caused by Erwinia chrysanthemi (abstract in Japanese). Ann Phytopathol Soc Jpn 63:197Google Scholar
  72. Young JM, Park DC (2007) Relationships of plant pathogenic enterobacteria based on partial atpD, carA, and recA as individual and concatenated nucleotide and peptide sequences. Syst App Microbiol 30:343–354CrossRefGoogle Scholar

Copyright information

© The Phytopathological Society of Japan and Springer Japan 2014

Authors and Affiliations

  • Radix Suharjo
    • 1
    • 2
  • Hiroyuki Sawada
    • 3
  • Yuichi Takikawa
    • 1
    Email author
  1. 1.Laboratory of Plant Pathology, Graduate School of Science and TechnologyShizuoka UniversityShizuokaJapan
  2. 2.Faculty of AgricultureUniversity of LampungBandar LampungIndonesia
  3. 3.National Institute of Agrobiological SciencesTsukubaJapan

Personalised recommendations