Abstract
We determined the species composition of 219 isolates of potato blackleg or soft rot pathogens in Japan collected after 2000 from potato plants by species-specific PCR. Of the total, Pectobacterium wasabiae (Pw) and P. carotovorum subsp. brasiliense (Pcb) comprised 88% (Pw: 94 isolates, Pcb: 98 isolates) of the isolates and Dickeya dianthicola (Ddi) 12% (27 isolates). P. atrosepticum (Pa) was not detected. Genetic diversity of Pw, Pcb and Ddi was investigated using repetitive sequence-based PCR (rep-PCR) fingerprinting with three primer pairs complementary to repetitive sequences in the bacterial genome (BOX, ERIC and REP). One hundred and twenty-one Pw isolates, one hundred Pcb isolates and thirty-three Ddi isolates were assigned to twenty-nine, twenty-one and eleven fingerprint genotypes (FGs) based on the combination of fingerprint patterns for each rep-PCR experiment (BOX-, ERIC- and REP-PCR). The genetic diversity of Pw and Ddi isolates in Japan was considered high, with Simpson’s diversity index and Shannon’s index of 0.87 and 2.44 for Pw, and 0.84 and 2.05 for Ddi, respectively. Pcb isolates were less diversified genetically (diversity index: 0.57 and 1.58). The FGs of the isolates obtained from blackleg-affected potato plants in the seed tuber field agreed with those of the isolates in the field where the seeds produced were grown. These results support the occurrence of seed-borne transmission of the blackleg pathogen between the fields.
Similar content being viewed by others
Data availability
The data sets analyzed during the current study available from the corresponding author on reasonable request.
References
Czajkowski, R., Grabe, G. J., & van der Wolf, J. M. (2009). Distribution of Dickeya spp. and Pectobacterium carotovorum subsp. carotovorum in naturally infected seed potatoes. European Journal of Plant Pathology, 125(2), 263–275. https://doi.org/10.1007/s10658-009-9480-9.
Czajkowski, R., Pérombelon, M., Jafra, S., Lojkowska, E., Potrykus, M., van der Wolf, J. M., & Sledz, W. (2015). Detection, identification and differentiation of Pectobacterium and Dickeya species causing potato blackleg and tuber soft rot: A review. Annals of Applied Biology, 166(1), 18–38.
Darrasse, A., Priou, S., Kotoujansky, A., & Bertheau, Y. (1994). PCR and restriction fragment length polymorphism of a pel gene as a tool to identify Erwinia carotovora in relation to potato disease. Applied and Environmental Microbiology, 60(5), 1437–1443.
De Boer, S. H. (2002). Relative incidence of Erwinia carotovora subsp. atroseptica in stolon end and peridermal tissue of potato tubers in Canada. Plant Disease, 86, 960–964.
De Boer, S. H., & Ward, L. J. (1995). PCR detection of Erwinia caotovora subsp. atroseptica associated with potato tissue. Phytopathology, 85, 854–858.
Degefu, Y., Potrykus, M., Golanowska, M., Virtanen, E., & Lojkowska, E. (2013). A new clade of Dickeya spp. plays a major role in potato blackleg outbreaks in North Finland. Annals of Applied Biology, 162(2), 231–241. https://doi.org/10.1111/aab.12020.
Duarte, V., De Boer, S. H., Ward, L. J., & de Oliveira, A. M. R. (2004). Characterization of atypical Erwinia carotovora strains causing blackleg of potato in Brazil. Journal of Applied Microbiology, 96(3), 535–545.
Fujimoto, T., Yasuoka, S., Aono, Y., Nakayama, T., Ohki, T., Sayama, M., & Maoka, T. (2017). First report of potato blackleg caused by Pectobacterium carotovorum subsp. brasiliense in Japan. Plant Disease, 101(1), 241.
Fujimoto, T., Yasuoka, S., Aono, Y., Nakayama, T., Ohki, T., Sayama, M., & Maoka, T. (2018). Biochemical, physiological, and molecular characterization of Dickeya dianthicola (formerly named Erwinia chrysanthemi) causing potato blackleg disease in Japan. Journal of General Plant Pathology, 84, 124–136.
Fujimoto, T., Yasuoka, S., Aono, Y., Nakayama, T., Ohki, T., & Maoka, T. (2020). First report of potato blackleg caused by Dickeya chrysanthemi in Japan. Journal of General Plant Pathology, 86, 423–427. https://doi.org/10.1007/s10327-020-00934-2.
Horita, M., Tanaka, F., & Fuwa, H. (2009). Characteristics of seed-borne bacterial diseases of potato and development of simple detection method of the pathogens. Plant Protection, 63(2), 98–103 (in Japanese).
Ishii, S., & Sadowsky, M. J. (2009). Applications of the rep-PCR DNA fingerprinting technique to study microbial diversity, ecology and evolution. Environmental Microbiology, 11(4), 733–740.
Kawakami, T., Oohori, H., & Tajima, K. (2015). Seed potato production system in Japan, starting from foundation seed of potato. Breeding Science, 65(1), 17–25.
Khayi, S., Blin, P., Pedron, J., Chong, T. M., Chan, K. G., Moumni, M., Hélias, V., Van Gijsegem, F., & Faure, D. (2015). Population genomics reveals additive and replacing horizontal gene transfers in the emerging pathogen Dickeya solani. BMC Genomics, 16, 788.
Khayi, S., Cigna, J., Chong, T. M., Quêtu-Laurent, A., Chan, K. G., Hélias, V., & Faure, D. (2016). Transfer of the potato plant isolates of Pectobacterium wasabiae to Pectobacterium parmentieri sp. nov. International Journal of Systematic and Evolutionary Microbiology, 66(12), 5379–5383.
Nassar, A., Darrasse, A., Lemattre, M., Kotoujansky, A., Dervin, C., Vedel, R., & Bertheau, Y. (1996). Characterization of Erwinia chrysanthemi by pectinolytic isozyme polymorphism and restriction fragment length polymorphism analysis of PCR-amplified fragments of pel genes. Applied and Environmental Microbiology, 62, 2228–2235.
Ngadze, E., Brady, C. L., Coutinho, T. A., & van der Waals, J. E. (2012). Pectinolytic bacteria associated with potato soft rot and blackleg in South Africa and Zimbabwe. European Journal of Plant Pathology, 134(3), 533–549.
Pérombelon, M, C, M., & van der Wolf, J, M. (Eds.). (2002). Methods for the detection and quantification of Erwinia carotovora subsp. atroseptica (Pectobacterium carotovorum subsp. atrosepticum) on potatoes: a laboratory manual (revised version 2002). Scottish Crop Research Institute Occasional Publication, No. 10, Invergowrie, Dundee, Scotland, UK, 82 pp.
Rademaker, J. L. W., & de Bruijn, F. J. (1997). Characterization and classification of microbes by rep-PCR genomic fingerprinting and computer assisted pattern analysis. In G. Caetano-Anollés & P. M. Gresshoff (Eds.), DNA markers: Protocols, applications and overviews (pp. 151-171). J. Wiley & Sons: Hoboken, NJ, USA.
Shannon, C. E. (1948). A mathematical theory of communication. The Bell System Technical Journal, 27, 379–423.
Simpson, E. H. (1949). Measurement of diversity. Nature, 163, 688.
Suharjo, R. (2013). Studies on the taxonomy and identification of Dickeya spp. and Pectobacterium spp. isolated in Japan. Ph. D. thesis, Shizuoka University, 235 pp.
Tanii, A. (1984). Studies on the blackleg disease of potato in Hokkaido. Report of Hokkaido Prefectural Agricultural Experiment Station, 45, 108 pp. (in Japanese with English abstract)
Toth, I. K., van der Wolf, J. M., Saddler, G., Lojkowska, E., Hélias, V., Pirhonen, M., Tsror (Lahkim), L., & Elphinstone, J. G. (2011). Dickeya species: an emerging problem for potato production in Europe. Plant Pathology, 60, 385–399.
Van der Wolf, J. M., Haan, E. G. D., Kastelein, P., Krijger, M., Haas, B. H. D., Velvis, H., Mendes, O., Kooman-Gersmann, M., & van der Zouwen, P. S. (2017). Virulence of Pectobacterium carotovorum subsp. brasiliense on potato compared with that of other Pectobacterium and Dickeya species under climatic conditions prevailing in the Netherlands. Plant Pathology, 66, 571–583.
Versalovic, J., Schneider, M., De Bruijn, F. J., & Lupski, J. R. (1994). Genomic fingerprinting of bacteria using repetitive sequence-based polymerase chain reaction. Methods in Molecular and Cellular Biology, 5, 25–40.
Zoledowska, S., Motyka, A., Zukowska, D., Sledz, W., & Lojkowska, E. (2018). Population structure and biodiversity of Pectobacterium parmentieri isolated from potato fields in temperate climate. Plant Disease, 102(1), 154–164.
Acknowledgments
The authors deeply appreciate Professor Dr. Yuichi Takikawa, Graduate School of Agriculture, Shizuoka University, for providing bacterial isolates and advice and Drs. Mitsuo Horita and Shingo Toyoshima for useful advice. This study was funded by the Science and Technology Research Promotion Program for the Agriculture (no. 27005C), Forestry, Fisheries, and Food industry, Ministry of Agriculture, Forestry and Fisheries.
Code availability
Not applicable.
Funding
This study was funded by the Science and Technology Research Promotion Program for the Agriculture, Forestry, Fisheries, and Food industry (no. 27005C), Ministry of Agriculture, Forestry and Fisheries.
Author information
Authors and Affiliations
Contributions
All authors contributed to the study conception and design. Collection of pathogenic bacteria was done by Shinji Yasuoka, Takahiro Ozawa, Yoshiyuki Aono and Yutaka Ushio. Material preparation, data collection and analysis were performed by Takato Nakayama. The first draft of the manuscript was written by Takato Nakayama. All authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.
Corresponding author
Ethics declarations
Ethics approval
Not applicable.
Consent to participate
Not applicable.
Consent for publication
Not applicable.
Conflict of interest
The authors declare that they have no competing interests.
Rights and permissions
About this article
Cite this article
Nakayama, T., Yasuoka, S., Ozawa, T. et al. Genetic diversity of potato blackleg pathogens, Pectobacterium wasabiae, P. carotovorum subsp. brasiliense and Dickeya dianthicola in Japan by rep-PCR fingerprinting. Eur J Plant Pathol 159, 917–939 (2021). https://doi.org/10.1007/s10658-021-02216-9
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10658-021-02216-9