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Phylotype and sequevar determination and AFLP fingerprinting of Ralstonia solanacearum strains causing bacterial wilt of potato in southeastern Iran

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Abstract

Bacterial wilt of potato caused by Ralstonia solanacearum is a severe threat to potato cultivation in Kerman province, located in southeastern Iran and the third largest potato producer in the country. The present study intends to determine the precise phylogenetic position, sequevar, and genetic diversity of R. solanacearum strains associated with the disease. To this end, the major potato-growing regions of the province (Jiroft and Laleh Zaar) were surveyed to collect tuber samples from affected potato plants showing typical wilt symptoms. Twenty-three strains were collectively purified and subjected to phenotypic and genotypic characterization. Biochemical tests showed that all the strains belonged to R. solanacearum biovar 2A. Furthermore, phylotype-specific multiplex polymerase chain reaction results indicated that the strains belonged to phylotype II. For sequevar typing as well as the determination of the phylotype subcluster (IIA/IIB), polymerase chain reaction amplicons of the endoglucanase precursor gene of 11 representative strains were sequenced. In phylogenetic analysis, the strains were grouped with the reference strains of phylotype IIB-1 retrieved from the GenBank. Then, to assess genetic diversity, 19 selected strains were subjected to genomic fingerprinting, i.e., amplified fragment length polymorphism (AFLP) using seven primer pair combinations. The AFLP data showed heterogeneity among the strains of R. solanacearum and were grouped into four clusters. With our knowledge, this is the first report of the phylotype, and sequevar determination (i.e., IIB-1) in addition to AFLP-based genomic fingerprinting of R. solanaceraum strains causing potato wilt in southeastern Iran.

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References

  • Abdurahman, A., Parker, M. L., Kreuze, J., Elphinstone, J. G., Struik, P. C., Kigundu, A., Arengo, E., & Sharma, K. (2019). Molecular epidemiology of Ralstonia solanacearum species complex strains causing bacterial wilt of potato in Uganda. Phytopathology, 109(11), 1922–1931.

    Article  CAS  PubMed  Google Scholar 

  • Amarnameh (2018). Statistical Book of Agriculture. Volume I. Published by Ministry of Agriculture-Jahad, Islamic Republic of Iran. pp. 116. (In Farsi).

  • Buddenhagen, I., Sequeira, L., & Kelman, A. (1962). Designation of races in Pseudomonas solanacearum. Phytopathology, 52, 726.

    Google Scholar 

  • Campanella, J. J., Bitincka, L., & Smalley, J. (2003). MatGAT: an application that generates similarity/identity matrices using protein or DNA sequences. BMC Bioinformatics, 4(1), 29.

    Article  PubMed  PubMed Central  Google Scholar 

  • Cellier, G., & Prior, P. (2010). Deciphering phenotypic diversity of Ralstonia solanacearum strains pathogenic to potato. Phytopathology, 100(11), 1250–1261.

    Article  CAS  PubMed  Google Scholar 

  • Cellier, G., Remenant, B., Chiroleu, F., Lefeuvre, P., & Prior, P. (2012). Phylogeny and population structure of brown rot-and Moko disease-causing strains of Ralstonia solanacearum phylotype II. Applied and Environmental Microbiology, 78(7), 2367–2375.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Champoiseau, P. G., Jones, J. B., & Allen, C. (2009). Ralstonia solanacearum race 3 biovar 2 causes tropical losses and temperate anxieties. Plant Health Progress, 10(1):35.

  • Chen, W. P., & Kuo, T. T. (1993). A simple and rapid method for the preparation of gram-negative bacterial genomic DNA. Nucleic Acids Research, 21(9), 2260.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Clarke, C. R., Studholme, D. J., Hayes, B., Runde, B., Weisberg, A., Cai, R., Wroblewski, T., Daunay, M.-C., Wicker, E., Castillo, J. A., & Vinatzer, B. A. (2015). Genome-enabled phylogeographic investigation of the quarantine pathogen Ralstonia solanacearum race 3 biovar 2 and screening for sources of resistance against its core effectors. Phytopathology, 105(5), 597–607.

    Article  CAS  PubMed  Google Scholar 

  • Danesh, D., & Bahar, M. (1984). Occurrence of bacterial wilt of potato in Iran. In Proceedings of the Ninth Triennial Conference of the European Association for Potato Research, Interlaken, Switzerland, 407–8.

  • Denny, P. T., & Hayward, A. C. (2001). Gram negative bacteria, Ralstonia. In N. W. Schaad, J. B. Jones & W. Chun (Eds.), Laboratory Guide for Identification of Plant Pathogenic Bacteria (pp. 151–174). St. Paul: American Phytopathology Society Press.

    Google Scholar 

  • Esfahani, S. T., Shiran, B., & Balali, G. (2009). AFLP markers for the assessment of genetic diversity in European and North American potato varieties cultivated in Iran. Crop Breeding and Applied Biotechnology, 9(1), 75–86.

    Article  Google Scholar 

  • Esfandiari, S., & khodakaramian, G. (2015). Diversity and physiological characteristics of Ralstonia solanacearum from potato fields in Hamedan province. Agricultural Biotechnology, 6(2), 23–31. (Abstract in English).

    Google Scholar 

  • Fegan, M., & Hayward, A. C. (2014). Ralstonia solanacearum Race 3, Biovar 2. In D. Liu (ed.), Manual of Security Sensitive Microbes and Toxins (pp. 807–818), CRC Press.

  • Fegan, M., & Prior, P. (2005). How complex is the Ralstonia solanacearum species complex? In C. Allen, P. Prior & A. C. Hayward (Eds.), Bacterial Wilt the Disease and the Ralstonia solanacearum Species Complex (pp. 449–461). St. Paul: American Phytopathology Society Press.

    Google Scholar 

  • Fegan, M., Taghavi, M., Sly, L. I., & Hayward, A. C. (1998). Phylogeny, diversity and molecular diagnostics of Ralstonia solanacearum. In P. Prior, C. Allen & J. Elphinstone (Eds.), Bacterial Wilt Disease: Molecular and Ecological Aspects (pp. 19–33). Berlin Heidelberg: Springer-Verlag.

    Chapter  Google Scholar 

  • García, R. O., Kerns, J. P., & Thiessen, L. (2019). Ralstonia solanacearum species complex: a quick diagnostic guide. Plant Health Progress, 20(1), 7–13.

  • Genin, S. (2010). Molecular traits controlling host range and adaptation to plants in Ralstonia solanacearum. New Phytologist, 187(4), 920–928.

    Article  PubMed  Google Scholar 

  • Guarischi-Sousa, R., Puigvert, M., Coll, N. S., Siri, M. I., Pianzzola, M. J., & Valls, M. (2016). Complete genome sequence of the potato pathogen Ralstonia solanacearum. UY031. Standards in Genomic Sciences, 11(1), 7.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Guidot, A., Prior, P., Schoenfeld, J., Carrere, S., Genin, S., & Boucher, C. (2007). Genomic structure and phylogeny of the plant pathogen Ralstonia solanacearum inferred from gene distribution analysis. Journal of Bacteriology, 189(2), 377–387.

    Article  CAS  PubMed  Google Scholar 

  • Gutarra, L., Herrera, J., Fernandez, E., Kreuze, J., & Lindqvist-Kreuze, H. (2017). Diversity, pathogenicity, and current occurrence of bacterial wilt bacterium Ralstonia solanacearum in Peru. Frontiers in Plant Science, 8, 1221.

    Article  PubMed  PubMed Central  Google Scholar 

  • Hall, T. A. (1999). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series, 41(41), 95–98.

  • Hayward, A. C. (1964). Characteristics of Pseudomonas solanacearum. Journal of Applied Bacteriology, 27(2), 265–277.

    Article  Google Scholar 

  • Hayward, A. C. (1991). Biology and epidemiology of bacterial wilt caused by Pseudomonas solanacearum. Annual Review of Phytopathology, 29(1), 65–87.

    Article  CAS  PubMed  Google Scholar 

  • Hayward, A. C. (1994). Systematics and phylogeny of Pseudomonas solanacearum and related bacteria. In A. C. Hayward & G. L. Hartman (Eds.), Bacterial Wilt: The Disease and its Causative Agent, Pseudomonas solanacearum (pp. 123–135). Wallingford: CAB International.

    Google Scholar 

  • Horita, M., Suga, Y., Ooshiro, A., & Tsuchiya, K. (2010). Analysis of genetic and biological characters of Japanese potato strains of Ralstonia solanacearum. Journal of General Plant Pathology, 76(3), 196–207.

    Article  CAS  Google Scholar 

  • Irandoust, H., Niknam, G., Ghasemi, A., Taghavi, S. M., & Torabi, E. (2008). Study on phenotypic and protein diversity of Ralstonia solanacearum strains in Iran. Journal of Science and Technology of Agriculture and Natural Resources, 12(43), 183–192.

    CAS  Google Scholar 

  • Izadiyan, M., & Taghavi, S. M. (2011). Genotypic diversity of Iranian strains of Ralstonia solanacearum. Phytopathologia Mediterranea, 50(2), 236–244.

    CAS  Google Scholar 

  • Izadiyan, M., & Taghavi, S. M. (2013). Host range variation and genetic diversity of Iranian isolates of Ralstonia solanacearum from potato and tomato with RAPD and (GTG) 5-PCR. Journal of Plant Pathology, 95(1), 87–97.

    Google Scholar 

  • Jeong, Y., Kim, J., Kang, Y., Lee, S., & Hwang, I. (2007). Genetic diversity and distribution of Korean isolates of Ralstonia solanacearum. Plant Disease, 91(10), 1277–1287.

    Article  CAS  PubMed  Google Scholar 

  • Kelman, A. (1954). The relationship of pathogenicity in Pseudomonas solanacearum to colony appearance on tetrazolium medium. Phytopathology, 44(12), 693–695.

    Google Scholar 

  • Kelman, A. (2013). One hundred and one years of research on bacterial wilt. In P. Prior, C. Allen, & J. Elphinstone (Eds.), Bacterial Wilt Disease: Molecular and Ecological Aspects (pp. 1–5). Springer Science & Business Media.

  • Kumar, A., Prameela, T. P., Bhai, S., Siljo, R., Biju, A., Anandaraj, C. N., M., & Vinatzer, B. A. (2012). Small cardamom (Elettaria cardamomum Maton.) and ginger (Zingiber officinale Roxb) bacterial wilt is caused by same strain of Ralstonia solanacearum: a result revealed by multilocus sequence typing (MLST). European Journal of Plant Pathology, 132(4), 477–482.

  • Kumar, A., Sarma, Y. R., & Anandaraj, M. (2004). Evaluation of genetic diversity of Ralstonia solanacearum causing bacterial wilt of ginger using REP-PCR and PCR-RFLP. Current Science, 87(11), 1555–1561.

    Google Scholar 

  • Laferriere, L. T., Helgeson, J. P., & Allen, C. (1999). Fertile Solanum tuberosum + S. commersonii somatic hybrids as sources of resistance to bacterial wilt caused by Ralstonia solanacearum. Theoretical and Applied Genetics, 98(8), 1272–1278.

    Article  Google Scholar 

  • Maghooli, M., Hayati, J., Taghavi, S. M., & Mostofezadeh Ghalamfarsa, R. (2004). Characteristics of Ralstonia solanacearum in Khuzestan. In: Proceedings of the Sixteenth Plant Protection Congress, 28 Aug.–1 Sep., Tabriz, Iran, p. 218.

  • Martin, C., French, E. R., & Nydegger, U. (1981). Bacterial wilt of potato in the Amazon Basin. Plant Disease, 65, 246–248.

    Article  Google Scholar 

  • Meng, F. (2013). Ralstonia solanacearum species complex and bacterial wilt disease. Journal of Bacteriology and Parasitology, 4(2), p.e 119.

  • Moradi-Beidokhti, H., Hosseini-pour, A., Rahimian, H., & Massumi, H. (2008). First report of Ralstonia solanacearum biovar N2 strains on potato in southeastern Iran. 18th Iranian Plant Protection Congress, 24–27 Aug., Hamedan, Iran. p. 436.

  • Morel, A., Peeters, N., Vailleau, F., Barberis, P., Jiang, G., Berthomé, R., & Guidot, A. (2018). Plant pathogenicity phenotyping of Ralstonia solanacearum strains. In Host-Pathogen Interactions (pp. 223–239). New York: Humana Press.

    Chapter  Google Scholar 

  • Nion, Y. A., & Toyota, K. (2015). Recent trends in control methods for bacterial wilt diseases caused by Ralstonia solanacearum. Microbes and Environments, 30(1), 1–11.

    Article  PubMed  PubMed Central  Google Scholar 

  • Nouri, S., Bahar, M., & Fegan, M. (2009). Diversity of Ralstonia solanacearum causing potato bacterial wilt in Iran and the first record of phylotype II/biovar 2T strains outside South America. Plant Pathology, 58(2), 243–249.

    Article  Google Scholar 

  • Opina, N., Tavner, F., Hollway, G., Wang, J. F., Li, T. H., Maghirang, R., Fegan, M., Hayward, A. C., Krishnapillai, V., Hong, W. F., Holloway, B. W., & Timmis, J. N. (1997). A novel method for development of species and strain-specific DNA probes and PCR primers for identifying Burkholderia solanacearum (formerly Pseudomonas solanacearum). Asia-Pacific Journal of Molecular Biology and Biotechnology, 5(1), 19–30.

    Google Scholar 

  • Patil, V. U., Girimalla, V., Sagar, V., Chauhan, R. S., & Chakrabarti, S. K. (2017). Genome sequencing of four strains of phylotype I, II and IV of Ralstonia solanacearum that cause potato bacterial wilt in India. Brazilian Journal of Microbiology, 48(2), 193–195.

    Article  CAS  PubMed  Google Scholar 

  • Pireh, S., & Harighi, B. (2017). Phenotypic and genetic properties of Ralstonia solanacearum strains the causal agent of bacterial wilt of potato isolated from Kurdistan province. Iranian Journal of Plant pathology, 53(1), 1–13. (Abstract in English).

    Google Scholar 

  • Poussier, S., Trigalet-Demery, D., Vandewalle, P., Goffinet, B., Luisetti, J., & Trigalet, A. (2000). Genetic diversity of Ralstonia solanacearum as assessed by PCR-RFLP of the hrp gene region, AFLP and 16S rRNA sequence analysis and identification of an African subdivision. Microbiology, 146(7), 1679–1692.

    Article  CAS  PubMed  Google Scholar 

  • Prior, P., & Fegan, M. (2005). Recent developments in the phylogeny and classification of Ralstonia solanacearum. Acta Horticulturae, 695, 127–136.

    Article  CAS  Google Scholar 

  • Prior, P., Ailloud, F., Dalsing, B. L., Remenant, B., Sanchez, B., & Allen, C. (2016). Genomic and proteomic evidence supporting the division of the plant pathogen Ralstonia solanacearum into three species. BMC Genomics, 17(1), 90.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Priou, S., Aley, P., Chujoy, E., Lemaga, B., French, E. R., & French, E. (1999). Integrated control of bacterial wilt of potato. In CIP Slide Training Series IV-3. International Potato. Available at http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.576.6546&rep=rep1&type=pdf.

  • Ravelomanantsoa, S., Vernière, C., Rieux, A., Costet, L., Chiroleu, F., Arribat, S., Cellier, G., Pruvost, O., Poussier, S., Robène, I., & Guérin, F. (2018). Molecular epidemiology of bacterial wilt in the Madagascar highlands caused by Andean (phylotype IIB-1) and African (phylotype III) brown rot strains of the Ralstonia solanacearum species complex. Frontiers in Plant Science, 8, 2258.

    Article  PubMed  PubMed Central  Google Scholar 

  • Safni, I., Cleenwerck, I., De Vos, P., Fegan, M., Sly, L., & Kappler, U. (2014). Polyphasic taxonomic revision of the Ralstonia solanacearum species complex: proposal to emend the descriptions of Ralstonia solanacearum and Ralstonia syzygii and reclassify current R. syzygii strains as Ralstonia syzygii subsp. syzygii subsp. nov., R. solanacearum phylotype IV strains as Ralstonia syzygii subsp. indonesiensis subsp. nov., banana blood disease bacterium strains as Ralstonia syzygii subsp. celebesensis subsp. nov. and R. solanacearum phylotype I and III strains as Ralstonia pseudosolanacearum sp. nov. International Journal of Systematic and Evolutionary Microbiology, 64(9), 3087–3103.

  • Sagar, V., Jeevalatha, A., Mian, S., Chakrabarti, S. K., Gurjar, M. S., Arora, R. K., Sharma, S., Bakade, R. R., & Singh, B. P. (2014). Potato bacterial wilt in India caused by strains of phylotype I, II and IV of Ralstonia solanacearum. European Journal of Plant Pathology, 138(1), 51–65.

    Article  Google Scholar 

  • Siri, M. I., Sanabria, A., & Pianzzola, M. J. (2011). Genetic diversity and aggressiveness of Ralstonia solanacearum strains causing bacterial wilt of potato in Uruguay. Plant Disease, 95(10), 1292–1301.

    Article  CAS  PubMed  Google Scholar 

  • Smith, J. J., Offord, L. C., Holderness, L. C., Holderness, M., & Saddler, G. S. (1995). Genetic diversity of Burkholderia solanacearum race 3 in Kenya. Applied and Environmental Microbiology, 61(12), 4263–4268.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Stulberg, M. J., & Huang, Q. (2016). A computer program for fast and easy typing of a partial endoglucanase gene sequence into genospecies and sequevars 1 & 2 of the Ralstonia solanacearum species complex. Journal of Microbiological Methods, 123, 101–107.

    Article  CAS  PubMed  Google Scholar 

  • Tamura, K., Stecher, G., Peterson, D., Filipski, A., & Kumar, S. (2013). MEGA6: molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution, 30(12), 2725–2729.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Toukam, M. S., Cellier, G., Wicker, G., Guilbaud, E., Kahane, C., Allen, R., C., & Prior, P. (2009). Broad diversity of Ralstonia solanacearum strains in Cameroon. Plant Disease, 93(11), 1123–1130.

  • Van Der Wolf, J. M., Bonants, P. J. M., Smith, J. J., Hagenaar, M., Nijhuis, E., Van Beckhoven, J. R. C. M., Saddler, G. S., Trigalet, A., & Feuillade, R. (1998). Genetic diversity of Ralstonia solanacearum race 3 in Western Europe determined by AFLP, RC-PFGE and Rep-PCR. In P. Prior, C. Allen & J. Elphinstone (Eds.), Bacterial Wilt Disease: Molecular and Ecological Aspects (pp. 44–49). Berlin Heidelberg: Springer-Verlag.

    Chapter  Google Scholar 

  • Vos, P., Hogers, R., Bleeker, M., Reijans, M., Lee, T. V. D., Hornes, M., Friters, A., Pot, J., Paleman, J., Kuiper, M., & Zabeau, M. (1995). AFLP: a new technique for DNA fingerprinting. Nucleic Acids Research, 23(21), 4407–4414.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang, L., Wang, B., Zhao, G., Cai, X., Jabaji, S., Seguin, P., & Chen, H. (2017). Genetic and pathogenic diversity of Ralstonia solanacearum causing potato brown rot in China. American Journal of Potato Research, 94(4), 403–416.

    Article  Google Scholar 

  • Yu, Q., Alvarez, A. M., Moore, P. H., Zee, F., Kim, M. S., de Silva, A., Hepperly, P. R., & Ming, R. (2003). Molecular diversity of Ralstonia solanacearum isolate from ginger in Hawaii. Phytopathology, 93(9), 1124–1130.

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

The office of vice-chancellor for research, Shahid Bahonar University of Kerman, Iran, funded this work, which is thankfully acknowledged.

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Authors and Affiliations

  1. Department of Plant Protection, College of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran

    Ali Mollae, Akbar Hosseinipour & Hossain Massumi

  2. Department of Plant Protection, South Kerman Agricultural and Natural Resources Research and Education Center, AREEO, Jiroft, Iran

    Mahdi Azadvar

  3. Research and Technology Institute of Plant Production, Shahid Bahonar University of Kerman, Kerman, Iran

    Fatemeh Ebrahimi

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Mollae, A., Hosseinipour, A., Azadvar, M. et al. Phylotype and sequevar determination and AFLP fingerprinting of Ralstonia solanacearum strains causing bacterial wilt of potato in southeastern Iran. Eur J Plant Pathol 157, 389–402 (2020). https://doi.org/10.1007/s10658-020-02018-5

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