Genomics-based Sensitive and Specific Novel Primers for Simultaneous Detection of Burkholderia glumae and Burkholderia gladioli in Rice Seeds |
Lee, Chaeyeong
(Department of Microbiology, Pusan National University)
Lee, Hyun-Hee (Department of Microbiology, Pusan National University) Mannaa, Mohamed (Department of Microbiology, Pusan National University) Kim, Namgyu (Department of Microbiology, Pusan National University) Park, Jungwook (Department of Microbiology, Pusan National University) Kim, Juyun (Department of Microbiology, Pusan National University) Seo, Young-Su (Department of Microbiology, Pusan National University) |
1 | Goto, K. and Ohata, K. 1956. New bacterial diseases of rice (brown stripe and grain rot). Ann. Phytopathol. Soc. Jpn. 21:46-47. |
2 | Ham, J. H., Melanson, R. A. and Rush, M. C. 2011. Burkholderia glumae: next major pathogen of rice?. Mol. Plant Pathol. 12:329-339. DOI |
3 | Hikichi, Y., Okuno, T. and Furusawa, I. 1993. Immunofluorescent antibody technique for detecting Pseudomonas glumae on rice plants. Ann. Phytopathol. Soc. Jpn. 59:477-480. DOI |
4 | Lee, C. J., Lee, J. T., Kwon, J. H., Kim, B. C. and Park, W. 2005. Occurrence of bacterial soft rot of onion plants caused by Burkholderia gladioli pv. alliicola in Korea. Aust. Plant Pathol. 34:287-292. DOI |
5 | Lee, C. J., Yun, H. S., Jhune, C. S., Cheong, J. C. and Yoo, Y. B. 2010. Occurrence of bacterial soft rot of Pleurotus ostreatus caused by Burkholderia gladioli pv. agaricicola in Korea. J. Plant Pathol. 92:235-240. |
6 | Lee, K. Y., Kong, H. G., Choi, K. H., Lee, S. W. and Moon, B. J. 2011. Isolation and identification of Burkholderia pyrrocinia CH-67 to control tomato leaf mold and damping-off on crisphead lettuce and tomato. Plant Pathol. J. 27:59-67. DOI |
7 | Maeda, Y., Shinohara, H., Kiba, A., Ohnishi, K., Furuya, N., Kawamura, Y., Ezaki, T., Vandamme, P., Tsushima, S. and 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. 56:1031-1038. DOI |
8 | Nandakumar, R., Bollich, P. A., Shahjahan, A. K. M., Groth, D. E. and Rush, M. C. 2008. Evidence for the soilborne nature of the rice sheath rot and panicle blight pathogen, Burkholderia gladioli 1. Can. J. Plant Pathol. 30:148-154. DOI |
9 | Nandakumar, R., Shahjahan, A. K. M., Yuan, X. L., Dickstein, E. R., Groth, D. E, Clark, C. A., Cartwright, R. D. and Rush, M. C. 2009. Burkholderia glumae and B. gladioli cause bacterial panicle blight in rice in the southern United States. Plant Dis. 93:896-905. DOI |
10 | Nzula, S., Vandamme, P. and Govan, J. R. 2000. Sensitivity of the Burkholderia cepacia complex and Pseudomonas aeruginosa to transducing bacteriophages. FEMS Immunol. Med. Microbiol. 28:307-312. DOI |
11 | Kawaradani, M., Okada, K. and Kusakari, S. 2000. New selective medium for isolation of Burkholderia glumae from rice seeds. J. Gen. Plant Pathol. 66:234-237. DOI |
12 | Rozen, S. and Skaletsky, H. 2000. Primer3 on the WWW for general users and for biologist programmers. Methods Mol. Biol. 132:365-386. |
13 | Tsushima, S., Wakimoto, S. and Mogi, S. 1986. Selective medium for detecting Pseudomonas glumae Jurita et Tabei, the causal bacterium of grain rot of rice. Ann. Phytopathol. Soc. Jpn. 52:253-259. DOI |
14 | Ura, H., Furuya, N., Iiyama, K., Hidaka, M., Tsuchiya, K. and Matsuyama, N. 2006. Burkholderia gladioli associated with symptoms of bacterial grain rot and leaf-sheath browning of rice plants. J. Gen. Plant Pathol. 72:98-103. DOI |
15 | Vandamme, P., Mahenthiralingam, E., Holmes, B., Coenye, T., Hoste, B., De Vos, P., Henry, D. and Speert, D. P. 2000. Identification and population structure of Burkholderia stabilis sp. nov. (formerly Burkholderia cepacia genomovar IV). J. Clin. Microbiol. 38:1042-1047. |
16 | Salles, J. F., De Souza, F. A. and van Elsas, J. D. 2002. Molecular method to assess the diversity of Burkholderia species in environmental samples. Appl. Environ. Microbiol. 68:1595-1603. DOI |
17 | Papaiakovou, M., Pilotte, N., Grant, J. R., Traub, R. J., Llewellyn, S., McCarthy, J. S., Krolewiecki, A. J., Cimino, R., Mejia, R. and Williams, S. A. 2017. A novel, species-specific, real-time PCR assay for the detection of the emerging zoonotic parasite Ancylostoma ceylanicum in human stool. PLoS Negl. Trop. Dis. 11:e0005734. DOI |
18 | Jeong, Y., Kim, J., Kim, S., Kang, Y., Nagamatsu, T. and Hwang, I. 2003. Toxoflavin produced by Burkholderia glumae causing rice grain rot is responsible for inducing bacterial wilt in many field crops. Plant Dis. 87:890-895. DOI |
19 | Jung, B., Park, J., Kim, N., Li, T., Kim, S., Bartley, L. E., Kim, J., Kim, I., Kang, Y., Yun, K., Choi, Y., Lee, H., Ji, S., Lee, K., Kim, B., Shon, J., Kim, W., Liu, K., Yoon, D., Kim, S., Seo, Y. and Lee, J. 2018. Cooperative interactions between seedborne bacterial and air-borne fungal pathogens on rice. Nat. Commun. 9:31. DOI |
20 | Kawanishi, T., Shiraishi, T., Okano Y., Sugawara, K., Hashimoto, M., Maejima, K., Komatsu, K., Kakizawa, S., Yamaji, Y., Hamamoto, H., Oshima, K. and Namba, S. 2011. New detection systems of bacteria using highly selective media designed by SMART: Selective Medium-Design Algorithm Restricted by Two Constraints. PLoS One 6:e16512. DOI |
21 | Yabuuchi, E., Kosako, Y., Oyaizu, H., Yano, I., Hotta, H., Hashimoto, Y., Ezaki, T. and Arakawa, M. 1992. Proposal of Burkholderia gen. nov. and transfer of seven species of the genus Pseudomonas homology group II to the new genus, with the type species Burkholderia cepacia (Palleroni and Holmes 1981) comb. nov. Microbiol. Immunol. 36:1251-1275. DOI |
22 | Yu, S., Chen, W., Wang, D., He, X., Zhu, X. and Shi, X. 2010. Species-specific PCR detection of the food-borne pathogen Vibrio parahaemolyticus using the irgB gene identified by comparative genomic analysis. FEMS Microbiol. Lett. 307:65-71. DOI |
23 | Zaid, A. M., Bonasera, J. M. and Beer, S. V. 2012. OEM-A new medium for rapid isolation of onion-pathogenic and onionassociated bacteria. J. Microbiol. Methods 91:520-526. DOI |
24 | Zhang, H., Hanada, S., Shigematsu, T., Shibuya, K., Kamagata, Y., Kanagawa, T. and Kurane, R. 2000. Burkholderia kururiensis sp. nov., a trichloroethylene (TCE)-degrading bacterium isolated from an aquifer polluted with TCE. Int. J. Syst. Evol. Microbiol. 50:743-749. DOI |
25 | Awika, J. M. 2011. Major cereal grains production and use around the world. In: Advances in cereal science: Implications to food processing and health promotion, eds. by J. M. Awika, V. Piironen and S. Bean, pp. 1-13. American Chemical Society, Washington, D. C., USA. |
26 | Stanier, R. Y., Palleroni, N. J. and Doudoroff, M. 1966. The aerobic pseudomonads: a taxonomic study. J. Gen. Microbiol. 43:159-271. DOI |
27 | Seo, Y. S., Lim, J., Choi, B. S., Kim, H., Goo, E., Lee, B., Lim, J. S., Choi, I. Y., Moon, J. S., Kim, J. and Hwang, I. 2011. Complete genome sequence of Burkholderia gladioli BSR3. J. Bacteriol. 193:3149. DOI |
28 | Sessitsch, A., Coenye, T., Sturz, A. V., Vandamme, P., Barka, E. A., Salles, J. F., Van Elsas, J. D., Faure, D., Reiter, B., Glick, B. R., Wang-Pruski, G. and Nowak, J. 2005. Burkholderia phytofirmans sp. nov., a novel plant-associated bacterium with plantbeneficial properties. Int. J. Syst. Evol. Microbiol. 55:1187-1192. DOI |
29 | Baek, I., Seo, B., Lee, I., Lee, K., Park, S. C., Yi, H. and Chun, J. 2015. Burkholderia megalochromosomata sp. nov., isolated from grassland soil. Int. J. Syst. Evol. Microbiol. 65:959-964. DOI |
30 | Stackebrandt, E. and 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. Bacteriol. 44:846-849. DOI |
31 | Takeuchi, T., Sawada, H., Suzuki, F. and Matsuda, I. 1997. Specific detection of Burkholderia plantarii and B. glumae. Jpn. J. Phytopathol. 63:455-462. DOI |
32 | Tao, T., Chen, Q., Bie, X., Lu, F. and Lu, Z. 2015. Mining of novel species-specific primers for PCR detection of Listeria monocytogenes based on genomic approach. World J. Microbiol. Biotechnol. 31:1955-1966. DOI |
33 | Trung, H. M., Van, N. V., Vien, N. V., Lam, D. T. and Lien, M. 1993. Occurrence of rice grain rot disease in Vietnam. Int. Rice Res. Notes 18:30. |
34 | Cottyn, B., Regalado, E., Lanoot, B., De Cleene, M., Mew, T. W. and Swings, J. 2001. Bacterial populations associated with rice seed in the tropical environment. Phytopathology 91:282-292. DOI |
35 | Baek, K. Y., Lee, H. H., Son, G. J., Lee, P. A., Roy, N., Seo, Y. S. and Lee, S. W. 2018. Specific and sensitive primers developed by comparative genomics to detect bacterial pathogens in grains. Plant Pathol. J. 34:104-112. |
36 | Cho, H. S., Park, S. Y., Ryu, C. M., Kim, J. F., Kim, J. G. and Park, S. H. 2007. Interference of quorum sensing and virulence of the rice pathogen Burkholderia glumae by an engineered endophytic bacterium. FEMS Microbiol. Ecol. 60:14-23. DOI |
37 | Cottyn, B., Van Outryve, M. F., Cerez, M. T., De Cleene, M., Swings, J. and Mew, T. W. 1996. Bacterial disease of rice. II. Characterization of pathogenic bacteria associated with sheath rot complex and grain discoloration of rice in the Philippines. Plant Dis. 80:438-445. DOI |
38 | Cottyn, B., Debode, J., Regalado, E., Mew, T. W. and Swings, J. 2009. Phenotypic and genetic diversity of rice seed-associated bacteria and their role in pathogenicity and biological control. J. Appl. Microbiol. 107:885-897. DOI |
39 | FAO. Feeding the world, eradicating hunger: executive summary. World summit on food security 2009. FAO Database. Version: 2009. URL http://www.fao.org/fileadmin/templates/wsfs/Summit/WSFS_Issues_papers/WSFS_Background_paper_Feeding_the_world.pdf [20 July 2018]. |
40 | Cui, Z., Ojaghian, M. R., Tao, Z., Kakar, K. U., Zeng, J., Zhao, W., Duan, Y., Vera Cruz, C. M., Li, B., Zhu, B. and Xie, G. 2016. Multiplex PCR assay for simultaneous detection of six major bacterial pathogens of rice. J. Appl. Microbiol. 120:1357-1367. DOI |
41 | Furuya, N., Ura, H., Iiyama, K., Matsumoto, M., Takeshita, M. and Takanami, Y. 2002. Specific oligonucleotide primers based on sequences of the 16S-23S rDNA spacer region for the detection of Burkholderia gladioli by PCR. J. Gen. Plant Pathol. 68:220-224. DOI |