Characterization and host range assessment of Dickeya zeae associated with pineapple soft rot disease in East Lampung, Indonesia
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Abstract. Aeny TN, Suharjo R, Ginting C, Hapsoro D, Niswati A. 2020. Characterization and host range assessment of Dickey zeae associated with pineapple soft rot disease in East Lampung, Indonesia. Biodiversitas 21: 587-595. The study aims to characterize the Dickeya zeae associated with pineapple soft rot in East Lampung, Indonesia and to assess the bacterial host range. From the blister-like lesion-symptom, bacteria were isolated with the morphological characteristics: circular, convex, cream white milk-colored, with diameter colonies ranging from 1-2 mm in diameter. Two strains (N-Unila 5 and N-Unila 10) were selected for further investigation including pathogenicity test on pineapple seedling, species identification by phenotypic characteristics and molecular techniques using sequence analysis of 16SrDNA, recA, and dnaX as well as host range test on 25 different plant species. The result of the pathogenicity test showed similar symptoms to those observed in the field. Physiological and biochemical characterization revealed that the two isolates were Gram-negative bacteria, fermentative, lecithinase positive, non-fluorescent on King’s B medium, able to grow on YDC medium at 41oC, did not produce H2S and did not grow in the presence of 5% NaCl. The isolates capable of using Myo-inositol, M-tartrate, mannitol, L-tartrate, lactose, glycerol, D-melibiose, D-arabinose, citrate, and cis-aconitic acid but did not utilize starch, S-ketoglucanate, L-ascorbic acid, inulin, folic acid, D-raffinose and tartrate as a sole carbon source. Phenotypic characteristics indicated that the strains were in the group of Dickeya spp. bv. 3 (phenon 1). Sequence analysis of 16S rDNA, recA, and dnaX revealed that the strains were placed in the same cluster with the reference strain of D. zeae. Host range assessment showed positive soft rot symptoms in Aloe vera, chinese cabbage, dragon-fruit, eggplant, lettuce, and welsh onion that have never been reported before.
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References
Aeny TN, Prasetyo J, Suharjo R, Dirmawati SR, Niswati A. 2018. Short Communication: Isolation and identification of actinomycetes potential as the antagonist of Dickeya zeae pineapple soft rot in Lampung, Indonesia. Biodivesitas 19: 2052–2058.
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Avrova AO, Hyman LJ, Toth RL, Toth IK. 2002. Application of amplified fragment length polymorphism fingerprinting for taxonomy and identification of the soft rot bacteria Erwinia carotovora and Erwinia chrysanthemi. App Environ Microbiol 68 :1499–1508.
Brady CL, Cleenwerck I, Denman S, Venter SN, Rodriguez-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 Lomsdalea 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. dieffenbachieae comb. nov., and emendation of the description of Dickeya dadantii. Int J Syst Evol Microbiol 62:1592–1602
Dickey RS. 1979. Erwinia chrysanthemi: a comparative study of phenotypic properties of strains from several hosts and other Erwinia species. Phytopathol 69:324–329
Dye DW. 1968. A taxonomic study of the genus Erwinia. I. The, ‘‘amylovora’’ group. New Zeal J Sci 11:590–607
Hall TA. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser, 41:95–98.
Hugh R, Leifson E. 1953. The taxonomic significance of fermentative versus oxidative metabolism of carbohydrates by various gram negative bacteria. J Bacteriol 66:24–26
Johnston A. 1957. Bacterial heart rot of the pineapple. Malay Agric J 40:2–8.
Kaneshiro WS, Burger M, Vine BG, De Silva AS, Alvarez AM. 2008. Characterization of Erwinia chrysanthemi from a Bacterial Heart Rot of Pineapple Outbreak in Hawaii. Plant Dis 92:1444–1450.
King EO, Ward MK, Raney DE. 1954. Two simple media for the demonstration of pyocyanin and fluorescin. J Lab Clin Med 44:301–307
Kumar S, Stecher G, Tamura K. 2016. MEGA:7 Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33: 1870–1874
Lelliot RA, Billing E, Hayward AC. 1966. A determinative scheme for the fluorescent plant pathogenic pseudmonads. J App Bacteriol: 29:470-489
Lim WH. 1974. The etiology of fruit collapse and bacterial heart rot of pineapple. MARDI Res Bull 2: 11-16
Ma B, Hibbing ME, Kim H-S, Reedy RM, Yedidia I, Breuer J, Breuer J, Glasner JD, Perna NT, Kelman A, Charkowski AO. 2007. Host Range and Molecular Phylogenies of the Soft Rot Enterobacterial Genera Pectobacterium and Dickeya. Phytopathol 97:1150–1163.
Ngwira N, Samson R. 1990. Erwinia chrysanthemi : description of two new biovar (bv 8 and bv 9) isolated from kalanchoe and maize host plant. Agronomie 10: 341-345
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 sequence. Int J Syst Evol Microbiol 59:2388–2393
Parkinson N, DeVos P, Pirhonen M, Elphinstone J. 2014. Dickeya aquatica sp. nov., isolated from waterways. Int J Syst Evol Microbiol 64: 2264–2266.
Prasetyo J, Aeny TN. 2014. Pineapple Fruit Collapse: Newly emerging disease of pineapple fruit in Lampung, Indonesia. J Hama dan Penyakit Tumbuhan Tropika 14: 96–99.
Ramachandran K, Manaf UA, Zakaria L. 2015. Molecular characterization and pathogenicity of Erwinia spp. associated with pineapple [Ananas comosus (L.) Merr.] and papaya (Carica papaya L.). J Plant Prot 55: 396–404.
Rohrbach KG, Johnson MW. 2003. Pests, Diseases and Weeds. In: Bartholomew DP, Paull RE, Rohrbach KG. The pineapple botany, production and uses. CABI Publising, New York
Samson R, Legendre JB, Christen R, Fischer-Le Saux M, Achouak W, Gardan L. 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. Int J Sys Evol Microbiol 55:1415–1427.
S?awiak 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. European J Plant Pathol 125: 245–261.
Society of American Bacteriologist. 1957. manual of microbiological methods. McGraw-Hill, New York
Suharjo R, Sawada H, Takikawa Y. 2014. Phylogenetic study of Japanese Dickeya spp. and development of new rapid identification methods using PCR-RFLP. J Gen Plant Pathol 80: 230-254
Suslow TV, Schroth MN, Isaka M. 1982. Application of a rapid method for gram differentiation of plant pathogenic and saprophytic bacteria without staining. Phytopathology 72: 917-918.
Tian Y, Zhao Y, Yuan X, Yi J, Fan J, Xu Z, Hu B, De Boer SH, Li X. 2016. Dickeya fangzhongdai sp. nov., a plant pathogenic bacterium isolated from pear trees (Pyrus pyrifolia). Int J Syst Evol Microbiol 66: 2831–2835.
van der Wolf JM, Nijhuis EH, Kowalewska MJ, Saddler GS, Parkinson N, Elphinstone JG, Pritchard L, Toth IK, Lojkowska E, Potrykus M, Waleron M, De Vos P, Cleenwerck I, Pirhonen M, Garlant L, Hélias V, Pothier JF, Pflüger V, et al. 2014. Dickeya solani sp. nov., a pectinolytic plant-pathogenic bacterium isolated from potato (Solanum tuberosum). Int J Syst Evol Microbiol 64:768–774.
Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 1991. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173: 697–703.
Zhang J, Shen, H, Pu X, Lin B, Hu J. 2014. Identification of Dickeya zeae as a causal agent of bacterial soft rot in banana in China. Plant Dis 98: 436-442.
Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K. 2003. Current Protocols in Molecular Biology. John Wiley & Sons, New York
Avrova AO, Hyman LJ, Toth RL, Toth IK. 2002. Application of amplified fragment length polymorphism fingerprinting for taxonomy and identification of the soft rot bacteria Erwinia carotovora and Erwinia chrysanthemi. App Environ Microbiol 68 :1499–1508.
Brady CL, Cleenwerck I, Denman S, Venter SN, Rodriguez-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 Lomsdalea 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. dieffenbachieae comb. nov., and emendation of the description of Dickeya dadantii. Int J Syst Evol Microbiol 62:1592–1602
Dickey RS. 1979. Erwinia chrysanthemi: a comparative study of phenotypic properties of strains from several hosts and other Erwinia species. Phytopathol 69:324–329
Dye DW. 1968. A taxonomic study of the genus Erwinia. I. The, ‘‘amylovora’’ group. New Zeal J Sci 11:590–607
Hall TA. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser, 41:95–98.
Hugh R, Leifson E. 1953. The taxonomic significance of fermentative versus oxidative metabolism of carbohydrates by various gram negative bacteria. J Bacteriol 66:24–26
Johnston A. 1957. Bacterial heart rot of the pineapple. Malay Agric J 40:2–8.
Kaneshiro WS, Burger M, Vine BG, De Silva AS, Alvarez AM. 2008. Characterization of Erwinia chrysanthemi from a Bacterial Heart Rot of Pineapple Outbreak in Hawaii. Plant Dis 92:1444–1450.
King EO, Ward MK, Raney DE. 1954. Two simple media for the demonstration of pyocyanin and fluorescin. J Lab Clin Med 44:301–307
Kumar S, Stecher G, Tamura K. 2016. MEGA:7 Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33: 1870–1874
Lelliot RA, Billing E, Hayward AC. 1966. A determinative scheme for the fluorescent plant pathogenic pseudmonads. J App Bacteriol: 29:470-489
Lim WH. 1974. The etiology of fruit collapse and bacterial heart rot of pineapple. MARDI Res Bull 2: 11-16
Ma B, Hibbing ME, Kim H-S, Reedy RM, Yedidia I, Breuer J, Breuer J, Glasner JD, Perna NT, Kelman A, Charkowski AO. 2007. Host Range and Molecular Phylogenies of the Soft Rot Enterobacterial Genera Pectobacterium and Dickeya. Phytopathol 97:1150–1163.
Ngwira N, Samson R. 1990. Erwinia chrysanthemi : description of two new biovar (bv 8 and bv 9) isolated from kalanchoe and maize host plant. Agronomie 10: 341-345
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 sequence. Int J Syst Evol Microbiol 59:2388–2393
Parkinson N, DeVos P, Pirhonen M, Elphinstone J. 2014. Dickeya aquatica sp. nov., isolated from waterways. Int J Syst Evol Microbiol 64: 2264–2266.
Prasetyo J, Aeny TN. 2014. Pineapple Fruit Collapse: Newly emerging disease of pineapple fruit in Lampung, Indonesia. J Hama dan Penyakit Tumbuhan Tropika 14: 96–99.
Ramachandran K, Manaf UA, Zakaria L. 2015. Molecular characterization and pathogenicity of Erwinia spp. associated with pineapple [Ananas comosus (L.) Merr.] and papaya (Carica papaya L.). J Plant Prot 55: 396–404.
Rohrbach KG, Johnson MW. 2003. Pests, Diseases and Weeds. In: Bartholomew DP, Paull RE, Rohrbach KG. The pineapple botany, production and uses. CABI Publising, New York
Samson R, Legendre JB, Christen R, Fischer-Le Saux M, Achouak W, Gardan L. 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. Int J Sys Evol Microbiol 55:1415–1427.
S?awiak 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. European J Plant Pathol 125: 245–261.
Society of American Bacteriologist. 1957. manual of microbiological methods. McGraw-Hill, New York
Suharjo R, Sawada H, Takikawa Y. 2014. Phylogenetic study of Japanese Dickeya spp. and development of new rapid identification methods using PCR-RFLP. J Gen Plant Pathol 80: 230-254
Suslow TV, Schroth MN, Isaka M. 1982. Application of a rapid method for gram differentiation of plant pathogenic and saprophytic bacteria without staining. Phytopathology 72: 917-918.
Tian Y, Zhao Y, Yuan X, Yi J, Fan J, Xu Z, Hu B, De Boer SH, Li X. 2016. Dickeya fangzhongdai sp. nov., a plant pathogenic bacterium isolated from pear trees (Pyrus pyrifolia). Int J Syst Evol Microbiol 66: 2831–2835.
van der Wolf JM, Nijhuis EH, Kowalewska MJ, Saddler GS, Parkinson N, Elphinstone JG, Pritchard L, Toth IK, Lojkowska E, Potrykus M, Waleron M, De Vos P, Cleenwerck I, Pirhonen M, Garlant L, Hélias V, Pothier JF, Pflüger V, et al. 2014. Dickeya solani sp. nov., a pectinolytic plant-pathogenic bacterium isolated from potato (Solanum tuberosum). Int J Syst Evol Microbiol 64:768–774.
Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 1991. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173: 697–703.
Zhang J, Shen, H, Pu X, Lin B, Hu J. 2014. Identification of Dickeya zeae as a causal agent of bacterial soft rot in banana in China. Plant Dis 98: 436-442.
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