Pantoea species (Pantoea spp.) is a diverse group of Gram-negative bacteria in the Enterobacteriaceae family that leads to devastating diseases in rice plants, thus affecting significant economic losses of rice production worldwide. Most critical rice diseases such as grain discoloration, bacterial leaf blight, stem necrosis and inhibition of seed germination have been reported to be caused by this pathogen. To date, 20 Pantoea spp. have been identified and recognized as having similar phenotypic and diverse characteristics. Detection via phenotypic and molecular-based approaches, for example the polymerase chain reaction (PCR) and multiplex PCR give us a better understanding of the diversity of Pantoea genus and helps to improve effective disease control strategies against this emergent bacterial pathogen of rice. In this review, we focused on the significance of rice diseases caused by Pantoea spp. and insights on the taxonomy and characteristics of this destructive pathogen via phenotypic and molecular identification.
We acknowledge Universiti Putra Malaysia (Grant 9494600) and Fundamental Research Grant Scheme from the Ministry of Education Malaysia (Grant 5540090) for financial support. Mohammad Malek Faizal Azizi is the recipient of the Research Fellowship from Universiti Putra Malaysia.
The authors have declared that no conflict of interests exist.
Achtman M. 2008. Evolution, population structure, and phylogeography of genetically monomorphic bacterial pathogens. Annual Review of Microbiology 62: 53–70. DOI:
Aksoy H.M., Boluk E. 2018. First report of Pantoea agglomerans on Oryza sativa in Turkey. Journal of Plant Pathology 101 (2): 449–449. DOI: 10.1007/s42161-018-00213-2.
Arshad H.M.I., Khan J.A., Naz S., Khan S.N., Akram M. 2009. Grain discoloration disease complex: a new threat for rice crop and its management. Pakistan Journal of Phytopathology 21 (1): 31–36.
Ashfaq M., Ali A., Siddique S., Haider M.S., Ali M., Hussain S.B., Mubashar U., Usman A.K. 2013. In vitro antibacterial activity of Parthenium hysterophorus against isolated bacterial species from discolored rice grains. International Journal of Agriculture & Biology 15 (6): 1119–1125.
Azegami K. 1983. Bacterial palea browning, a new disease of rice caused by Erwinia herbicola. Bulletin of the National Institute of Agricultural Sciences 37: 1–12.
Azizi M.M.F., Ismail S.I., Hata E.M., Zulperi D., Ina-Salwany M.Y., Abdullah M.A.F. 2019a. First report of Pantoea stewartii subsp. indologenes causing leaf blight on rice in Malaysia. Plant Disease 103 (6): 1407–1407. DOI: 10.1094/PDIS-08-18-1403-PDN.
Azizi M.M.F., Zulperi D., Rahman M.A.A., Abdul-Basir B., Othman N.A., Ismail S.I., Hata E.M., Ina-Salwany M.Y., Abdullah M.A.F. 2019b. First report of Pantoea ananatis causing leaf blight disease of rice in Peninsular Malaysia. Plant Disease 103 (8): 2122. DOI:
Beijerinck M.W. 1888. Die bakterien der papilionaceenknollchen. Botanische Zeitung 46: 725–804. (in German).
Brady C., Cleenwerck I., Venter S., Vancanneyt M., Swings J., Coutinho T. 2008. Phylogeny and identification of Pantoea species associated with plants, humans and the natural environment based on multilocus sequence analysis (MLSA). Systematic and Applied Microbiology 31 (6–8): 447–460. DOI:
Brady C.L., Goszczynska T., Venter S.N., Cleenwerck I., De Vos P., Gitaitis R.D., Coutinho T.A. 2011. Pantoea allii sp. nov., isolated from onion plants and seed. International Journal of Systematic and Evolutionary Microbiology 61: 932–937. DOI:
Brady C.L., Venter S.N., Cleenwerck I., Engelbeen K., De Vos P., Wingfield M.J., Telechea N., Coutinho T.A. 2009a. Isolation of Enterobacter cowanii from eucalyptus showing symptoms of bacterial blight and dieback in Uruguay. Letters in Applied Microbiology 49 (4): 461–465. DOI:
Brady C.L., Venter S.N., Cleenwerck I., Engelbeen K., Vancanneyt M., Swings J., Coutinho T.A. 2009b. Pantoea vagans sp. nov., Pantoea eucalypti sp. nov., Pantoea deleyi sp. nov. and Pantoea anthophila sp. nov. International Journal of Systematic and Evolutionary Microbiology 59 (9): 2339–2345.DOI:
Bruton B.D., Wells J.M., Lester G.E, Patterson C.L. 1991. Pathogenicity and characterization of Erwinia ananas causing a postharvest disease of cantaloup fruit. Plant Disease 75 (2): 180–183. DOI:
Carrer Filho R., Rodrigues L.L., Abreu A.G., Souza R.R., Rangel P.H.N., Mello R.N., Rocha G.A., Cunha M.G. 2018. Detection of Pantoea agglomerans in germplasm rice accessions (Oryza sativa) in Brazil. Plant Disease 102 (1): 237. DOI:
Chandramani B., Awadhiya G.K. 2014. Assessment of percent grain discoloration in important rice varieties. International Journal of Current Research in Biosciences and Plant Biology 1 (4): 61–64. DOI:
Cother E.J., Reinke R., McKenzie C., Lanoiselet V.M., Noble D.H. 2004. An unusual stem necrosis of rice caused by Pantoea ananas and the first record of this pathogen on rice in Australia. Australasian Plant Pathology 33 (4): 495–503. DOI:
Countinho T.A., Preisig O., Mergaert J., Cnockaert M.C., Riedel K.H., Swings J., Wingfield M.J. 2002. Bacterial blight and dieback of Eucalyptus species, hybrids, and clones in South Africa. Plant Disease 86 (1): 20–25. DOI:
Coutinho T.A., Venter S.N. 2009. Pantoea ananatis: an unconventional plant pathogen. Molecular Plant Pathology 10 (3): 325–335. DOI:
Delétoile A., Decré D., Courant S., Passet V., Audo J., Grimont P., Arlet G., Brisse S. 2009. Phylogeny and identification of Pantoea species and typing of Pantoea agglomerans strains by multilocus gene sequencing. Journal of Clinical Microbiology 47 (2): 300–310. DOI:
Doni F., Suhaimi N.S.M., Mohamed Z., Ishak N., Mispan M.S. 2019. Pantoea: a newly identified causative agent for leaf blight disease in rice. Journal of Plant Diseases and Protection 126 (6): 491–494. DOI:
Egorova M., Mazurin E., Ignatov A.N. 2015. First report of Pantoea ananatis causing grain discolouration and leaf blight of rice in Russia. New Disease Reports 32: 21. DOI:
Ewing W.H., Fife M.A. 1972. Enterobacter agglomerans (Beije rinck) comb. nov. (the herbicola-lathyri bacteria). International Journal of Systematic and Evolutionary Microbiology 22 (1): 4–11. DOI:
Gavini F., Mergaert J., Beji A., Mielcarek C., Izard D., Kersters K., De Ley J. 1989. Transfer of Enterobacter agglomerans (Beijerinck 1888) Ewing and Fife 1972 to Pantoea gen. nov. as Pantoea agglomerans comb. nov. and Description of Pantoea dispersa sp. nov. International Journal of Systematic and Evolutionary Microbiology 39: 337–345.
Gehring I., Wensing A., Gernold M., Wiedemann W., Coplin D.L., Geider K. 2014. Molecular differentiation of Pantoea stewartii subsp. indologenes from subspecies stewartii and identification of new isolates from maize seeds. Journal of Applied Microbiology 116 (6): 1553–1562. DOI:
Gitaitis R.D., Gay J.D. 1997. First report of a leaf blight, seed stalk rot, and bulb decay of onion by Pantoea ananas in Georgia. Plant Disease 81 (9): 1096–1096. DOI:
González A.D., Franco M.A., Contreras N., Galindo-Castro I., Jayaro Y., Graterol E. 2015. First report of Pantoea agglomerans causing rice leaf blight in Venezuela. Plant Disease 99 (4): 552–552. DOI:
Grimont P.A., Grimont F. 2015. Klebsiella. Bergey’s Manual of Systematics of Archaea and Bacteria, John Wiley & Sons, Inc., in association with Bergey’s Manual Trust. DOI:
Hasegawa M., Azegami K., Yoshida H., Otani H. 2003. Behavior of Erwinia ananas transformed with bioluminescence genes on rice plants. Journal of General Plant Pathology 69 (4): 267–270. DOI:
Holding A.J., Collee J.G. 1971. Chapter I: Routine biochemical tests. Methods in Microbiology 6: 267–270. DOI:
Hong Y.C., Hu F.P., Huang X.N. 2002. Pathogenicity of Pantoea agglomerans on rice seeds. Journal of Fujian Agricultural and Forestry University 31: 32–36 [Natural Science Edition].
Ilsan N.A., Nawansih A.A., Wahyudi A.T. 2016. Rice phyllosphere actinomycetes as biocontrol agent of bacterial leaf blight disease on rice. Asian Journal of Plant Pathology 10: 1–8. DOI:
Kageyama B., Nakae M., Yagi S., Sonoyama T. 1992. Pantoea punctata sp. nov., Pantoea citrea sp. nov., and Pantoea terrea sp. nov. isolated from fruit and soil samples. International Journal of Systematic and Evolutionary Microbiology 42 (2): 203–210. DOI:
Kala A., Soosairaj S., Mathiyazhagan S., Raja P. 2015. Isolation and identification of Xanthomonas oryzae pv. oryzae the causal agent of rice bacterial leaf blight and its activities against of six medicinal plants. Asian Journal of Plant Science and Research 5 (6): 80–83.
Khalimi K., Suprapta D.N., Nitta Y. 2012. Effect of Pantoea agglomerans on growth promotion and yield of rice. Agricultural Science Research Journal 2 (5): 240–249.
Kido K., Adachi R., Hasegawa M., Yano K., Hikichi Y., Takeuchi S., Takikawa Y. 2008. Internal fruit rot of netted melon caused by Pantoea ananatis (= Erwinia ananas) in Japan. Journal of General Plant Pathology 74 (4): 302–312. DOI:
Kim H., Lee Y.H. 2019. The rice microbiome: a model platform for crop holobiome. Phytobiomes Journal 4 (1): 5–18. DOI:
Kini K., Agnimonhan R., Afolabi O., Milan B., Soglonou B., Gbogbo V., Koebnik R., Silué D. 2017a. First report of a new bacterial leaf blight of rice caused by Pantoea ananatis and Pantoea stewartii in Benin. Plant Disease 101 (1): 242–242. DOI:
Kini K., Agnimonhan R., Afolabi O., Soglonou B., Silué D., Koebnik R. 2017b. First report of a new bacterial leaf blight of rice caused by Pantoea ananatis and Pantoea stewartii in Togo. Plant Disease 101 (1): 241. DOI:
Kini K., Agnimonhan R., Dossa R., Silue D., Koebnik R. 2018. A diagnostic multiplex PCR scheme for identification of plant-associated bacteria of the genus Pantoea. BioRxiv: 456806. DOI:
Kini K., Dossa R., Dossou B., Mariko M., Koebnik R, Silué D. 2019. A semi-selective medium to isolate and identify bacteria of the genus Pantoea. Journal of General Plant Pathology 85 (6): 424–427. DOI:
Lakshmanan V., Shantharaj D., Li G., Seyfferth A.L., Janine Sherrier D., Bais H.P. 2015. A natural rice rhizospheric bacterium abates arsenic accumulation in rice (Oryza sativa L.). Planta 242 (4): 1037–1050. DOI:
Lee H.B., Hong J.P., Kim S.B. 2010. First report of leaf blight caused by Pantoea agglomerans on rice in Korea. Plant Disease 94 (11): 372–1372. DOI:
Manulis S., Kogan N., Valinsky L., Dror O., Kleitman F. 1998. Detection of Erwinia herbicola pv. gypsophilae in gypsophila plants by PCR. European Journal of Plant Pathology 104 (1): 5–91. DOI:
Medrano E.G., Bell A.A. 2007. Role of Pantoea agglomerans in opportunistic bacterial seed and boll rot of cotton (Gossypium hirsutum) grown in the field. Journal of Applied Microbiology 102 (1): 134–143. DOI:
Mergaert J., Verdonck L., Kersters K. 1993. Transfer of Erwinia ananas (synonym, Erwinia uredovora) and Erwinia stewartii to the genus Pantoea emend as Pantoea ananas (Serrano 1928) comb. nov., and Pantoea stewartii (Smith 1898) comb. nov., respectively, and description of Pantoea stewartii subsp. Indologenes subsp. nov. International Journal of Systematic and Evolutionary Microbiology 43: 162–173. DOI: 10.1099/00207713-43-1-162.
Mew T.W., Alvarez A.M., Leach J.E., Swings J. 1993. Focus on bacterial blight of rice. Plant Disease 77 (1): 5–12. DOI: 10.1094/PD-77-0005.
Mew T.W., Leung H., Savary S., Vera Cruz C.M., Leach J.E. 2004. Looking ahead in rice disease research and management. Critical Reviews in Plant Sciences 23 (2): 103–127. DOI:
Mondal K.K., Mani C., Singh J., Kim J.G., Mudgett M.B. 2011. A new leaf blight of rice caused by Pantoea ananatis in India. Plant Disease 95 (12): 1582–1582. DOI:
Morales H., Sanchis V., Usall J., Ramos A.J., Marín S. 2008. Effect of biocontrol agents Candida sake and Pantoea agglomerans on Penicillium expansum growth and patulin accumulation in apples. International Journal of Food Microbiology 122 (1–2): 61–67.
Morin A. 2014. Pantoea. Encycopledia of Food Microbiology 1623–1630. DOI:
Muraschi T.F., Friend M., Bolles D. 1965. Erwinia-like microorganisms isolated from animal and human hosts. Applied Microbiology 13 (2): 128–131.
Nadarasah G., Stavrinides J. 2014. Quantitative evaluation of the host-colonizing capabilities of the enteric bacterium Pantoea using plant and insect hosts. Microbiology 160 (3): 602–615. DOI: 10.1099/mic.0.073452-0.
Naqvi S.A.H., Perveen R., Umer U.U.D., Malik O., Rehman A.U., Wazeer S., Majid T. 2014. Determination of antibacterial activity of various broad spectrum antibiotics against Xanthomonas oryzae pv. oryzae, a cause of bacterial leaf blight of rice. International Journal of Microbiology and Mycology 2: 12–19. DOI:
Ou S.H. 1983. Rice Disease. The Commonwealth Mycological Institute. 3rd ed. Commonwealth Mycological Institute, Kew, 380 pp.
Popp A., Cleenwerck I., Iversen C., De Vos P., Stephan R. 2010. Pantoea gaviniae sp. nov and Pantoea calida sp. nov., isolated from infant formula and an infant formula production environment. International Journal of Systematic and Evolutionary Microbiology 60 (12): 2786–2792. DOI:
Prabhu A.S., Barbosa Filho M.P., Datnoff L.E., Snyder G.H., Berni R.F., Rodrigues F.A., Dallagnol L.J. 2012. Silicon reduces brown spot severity and grain discoloration on several rice genotypes. Tropical Plant Pathology 37: 409–414. DOI:
Raaijmakers J.M., Mazzola M. 2012. Diversity and natural functions of antibiotics produced by beneficial and plant pathogenic bacteria. Annual Review of Phytopathology 50: 403–424. DOI:
Schaad N.W., Jones J.B., Chun W. 2001. Laboratory Guide for the Identification of Plant Pathogenic Bacteria. 3rd ed. American Phytopathological Society (APS Press), USA.
Séré Y., Fargette D., Abo M.E., Wydra K., Bimerew M., Onasanya A., Akator S.K. 2013. Managing the major diseases of rice in Africa. p. 213–228. In: “Realizing Africa’s Rice Promise” (D.E. Johnson, N. Ahmadi, E. Tollens, A. Jalloh, eds.). Wopereis MCS, CABI, Wallingford, USA.
Simeya N., Numata S., Nakjima M., Haseba A., Hibi T., Akutsu K. 2003. Biological control of rice blast by the epiphytic bacterium Erwinia ananas transformed with a chitinolytic enzyme gene from an antagonistic bacterium, Serratia marcescens. Journal of General Plant Pathology 69: 276–282. DOI:
Spratt D.A. 2004. Significance of bacterial identification by molecular biology methods. Endodontic Topics 9: 5–14. DOI:
Tabei H., Azegami K., Fukuda T. 1988. Infection site of rice grain with Erwinia herbicola, the causal agent of bacterial palea browning of rice. Japanese Journal of Phytopathology 54: 637–639. DOI:
Tagami Y. 1962. Historical review of the researchers on bacterial leaf blight of rice caused by Xanthomonas oryzae (Uyeda et Ishiyama) Dowson; Special report. Plant Disease and Insect Pests Forecasting Service 10: 112.
Tindall B.J. 2014. The combination Enterobacter agglomerans is to be cited as Enterobacter agglomerans (Beijerinck 1888) Ewing & Fife 1972 and the combination Pantoea agglomerans is to be cited as Pantoea agglomerans (Beijerinck 1888) Gavini et al. 1989 Opinion 90. Judicial Commission of the International Committee on Systematics of Prokaryotes. International Journal of Systematic and Evolutionary Microbiology 64: 3582–3583.
Toh W.K., Loh P.C., Wong H.L. 2019. First report of leaf blight of rice caused by Pantoea ananatis and Pantoea dispersa in Malaysia. Plant Disease 103 (7): 1764–1764. DOI:
Trung H.M., Van Van N., Vien N.V., Lam D.T., Lien M. 1993. Occurrence of rice grain rot disease in Vietnam. International Rice Research Notes (Philippines) 18: 30.
Turner S., Pryer K.M., Miao V.P., Palmer J.D. 1999. Investigating deep phylogenetic relationships among cyanobacteria and plastids by small subunit rRNA sequence analysis. Journal of Eukaryotic Microbiology 46 (4): 327–338. DOI:
Vinodhini J., Kannan R., Sankareswari R.U., Akila R., Pillai M.A. 2017. Characterization of new bacterial leaf blight of rice caused by Pantoea stewartii subsp. indologenes in southern districts of Tamil Nadu. International Journal of Environment, Agriculture and Biotechnology 2 (6): 3279–3284. DOI:
Völksch B., Thon S., Jacobsen I.D., Gube M. 2009. Polyphasic study of plant and clinic associated Pantoea agglomerans strains reveals indistinguishable virulence potential Infection, Genetics and Evolution Infection. Genetics and Evolution 9 (6): 1381–1391. DOI:
Walcott R.R., Gitaitis R.D., Castro A.C., Sanders Jr. F.H., Diaz-Perez J.C. 2002. Natural infestation of onion seed by Pantoea ananatis, causal agent of center rot. Plant Disease 86 (2): 106–111. DOI:
Walterson A.M., Stavrinides J. 2015. Pantoea: insights into a highly versatile and diverse genus within the Enterobacteriaceae. FEMS Microbiology Reviews 39 (6): 968–984. DOI:
Watanabe K., Kawakita H., Sato M. 1996. Epiphytic bacterium, Erwinia ananas, commonly isolated from rice plants and brown planthoppers (Nilaparvata lugens) in hopperburn patches. Applied Entomology and Zoology 31 (3): 459–462. DOI:
Xie G. 2001. First report of palea browning in China and characterization of the causal organism by phenotypic tests and Biolog. International Rice Research Notes 26 (1): 25–26.
Yan H., Yu S.H., Xie G.L., Fang W., Su T., Li B. 2010. Grain discoloration of rice caused by Pantoea ananatis (synonym Erwinia uredovora) in China. Plant Disease 94 (4): 482–482. DOI:
Zeigler R.S., Alvarez E. 1990. Characteristics of Pseudomonas spp. causing grain discoloration and sheath rot of rice, and associated pseudomonad epiphytes. Plant Disease 74 (11): 917–922. DOI:
Journals System - logo
Scroll to top