- Ecological and Environmental Microbiology
- Original Articles
- Published:
Genetic diversity among ‘Candidatus Liberibacter asiaticus’ isolates based on single nucleotide polymorphisms in 16S rRNA and ribosomal protein genes
Annals of Microbiology volume 59, pages 681–688 (2009)
Abstract
Citrus Huanglongbing (HLB) is one of the most destructive and widespread diseases of citrus, caused by ‘Candidates Liberibacter’, a non-cultured, phloem-restricted alpha-proteobacterium. In the present study, ‘Ca. Liberibacter’ was detected in symptomatic citrus plants growing in the Karnataka state (South India) by amplification of 16S rRNA and β-operon ribosomal protein (β-rp) genes, using PCR primers specific for African and Asian ‘Ca. Liberibacter’. Sequencing of the 16S rRNA amplified fragment revealed that ‘Ca. Liberibacter’, here identified belongs to the species ‘Ca. Liberibacter asiaticus’. The alignments of 16S rRNA and ribosomal protein gene sequences of all known ‘Ca. Liberibacter asiaticus’related, allowed to recognize Single Nucleotide Polymorphisms (SNPs). Basing on SNP analysis, the strains were grouped in fourteen 16SrRNA SNP genetic lineages (16Sr-I to 16Sr-XIV) and three β-rp SNP genetic lineages (rp-I to rp-III). Only the strains of ‘Ca. Liberibacter asiaticus’ from the Karnataka state belonged to the genetic lineages 16Sr-I and rp-I. RFLP diagnostic tests on the discriminative 16S rRNA SNPs were set up to identify this lineage. These results revealed the presence of a new ‘Ca. Liberibacter asiaticus’ genetic lineage in the Indian sub-continent, where at least four genetically diverse SNP lineages were found. These findings could open new opportunities for in-depth studies on biological niches and traits of ‘Ca. Liberibacter asiaticus’.
References
Adkar-Purushothama C.R., Gottravalli-Ramanayaka J., Sano T., Casati P., Bianco P.A. (2007). Are phytoplasmas the etiological agent of yellow leaf disease ofAreca catechu in India? B. Insectol., 60: 161–162.
Appunu C., N’Zoue A., Laguerre G. (2008). Genetic diversity of native bradyrhizobia isolated from soybeans (Glycine max L.) in different agricultural-ecological-climatic regions of India. Appl. Environ. Microbiol., 74: 5991–5996.
Aubert B. (1987).Trioza erytreae del Guercio andDiaphorina citri Kuwayama (Homoptera: Psyllidae), the two vectors of citrus greening disease: Biological aspects and possible control stratergies. Fruits, 42: 149–162.
Batool A., Iftikhar Y., Mughal S.M., Khan M.M., Jaskani M.J., Abbas M., Khan I.A. (2007). Citrus greening disease — A major cause of citrus decline in the world — A Review. Hort. Sci. (Prague), 4: 159–166.
Bové J.M. (2006). Huanglongbing: A destructive, newlyemerging, century-old disease of citrus. J. Plant Pathol., 88: 7–37.
Cai H., Wei W., Davis R.E., Chen H., Zhao Y. (2008). Genetic diversity among phytoplasmas infecting Opuntia: virtual RFLP analysis identifies new subgroups in the peanut witches’-broom phytoplasma group. Int. J. Syst. Evolut. Microbiol., 58: 1448–1457.
Capoor S.P. (1963). Decline of citrus trees in India. Bulletin National Institute of Science India, 24: 48–64.
Capoor S.P., Rao D.G., Vishwanath S.M. (1967).Diaphorina citri Kuway., a vector of greening disease of citrus in India. Indian J. Agri. Sci., 37: 572–576.
Coletta-Filho H.D., Takita M.A., Targon M.L.P.N., Machado M.A. (2005). Analysis of 16S rDNA sequences from Citrus Huanglongbing bacteria reveal a different “Ca. Liberibacter” isolate associated with Citrus disease in São Paulo. Plant Dis., 89: 848–852.
da Graça J.V. (1991). Citrus greening disease. Annu. Rev. Phytopathol., 29: 109–136.
Das A.K., Rao C.N., Singh S. (2007). Presence of citrus greening (Huanglongbing) disease and its psyllid vector in the North-Eastern region of India confirmed by PCR technique. Curr. Sci. India, 92: 1759–1763.
Elizabeth E., Godfrey K.E., Rogers M.E., Childers C.C., Stansly P.A. (2005). Asian citrus psyllids. Division of Agriculture and Natural Resources. Riverside, University of California. http://anrcatalog.ucdavis.edu
Gamier M., Jagoueix S., Cronje P.R., Le Roux H.F., Bové J.M. (2000). Genomic characterization of a liberibacter present in an ornamental rutaceous tree, Calodendrum capense, in the Western Cape province of South Africa. Proposal of ‘Candidatus Libribacter Africans subsp. Capensis’. Int. J. Syst. Evol. Microbiol., 50: 2119–2125.
Haibert S.E. (2005). The discovery of huanglongbing in Florida. Abstr. H-3. In: Proceedings of the 2nd International Citrus Canker and Huanglongbing Research Workshop: Florida Citrus Mutual, Orlando.
Haibert S.E., Manjunath K.L. (2004). Asian citrus psyllids (Sternorryncha: Psyllidae) and greening disease of citrus: a literature review and assessment of risk in Florida. Fla. Entomol., 87: 330–353.
Hall T.A. (1999). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Sen, 41: 95–98.
Hansen A.K., Trumble J.T., Stouthamer R., Paine T.D. (2008). A New Huanglongbing Species, “Candidatus Liberibacter psyllaurous,” Found To Infect Tomato and Potato, Is Vectored by the PsyllidBactericera cockerelli (Sulc). Appl. Environ. Microbiol., 74: 5862–5865.
Hocquellet A., Toorawa P., Bove J.M., Gamier M. (1999). Detection and identification of the two ‘Candidatus Liberobacter’ species associated with citrus huanglongbing by PCR amplification of ribosomal protein genes of the β Operon. Mol. Cell Probe, 13: 373–379.
Jagoueix S., Bové J.M., Gamier M. (1994). The phloem-limited bacterium of greening disease of citrus is a member of the alpha subdivision of the proteobacteria. Int. J. Syst. Bacteriol., 44: 379–368.
Jagoueix S., Bové J.M., Gamier M. (1996). PCR detection of the two ‘Candidatus’ liberibacter species associated with greening disease of citrus. Mol. Cell. Probe, 10: 43–50.
Liefting L.W., Sutherland P.W., Ward L.I., Paice K.L., Weir B.S., Clover G.R.G. (2009). A new ‘Candidates Liberibacter’ species associated with diseases of Solanaceous crops. Plant Dis., 93: 208–214.
Martinez A.L., Wallace J.M. (1967). Citrus leaf mottle-yellows disease in the Philippines and transmission of the causal virus by a psyllid,Diaphorina citri. Plant Dis. Report, 51: 692–695.
Oberholzer P.C.J., von Standen D.F.A., Basson W.J. (1965). Greening disease of sweet orange in South Africa. In: Proceedings of 3rd Conference IOCV. University Florida Press, Gainesville, pp. 213–219.
Quaglino F., Zhao Y., Bianco P.A., Wei W., Casati P., Durante G., Davis R.E. (2009). New 16Sr subgroups and distinct SNP lineages among grapevine Bois noir phytoplasma populations. Ann. Appl. Biol., 154: 279–289.
Reinking O.A. (1919). Diseases of economic plants in southern China. Philippine Agricultural, 8: 109–135.
Salibe A.A., Cortez R.E. (1968). Leaf mottling, a serious virus disease of citrus in the Philippines. In: Proceedings of 4th Conference IOCV. University Florida Press, Gainesville, pp. 131–136.
Subandiyah S., Iwanami T., Tsuyumu S., Ikki H. (2000). Comparison of 16S RNA and 16S23S intergenic region sequences among citrus greening organisms in Asia. Plant Dis., 84: 15–18.
Tamura K., Dudley J., Nei M., Kumar S. (2007). MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol., 24: 1596–1599.
Texeira D.C., Ayres A.J., Kitajima E.W., Tanaka F.A.O., Danet J.L., Jagoueix-Eveillard S., Saillard C., Bové J.M. (2005). First report of a Haunglongbing-like disease of Citrus in São Paulo State, Brazil and association of a new Liberibacter species, “Candidates Liberibacter americanus”, with the disease. Plant Dis., 89: 107.
Texeira D.C., do Carmo C., Saillard C., Jagoueix-Eveillard S., Danet J.L., Ayres A.J., Bové J.M. (2005). “Candidates Liberibacter americanus”, associated with citrus huanglongbing (greening disease) in São Paulo State, Brazil. Int. J. Syst. Evol. Microbiol., 55: 1857–1862.
Tirtawidjaja S., Hadewidjaja T., Lasheen A.M. (1965). Citrus vein phloem degeneration virus, a possible cause of citrus chlorosis in Java. In : Proceedings of the American Society of Horticultural Science, 86: 235–243.
Tomimura K., Miyata S.-I., Furuya N., Kubota K., Okuda M., Subandiyah S., Hung T.-H., Su H.-J., Iwanami T. (2009). Evaluation of genetic diversity among ‘Candidates Liberibacter asiaticus’ isolates collected in Southeast Asia. Phytopathology, 99: 1062–1069.
Urasaki N., Kawano S., Mukai H., Uemori T., Takeda O., Sano T. (2008). Rapid and sensitive detection of “Candidates Liberibacter asiaticus” by cycleave isothermal and chimeric primer-initiated amplification of nucleic acids. J. Gen. Plant Pathol., 74: 151–155.
Varma A., Ahlawar Y.S., Chakraborty N.K., Gamier M., Bové J.M. (1993). Detection of the greening BLO by electron microscopy, DNA hybridization and ELISA in citrus leaves with and without mottle from various regions in India. In: Proceedings of 12th Conference IOCV: Riverside, CA, USA, pp. 280–286.
Wei W., Davis R.E., Lee I.-M., Zhao Y. (2007). Computer simulated RFLP analysis of 16S rRNA genes: identification of ten new phytoplasma groups. Int. J. Syst. Evol. Microbiol., 57: 1855–1867.
Wei W., Lee I.M., Davis R.E., Suo X., Zhao Y. 2008. Automated RFLP pattern comparison and similarity coefficient calculation for rapid delineation of new and distinct phytoplasma 16Sr subgroup lineages. Int. J. Syst. Evol. Microbiol., 58: 2368–2377.
Zhang J.H., Hogenhout S.A., Nault L.R., Hoy C.W., Miller S.A. (2004). Molecular and symptom analyses of phytoplasma isolates from lettuce reveal a diverse population. Phytopathology, 94: 842–849.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Adkar-Purushothama, C.R., Quaglino, F., Casati, P. et al. Genetic diversity among ‘Candidatus Liberibacter asiaticus’ isolates based on single nucleotide polymorphisms in 16S rRNA and ribosomal protein genes. Ann. Microbiol. 59, 681–688 (2009). https://doi.org/10.1007/BF03179208
Received:
Accepted:
Issue Date:
DOI: https://doi.org/10.1007/BF03179208