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 Analysing Pandoraea associated with Brassica oleracea using 16S rDNA from Limpopo Province, South Africa


Citation :- Analysing Pandoraea associated with Brassica oleracea using 16S rDNA from Limpopo Province, South Africa. Res. Crop. 25: 269-272
MEHRNOUSH AMINISARTESHNIZI Mehrnoush.aminisarteshnizi@ul.ac.za
Address : Aquaculture Research Unit, School of Agricultural and Environmental Sciences, University of Limpopo, Private Bag X1106, Sovenga, 0727, South Africa
Submitted Date : 7-03-2024
Accepted Date : 30-04-2024

Abstract

The genus Pandoraea comprises gram-negative, motile, non-spore-forming, rod-shaped, oxidase-positive, and obligate aerobes bacteria with a single polar flagellum. Several species belonging to this genus have been identified as potentially risky pathogenic bacteria, which can adversely impact the yield of white cabbage plants. A study was conducted at the University of Limpopo in 2023 to isolate and identify the Pandoraea bacterium from a white cabbage field and a free-living nematode, Acrobeles complexus, in South Africa. The molecular study used the 16S rDNA marker to identify the bacterium associated with nematode and white cabbage fields from South Africa's soils. The DNA was extracted using the Chelex method, and the bacterium was identified as Pandoraea. Specific primers were used to amplify the 16S rDNA to identify the nematode. The Nblast analysis showed that South African Pandoraea has a 99% similarity with a population from India (AB510957). Phylogenetic analysis using maximum likelihood placed this species with those molecularly identified as Pandoraea in the same clade with highly supported (100) bootstrap values. In conclusion, this study has demonstrated that the 16S rDNA marker can be effectively used to identify Pandoraea species. However, the use of additional DNA markers is recommended to achieve a better understanding of Pandoraea's phylogeny.

Keywords

16S rDNA bacterium free-living nematode Pandoraea phylogeny

References

Ambrose, M., Malley, R. C., Warren, S. J. C., Beggs, S. A., Swallow, O. F. E., McEwan, B., Stock, D. and Roddam, L. F. (2016). Pandoraea pnomenusa isolated from an Australian patient with cystic fibrosis. Front. Microbiol. 7: doi:10.3389/fmicb.2016.00692.
Aminisarteshnizi, M. (2023). Molecular characterization of Burkholderia using 16S rDNA isolated from cabbage, Limpopo Province, South Africa. Res. Crop. 24: 316-18. doi:10.31830/2348-7542.2023.ROC-952. 
Anandham, R., Indiragandhi, P., Kwon, S. W., Sa, T. M., Jeon, C. O., Kim, Y. K. and Jee, H. J. (2010). Pandoraea thiooxydans sp. nov., a facultatively chemolithotrophic, thiosulfate- oxidizing bacterium isolated from rhizosphere soils of sesame (Sesamum indicum L.). Int. J. Syst. Evol. Microbiol. 60: 21-26. doi:10.1099/ijs.0.012823-0.
Coenye, T., Falsen, E., Hoste, B., Ohlen, M., Goris, J. and Govan, J. R., Gillis, M. and Vandamme, P. (2000). Description of Pandoraea gen. nov. with Pandoraea apista sp. nov., Pandoraea pulmonicola sp. nov., Pandoraea pnomenusa sp. nov., Pandoraea sputorum sp. nov. and Pandoraea norimbergensis comb. nov. Int. J. Syst. Evol. Microbiol. 50: 887-99.
Jeong, S. E., Lee, H. J., Jia, B. and Jeon, C. O. (2016). Pandoraea terrae sp. nov., isolated from forest soil, and emended description of the genus Pandoraea Coenye et al. 2000. Int. J. Syst. Evol. Microbiol. 66: 3524-30. doi:10.1099/ijsem.0.001229.
Kumar, S., Stecher, G., Li, M., Knyaz, C. and Tamura, K. (2018). MEGA X: molecular evolutionary genetics analysis across computing platforms. Mole. Biol. Evol. 35: 1547–49. doi:10.1093/molbev/msy096.
Lane, D. J. (1991). 16S/23S rRNA sequencing. In nucleic acid techniques in bacterial systematics. Edited by E. Stackebrandt and M. Goodfellow. Chichester: Wiley. Pp. 115-75.
Martina, P. F., Martínez, M., Frada, G., Alvarez, F., Leguizamón, L., Prieto, C., Barrias, C., Bettiol, M., Lagares, A., Bosch, A., Ferreras, J. and Specht, M. V. (2017). First time identification of Pandoraea sputorum from a patient with cystic fibrosis in Argentina: A case report. BMC Pulm. Med. 17: doi:10.1186/s12890-017-0373-y.
Peeters, C., Canck, E., De, Cnockaert, M., Brandt, E., Snauwaert, C., Verheyde, B., Depoorter, E., Spilker, T., Lipuma, J. J. and Vandamme, P. (2019). Comparative genomics of Pandoraea, a genus enriched in xenobiotic biodegradation and metabolism. Front. Microbiol. 10: 1-21. doi:10.3389/fmicb.2019.02556.
Sahin, N., Tani, A., Kotan, R., Sedlacek, I., Kimbara, K. and Tamer, A. U. (2011). Pandoraea oxalativorans sp. nov., Pandoraea faecigallinarum sp. nov. and Pandoraea vervacti sp. nov., isolated from oxalate-enriched culture. Int. J. Syst. Evol. Microbiol. 61: 2247–53. doi:10.1099/ijs.0.026138-0.
See-Too, W. S., Ambrose, M., Malley, R., Ee, R., Mulcahy, E., Manche, E., Lazenby, J., McEvan, B., Pagnon, J., Chen, J. W., Chan, K. G., Turnbull, L., Whitchurch, C. B. and Roddam, L. F.  (2019). Pandoraea fibrosis sp. nov., a novel Pandoraea species isolated from clinical respiratory samples. Int. J. Syst. Evol. Microbiol. 69: 645–51. doi:10.1099/ ijsem.0.003147.
Shokoohi, E. (2021). Morphological and molecular characters of Scutellonema brachyurus (Steiner, 1938) Andrássy, 1958 from South Africa. J. Nematol. 53: 1-13. doi:10. 21307/jofnem-2021-027.
Shokoohi, E. and Duncan, L. W. (2018). Nematode parasites of citrus. In: Sikora R, Timper P, Coyne D (eds) Plant-parasitic nematodes in tropical & subtropical agriculture, 3rd Edition. CAB International, St. Albans, UK. pp. 446-76.
 

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