Molecular characters of Pandoraea, a bacterium associated with tomato (Solanum lycopersicum) using 16S rDNA from Limpopo Province, South Africa

Citation :- Molecular characters of Pandoraea, a bacterium associated with tomato (Solanum lycopersicum) using 16S rDNA from Limpopo Province, South Africa. Res. Crop. 25: 202-205
GAVIN GELDENHUYS gavin.geldenhuys@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 : 30-04-2023
Accepted Date : 5-01-2024


Tomato is one of the premier vegetables in the world and is widely cultivated for higher yield and economic importance; thus, the area under cultivation is increasing. Pandoraea species can be a risky pathogenic bacterium to tomato plants, impacting the yield. They are gram-negative, motile, and rod-shaped. In 2022, the University of Limpopo conducted a study to identify and name the Pandoraea bacterium found in a tomato field located in Limpopo Province, South Africa. Molecular methods were employed, and the Chelex approach was utilized to extract the 16S rDNA marker, enabling the identification of bacteria present in the soil of tomato fields in South Africa. After conducting tests using specific primers to amplify the 16S rDNA, we have identified the bacterium as Pandoraea. Our analysis indicates that the strain of Pandoraea found in South Africa shares a 90% similarity with a population from Belgium (LR536859). Furthermore, maximum likelihood phylogenetic analysis indicates that this species is grouped with other Pandoraea species, with highly supported (100) bootstrap values. While the 16S rDNA method successfully identified this species, we recommend utilizing other DNA markers for a more comprehensive understanding of the Pandoraea phylogeny.


16S rDNA bacterium Pandoraea phylogeny tomato


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. (2021). Study of bacterium associated with maize and nematode, Pandoraea using 16S rDNA from Rustenburg, North West Province, South Africa. Res. Crop. 22: 930-34. doi:10.31830/2348-7542.2021.152. 
Aminisarteshnizi, M. (2022). Molecular characters of Dechloromonas, a bacterium associated with peanut and nematode from North West Province, South Africa, using 16S rDNA. Res. Crop. 23: 202-05.
Coenye, T., Falsen, E., Hoste, B., Ohle´n, M., Goris, J., Govan, J. R. W. 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.
Kumar, S., Stecher, G., Li, M., Knyaz, C. and Tamura, K. (2018). MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 35 : 1547-49. doi:10.1093/molbev/msy096.
Martina, P. F., Martínez, M., Frada, G., Alvarez, F., Leguizamón, L., Prieto, C., Barrias, C., Bettiol, M., Lagares, A., Bosch, A. and Ferreras, J. (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.
Moore, J. E., Coenye, T., Vandamme, P. and Elborn, J. S. (2001). First report of Pandoraea norimbergensis isolated from food—potential clinical significance. Food Microbiol. 18: 113-14. doi:10.1006/FMIC.2000.0375.
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: doi:10.3389/fmicb.2019.02556.
See-Too, W. S., Ambrose, M., Malley, R. E. R., Mulcahy, E. and Manche, E. (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. (2023a). Impact of Agricultural Land Use on Nematode Diversity and Soil Quality in Dalmada, South Africa. Horticulturae 9: doi:10.3390/ horticulturae9070749.
Shokoohi, E. (2023b). First observation on morphological and molecular characters of Bitylenchus ventrosignatus (Tobar Jiménez, 1969) Siddiqi, 1986 isolated from tomato in Dalmada, South Africa. Biologia 78: 3599-3607. doi:10.1007/s11756-023-01494-4.
Tabatabaei, M., Dastbarsar, M. and Moslehi, M.A. (2019). Isolation and identification of Pandoraea spp. from bronchoalveolar lavage of cystic fibrosis patients in Iran. Ital. J. Pediatr. 45: doi:10.1186/s13052-019-0687-x.

Global Footprints