In Vitro and In Silico Analysis of the Gut Microbiome of Zebrafish for Bioremediation Approach of Zinc-Contaminated Aquatic Environments
Main Article Content
Keywords
Bioremediation, Bioaccumulation, Gut microbiome, zinc-resistant bacteria, Zinc binding protein (ZBP)
Abstract
The discovery of bacterial organisms that aid in heavy metal bioremediation opens up new possibilities for removing radioactive compounds and heavy metals from polluted water sources. Accordingly, this study aims to the identification of Zinc resistant bacteria from the gut microbiome of zebrafish and to evaluate its bioremediation capability. The isolates, namely FG01 (Enterobacter cloacae), FG02 (Citrobacter freundii), and FG03 (Aeromonas hydrophila) identified based on 16S rRNA gene sequencing resistant to Zinc and antibiotics like Ampicillin and Amoxicillin and also selected for bioaccumulation studies. The MTC values of the three zinc-resistant bacteria from the Zebrafish gut were evaluated, and the results revealed that the growth of the isolate FG02 was better than the others, while the growth of FGO3 and FG01 decreased at the concentrations of 10 ppm and 15 ppm. By docking studies, the Zinc binding proteins (ZBPs) were discovered and beta-lactamase showed the best binding affinity compared to the other protein. In the process of treating wastewater, zinc-resistant bacteria from the gut microbiome of zebrafish are normally present and can demonstrate their capacity to adsorb heavy metals. The ZBP can be used later as a novel absorbent for heavy metal removal technology.
References
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27. G. Bitencourt-Ferreira and W. F. de Azevedo, “Molecular Docking Simulations with ArgusLab,” 2019, pp. 203–220. doi: 10.1007/978-1-4939-9752-7_13.
28. R. Chaudhari and Z. Li, “PyMine: a PyMOL plugin to integrate and visualize data for drug discovery,” BMC Res Notes, vol. 8, no. 1, p. 517, Dec. 2015, doi: 10.1186/s13104-015-1483-3.
29. S. A. Smith, J. M. Beaulieu, and M. J. Donoghue, “Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches,” BMC Evol Biol, vol. 9, no. 1, p. 37, 2009, doi: 10.1186/1471-2148-9-37.
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33. K. Sunda and R. Vidya, “High Chromium Tolerant Bacterial Strains from Palar River Basin: Impact ofTannery Pollution,” Research Journal of Environmental and Earth Sciences, vol. 2, pp. 112–117, 2010.
34. Vashishth and S. Khanna, “Toxic Heavy Metals Tolerance in Bacterial Isolates Based On Their Inducible Mechanism,” Jan. 2018.
35. K. Ghaima, A. Mohamed, W. Yehia, A. Meshhdany, and A. Abdulhassan, “Resistance and bioadsorption of Cadmium by Pseudomonas aeruginosa isolated from agricultural soil,” International Journal of Applied Environmental Sciences, vol. 12, Jan. 2017.
36. G. Haferburg and E. Kothe, “Microbes and metals: interactions in the environment,” J Basic Microbiol, vol. 47, no. 6, pp. 453–467, Dec. 2007, doi: 10.1002/jobm.200700275.
37. S. Sinha and S. Mukherjee, “Pseudomonas aeruginosa KUCD1, a possible candidate for cadmium bioremediation,” Braz J Microbiol, vol. 40, pp. 655–662, Jan. 2009, doi: 10.1590/S1517-838220090003000030.
38. de Vicente, M. Avilés, J. C. Codina, J. J. Borrego, and P. Romero, “Resistance to antibiotics and heavy metals of Pseudontonas aeruginosa isolated from natural waters,” Journal of Applied
Bacteriology, vol. 68, no. 6, pp. 625–632, Jun. 1990, doi: 10.1111/j.1365-2672.1990.tb05228.x.
39. G. O. Oyetibo, M. O. Ilori, S. A. Adebusoye, O. S. Obayori, and O. O. Amund, “Bacteria with dual resistance to elevated concentrations of heavy metals and antibiotics in Nigerian contaminated systems,” Environ Monit Assess, vol. 168, no. 1–4, pp. 305–314, Sep. 2010, doi: 10.1007/s10661-009-1114-3.
40. S. Hussain et al., “Zinc Essentiality, Toxicity, and Its Bacterial Bioremediation: A Comprehensive Insight,” Front Microbiol, vol. 13, May 2022, doi: 10.3389/fmicb.2022.900740.
41. V. N. Kavamura and E. Esposito, “Biotechnological strategies applied to the decontamination of soils polluted with heavy metals,” Biotechnol Adv, vol. 28, no. 1, pp. 61–69, Jan. 2010, doi: 10.1016/j.biotechadv.2009.09.002.
42. J. Scherer and D. H. Nies, “CzcP is a novel efflux system contributing to transition metal resistance in Cupriavidus metallidurans CH34,” Mol Microbiol, vol. 73, no. 4, pp. 601–621, Aug. 2009, doi: 10.1111/j.1365-2958.2009.06792.x.
43. J. Xiong et al., “Genome analysis and characterization of zinc efflux systems of a highly zinc-resistant bacterium, Comamonas testosteroni S44,” Res Microbiol, vol. 162, no. 7, pp. 671–679, Sep. 2011, doi: 10.1016/j.resmic.2011.06.002.
44. Y. Hou et al., “Biosorption of Cadmium and Manganese Using Free Cells of Klebsiella sp. Isolated from Waste Water,” PLoS One, vol. 10, no. 10, p. e0140962, Oct. 2015, doi: 10.1371/journal.pone.0140962.
45. M. Dalben et al., “Investigation of an outbreak of Enterobacter cloacae in a neonatal unit and review of the literature,” Journal of Hospital Infection, vol. 70, no. 1, pp. 7–14, Sep. 2008, doi: 10.1016/j.jhin.2008.05.003.
46. G. Delgado et al., “Genetic Characterization of Atypical Citrobacter freundii,” PLoS One, vol. 8, no. 9, p. e74120, Sep. 2013, doi: 10.1371/journal.pone.0074120.
47. J. Martinez-Murcia, S. Benlloch, and M. D. Collins, “Phylogenetic Interrelationships of Members of the Genera Aeromonas and Plesiomonas as Determined by 16S Ribosomal DNA Sequencing: Lack of Congruence with Results of DNA-DNA Hybridizations,” Int J Syst Bacteriol, vol. 42, no. 3, pp. 412–421, Jul. 1992, doi: 10.1099/00207713-42-3-412.
48. J. Thompson, “The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysistools,” Nucleic Acids Res, vol. 25, no. 24, pp. 4876–4882, Dec. 1997, doi: 10.1093/nar/25.24.4876.
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Apr 18, 2023
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Sugitha S, & Abirami G. (2023). In Vitro and In Silico Analysis of the Gut Microbiome of Zebrafish for Bioremediation Approach of Zinc-Contaminated Aquatic Environments. Journal of Population Therapeutics and Clinical Pharmacology, 30(8), 222–236. https://doi.org/10.47750/jptcp.2023.30.08.024
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