Abstract
Purpose
In this study, the culturable halophilic and halotolerant bacterial diversity was determined in Aran-Bidgol as a thalassohaline seasonal hypersaline lake in Iran.
Methods
Thirty water, soil, sediments, coastal mud, multi-color brines and salt crystals samples were extracted and cultured using different media and incubation conditions. Totally 958 isolates were obtained and 87 isolates were selected for further studies, based on morphological, physiological and biochemical tests, representing different morphotypes.
Results
Based on 16S rRNA gene sequence analyses, the isolates exhibited 94.6–100% sequence similarity to the closest known species of the genera Bacillus, Halomonas, Oceanobacillus, Salinicoccus, Thalassobacillus, Ornithinibacillus, Halobacillus, Salicola, Virgibacillus, Aerococcus, Arthrobacter, Idiomarina, Paraliobacillus, Staphylococcus, Acinetobacter, Aneurinibacillus, Brevibacillus, Brevundimonas, Chromohalobacter, Gracilibacillus, Jeotgalicoccus, Kocuria, Marinilactibacillus, Marinobacter, Microbacterium, Paenibacillus, Paracoccus, Piscibacillus, Pseudomonas and Sediminibacillus and also, comparison of ARDRA patterns among the sequenced strains, using AluI, Bst UI and Hpa II enzymes showed that these patterns are in accordance with the phylogenetic position of these strains.
Conclusion
The PCR-RFLP analyses suggested that ARDRA possess a functional potential for distinguishing halophilic bacteria to be used for further studies in elementary steps of isolation to reduce the tedious duplication of isolates.
Similar content being viewed by others
References
Oren A. Halophilic microorganisms and their environments. Kluwer Academic Publishers; 2002.
Kushner D, Kamekura M. Physiology of halophilic eubacteria. In: Rodriguez-Valera F, editor. Halophilic bacteria. Florida: CRC Press; 1988. p. 109–40.
Oren A. Life at high salt concentrations. In: Stanley Falkow ER, editor. Karl-Heinz Schleifer, Erko Stackebrandt, Martin Dworkin, editor. The Prokaryotes: Ecophysiology and biochemistry: Springer; 2006. p. 263–82.
Ventosa A, Nieto J, Oren A. Biology of moderately halophilic aerobic bacteria. Microbiol Mol Biol Rev. 1998;62(2):504–44.
Oren A, Stambler N, Dubinsky Z. On the red coloration of saltern crystallizer ponds. Int J Salt Lake Res. 1992;1(2):77–89.
Oren A, Dubinsky Z. On the red coloration of saltern crystallizer ponds. II. Additional evidence for the contribution of halobacterial pigments. Int J Salt Lake Res. 1994;3(1):9–13.
Alain K, Querellou J. Cultivating the uncultured: limits, advances and future challenges. Extremophiles. 2009;13(4):583–94.
Babavalian H, Amoozegar M, Pourbabaei A. Isolation, identification and characterization of moderately halophilic bacteria producing hydrolytic enzymes from Aran-Bidgol salt Lake. Iranian J Biol. 2009;22(1):24–45.
Atlas R. Handbook of microbiological media. Boca Raton (Florida): CRC press; 2004.
Ventosa A, Quesada E, Rodriguez-Valera F, Ruiz-Berraquero F, Ramos-Cormenzana A. Numerical taxonomy of moderately halophilic gram-negative rods. Microbiology. 1982;128(9):1959–68.
Janssen P, Yates P, Grinton B, Taylor P, Sait M. Improved culturability of soil bacteria and isolation in pure culture of novel members of the divisions Acidobacteria, Actinobacteria, Proteobacteria, and Verrucomicrobia. Appl Environ Microbiol. 2002;68(5):2391–6.
Wilson K. Preparation of genomic DNA from bacteria. In: Ausubel FMBR, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K, editors. Current protocols in molecular biology. New York: John Wiley & Sons; 1987.
Thompson J, Gibson T, Plewniak F, Jeanmougin F, Higgins D. The CLUSTAL X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 1997;25(24):4876–82.
Kashi FJ, Owlia P, Amoozegar MA, Yakhchali B, Kazemi B. Diversity of cultivable microorganisms in the eastern part of Urmia salt lake, Iran. J Microbiol Biotechnol Food Sci. 2020;9(4):36–43.
Garcia-Vallvé S, Palau J, Romeu A. Horizontal gene transfer in glycosyl hydrolases inferred from codon usage in Escherichia coli and Bacillus subtilis. Mol Biol Evol. 1999;16(9):1125–34.
Tamura K, Dudley J, Nei M, Kumar S. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol. 2007;24(8):1596–9.
Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987;4(4):406–25.
Fitch W. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool. 1971;20(4):406–16.
Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, et al. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 2007;35(21):7188–96.
Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution. 1985;39(4):783–91.
Maturrano L, Valens-Vadell M, Rossello-Mora R, Anton J. Salicola marasensis gen. nov., sp. nov., an extremely halophilic bacterium isolated from the Maras solar salterns in Peru. Int J Syst Evol Microbiol. 2006;56(7):1685.
Rohban R, Amoozegar M, Ventosa A. Screening and isolation of halophilic bacteria producing extracellular hydrolyses from Howz Soltan Lake. Iran J Ind Microbiol Biotechnol. 2009;36:333–40.
Ventosa A. Unusual micro-organisms from unusual habitats: hypersaline environments. In: Logan N. A. L-S, H. M., Oyston, P. C. F., editor. Prokaryotic Diversity Mechanisms and Significance. Society for General Microbiology Symposia: Cambridge University Press; 2006. p. 223–54.
Gunde-Cimerman N, Oren A, Plemenitaš A. Adaptation to life at high salt concentrations in Archaea, Bacteria, and Eukarya. Dordrecht, Netherlands: Kluwer Academic Pub; 2005.
Huang C, Garcia J, Patel B, Cayol J, Baresi L, Mah R. Salinivibrio costicola subsp. vallismortis subsp. nov., a halotolerant facultative anaerobe from Death Valley, and emended description of Salinivibrio costicola. Int J Syst Evol Microbiol. 2000;50(2):615–22.
Marquez M, Ventosa A, Ruiz-Berraquero F. A taxonomic study of heterotrophic halophilic and non-halophilic bacteria from a solar saltern. J Gen Microbiol. 1987;133(1):45–56.
Martinez-Canovas M, Bejar V, Martinez-Checa F, Paez R, Quesada E. Idiomarina fontislapidosi sp. nov. and Idiomarina ramblicola sp. nov., isolated from inland hypersaline habitats in Spain. Int J Syst Evol Microbiol. 2004;54(5):1793.
Donachie S, Hou S, Gregory T, Malahoff A, Alam M. Idiomarina loihiensis sp. nov., a halophilic gamma-Proteobacterium from the Lo'ihi submarine volcano, Hawai'i. Int J Syst Evol Microbiol. 2003;53(6):1873–9.
Yoon J, Jung S, Jung Y, Oh T. Idiomarina salinarum sp. nov., isolated from a marine solar saltern in Korea. Int J Syst Evol Microbiol. 2007;57(11):2503–6.
Arens M. Methods for subtyping and molecular comparison of human viral genomes. Clin Microbiol Rev. 1999;12(4):612–26.
Yang Z, Huang J, Yao Y. Auto-screening of restriction endonucleases for PCR-RFLP identification of fungal species, using Pleurotus as an example. Appl Environ Microbiol. 2007:842–745.
Liu W, Marsh T, Cheng H, Forney L. Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl Environ Microbiol. 1997;63(11):4516–22.
Acknowledgments
The authors would like to express their gratitude to the research council of the University of Tehran. This work was supported by a grant from the Spanish Ministery of Econmoy and Copetitiveness (MINECO) throurgh project CGL2017-83385-P and the Junta de Andalucia (Spain) (Bio-213, US-1263771), all including European (FEDER) funds.
Author information
Authors and Affiliations
Contributions
Mohammad Ali Amoozegar and Antonio Ventosa planned the experiments. Maryam Didari, Maryam Bagheri, Dr. Saied Bouzari, Hamid Babavalian, Hamid Tebyanian and Mehdi Hassanshahian carried out the experimental work and prepared the draft manuscript. All authors revised and contributed to the preparation of the final manuscript.
Corresponding author
Ethics declarations
Conflict of interest
The authors declare no conflict of interest.
Ethical approval
This article does not contain any studies with human participants or animal experiments by any of the authors.
Additional information
Publisher’s note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
About this article
Cite this article
Didari, M., Bagheri, M., Amoozegar, M.A. et al. Diversity of halophilic and halotolerant bacteria in the largest seasonal hypersaline lake (Aran-Bidgol-Iran). J Environ Health Sci Engineer 18, 961–971 (2020). https://doi.org/10.1007/s40201-020-00519-3
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s40201-020-00519-3