Effect of salinity on community structure and naphthalene dioxygenase gene diversity of a halophilic bacterial consortium

Abstract

Various salinities affected the PAH-biodegrading community structure.

Various salinities affected the growth of strains with different salt tolerance.

The two ndo genes belonged to a new divergent cluster of the known nah-like genes.

The two main ndo genes had correlations with the phenanthrene degradation.

The aim of this study is to analyze the effect of salinity on polycyclic aromatic hydrocarbons (PAHs) biodegradation, community structure and naphthalene dioxygenase gene (ndo) diversity of a halophilic bacterial consortium with the denaturing gradient gel electrophoresis (DGGE) approach. The consortium was developed from oil-contaminated saline soil after enrichment for six times, using phenanthrene as the substrate. The prominent species in the bacterial consortium at all salinities were identified as halophilic bacteria Halomonas, Alcanivorax, Marinobacter, Idiomarina, Martelella and uncultured bacteria. The predominant microbes gradually changed associating with the saline concentration fluctuations ranging from 0.1% to 25% (w/v). Two ndo alpha subunits were dominant at salinities ranging from 0.1% to 20%, while not been clearly detected at 25% salinity. Consistently, the biodegradation occurred at salinities ranging from 0.1% to 20%, while no at 25% salinity, suggesting the two ndo genes played an important role in the degradation. The phylogenetic analysis revealed that both of the two ndo alpha subunits were related to the classic nah-like gene from Pseudomonas stutzeri AN10 and Pseudomonas aeruginosa PaK1, while one with identity of about 82% and the other one with identity of 90% at amino acid sequence level. We concluded that salinity greatly affected halophilic bacterial community structure and also the functional genes which were more related to biodegradation.

Graphical abstract

Keywords

Phenanthrene / Halophilic bacteria / Gene diversity / Naphthalene dioxygenase genes

References

[1] Díaz M P, Boyd K G, Grigson S J, Burgess J G. Biodegradation of crude oil across a wide range of salinities by an extremely halotolerant bacterial consortium MPD-M, immobilized onto polypropylene fibers. Biotechnology and Bioengineering, 2002, 79(2): 145–153

[2] Kleinsteuber S, Riis V, Fetzer I, Harms H, Müller S. Population dynamics within a microbial consortium during growth on diesel fuel in saline environments. Applied and Environmental Microbiology, 2006, 72(5): 3531–3542

[3] Santodonato J. Review of the estrogenic and antiestrogenic activity of polycyclic aromatic hydrocarbons: relationship to carcinogenicity. Chemosphere, 1997, 34(4): 835–848

[4] Chen Q, Liu J, Liu F, Wang B, Cao Z. Biologic risk and source diagnose of 16 PAHs from Haihe River Basin, China. Frontiers of Environmental Science & Engineering, 2016, 10(1): 46–52

[5] Zhang H, Xu L, Zhang Y, Jiang M. The transformation of PAHs in the sewage sludge incineration treatment. Frontiers of Environmental Science & Engineering, 2016, 10(2): 336–340

[6] Guo G, Fang T, Wang C, Huang Y, Tian F, Cui Q, Wang H. Isolation and characterization of two novel halotolerant Catechol 2,3-dioxygenases from a halophilic bacterial consortium. Scientific Reports, 2015, 5: 17603

[7] Guo G, He F, Tian F, Huang Y, Wang H. Effect of salt contents on enzymatic activities and halophilic microbial community structure during phenanthrene degradation. Int Biodete Biodegr, 2016, 110: 8–15

[8] Arulazhagan P, Vasudevan N. Role of a moderately halophilic bacterial consortium in the biodegradation of polyaromatic hydrocarbons. Marine Pollution Bulletin, 2009, 58(2): 256–262

[9] Zhao B, Wang H, Mao X, Li R. Biodegradation of phenanthrene by a halophilic bacterial consortium under aerobic conditions. Current Microbiology, 2009, 58(3): 205–210

[10] Minai-Tehrani D, Minoui S, Herfatmanesh A. Effect of salinity on biodegradation of polycyclic aromatic hydrocarbons (PAHs) of heavy crude oil in soil. Bulletin of Environmental Contamination and Toxicology, 2009, 82(2): 179–184

[11] Zhong Y, Wang J, Song Y, Liang Y, Li G. Microbial community and functional genes in the rhizosphere of alfalfa in crude oil-contaminated soil. Frontiers of Environmental Science & Engineering, 2012, 6(6): 797–805

[12] Peng J, Li H, Su J, Zhang Q, Rui J, Cai C. Response of bacterial communities to short-term pyrene exposure in red soil. Frontiers of Environmental Science & Engineering, 2013, 7(4): 559–567

[13] Zhou J, Bruns M A, Tiedje J M. DNA recovery from soils of diverse composition. Applied and Environmental Microbiology, 1996, 62(2): 316–322

[14] Nübel U, Engelen B, Felske A, Snaidr J, Wieshuber A, Amann R I, Ludwig W, Backhaus H. Sequence heterogeneities of genes encoding 16S rRNAs in Paenibacillus polymyxa detected by temperature gradient gel electrophoresis. Journal of Bacteriology, 1996, 178(19): 5636–5643

[15] Gomes N C, Borges L R, Paranhos R, Pinto F N, Krögerrecklenfort E, Mendonça-Hagler L C, Smalla K. Diversity of ndo genes in mangrove sediments exposed to different sources of polycyclic aromatic hydrocarbon pollution. Applied and Environmental Microbiology, 2007, 73(22): 7392–7399

[16] Pieper U, Kapadia G, Mevarech M, Herzberg O. Structural features of halophilicity derived from the crystal structure of dihydrofolate reductase from the Dead Sea halophilic archaeon, Haloferax volcanii. Structure (London, England), 1998, 6(1): 75–88

[17] Kushner D J. The halobactefiaceae. In: Woese, Wolfe, eds. The Bacteria, a Treatise on the Structure and Function, Vol. VIII, The Archaebacteria.New York: Academic Press, 1985, 171–206

[18] Kim K K, Jin L, Yang H C, Lee S T. Halomonas gomseomensis sp. nov., Halomonas janggokensis sp. nov., Halomonas salaria sp. nov. and Halomonas denitrificans sp. nov., moderately halophilic bacteria isolated from saline water. International Journal of Systematic and Evolutionary Microbiology, 2007, 57(Pt 4): 675–681

[19] Choi D H, Cho B C. Idiomarina seosinensis sp. nov., isolated from hypersaline water of a solar saltern in Korea. International Journal of Systematic and Evolutionary Microbiology, 2005, 55(Pt 1): 379–383

[20] Liu C, Shao Z. Alcanivorax dieselolei sp. nov., a novel alkane-degrading bacterium isolated from sea water and deep-sea sediment. International Journal of Systematic and Evolutionary Microbiology, 2005, 55(Pt 3): 1181–1186

[21] Brettar I, Christen R, Höfle M G. Idiomarina baltica sp. nov., a marine bacterium with a high optimum growth temperature isolated from surface water of the central Baltic Sea. International Journal of Systematic and Evolutionary Microbiology, 2003, 53(Pt 2): 407–413

[22] Okamoto T, Maruyama A, Imura S, Takeyama H, Naganuma T. Comparative phylogenetic analyses of Halomonas variabilis and related organisms based on 16S rRNA, gyrB and ectBC gene sequences. Systematic and Applied Microbiology, 2004, 27(3): 323–333

[23] Riis V, Kleinsteuber S, Babel W. Influence of high salinities on the degradation of diesel fuel by bacterial consortia. Canadian Journal of Microbiology, 2003, 49(11): 713–721

[24] Lozada M, Riva Mercadal J P, Guerrero L D, Di Marzio W D, Ferrero M A, Dionisi H M. Novel aromatic ring-hydroxylating dioxygenase genes from coastal marine sediments of Patagonia. BMC Microbiology, 2008, 8(1): 50

[25] Nicholson C A, Fathepure B Z. Aerobic biodegradation of benzene and toluene under hypersaline conditions at the Great Salt Plains, Oklahoma. FEMS Microbiology Letters, 2005, 245(2): 257–262

[26] Cui Z, Lai Q, Dong C, Shao Z. Biodiversity of polycyclic aromatic hydrocarbon-degrading bacteria from deep sea sediments of the Middle Atlantic Ridge. Environmental Microbiology, 2008, 10(8): 2138–2149

[27] Rivas R, Sánchez-Márquez S, Mateos P F, Martínez-Molina E, Velázquez E. Martelella mediterranea gen. nov., sp. nov., a novel alpha-proteobacterium isolated from a subterranean saline lake. International Journal of Systematic and Evolutionary Microbiology, 2005, 55(Pt 2): 955–959

[28] Habe H, Omori T. Genetics of polycyclic aromatic hydrocarbon metabolism in diverse aerobic bacteria. Bioscience, Biotechnology, and Biochemistry, 2003, 67(2): 225–243

[29] Hedlund B P, Geiselbrecht A D, Staley J T. Marinobacter strain NCE312 has a Pseudomonas-like naphthalene dioxygenase. FEMS Microbiology Letters, 2001, 201(1): 47–51

[30] Ferrero M, Llobet-Brossa E, Lalucat J, García-Valdés E, Rosselló-Mora R, Bosch R. Coexistence of two distinct copies of naphthalene degradation genes in Pseudomonas strains isolated from the western Mediterranean region. Applied and Environmental Microbiology, 2002, 68(2): 957–962

Acknowledgements

This research was supported by the Key Program of the Natural Science Foundation of China (Nos. 41573065 and 51138006), the National Key Research Project on Water Environmental Pollution Control in China (No. 2012ZX07313-001) and the National High Technology Research and Development Program of China (No. 2013AA06A210).

Funding

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2016 Higher Education Press and Springer-Verlag Berlin Heidelberg