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Detection of Horizontal Transfer of Housekeeping and Hydrocarbons Catabolism Genes in Bacterial Genus with Potential to Application in Bioremediation Process

DOI: 10.4236/oalib.1104454, PP. 1-10

Subject Areas: Molecular Biology, Microbiology, Marine Biology, Evolutionary Studies, Ecosystem Science, Ecology, Bioinformatics

Keywords: Bacterial Community, Microbial Ecology, Gene Transfer, Catabolic Genes

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Abstract

In silico analysis can be useful to infer about the horizontal gene transfer (HGT) as well as to deduce about the evolutionary relations of catabolic genes. In this study, we performed the analysis of two housekeeping genes (fabD and rpoD) and two catabolic genes (alkB and catA) from 12 bacterial genus usually founded in marine environments. Comparing the trees obtained from Bayesian Inference hypotheses of these genes with 16S rDNA sequences, we noted the topologies are different among housekeeping or catabolic genes trees comparing to 16S gene tree. The HGT may be used with the purpose to spread genes within bacterial community according to environmental conditions in marine ecosystems. In this way, using our analysis, we concluded that hydrocarbons catabolism genes as well as housekeeping genes can be subject to horizontal gene transfers among marine bacterial communities.

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Rodrigues, E. M. , Freitas, F. D. S. and Siqueira, T. D. P. (2018). Detection of Horizontal Transfer of Housekeeping and Hydrocarbons Catabolism Genes in Bacterial Genus with Potential to Application in Bioremediation Process. Open Access Library Journal, 5, e4454. doi: http://dx.doi.org/10.4236/oalib.1104454.

References

[1]  Olsen, G.J., Lane, D.J., Giovannoni, S.J. and Pace, N.R. (1986) Microbial Ecology and Evolution: A Ribosomal RNA Approach. Annual Review of Microbiology, 40, 337-365.
https://doi.org/10.1146/annurev.mi.40.100186.002005
[2]  Woese, C.R., Kandler, O. and Wheelis, M.L. (1990) Towards a Natural System of Organisms: Proposal for the Domains Archaea, Bacteria, and Eucarya. Proceedings of the National Academy of Sciences of the United States of America, 87, 4576-4579.
https://doi.org/10.1073/pnas.87.12.4576
[3]  Sasser, M. (2001) Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids. Technical Note 101. Microbial ID, Inc., Newark, Del.
[4]  Zuckerkandl, E. and Pauling, L. (1965) Molecules as Documents of Evolutionary History. Journal of Theoretical Biology, 8, 357-366.
https://doi.org/10.1016/0022-5193(65)90083-4
[5]  Tang, Y.-W., Ellis, N.M., Hopkins, M.K., Smith, D.H., Dodge, D.E. and Persing, D.H. (1998) Comparison of Phenotypic and Genotypic Techniques for Identification of Unusual Aerobic Pathogenic Gram-Negative Bacilli. Journal of Clinical Microbiology, 36, 3674.
[6]  Ochman, H., Lawrence, J.G. and Groisman, E.A. (2000) Lateral Gene Transfer and the Nature of Bacterial Innovation. Nature, 405, 299-304.
https://doi.org/10.1038/35012500
[7]  Thomas, C. and Nielsen, K. (2005) Mechanisms of, and Barriers to, Horizontal Gene Transfer between Bacteria. Nature Reviews Microbiology, 3, 711-721.
https://doi.org/10.1038/nrmicro1234
[8]  Nakamura, Y., Itoh, T., Matsuda, H. and Gojobori, T. (2004) Biased Biological Functions of Horizontally Transfered Genes in Prokaryotic Genomes. Nature Genet, 36, 760-766.
https://doi.org/10.1038/ng1381
[9]  Miyazaki, R., Minoia, M., Pradervand, N., Sulser, S., Reinhard, F. and Meer, J.R. (2012) Cellular Variability of RpoS Expression. Underlies Subpopulation Activation of an Integrative and Conjugative Element. Plos Genetics, 8, e1002818.
https://doi.org/10.1371/journal.pgen.1002818
[10]  Riser-Roberts, E. (1992) Bioremediation of Petroleum Contaminated Sites. CRC Press, Boca Raton, FL.
[11]  Aske, N., Kallevik, H. and Sjoblom, J. (2002) Water-in-Crude Oil Emulsion Stability Studied by Critical Electric Field Measurements. Correlation to Physico-Chemical Parameters and Near-Infrared Spectroscopy. Journal of Petroleum Science and Engineering, 36, 1-17.
https://doi.org/10.1016/S0920-4105(02)00247-4
[12]  Ghazali, F.M., Rahman, R.N.Z.A., Salleh, A.B. and Basri, M. (2004) Biodegradation of Hydrocarbons in Soil by Microbial Consortium. International Biodeterioration & Biodegradation, 54, 61-67.
https://doi.org/10.1016/j.ibiod.2004.02.002
[13]  La Rocca, C., Conti, L., Crebelli, R., Crochi, B., Iacovella, N., Rodriguez, F., Turrio-Baldassarri, L. and di Domenico, A. (1996) PAH Content and Mutagenicity of Marine Sediments from the Venice Lagoon. Ecotoxicology and Environmental Safety, 33, 236-245.
https://doi.org/10.1006/eesa.1996.0030
[14]  Ritter, K.S. and Paul, S.L. (2002) Sources, Pathways, and Relative Risks of Contaminants in Surface Water and Groundwater: A Perspective Prepared for the Walkerton Inquiry. Journal of Toxicology and Environmental Health, Part A, 65, 1-142.
https://doi.org/10.1080/152873902753338572
[15]  Chen, G. and White, P.A. (2004) The Mutagenic Hazards of Aquatic Sediments: A Review. Mutation Research, 567, 151-225.
https://doi.org/10.1016/j.mrrev.2004.08.005
[16]  Shimada, T. and Fujii-Kuriyama, Y. (2004) Metabolic Activation of Polycyclic Aromatic Hydrocarbons to Carcinogens by Cytochromes P450 1A1 and 1B1. Cancer Science, 95, 1-6.
https://doi.org/10.1111/j.1349-7006.2004.tb03162.x
[17]  Whitehead, A. (2013) Interactions between Oil-Spill Pollutants and Natural Stressors Can Compound Ecotoxicological Effects. Integrative and Comparative Biology, 53, 635-647.
https://doi.org/10.1093/icb/ict080
[18]  Cerniglia, C.E. (1992) Biodegradation of Polycyclic Aromatic Hydrocarbons. Biodegradation, 3, 351-368.
https://doi.org/10.1007/BF00129093
[19]  McCay, D.F., Rowe, J.J., Whittier, N., Sanka-ranarayanan, S. and Etkin, D.S. (2004) Estimation of Potential Impacts and Natural Resource Damages of Oil. Journal of Hazardous Materials, 107, 11-25.
https://doi.org/10.1016/j.jhazmat.2003.11.013
[20]  Rodrigues, E. and Tótola, M. (2015) Petroleum: From Basic Features to Hydrocarbons Bioremediation in Oceans. Open Access Library Journal, 2, 1-17.
https://doi.org/10.4236/oalib.1102136
[21]  Rodrigues, E., Morais, D., Pylro, V., Redmile-Gordon, M., Oliveira, J., Roesch, L., Cesar, D. and Tótola, M. (2017) Aliphatic Hydrocarbon Enhances Phenanthrene Degradation by Autochthonous Prokaryotic Communities from a Pristine Seawater. Microbial Ecology.
https://doi.org/10.1007/s00248-017-1078-8
[22]  Obayori, O.S. and Salam, L.B. (2010) Degradation of Polycyclic Aromatic Hydrocarbons: Role of Plasmids. Scientific Research and Essays, 5, 4093-4106.
[23]  Johnsen, A.R., Wick, L.Y. and Harms, H. (2005) Principles of Microbial PAH-Degradation in Soil. Environmental Pollution, 133, 71-84.
https://doi.org/10.1016/j.envpol.2004.04.015
[24]  Foght, J.M. and Westlake, D.W. (1996) Transposon and Spontaneous Deletion Mutants of Plasmid-Borne Genes Encoding Polycyclic Aromatic Degradation by a Strain of Pseudomonas fluorescens. Biodegradation, 7, 353-366.
https://doi.org/10.1007/BF00115749
[25]  Top, E.M. and Springael, D. (2003) The Role of Mobile Genetic Elements in Bacterial Adaptation to Xenobiotic Organic Compounds. Current Opinion in Biotechnology, 14, 262-269.
https://doi.org/10.1016/S0958-1669(03)00066-1
[26]  Bosma, T.N.P., Harms, H. and Zehnder, A.J.B. (2001) Biodegradation of Xenobiotics in Environment and Technosphere. In: Beek, B., Ed., The Handbook of Environmental Chemistry Vol. 2 Part K, Biodegradation and Persistence, Springer-Verlag, Berlin, Heidelberg, 163-202.
https://doi.org/10.1007/10508767_2
[27]  Tamura, K., Stecher, G., Peterson, D., Filipski, A. and Kumar, S. (2013) MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0. Molecular Biology and Evolution, 30, 2725-2729.
https://doi.org/10.1093/molbev/mst197
[28]  Yang, Z. and Ranalla, B. (1997) Bayesian Phylogenetic Inference Using DNA Sequences: A Markov Chain Monte Carlo Method. Molecular Biology and Evolution, 14, 717-724.
https://doi.org/10.1093/oxfordjournals.molbev.a025811
[29]  Huelsenbeck, J.P. and Ronquist, F. (2001) MRBAYES: Bayesian Inference of Phylogenetic Trees. Bioinformatics Applications Note, 17, 754-755.
https://doi.org/10.1093/bioinformatics/17.8.754
[30]  Smith, S.E., Showers-Corneli, P., Dardenne, C.N., Harpending, H.H., Martin, D.P. and Beiko, R.G. (2012) Comparative Genomic and Phylogenetic Approaches to Characteriza the Role of Genetic Recombination in Mycobacterial Evolution. PLoS ONE, 7, e50070.
https://doi.org/10.1371/journal.pone.0050070
[31]  Arenskotter, M., Broker, D., Arensko, M., Bro, D. and Steinbu, A. (2004) Biology of the Metabolically Diverse Genus Gordonia Biology of the Metabolically Diverse Genus Gordonia. Applied and Environmental Microbiology, 70, 3195-3204.
https://doi.org/10.1128/AEM.70.6.3195-3204.2004
[32]  Shen, F.-T., Lu, H.-L., Lin, J.-L., Huang, W.-S., Arun, A.-B. and Young, C.-C. (2006) Phylogenetic Analysis of Members of the Metabolically Diverse Genus Gordonia Based on Proteins Encoding the gyrB Gene. Research in Microbiology, 157, 367-375.
https://doi.org/10.1016/j.resmic.2005.09.007
[33]  Jeffroy, O., Brinkmann, H., Delsuc, F. and Philippe, H. (2006) Phylogenomics: The Beginning of Incongruence? Trends in Genetics, 22, 225-231.
https://doi.org/10.1016/j.tig.2006.02.003
[34]  Yamamoto, S. and harayama, S. (1998) Phylogenetic Relationships of Pseudomonas putida Strains Deduced from the Nucleotide Sequences of gyrB, rpoD and 16S rRNA Genes. International Journal of Systematic Bacteriology, 48, 813-819.
https://doi.org/10.1099/00207713-48-3-813
[35]  Soler, L., Yánez, M.A., Chacon, M.R., Aguilera-Arreola, M.G., Catalán, V., Figueras, M.J. and Martínez-Murcia, A.J. (2004) Phylogenetic Analysis of the Genus Aeromonas Based on Two Housekeeping Genes. International Journal of Systematic and Evolutionary Microbiology, 54, 1511-1519.
https://doi.org/10.1099/ijs.0.03048-0
[36]  Stackebrandt, E., Frederiksen, W., Garrity, G.M., Grimont P.A.D., Kampfer, P., Maiden, M.C.J., Nesme, X., Rosselló-Mora, R., Swings, J., Truper, H.G., Vauterin, L., Ward, A.C. and Whitman, W.B. (2002) Report of the Ad Hoc Committee for the Re-Evaluation of the Species Definition in Bacteriology. International Journal of Systematic and Evolutionary Microbiology, 52, 1043-1047.
[37]  Heled, J. and Drummond, A.J. (2010) Baysian Inference of Species Trees from Multilocus Data. Molecular Biology and Evolution, 27, 570-580.
https://doi.org/10.1093/molbev/msp274
[38]  Leahy, J.G. and Colwell, R.R. (1990) Microbial Degradation of Hydrocarbons in the Environment. Microbiological Reviews, 54, 305-315.
[39]  Wilson, M.S., Harrick, J.B., Jeon, C.O., Hinman, D.E. and Madsen, E.L. (2003) Horizontal Transfer of phnAc Dioxygenase Genes within One og Two Phenotypically and Genotypically Distinctive Naphthalene-Degrading Guilds from Adjacent Soil Environments. Applied and Environmental Microbiology, 69, 2172-2181.
https://doi.org/10.1128/AEM.69.4.2172-2181.2003
[40]  Ma, Y., Wang, L. and Shao, Z. (2006) Pseudomonas, the Dominant Polycyclic Aromatic Hydrocarbon-Degrading Bacteria Isolated from Antartic Soils and the Role of Large Plasmids in Horizontal Gene Transfer. Environmental Microbiology, 8, 455-465.
https://doi.org/10.1111/j.1462-2920.2005.00911.x
[41]  Atlas, R.M. (1981) Microbial Degradation of Petroleum Hydrocarbons: An Environmental Perspective. Microbiological Reviews, 45, 180-209.
[42]  Habe, H. and Omori, T. (2003) Genetics of Polycyclic Aromatic Hydrocarbon Metabolism in Diverse Aerobic Bacteria. Bioscience, Biotechnology, and Biochemistry, 67, 225-243.
https://doi.org/10.1271/bbb.67.225
[43]  Coates, J.D., Woodward, J., Allen, J., Philp, P. and Lovley, D.R. (1997) Anaerobic Degradation of Polycyclic Aromatic Hydrocarbons and Alkanes in Petroleum-Contaminated Marine Harbor Sediments. Applied and Environmental Microbiology, 63, 3589-3593.
[44]  Nie, Y., Chi, C.Q., Fang, H., Liang, J.L., Lu, S.L., Lai, G.L., Tang, Y.Q. and Wu, X.L. (2014) Diverse Alkane Hydroxylase Genes in Microorganisms and Environments. Scientific Reports, 4, 4968-4978.
[45]  van Beilen, J.B., Funhoff, E., van Loon, A., Just, A., Jaysser, L., Bouza, M., Holtackers, R., Rothisberger, M., Li, Z. and Witholt, B. (2006) Cytochrome P450 Alkane Hydroxylases of the CYP153 Family Are Common in Alkane-Degrading Eubacteria Lacking Integral Membrane Alkane Hydroxylases. Applied and Environmental Microbiology, 72, 59-65.
https://doi.org/10.1128/AEM.72.1.59-65.2006
[46]  Prince, R.C. (2005) The Microbiology of Marine Oil Spill Bioremediation. In: Ollivier, B. and Magot, M., Eds., Petroleum Microbiology, ASM Press, Washington DC, 317-336.
https://doi.org/10.1128/9781555817589.ch16
[47]  Rodrigues, E.M., Kalks, K.H.M. and Tótola, M.R. (2015) Prospect, Isolation, and Characterization of Microorganisms for Potential Use in Cases of Oil Bioremediation along the Coast of Trindade Island. Journal of Environmental Management, 156, 15-22.
https://doi.org/10.1016/j.jenvman.2015.03.016
[48]  Whyte, L.G., Smits, T.H.M., Labbe, D., Witholt, B., Greer, C.W. and van Beilen, J.B. (2002) Gene Cloning and Characterization of Multiple Alkane Hydroxylase Systems in Rhodococcus Strains Q15 and NRRL B-16531. Applied and Environmental Microbiology, 68, 5933-5942.
https://doi.org/10.1128/AEM.68.12.5933-5942.2002
[49]  Amouric, A., Quemeneur, M., Grossi, V., Liebgott, P., Auria, R. and Casalot, L. (2009) Identification of Different Alkane Hydroxylase Systems in Rhodococcus Ruber Strain SP2B, an Hexane-Degrading Actinomycete. Journal of Applied Microbiology, 108, 1903-1916.
https://doi.org/10.1111/j.1365-2672.2009.04592.x
[50]  Atlas, R.M. (1991) Microbial Hydrocarbon Degrada-tion-Bioremediation Oil Spills. Journal of Chemical Technology and Biotechnology, 52, 149-156.
https://doi.org/10.1002/jctb.280520202
[51]  Haritash, A.K. and Kaushik, C.P. (2009) Biodegradation Aspects of Polycyclic Aromatic Hydrocarbons (PAHs): A Review. Journal of Hazardous Materials, 169, 1-15.
https://doi.org/10.1016/j.jhazmat.2009.03.137
[52]  Simpson, C.D., Mosi, A.A., Cullen, W.R. and Reimer, K.J. (1996) Composition and Distribution of Polycyclic Aromatic Hydrocarbon Contamination in Surficial Marine Sediments from Kitimat Harbor, Canada. Science of the Total Environment, 181, 265-278.
https://doi.org/10.1016/0048-9697(95)05026-4
[53]  Morales-Caselles, C., Jiménez-Tenorio, N., de Canales, M.L.G., Sarasquete, C. and DelValls, T.A. (2006) Ecotoxicity of Sediments Contaminated by the Oil Spill Associated with the Tanker “Prestige” Using Juveniles of the Fish Sparus aurata. Archives of Environmental Contamination and Toxicology, 51, 652-660.
https://doi.org/10.1007/s00244-005-0251-0

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