Molecular Phylogeny of Arctic Microbes Using Metagenomic Approach
Affiliation(s)
1 Department of Biotechnology, Burdwan University, Burdwan, India. 2 National Facility for Marine Cyanobacteria, Bharathidasan University, Tiruchirappalli, India. 3 Department of Biotechnology, Haldia Institute of Technology, Haldia, India.
1 Department of Biotechnology, Burdwan University, Burdwan, India. 2 National Facility for Marine Cyanobacteria, Bharathidasan University, Tiruchirappalli, India. 3 Department of Biotechnology, Haldia Institute of Technology, Haldia, India.
ABSTRACT
Metagenomic approach to the characterization of uncultured and mixed bacterial consortium has been used in this study for a few arctic micro-organisms. Arctic soil, collected from one spot at Ny Alesund in Svalbard was used as the source of such organisms and enriched in culture medium. Only psychrotrophic microbes were chosen which could grow from 5°C to 20°C. Total genomic DNA isolated from the consortium was used as template for amplifying the 16S rRNA genes using the conserved forward and reverse primers. The amplified mixture of 1.4 kb DNA was cloned in pGEMT Easy vector and individual 16S rDNA sequences were determined by automated sequencing. A phylogenetic tree was constructed using MEGA 5 software which enlists 19 isolates in the consortium. Most of these arctic bacteria were Bacillus species as these were isolated from a single spot.
Metagenomic approach to the characterization of uncultured and mixed bacterial consortium has been used in this study for a few arctic micro-organisms. Arctic soil, collected from one spot at Ny Alesund in Svalbard was used as the source of such organisms and enriched in culture medium. Only psychrotrophic microbes were chosen which could grow from 5°C to 20°C. Total genomic DNA isolated from the consortium was used as template for amplifying the 16S rRNA genes using the conserved forward and reverse primers. The amplified mixture of 1.4 kb DNA was cloned in pGEMT Easy vector and individual 16S rDNA sequences were determined by automated sequencing. A phylogenetic tree was constructed using MEGA 5 software which enlists 19 isolates in the consortium. Most of these arctic bacteria were Bacillus species as these were isolated from a single spot.
Cite this paper
Ray, D. , Mohandass, S. and Roy, P. (2014) Molecular Phylogeny of Arctic Microbes Using Metagenomic Approach. Advances in Microbiology, 4, 1278-1284. doi: 10.4236/aim.2014.416137.
Ray, D. , Mohandass, S. and Roy, P. (2014) Molecular Phylogeny of Arctic Microbes Using Metagenomic Approach. Advances in Microbiology, 4, 1278-1284. doi: 10.4236/aim.2014.416137.
References
[1] Whitman, W.B., Coleman, D.C. and Wiebe, W.J. (1998) Prokaryotes: The Unseen Majority. Proceedings of the National Academy of Sciences of the United States of America, 95, 6578-6583.
http://dx.doi.org/10.1073/pnas.95.12.6578 [2] Turnbaugh, P.J. and Gordon, J.I. (2008) An Invitation to the Marriage of Metagenomics and Metabolomics. Cell, 134, 708-713. [3] Sleator, R.D., Shortall, C. and Hill, C. (2008) Metagenomics. Letters in Applied Microbiology, 47, 361-366. http://dx.doi.org/10.1111/j.1472-765X.2008.02444.x [4] Venter, J.C., et al. (2004) Environmental Genome Shotgun Sequencing of the Sargasso Sea. Science, 304, 66-74. http://dx.doi.org/10.1126/science.1093857 [5] Daniel, R. (2005) The Metagenomics of Soil. Nature Reviews Microbiology, 3, 470-478.
http://dx.doi.org/10.1038/nrmicro1160 [6] Ferrer, M., Beloqui, A., Timmis, K.N. and Golyshin, P.N. (2009) Metagenomics for Mining New Genetic Resources of Microbial Communities. Journal of Molecular Microbiology and Biotechnology, 16, 109-123. http://dx.doi.org/10.1159/000142898 [7] Handelsman, J. (2004) Metagenomics: Application of Genomics to Uncultured Microorganisms. Microbiology and Molecular Biology Reviews, 68, 669-685.
http://dx.doi.org/10.1128/MMBR.68.4.669-685.2004 [8] Pace, N.R., Stahl, D.A., Lane, D.J. and Olsen, G.J. (1985) Analyzing Natural Microbial Populations by rRNA Sequences. ASM News, 51, 4-12. [9] Maniatis, T., Fritsch, E.F. and Sambrook, J. (1982) Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York. [10] Mezei, L.M. and Storts, D.R. (1994) Purification of PCR Products. In: Griffin, H.G. and Griffin, A.M., Eds., PCR Technology: Current Innovations, CRC Press, Boca Raton, 21-27. [11] Birnboim, H.C. and Doly, J. (1979) A Rapid Alkaline Extraction Procedure for Screening Recombinant Plasmid DNA. Nucleic Acids Research, 7, 1513-1523. http://dx.doi.org/10.1093/nar/7.6.1513 [12] Lane, D.J., Pace, B., Olsen, G.J., Stahl, D.A., Sogin, M.L. and Pace, N.R. (1985) Rapid Determination of 16S Ribosomal RNA Sequences for Phylogenetic Analysis. Proceedings of the National Academy of Sciences of the United States of America, 82, 6955-6959. http://dx.doi.org/10.1073/pnas.82.20.6955 [13] Weisburg, W.G., Oyaizu, Y., Oyaizu, H. and Woese, C.R. (1985) Natural Relationship between Bacteroides and Flavobacteria. Journal of Bacteriology, 164, 230-236.
[1] Whitman, W.B., Coleman, D.C. and Wiebe, W.J. (1998) Prokaryotes: The Unseen Majority. Proceedings of the National Academy of Sciences of the United States of America, 95, 6578-6583.
http://dx.doi.org/10.1073/pnas.95.12.6578 [2] Turnbaugh, P.J. and Gordon, J.I. (2008) An Invitation to the Marriage of Metagenomics and Metabolomics. Cell, 134, 708-713. [3] Sleator, R.D., Shortall, C. and Hill, C. (2008) Metagenomics. Letters in Applied Microbiology, 47, 361-366. http://dx.doi.org/10.1111/j.1472-765X.2008.02444.x [4] Venter, J.C., et al. (2004) Environmental Genome Shotgun Sequencing of the Sargasso Sea. Science, 304, 66-74. http://dx.doi.org/10.1126/science.1093857 [5] Daniel, R. (2005) The Metagenomics of Soil. Nature Reviews Microbiology, 3, 470-478.
http://dx.doi.org/10.1038/nrmicro1160 [6] Ferrer, M., Beloqui, A., Timmis, K.N. and Golyshin, P.N. (2009) Metagenomics for Mining New Genetic Resources of Microbial Communities. Journal of Molecular Microbiology and Biotechnology, 16, 109-123. http://dx.doi.org/10.1159/000142898 [7] Handelsman, J. (2004) Metagenomics: Application of Genomics to Uncultured Microorganisms. Microbiology and Molecular Biology Reviews, 68, 669-685.
http://dx.doi.org/10.1128/MMBR.68.4.669-685.2004 [8] Pace, N.R., Stahl, D.A., Lane, D.J. and Olsen, G.J. (1985) Analyzing Natural Microbial Populations by rRNA Sequences. ASM News, 51, 4-12. [9] Maniatis, T., Fritsch, E.F. and Sambrook, J. (1982) Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York. [10] Mezei, L.M. and Storts, D.R. (1994) Purification of PCR Products. In: Griffin, H.G. and Griffin, A.M., Eds., PCR Technology: Current Innovations, CRC Press, Boca Raton, 21-27. [11] Birnboim, H.C. and Doly, J. (1979) A Rapid Alkaline Extraction Procedure for Screening Recombinant Plasmid DNA. Nucleic Acids Research, 7, 1513-1523. http://dx.doi.org/10.1093/nar/7.6.1513 [12] Lane, D.J., Pace, B., Olsen, G.J., Stahl, D.A., Sogin, M.L. and Pace, N.R. (1985) Rapid Determination of 16S Ribosomal RNA Sequences for Phylogenetic Analysis. Proceedings of the National Academy of Sciences of the United States of America, 82, 6955-6959. http://dx.doi.org/10.1073/pnas.82.20.6955 [13] Weisburg, W.G., Oyaizu, Y., Oyaizu, H. and Woese, C.R. (1985) Natural Relationship between Bacteroides and Flavobacteria. Journal of Bacteriology, 164, 230-236.