SOME MOLECULAR TECHNIQUES APPLIED in DETERMINATION of ENVIRONMENTAL MICROBIAL DIVERSITY

Year 2015, Volume: 33 Issue: 1, 54 - 64, 01.03.2015

Nihal Doğruöz Güngör

Abstract

The most important questions to be answered in the studies regarding the diversity of microorganisms in natural ecosystems are the functions of bacterial communities and how the compositions of these communities are affected by environmental changes. In order to answer these questions, there needs to be conducted advanced studies concerning the community structure. The total bacteria community studies require a huge amount of genetic data and high range of genetic diversity. Molecular techniques are quite valuable in researching the structure and diversity of bacterial communities. To combine various complementary molecular techniques is a nice strategy to keep track of microbial community changes in natural ecosystems. Combining some commonly-used techniques, i.e. polymerase chain reaction (PCR), denaturing gradient gel electrophoresis (DGGE), molecular cloning and fluorescence in situ hybridization (FISH), this review evaluates the advantages of using these techniques together in determining microbial diversity in environmental samples.

Keywords

Enviromental samples, molecular techniques, microbial diversity.

References

• [1] V.L. Torsvik, Øvreås L. DNA Reassociation Yields Broad-Scale Information on Metagenome Complexity and Microbial Diversity. In: Handbook of Molecular Microbial Ecology I. John Wiley & Sons, Inc., 3-16, 2011.
• [2] J.M. Gonzalez, A. Ortiz-Martinez, M.A. Gonzalez-del Valle, L. Laiz, C. Saiz- Jimenez. An efficient strategy for screening large cloned libraries of amplified 16S rRNA sequences from complex environmental communities. J. Microbiol. Methods. 55: 459–46, 2003.
• [3] C. Schabereiter-Gurtner, G. Pinar, W. Lubitz, S. Rölleke. An advanced strategy to identify bacterial communities on art objects. J. Microbiol. Methods. 45: 77–87, 2001.
• [4] S.J. Giovannoni, T.B. Britschgi, C.L. Moyer, K.G. Field. Genetic diversity in Saragasso Sea Bacterioplankton. Nature. 345: 60-62, 1990.
• [5] D.L. Kirchman. Introduction and overview. In: Microbial Ecology of the Oceans. Wiley-Blackwell: New Jersey, 1-26, 2008.
• [6] R. Daniel. Soil-Based Metagenomics. In: Handbook of Molecular Microbial Ecology II: Metagenomics in Diff erent Habitats. Wiley-Blackwell, 83-92, 2011.
• [7] J.M. Gonzalez, C. Saiz-Jimenez. Unknown microbial communities on rock art painting. Consequences for conservation and future perspectives. Coalitio., 10: 4–7, 2005.
• [8] J. Wang, S. Krause, G. Muyzer, M. Meima-Franke, H. J. Laanbroek, P. L. Bodelier. Spatial patterns of iron-and methane-oxidizing bacterial communities in an irregularly flooded, riparian wetland. Frontiers in microbiology. 3: 1-13, 2012.
• [9] D. Liu, H. Ishikawa, M. Nishida, K.Tsuchiya, T. Takahashi, M. Kimura, S. Asakawa. Effect of Paddy-Upland Rotation on Methanogenic Archaeal Community Structure in Paddy Field Soil. Microb. Ecol. 1-9, 2014.
• [10] G. Muyzer, K. Smalla. Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis in microbial ecology. Antonie van Leeuwenhock. 73: 127– 141, 1999.
• [11] L.M. Feinstein, W.J. Sul, C.B. Blackwood. Assessment of bias associated with incomplete extraction of microbial DNA from soil. Appl. Environ. Microbiol.75:5428–5433, 2009.
• [12] K.B. Mullis, F.A. Faloona. Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction. Methods. Enzymol. 155:335–350, 1987.
• [13] T.C. Dakal, P.K. Arora. Evaluation of potential of molecular and physical techniques in studying biodeterioration. Rev. Environ. Sci. Biotechnol. 11: 71–104, 2012.
• [14] G. Rastogi, R.S. Sani. Molecular techniques to asses microbial community structure, function and dynamics in the environment. In Microbes and microbial technology: agricultural and environmental applications. Ahmad I., Ahmad F., Pichtel J., eds, Springer, New York, 29–57, 2011.
• [15] L.A. O'Sullivan, A.M. Sass, G. Webster, J.C. Fry, R.J. Parkes, A. J. Weightman. Contrasting relationships between biogeochemistry and prokaryotic diversity depth profiles along an estuarine sediment gradient. FEMS. Microbiol. Ecol. 85: 143-157, 2013.
• [16] E. W. Vissers, F. S. Anselmetti, P. L. Bodelier, G. Muyzer, C. Schleper, M. Tourna, H. J. Laanbroek. Temporal and Spatial Coexistence of Archaeal and Bacterial amoA Genes and Gene Transcripts in Lake Lucerne. Archae. 2013:1-11, 2013.
• [17] G. Muyzer, E.C. de Waal, A.G. Uitterlinden. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes encoding for 16S rRNA. Appl. Environ. Microbiol. 59: 695-700, 1993.
• [18] C.C. Gaylarde, C.H. Rodriguez, Y.E. Navarro-Noya, B.O. Ortega-Morales. Microbial biofims on the sandstone monuments of the Angkor Wat Complex, Cambodia. Curr. Microbiol. 64: 85–92, 2012.
• [19] S. Mocali, A. Benedetti. Exploring research frontiers in microbiology: the challenge of metagenomics in soil microbiology. Res. Microbiol. 161: 497–505, 2010.
• [20] Promega (2007) pGEM-T easy vector manual. Available from: http://www.promega.com/~/media/files/resources/protocols/technical%20manuals/0/pgem-t%20and%20pgem-t%20easy%20vector%20systems%20protocol.pdf [accessed April 12, 2014].
• [21] W.J. Thieman, M.A. Palladino. Biyoteknolojiye Giriş. Palme Yayıncılık, Çeviri ed. Tekeoğlu M. Ankara, 2013.
• [22] M.T. Madigan, J.M. Martinko. Mikroorganizmaların biyolojisi. Palme Yayıncılık, Çeviri ed. Çökmüş C. Ankara, 2010.
• [23] F. Sanger, A.R. Coulson. A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. J. Mol. Biol. 94: 441-448, 1975.
• [24] A.M. Maxam, W. Gilbert. A new method for sequencing DNA. Proceedings of the National Academy of Science. 74: 560-564, 1977.
• [25] I. Mecler, U. Nawrot. Techniki molekularne stosowane w diagnostyce mikrobiologicznej. Mikol. Lek. 14: 280–284, 2007.
• [26] A. Raszka, A. Ziembinska, A. Wiechetek. Techniki molekularne stosowane w diagnostyce mikrobiologicznej. Środowisko, 2: 101–114, 2009.
• [27] M.L. Metzker. Sequencing technologies mdash] the next generation. Nat. Rev. Genet. 11: 31-46, 2010.
• [28] S. Balzer, K. Malde, A. Lanzen, A. Sharma, I. Jonassen. Characteristics of 454 pyrosequencing data-enabling realistic simulation with flowsim. Bioinformatics. 26: 420-425, 2010.
• [29] M. Ronaghi. Pyrosequencing sheds light on DNA sequencing. Genome. Res. 11: 3–11, 2013.
• [30] T.Z. DeSantis, E.L. Brodie, J.P. Moberg, I.X. Zubieta, Y.M. Piceno, G.L. Andersen. High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment. Microbial. Ecol. 53: 371–383, 2007.
• [31] T.A. Tatusova, T.L. Madden. BLAST 2 SEQUENCES, a new tool for comparing protein and nucleotide sequences. FEMS Microbiol. Lett.174: 247–250, 1999.
• [32] J. Dunbar, S.M. Barns, L.O. Ticknor, C.R. Kuske. Empirical and theoretical bacterial diversity in four Arizona soils. Appl. Environ. Microbiol. 68: 3035–3045, 2002.
• [33] R.I. Amann, W. Ludwig, K.H. Schleifer. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59:143–169, 1995.
• [34] S.W. Rogers, T.B. Moorman, S.K. Ong. Fluorescent in situ hybridization and microautoradiography applied to ecophysiology in soil. Soil. Sci. Soc. Am. J. 71: 620–631, 2007.
• [35] S.A. Bustin, V. Benes, T. Nolan, M.W. Pfaffl. Quantitative real-time RT-PCR – a perspective. J. Mol. Endocrinol. 34: 597–601, 2005.
• [36] C.J. Smith, A.M. Osborn. Advantages and limitations of quantitative PCR (Q-PCR)-based approaches in microbial ecology. FEMS. Microbiol. Ecol. 67: 6–20, 2009.
• [37] M. Foti, D.Y. Sorokin, B. Lomans, M. Mussman, E.E. Zacharova, N.V. Pimenov, J.G. Kuenen, G. Muyzer. Diversity, activity, and abundance of sulfate-reducing bacteria in saline and hypersaline soda lakes. Appl. Environ. Microbiol. 73: 2093–3000, 2007.