Abstract
Culture independent metagenomic methods represent promising approach for the identification of novel genes and genomes of uncultivable microorganisms. A wide range of protocols have been developed for the isolation of community DNA from environmental sources. Three important steps in DNA isolation from soil are (a) cell lysis, (b) removal of contaminants, in particular humic acid, and (c) purification of isolated community DNA. Depending on the nature of the environmental DNA source, modifications are usually performed in any of the above steps. The steps involved in the isolation of DNA and RNA from soil samples and the appropriate purification strategies are described in this chapter. Additionally, protocols for the microbial diversity analysis using 16S ribosomal RNA analysis and construction of metagenomic library for screening of functional genes from metagenomic DNA are given.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Cullen DW, Hirsch PR (1998) Simple and rapid method for direct extraction of microbial DNA from soil for PCR. Soil Biol Biochem 30: 983–993
Handelsman J (2004) Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 68:669–685
Liles MR, Williamson LL, Rodbumrer J, Torsvik V, Goodman RM, Handelsman J (2008) Recovery, purification and cloning of high molecular weight DNA from soil microorganisms. Appl Environ Microbiol 74:3302–3305
Rajendhran J, Gunasekaran P (2008) Strategies for accessing soil metagenome for desired applications. Biotechnol Adv 6:576–590
Rajesh T, Rajendhran J, Lavanya Pushpam P, Gunasekaran P (2011) Methods in metagenomic DNA and RNA isolation from soil. In: Frans. J. de Bruijin (ed) Handbook of molecular microbial ecology II: metagenomics in different habitats, John Wiley & Sons Inc. vol 2, pp 93–107
Sagova-Mareckova M, Cermak L, Novotna J, Plhackova K, Forstova J, Kopecky J (2008) Innovative methods for soil DNA purification tested in soils with widely differing characteristics. Appl Environ Microbiol 74: 2902–2907
Sharma PK, Capalash N, Kaur J (2007) An improved method for single step purification of metagenomic DNA. Mol Biotechnol 36: 61–63
Tsai Y, Park MJ, Olson BH (1991) Rapid method for direct extraction of mRNA from seeded soils. Appl Environ Microbiol 57:765–768
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2013 Springer-Verlag Berlin Heidelberg
About this protocol
Cite this protocol
Rajesh, T., Rajendhran, J., Gunasekaran, P. (2013). Analysis of Microbial Diversity and Construction of Metagenomic Library. In: Arora, D., Das, S., Sukumar, M. (eds) Analyzing Microbes. Springer Protocols Handbooks. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-34410-7_14
Download citation
DOI: https://doi.org/10.1007/978-3-642-34410-7_14
Published:
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-34409-1
Online ISBN: 978-3-642-34410-7
eBook Packages: Springer Protocols