Abstract
DNA fingerprints are commonly generated for a genetic characterisation of microbial populations or communities. The respective techniques are based either on hybridisation or on polymerase chain reaction (PCR). We present an overview and detailed protocols of the most frequently DNA fingerprinting techniques currently used in microbial ecology, including isolation of respective target sequences, set-ups of PCR reactions, and ways of detecting markers for generating fingerprints.
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References
Head IM, Saunders JR, Pickup RW (1998) Microbial evolution, diversity, and ecology: a decade of ribosomal RNA analysis of uncultivated microorganisms. Microb Ecol 35:1–21
White TJ, Bruns T, Lee S et al (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ (eds) PCR protocols: a guide to methods and applications. Academic, San Diego, pp 315–322
Zinger L, Gury J, Alibeu O et al (2008) CE-SSCP and CE-FLA, simple and high-throughput alternatives for fungal diversity studies. J Microbiol Methods 72:42–53
Glass NL, Donaldson GC (1995) Development of primer sets designed for use with the PCR to amplify conserved genes from filamentous Ascomycetes. Appl Environ Microbiol 61:1323–1330
Devi KU, Reineke A, Rao UC et al (2007) AFLP and single-strand conformation polymorphism studies of recombination in the entomopathogenic fungus Nomuraea rileyi. Mycol Res 111:716–725
Weisburg WG, Barns SM, Pelletier DA et al (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697–703
Sun L, Qiu F, Zhang X et al (2007) Endophytic bacterial diversity in rice (Oryza sativa L.) roots estimated by 16S rDNA sequence analysis. Microb Ecol 55:415–424
Medlin L, Elwood HJ, Stickel S et al (1988) The characterization of enzymatically amplified eukaryotic 16S-like rRNA-coding regions. Gene 71:491–499
Stoeck T, Epstein S (2003) Novel eukaryotic lineages inferred from small-subunit rRNA analyses of oxygen-depleted marine environments. Appl Environ Microbiol 69:2657–2663
Borneman J, Hartin RJ (2000) PCR primers that amplify fungal rRNA genes from environmental samples. Appl Environ Microbiol 66:4356–4360
Edel-Hermann W, Dreumont C, Perez-Piqueres A et al (2004) Terminal restriction fragment length polymorphism analysis of ribosomal RNA genes to assess changes in fungal community structure in soils. FEMS Microbiol Ecol 47:397–404
Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley, West Sussex, pp 115–175
Dees PM, Ghiorse WC (2001) Microbial diversity in hot synthetic compost as revealed by PCR-amplified rRNA sequences from cultivated isolates and extracted DNA. FEMS Microbiol Ecol 35:207–216
Schütte UME, Abdo Z, Bent SJ et al (2008) Advances in the use of terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes to characterize microbial communities. Appl Microbiol Biotechnol 80:365–380
Gothwal RK, Nigam VK, Mohan MK et al (2007) Extraction of bulk DNA from Thar Desert soils for optimization of PCR-DGGE based microbial community analysis. Electron J Biotechnol 10:400–408
Muyzer G, de Waal EC, Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction amplified genes coding for 16S rRNA. Appl Environ Microbiol 59:695–700
Welsh J, McClelland M (1990) Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res 18:7213–7218
Williams JGK, Kubelik AR, Livak KJ et al (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 18:6531–6535
Meunier JR, Grimont PAD (1993) Factors affecting reproducibility of random amplified polymorphic DNA fingerprinting. Res Microbiol 144:373–379
Muralidharan K, Wakeland EK (1993) Concentration of primer and template qualitatively affects products in random-amplified polymorphic DNA PCR. Biotechniques 14:362–364
Schierwater B, Ender A (1993) Different thermostable DNA polymerases may amplify different RAPD products. Nucleic Acids Res 21:4647–4648
Vos P, Hogers R, Bleeker M et al (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414
Meudt HM, Clark AC (2006) Almost forgotten or latest practice? AFLP applications, analyses and advances. Trends Plant Sci 12:106–117
Mueller UG, Wolfenbarger LL (1999) AFLP genotyping and fingerprinting. Trends Ecol Evol 14:389–394
Savelkoul PHM, Aarts HJM, de Haas J et al (1999) Amplified-fragment length polymorphism analysis: the state of an art. J Clin Microbiol 37:3083–3091
Goldstein DB, Schlötterer C (1999) Microsatellites: evolution and applications. Oxford University Press, Oxford
MacGregor BJ, Amann R (2006) Single-stranded conformational polymorphism for separation of mixed rRNAs (rRNA-SSCP), a new method for profiling microbial communities. Syst Appl Microbiol 29:661–670
Oto M, Suda W, Shinoyama H (2006) 16S rRNA gene-based analysis of microbial community by whole-genome amplification and minigel-single-strand conformation polymorphism technique. J Biosci Bioeng 102:482–484
Sunnucks P, Wilson ACC, Beheregaray LB et al (2000) SSCP is not so difficult: the application and utility of single-strand conformation polymorphism in evolutionary biology and molecular ecology. Mol Ecol 9:1699–1710
Zinger L, Gury J, Giraud F et al (2007) Improvements of polymerase chain reaction and capillary electrophoresis single-strand conformation polymorphism methods in microbial ecology: toward a high-throughput method for microbial diversity studies in soil. Microb Ecol 54:203–216
Gich FB, Amer E, Figueras JB et al (2000) Assessment of microbial community structure changes by amplified ribosomal DNA restriction analysis ARDRA. Int Microbiol 3:103–106
Wu XY, Walker MJ, Hornitzky M et al (2006) Development of a group-specific PCR combined with ARDRA for the identification of Bacillus species of environmental significance. J Microbiol Methods 64:107–119
Liu WT, Marsh TL, Cheng H et al (1997) Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl Environ Microbiol 63:4516–4522
de Souza FA, Kowalchuk GA, Leeflang P et al (2004) PCR-denaturing gradient gel electrophoresis profiling of inter- and intraspecies 18S rRNA gene sequence heterogeneity is an accurate and sensitive method to assess species diversity of arbuscular mycorrhizal fungi of the genus Gigaspora. Appl Environ Microbiol 70:1413–1424
Etscheid M, Riesner D (1998) TGGE and DGGE. In: Karp A, Isaac PG, Ingram DS (eds) Molecular tools for screening biodiversity: plants and animals. Chapman and Hall, London, pp 135–151
Sambrook J, Russel DW (2001) Molecular cloning: a laboratory manual, vol 3. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
Zane L, Bargelloni L, Patarnello T (2002) Strategies for microsatellite isolation: a review. Mol Ecol 11:1–16
Hamilton MB, Pincus EL, Di Fiore A et al (1999) Universal linker and ligation procedures for construction of genomic DNA libraries enriched for microsatellites. Biotechniques 27:500–507
Nunome T, Negoro S, Miyatake K et al (2006) Protocol for the construction of microsatellite enriched genomic library. Plant Mol Biol Rep 24:305–312
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Reineke, A., Devi, K.U. (2013). Genetic Fingerprinting Techniques for Molecular Characterisation of Microbes. 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_4
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DOI: https://doi.org/10.1007/978-3-642-34410-7_4
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