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Optimisation of automated ribosomal intergenic spacer analysis for the estimation of microbial diversity in fynbos soil

By Karin Jacobs, Carel J. van Heerden and Etienne Slabbert

Abstract

Automated ribosomal intergenic spacer analysis (ARISA) has become a commonly used molecular technique for the study of microbial populations in environmental samples. The reproducibility and accuracy of ARISA, with and without the polymerase chain reaction (PCR) are important aspects that influence the results and effectiveness of these techniques. We used the primer set ITS4/ITS5 for ARISA to assess the fungal community composition of two sites situated in the Sand Fynbos. The primer set proved to deliver reproducible ARISA profiles of the fungal community composition with little variation observed between ARISA-PCRs. Variation that occurred in a sample due to repeated DNA extraction is expected for ecological studies. This reproducibility made ARISA a useful tool for the assessment and comparison of diversity in ecological samples. In this paper, we also offered particular suggestions concerning the binning strategy for the analysis of ARISA profiles

Topics: automated ribosomal intergenic spacer analysis, binning, fungal ecology, fynbos fungi, molecular community fingerprinting, soil fungi, General Works, A, DOAJ:Multidisciplinary, DOAJ:General Works, Science, Q, Science (General), Q1-390, Social Sciences, H, Social sciences (General), H1-99
Publisher: Academy of Science of South Africa
Year: 2010
DOI identifier: 10.4102/sajs.v106i7
OAI identifier: oai:doaj.org/article:3f351a3aad994776b2e357b1dd562b34
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