Research Letters

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

Etienne Slabbert, Carel J. van Heerden, Karin Jacobs
South African Journal of Science | Vol 106, No 7/8 | a329 | DOI: https://doi.org/10.4102/sajs.v106i7/8.329 | © 2010 Etienne Slabbert, Carel J. van Heerden, Karin Jacobs | This work is licensed under CC Attribution 4.0
Submitted: 23 June 2010 | Published: 04 August 2010

About the author(s)

Etienne Slabbert, Stellenbosch University, South Africa
Carel J. van Heerden, Stellenbosch University, South Africa
Karin Jacobs, Stellenbosch University, South Africa

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.

Keywords

automated ribosomal intergenic spacer analysis; binning; fungal ecology; fynbos fungi; molecular community fingerprinting; soil fungi

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