Optimization of automated ribosomal intergenic spacer analysis for the estimation of microbial diversity in fynbos soil
Date
2010-08
Journal Title
Journal ISSN
Volume Title
Publisher
Academy of Science of South Africa -- ASSAF
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.
Description
The original publication is available at http://www.scielo.org.za/
Keywords
Automated ribosomal intergenic spacer analysis (ARISA), Fungal ecology, Fynbos fungi