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Application of an automated ribosomal intergenic spacer analysis database for identification of cultured Antarctic fungi

Published online by Cambridge University Press:  06 November 2012

Caleb Slemmons ,
Gregory Johnson  and
Laurie B. Connell
Caleb Slemmons
Affiliation:
University of Maine, School of Marine Sciences, 5735 Hitchner Hall, Orono, ME 04468, USA
Gregory Johnson
Affiliation:
University of Maine, School of Marine Sciences, 5735 Hitchner Hall, Orono, ME 04468, USA
Laurie B. Connell*
Affiliation:
University of Maine, School of Marine Sciences, 5735 Hitchner Hall, Orono, ME 04468, USA
*
*corresponding author: laurie.connell@umit.maine.edu
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Abstract

We utilized an automated ribosomal intergenic spacer analysis (ARISA) method as a more rapid alternative to classical morphological/nutritional identification and a less expensive alternative to sequencing for identification and grouping of isolates in culture-based fungal abundance studies. This method is well suited for the study of culturable Antarctic soil fungal communities where both abundance and diversity are relatively low. We optimized template concentration and verified the effect of primer selection from eight commonly used fungal polymerase chain reaction primers on ARISA chromatographs for 46 fungal species commonly isolated from south Victoria Land. A database of Antarctic fungal electropherograms was produced containing each of the species and was used as the first step in a tiered system for species identification. In addition, isolates containing more than one species were identified, allowing isolates not in the database to be sequenced for further analysis. This method unambiguously identified 78% of the fungal taxa in this study and we were able to rapidly determine which isolates should be subjected to further analysis by DNA sequencing. Using this approach, the cost of analysis for abundance studies can be greatly reduced compared to DNA sequencing of each isolate.

Keywords

ARISAARISA-AFFfungal abundanceMcMurdo Dry Valleyssoil microbial community
Type
Biological Sciences
Information
Antarctic Science , Volume 25 , Issue 1 , February 2013 , pp. 44 - 50
Copyright
Copyright © Antarctic Science Ltd 2012

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