Comparison of DNA and RNA, and Cultivation Approaches for the Recovery of Terrestrial and Aquatic Fungi from Environmental Samples

• Published in: Current microbiology Vol. 66; no. 2; pp. 185 - 191
• Main Authors: Rao, Subramanya, Hyde, Kevin D, Pointing, Stephen B
• Format: Journal Article
• Language: English
• Published: New York Springer-Verlag 01.02.2013; Springer Nature B.V
• Subjects: Anguillospora; Aquatic fungi; Ascomycota; Basidiomycota; Biodiversity; Biomedical and Life Sciences; Biotechnology; classification; Cultivation; Deoxyribonucleic acid; DNA; DNA libraries; DNA, Fungal; DNA, Fungal - genetics; Environmental Microbiology; forests; freshwater; Fungi; Fungi - classification; Fungi - isolation & purification; genetics; isolation & purification; Life Sciences; Metagenomics; Metagenomics - methods; methods; Microbiological Techniques; Microbiological Techniques - methods; Microbiology; Molecular Sequence Data; phylogeny; Ribonucleic acid; RNA; RNA libraries; RNA, Fungal; RNA, Fungal - genetics; Sequence Analysis, DNA; soil; Terminal Restriction Fragment Length Polymorphism; Trichoderma; Clone Library; Fungal Community; Internal Transcribe Spacer
• ISSN: 0343-8651; 1432-0991; 1432-0991
• DOI: 10.1007/s00284-012-0256-7

Estimates of fungal biodiversity from environmental samples are all subject to bias. Major issues are that the commonly adopted cultivation-based approaches are suitable for taxa which grow readily under laboratory conditions, while the DNA-based approaches provide more reliable estimates, but do not indicate whether taxa are metabolically active. In this study, we have evaluated these approaches to estimate the fungal diversity in soil and freshwater samples from a subtropical forest, and compared these to RNA-based culture-independent approach intended to indicate the metabolically active fungal assemblage. In both soil and freshwater samples, the dominant taxon recovered by all three approaches was the same (Anguillospora furtiva). This taxon was cultivable from all samples and comprised 85–86 % DNA libraries and 90–91 % RNA libraries. The remaining taxa were phylogenetically diverse and spanned the Ascomycota, Basidiomycota, and Fungi incertae sedis. Their recovery was not consistent among the three approaches used and suggests that less abundant members of the assemblage may be subjected to greater bias when diversity estimates employ a single approach.