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Comparison of taxonomic, colony morphotype and PCR-RFLP methods to characterize microfungal diversity

     U.S. Environmental Protection Agency, Office of Research and Development, National Health and Environmental Effects Research Laboratory, Western Ecology Division, 200 SW 35th Street, Corvallis, Oregon 97333

Kendall Martin
Kelly K. Donegan

     Dynamac Corp., 200 SW 35th Street, Corvallis, Oregon 97333

Jeffrey K. Stone

     Oregon State University, Department of Botany and Plant Pathology, Corvallis, Oregon 97331

Clarace G. Coleman

     National Asian Pacific Center on Aging, 1511 Third Avenue, Seattle, Washington 98101

We compared three methods for estimating fungal species diversity in soil samples. A rapid screening method based on gross colony morphological features and color reference standards was compared with traditional fungal taxonomic methods and PCR-RFLP for estimation of ecological indices of soil microfungal community composition. Normalized counts of colony morphotypes on dichloran rose bengal medium were used to estimate species richness (S) and evenness ( J) and to calculate Shannon’s diversity (H) and Simpson’s (SI) dominance indices. Isolates were obtained by dilution plating techniques from litter and soil layer samples taken from Douglas-fir forest and clear-cut areas at two locations in the Cascade Mountains. The highest correspondence (97%) was observed between taxonomic identification and RFLP patterns (32:33). Cladistic analyses of PCR-RFLP patterns indicated an 81% correspondence between RFLP patterns:colony morphotypes (33:41). A correspondence of 78% was observed between traditional taxonomic identification:colony morphotypes (32:41). Statistical analyses of ecological indices based on quantitative application of the colony morphotyping method indicated significant differences (P < 0.05) in fungal community composition between forested and clear-cut areas at the Toad Road site but not at the Falls Creek site. Comparisons of ecological indices based on traditional identification of taxa by microscopic characterization on defined culture media resulted in identical findings of statistical significance. The colony morphotyping approach is proposed as a screening method to identify potential effects of land management practices, edaphic factors and pollutants on microfungal diversity.

Key words: ecological indices, fungi, litter, soil ecology