Supplemental files for O'Brien et al (manuscript submitted Nov/2004) :
earlier abstract (poster presentation)
FUNGAL COMMUNITY ANALYSIS BY LARGE-SCALE SEQUENCING OF ENVIRONMENTAL SAMPLES
Heath E. O'Brien, Jeri Lynn Parrent, Jason A. Jackson, Jean-Marc Moncalvo, and Rytas Vilgalys
Department of Biology
Duke University
Durham NC 27708
We investigated the soil fungal diversity at two sites in a temperate forest with distinct vegetation differences using direct isolation of SSU and ITS rDNA by PCR and high-throughput sequencing of cloned fragments. Using a 97% ITS sequence similarity cutoff, we recovered 403 OTUs from 830 fungal sequences, as well as 108 sequences from other Eukaryotic microorganisms. Approximately equal proportions of Basidiomycota and Ascomycota sequences were present in both ITS and SSU libraries while members of other fungal phyla were present at much lower frequencies. We recovered a large number of sequences with close matches to mycorrhizal, plant pathogenic and saprophytic fungi. Major differences were observed in the taxonomic composition of communities at different soil depths, with mycorrhizal species predominating in the middle soil depths and saprophytic species more common in the litter layer. Diversity was consistently lowest in the deepest soil horizon samples. These differences in abundance of major taxonomic groups indicate that this approach is able to detect community response to environmental variables. Comparable levels of fungal diversity have been obtained with traditional specimen based collecting and culturing surveys only after much more extensive sampling. The high rate at which new OTUs are recovered even after sampling 800 sequences and the dominance of fungi in our libraries relative to other eukaryotes suggest that the abundance and diversity of fungi in forest soils may be much higher than previously appreciated.