Fungal community analysis by large-scale sequencing of environmental samples

HE O'Brien*, JL Parrent, JA Jackson, JM Moncalvo, R Vilgalys

*Corresponding author for this work

Research output: Contribution to journalArticle (Academic Journal)peer-review

619 Citations (Scopus)

Abstract

Fungi are an important and diverse component of soil communities, but these communities have proven difficult to study in conventional biotic surveys. We evaluated soil fungal diversity at two sites in a temperate forest using direct isolation of small-subunit and internal transcribed spacer (ITS) rRNA genes by PCR and high-throughput sequencing of cloned fragments. We identified 412 sequence types from 863 fungal ITS sequences, as well as 112 ITS sequences from other eukaryotic microorganisms. Equal proportions of Basidiomycota and Ascomycota sequences were present in both the ITS and small-subunit libraries, while members of other fungal phyla were recovered at much lower frequencies. Many sequences closely matched sequences from mycorrhizal, plant-pathogenic, and saprophytic fungi. Compositional differences were observed among samples from different soil depths, with mycorrhizal species predominating deeper in the soil profile and saprophytic species predominating in the litter layer. Richness was consistently lowest in the deepest soil horizon samples. Comparable levels of fungal richness have been observed following traditional specimen-based collecting and culturing surveys, but only after much more extensive sampling. The high rate at which new sequence types were recovered even after sampling 863 fungal ITS 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 hypothesized.

Original languageEnglish
Pages (from-to)5544-5550
Number of pages7
JournalApplied and Environmental Microbiology
Volume71
Issue number9
DOIs
Publication statusPublished - Sep 2005

Keywords

  • PINUS-MURICATA FOREST
  • ECTOMYCORRHIZAL FUNGI
  • MYCORRHIZAL FUNGI
  • SPECIES RICHNESS
  • SOIL FUNGI
  • DIVERSITY
  • EVOLUTION
  • DYNAMICS
  • GRADIENT
  • REGIONS

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