Molecular Identification of Ectomycorrhizal Mycelium in Soil Horizons
Open Access
- 1 January 2003
- journal article
- Published by American Society for Microbiology in Applied and Environmental Microbiology
- Vol. 69 (1) , 327-333
- https://doi.org/10.1128/aem.69.1.327-333.2003
Abstract
Molecular identification techniques based on total DNA extraction provide a unique tool for identification of mycelium in soil. Using molecular identification techniques, the ectomycorrhizal (EM) fungal community under coniferous vegetation was analyzed. Soil samples were taken at different depths from four horizons of a podzol profile. A basidiomycete-specific primer pair (ITS1F-ITS4B) was used to amplify fungal internal transcribed spacer (ITS) sequences from total DNA extracts of the soil horizons. Amplified basidiomycete DNA was cloned and sequenced, and a selection of the obtained clones was analyzed phylogenetically. Based on sequence similarity, the fungal clone sequences were sorted into 25 different fungal groups, or operational taxonomic units (OTUs). Out of 25 basidiomycete OTUs, 7 OTUs showed high nucleotide homology (≥99%) with known EM fungal sequences and 16 were found exclusively in the mineral soil. The taxonomic positions of six OTUs remained unclear. OTU sequences were compared to sequences from morphotyped EM root tips collected from the same sites. Of the 25 OTUs, 10 OTUs had ≥98% sequence similarity with these EM root tip sequences. The present study demonstrates the use of molecular techniques to identify EM hyphae in various soil types. This approach differs from the conventional method of EM root tip identification and provides a novel approach to examine EM fungal communities in soil.Keywords
This publication has 39 references indexed in Scilit:
- Investigation of the influence of prescribed burning on ITS profiles of ectomycorrhizal and other soil fungi at three Australian sclerophyll forest sitesMycological Research, 2002
- Molecular approach to the characterisation of fungal communities: methods for DNA extraction, PCR amplification and DGGE analysis of painted art objectsFEMS Microbiology Letters, 2001
- Diversity of soil fungi studied by PCR-RFLP of ITSMycological Research, 2000
- Direct analysis of wood-inhabiting fungi using denaturing gradient gel electrophoresis of amplified ribosomal DNAMycological Research, 2000
- Primers based on specific rDNA-ITS sequences for PCR detection of Rhizoctonia solani, R. solani AG 2 subgroups and ecological types, and binucleate RhizoctoniaMycological Research, 2000
- General description of the sampling techniques and the sites investigated in the Fennoscandinavian podzolization projectGeoderma, 2000
- Molecular identification of co-occurring Cortinarius and Dermocybe species from southeastern Australian sclerophyll forestsMycorrhiza, 1999
- Phylogenetic relationships inDermocybeand relatedCortinariustaxa based on nuclear ribosomal DNA internal transcribed spacersCanadian Journal of Botany, 1997
- Rapid DNA extraction protocol from soil for polymerase chain reaction‐mediated amplificationJournal of Applied Bacteriology, 1993
- Mycorrhizas in ecosystemsCellular and Molecular Life Sciences, 1991