title: Molecular identification of ectomycorrhizal mycelium in soil horizons.
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 (> or = 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 > or = 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.
authors.affiliation: Subdepartment of Soil Quality, Wageningen University, NL-6700 EC Wageningen, The Netherlands. renske.landeweert@wur.nl
authors.forename: Renske
authors.initials: R
authors.lastname: Landeweert
authors.forename: Paula
authors.initials: P
authors.lastname: Leeflang
authors.forename: Thom W
authors.initials: TW
authors.lastname: Kuyper
authors.forename: Ellis
authors.initials: E
authors.lastname: Hoffland
authors.forename: Anna
authors.initials: A
authors.lastname: Rosling
authors.forename: Karel
authors.initials: K
authors.lastname: Wernars
authors.forename: Eric
authors.initials: E
authors.lastname: Smit
mesh_terms: D001487:Basidiomycota / Q000145:classification* / Q000235:genetics; D004271:DNA, Fungal / Q000032:analysis* / Q000302:isolation & purification; D008969:Molecular Sequence Data; D038821:Mycorrhizae; D010802:Phylogeny; D028222:Picea / Q000382:microbiology*; D028223:Pinus / Q000382:microbiology*; D018517:Plant Roots / Q000382:microbiology; D017422:Sequence Analysis, DNA; D012987:Soil / Q000032:analysis; D012988:Soil Microbiology
chemical_list: D004271:DNA, Fungal; D012987:Soil