title: A new cultivation independent approach to detect and monitor common Trichoderma species in soils.
abstract: A set of primers was developed for the detection, identification and quantification of common Trichoderma species in soil samples. Based on a broad range master alignment primers were derived to amplify an approximate 540 bp fragment comprising the internal transcribed spacer region 1 (ITS 1), 5.8S rDNA and internal transcribed spacer region 2 (ITS 2) from all taxonomic Clades of the genus Trichoderma. The primer set was applied to test strains as well as community DNA isolated from arable and forest soil. For all tested isolates the corresponding internal transcribed spacer regions of Trichoderma spp. strains were amplified, but none of non-Trichoderma origin. PCR with community DNA from soil yielded products of the expected size. Analysis of a clone library established for an arable site showed that all amplified sequences originated exclusively from Trichoderma species mainly being representatives of the Clades Hamatum, Harzianum and Pachybasioides and comprising most of the species known for biocontrol ability. In a realtime PCR approach the primer set uTf/uTr also proved to be a suitable system to quantify DNA of Trichoderma spp. in soils.
authors.affiliation: GSF-National Research Center for Environment and Health, Institute of Soil Ecology, Ingolstädter Landstrasse 1, 85758 Neuherberg, Germany.
authors.forename: Alexandra
authors.initials: A
authors.lastname: Hagn
authors.forename: Stefanie
authors.initials: S
authors.lastname: Wallisch
authors.forename: Viviane
authors.initials: V
authors.lastname: Radl
authors.forename: Jean
authors.initials: J
authors.lastname: Charles Munch
authors.forename: Michael
authors.initials: M
authors.lastname: Schloter
mesh_terms: D001483:Base Sequence; D017931:DNA Primers / Q000378:metabolism; D004271:DNA, Fungal / Q000378:metabolism; D021903:DNA, Ribosomal Spacer / Q000378:metabolism; D008969:Molecular Sequence Data; D016533:Mycological Typing Techniques / Q000379:methods*; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D012987:Soil; D012988:Soil Microbiology; D014242:Trichoderma / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*
chemical_list: D017931:DNA Primers; D004271:DNA, Fungal; D021903:DNA, Ribosomal Spacer; D012987:Soil