title: Development of a molecular approach to describe the composition of Trichoderma communities.
abstract: Trichoderma and its teleomorphic stage Hypocrea play a key role for ecosystem functioning in terrestrial habitats. However, little is known about the ecology of the fungus. In this study we developed a novel Trichoderma-specific primer pair for diversity analysis. Based on a broad range master alignment, specific Trichoderma primers (ITSTrF/ITSTrR) were designed that comprise an approximate 650bp fragment of the internal transcribed spacer region from all taxonomic clades of the genus Trichoderma. This amplicon is suitable for identification with TrichoKey and TrichoBLAST. Moreover, this primer system was successfully applied to study the Trichoderma communities in the rhizosphere of different potato genotypes grown at two field sites in Germany. Cloning and sequencing confirmed the specificity of the primer and revealed a site-dependent Trichoderma composition. Based on the new primer system a semi-nested approach was used to generate amplicons suitable for denaturing gradient gel electrophoresis (DGGE) analysis and applied to analyse Trichoderma communities in the rhizosphere of potatoes. High field heterogeneity of Trichoderma communities was revealed by both DGGE. Furthermore, qPCR showed significantly different Trichoderma copy numbers between the sites.
authors.affiliation: Environmental Biotechnology, Graz University of Technology, Petersgasse 12, A-8010 Graz, Austria.
authors.forename: Remo
authors.initials: R
authors.lastname: Meincke
authors.forename: Nicole
authors.initials: N
authors.lastname: Weinert
authors.forename: Viviane
authors.initials: V
authors.lastname: Radl
authors.forename: Michael
authors.initials: M
authors.lastname: Schloter
authors.forename: Kornelia
authors.initials: K
authors.lastname: Smalla
authors.forename: Gabriele
authors.initials: G
authors.lastname: Berg
mesh_terms: D044822:Biodiversity; D016172:DNA Fingerprinting / Q000379:methods*; D017931:DNA Primers / Q000235:genetics; D004271:DNA, Fungal / Q000235:genetics; D008969:Molecular Sequence Data; D016533:Mycological Typing Techniques / Q000379:methods*; D010802:Phylogeny; D012988:Soil Microbiology; D011198:Solanum tuberosum / Q000382:microbiology; D014242:Trichoderma / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*
chemical_list: D017931:DNA Primers; D004271:DNA, Fungal