Specific PGR primers to identify arbuscular mycorrhizal fungi within colonized roots

A set of PCR primers targeted at five major phylogenetic subgroups of arbuscular mycorrhizal fungi (Glomales) was designed to facilitate specific amplification of internal transcribed spacers and 18 S rRNA gene fragments from colonized roots in the absence of spores. The subgroups include the recently discovered deeply divergent lineages of Glomales, which could not be detected by previously reported PCR primers, and the former genus Sclerocystis. Restriction fragment length polymorphism patterns presented allow identification of presently known members of these groups. The resulting PCR products can be used to identify the fungal symbionts at the genus or species level by restriction digests or DNA sequencing. A novel DNA extraction method allows visual control of the analyzed roots by staining procedures after analysis by PCR.