Methods for identifying and measuring the diversity of ectomycorrhizal fungi

Abstract

Abstract Mycorrhiza is a mutualistic symbiosis between some plant species and a diverse group of soil fungi. Mycorrhizal symbiosis is categorized into discrete types based on the structural differences and the taxonomic position of involved plants and fungi. The main types of mycorrhiza include arbuscular, ericoid, orchid, monotropoid and ectomycorrhiza, the latter being the main focus of this review. Identifying ectomycorrhizal fungi (EMF) is crucial for understanding the ecology and preservation of rare and endangered plants, fungi and habitats. Thus, since the discovery of ectomycorrhiza, new identification methods have been constantly developed. This review tracks the history of EMF identification methods, presents their limitations and aims to discern the frontier of the field. The early methods were based on the morphology and anatomy of EMF, which allowed ectomycorrhizae formed by different EMF to be distinguished. Recognizing the EMF species that formed them, however, was difficult. The introduction of molecular methods that analysed taxon-specific DNA barcodes was a breakthrough in EMF identification, and the internal transcribed spacer gene was adopted as a routine fungal barcoding sequence. Identifying EMF from randomly sampled roots by morphology or polymerase chain reaction (PCR)-based methods results in rare EMF taxa being missed and underreported. This is addressed by bulk sampling combined with environmental DNA metabarcoding methods, which, in turn, yield a lower resolution of taxonomic identification. Most EMF identification methods incorporate PCR reactions, which are biased against some groups of EMF; developing PCR-free molecular methods would constitute a significant advancement. As the traditional concept of species is challenging for fungi, studying EMF functional rather than taxonomic diversity appears to be promising.