An increasing number of case studies are reporting Glomeromycota molecular diversity from ecosystems worldwide. Typically, phylogroups that can be related to morphospecies and those that remain unidentified (“environmental”) are recorded. To compare such data and generalise observed patterns, the principles underlying sequence identification should be unified. Data from case studies are collected and systematized in a public database MaarjAM ( http://www.maarjam.botany.ut.ee ), which applies a unique molecular operational taxonomic unit (MOTU) nomenclature: virtual taxa (VT) are phylogenetically defined sequence groups roughly corresponding to species-level taxa. VT are based on type sequences, making them consistent in time, but they also evolve: they can be split or merged, when necessary. This system allows standardisation of original MOTU designations and, much like binomial taxonomic nomenclature, comparison and consistency between studies. Refinement of VT delimitation principles and comparability with traditional Glomeromycota taxonomy will benefit from more information about intra- vs. inter-specific nucleotide variation in Glomeromycota, sequencing of morphospecies, and resolution of issues in Glomeromycota taxonomy. As the recorded number of VT already exceeds the number of Glomeromycota morphospecies, designation of species based on DNA alone appears a necessity in the near future. Application of VT is becoming widespread, and MaarjAM database is increasingly used as a reference for environmental sequence identification. The current status and future prospects of arbuscular mycorrhizal fungi (AMF) DNA-based identification and community description are presented.
