Progress in molecular and morphological taxon discovery in Fungi and options for formal classification of environmental sequences

Fungal taxonomy seeks to discover, describe, and classify all species of Fungi and provide tools for their identification. About 100,000 fungal species have been described so far, but it has been estimated that there may be from 1.5 to 5.1 million extant fungal species. Over the last decade, about 1200 new species of Fungi have been described in each year. At that rate, it may take up to 4000 y to describe all species of Fungi using current specimen-based approaches. At the same time, the number of molecular operational taxonomic units (MOTUs) discovered in ecological surveys has been increasing dramatically. We analyzed ribosomal RNA internal transcribed spacer (ITS) sequences in the GenBank nucleotide database and classified them as “environmental” or “specimen-based”. We obtained 91,225 sequences, of which 30,217 (33 %) were of environmental origin. Clustering at an average 93 % identity in extracted ITS1 and ITS2 sequences yielded 16,969 clusters, including 6230 (37 %) clusters with only environmental sequences, and 2223 (13 %) clusters with both environmental and specimen-based sequences. In 2008 and 2009, the number of purely environmental clusters deposited in GenBank exceeded the number of species described based on specimens, and this does not include the huge number of unnamed MOTUs discovered in pyrosequencing studies. To enable communication about fungal diversity, there is a pressing need to develop classification systems based on environmental sequences. Assigning Latin binomials to MOTUs would promote their integration with specimen-based taxonomic databases, whereas the use of numerical codes for MOTUs would perpetuate a disconnect with the taxonomic literature. MOTUs could be formally named under the existing International Code of Botanical Nomenclature if the concept of a nomenclatural type was expanded to include environmental samples or illustrations of sequence chromatograms (or alignments). Alternatively, a “candidate species” category could be created for Fungi, based on the candidatus taxon status employed by microbiologists.