Data processing can mask biology: towards better reporting of fungal barcoding data?

Fungal barcoding, that is the use of genetic markers to identify fungal species, has contributed enormously to the rise of mycorrhizal research in the last decade (van der Heijden et al., 2015) because it allows quick and easy en masse identification of species or higher taxonomic ranks and grouping of sequences into entities; this speeds up ecological analyses and the discovery of new species (Hibbett et al., 2011; Herr et al., 2015). Marker sequences allow the delineation of operational taxonomic units (OTUs) on the basis of sequence similarities (Lindahl et al., 2013). Specific cases of OTUs delimited across datasets are internal transcribed spacer (ITS)-based fungal Species Hypotheses (SH; K~oljalg et al., 2013) and small subunit (SSU) rRNA gene–based Glomeromycota Virtual Taxa (VT; € Opik et al., 2014), which allow a stable naming and databases of sequence-associated ecological metadata (SH; UNITE, K~oljalg et al., 2013; VT; MaarjAM, € Opik et al., 2010). Such OTUs allow us to answer ecological questions, such as the exploration of diversity patterns between habitats, hosts or experimental treatments (Merckx et al., 2012; Ohsowski et al., 2014), and to describe distribution ranges and large-scale patterns (Tedersoo et al., 2014; Davison et al., 2015). Moreover, the phylogenetic signal conveyed by the sequences can detect phylogenetic diversity patterns and identify phylogenetic signals in functional traits of organisms and communities (Martos et al., 2012;Grilli et al., 2015).Mycorrhizal fungal research often uses the nuclear ribosomal ITS (Box 1), now the most acknowledged taxonomic barcode for fungi (Schoch et al., 2012), especially in ectomycorrhizal (ECM) models. Molecular ecological research on Glomeromycota, the arbuscular mycorrhizal (AM) fungi, uses a broader range of markers, among which the nuclear SSU rRNA gene is most often used in community surveys, whilst the ITS and large subunit (LSU) rRNA gene are more common in taxonomic research into Glomeromycota (€ Opik et al., 2014). Alternative markers, such as the beta-tubulin gene, COI or RPB1 genes, are also being tested (reviewed in € Opik et al., 2014 andHart et al., 2015). While the data processing that delivers the final sequence in the International Nucleotide Sequence Database (INSD) is often well