2 %) and 342 ITS3/4-OTUs (94.0 %) were minor with frequencies lower than 0.2 %, a frequency equivalent to 1 detection from 500 clones, reflecting the power of deep sequencing (Mardis 2008). Primer preference undoubtedly biases estimations of the species composition in a community (Bellemain et al. 2010). In this

study, up to one third of the OTUs detected using the mtLSU were assigned to bacteria, likely from the low specificity of the primers for fungi (Table 2). The mtLSU primers were designed for conserved regions of the large subunit buy Captisol rDNA of the mitochondrion, which share high similarities with bacterial ribosomal components (Kanagawa 2003). Likewise, the low efficiency

of the nrLSU-LR barcode in detecting fungal species may also have resulted from low primer specificity, as shown by the fact that ~80 % of the reads were assigned to plants instead of fungi. Even so, the nrLSU-LR was useful for identifying 17 unique genera (Table S4). Another extreme was with the mtATP6 amplification, that yielded all of the reads belonging to the Basidiomycota, 95.5 % of which were assigned to Ceratobasidium, a mycorrhizal learn more genus associated with orchids (Irwin et al. 2007). On the other hand, 83.8 % of the mtATP6 OTUs representing 0.7 % of the reads remained unidentified likely due to JPH203 insufficient information of mtATP6 sequences. All of these facts revealed high inconsistency across barcodes. Apparently, using one or few barcodes likely increases the risks of misidentifying the species composition in a microbial community, although nrITS is one of the best barcodes for fungal species discrimination (Schoch et al. 2012). Using multiple barcodes is therefore necessary and has been strongly recommended (Nilsson et al. 2008; Gazis et al. 2011). Among the barcodes utilized in this study, ITS1/2, ITS3/4, and nrLSU-U were the most competent in uncovering the diversity of the fungal community

in Phalaenopsis roots (Fig. 1), while mitochondrial markers (mtLSU and mtATP6) yielded a low alpha diversity with rarely detected genera (Tables 3 Metalloexopeptidase and 4). Species composition and ecological roles of constituent fungi within orchid roots Orchid roots represent an ecosystem that fosters a high diversity of microbial species. Noticeably, genetic barcodes identified different floristic compositions at the class level (Fig. 2) and different common species from the same root community (Table S4). For example, for various barcodes, the most common species (with percentage reads) were as follows: ITS1/2, Alternaria sp. (up to 30.4 %); ITS3/4, Penicillium sp. (37.8 %); nrLSU-LR, Trechispora farinacea (48.9 %); nrLSU-U, Trechispora sp. (39.2 %); mtLSU, Serpula sp. (64.7 %).