Table 1.
Primers used in the current study.
Figure 1.
Rarefaction curves for each of the three primer pairs used in this study: ITS1F/ITS2, ITS3/ITS4 and ITS86F/ITS4.
In these graphs, the number of samples is plotted against the rarefied number of operational taxonomic units (OTUs) that were created based on a 97% sequence similarity cut-off value.
Figure 2.
Parametrical comparison between the three primer pairs used in this study (ITS1F/ITS2, ITS3/ITS4 and ITS86F/ITS4).
A. Average number of sequences obtained after quality trimming. B. Average number of operational taxonomic units (OTUs), based on a 97% sequence similarity cut-off value. C. Average inverse Simpson index. D. Average Good's coverage. Averages were calculated across replicates (four) and samples (seven) for each primer pair. Differences at the 95% significance level are indicated with an asterisk “*”.
Figure 3.
Relative abundance for the top ten most abundant species-level operational taxonomic units (OTUs), based on a 97% sequence similarity cut-off value, obtained for each of the three primer pairs studied (ITS1F/ITS2, ITS3/ITS4 and ITS86F/ITS4).
Reads that did not result in a BLAST hit against the UNITE or INSD databases were indicated as “not applicable (NA)”. Ecological functions of OTUs are indicated between brackets behind the OTU identities (ECM: ectomycorrhizal, ERM: ericoid mycorrhizal, SAP: saprotrophic, LICH: lichenized, END: endophytic). OTUs not belonging to the top ten most abundant OTUs were pooled in the category “Remaining taxa”. OTUs that appear exclusively in a single chart are indicated in grayscale. OTUs that can be found in multiple pie charts are indicated in colour. OTU abundance scores were averaged across replicates (four) and samples (seven). A. ITS1F/ITS2. B. ITS3/ITS4. C. ITS86F/ITS4.
Figure 4.
Relative number of OTUs belonging to different fungal phyla. OTUs that could not be assigned to a phylum were grouped together under “not applicable (NA)”.
Averages were calculated across replicates (four) and samples (seven). A. ITS1F/ITS2. B. ITS3/ITS4. C. ITS86F/ITS4.
Table 2.
Average PCR amplification efficiencies obtained for twelve environmental DNA samples using quantitative real-time PCR.
Figure 5.
Phylum-level PCR bias assessed using qPCR.
Average PCR efficiencies were calculated for each phylum using 5 basidiomycetes, 5 ascomycetes, 2 glomeromycetes and 3 zygomycetes. Error bars represent standard errors. No significant differences between primer pairs and phyla were found at the 95% significance level.
Table 3.
Results of in silico testing of primers using PrimerProspector 1.0.1 [34].