Suitable DNA barcode for DNA metabarcoding
Whether a soil sample could be traced back to its original source localities depends on the suitable DNA barcode to be used. Although there is incompatibility between the universality of primers and the resolution of barcodes for higher plants, the universality of primers is more important for DNA metabarcoding of lower plants in soil samples because almost all DNA barcodes are variable enough to resolve most known taxonomic units (Liu et al., 2020b). Lower plants have shorter lifetime, evolve much more quickly and accumulate more genetic variations in their genomes than higher plants. However, lower plants are the least known creatures to taxonomists and quite large of them can only be identified to genus or even family levels. For example,rbcL is one of the least variable gene of seed plants, but its variability in lower plants is much higher (Dong et al., 2014) and can serve as a DNA barcode for lower plants such as diatoms (Liu et al., 2020a).
Another advantage of using rbcL as a DNA barcode for lower plants is that this gene locates in plastid genome, implying that contaminations of plastid genome free organisms bring no trouble to the data analyses. There is usually a vast range of microorganisms in soil samples, for example, insects, fungi, bacteria, etc.. When using DNA barcodes from nuclear genome such as 18S, amplification of these organisms is usually inevitable, which needs quite large experimental and analysis resources.