A relatively novel alternative to traditional qPCR is digital PCR (dPCR) which requires no external standard for quantification, offers higher precision, and is relatively unaffected by the presence of PCR inhibitors. This represents a tremendous advantage when working with nucleic acid extracts from soil \citep{Dong_2015}. However, like standard qPCR, the efficiency of this method is affected by the degeneracy of the primers, which means particular care must be taken during primer design (see section 3.1). In addition, both dPCR and qPCR are limited in terms of absolute quantification of the fungal ITS gene due to the hypervariable target region and its variable-length \citep{Nilsson2019}.
A major advantage of both quantitative PCR approaches is the possibility of using the same DNA extracts as for the community profiling without additional sample processing that would be required for other methods (see sections 4.2.2- 4.2.4). Consequently, quantitative PCR approaches have been used successfully to address the compositionality of sequencing data and can aid in the interpretation of microbial community data in soil (e.g., \citealt{Tkacz_2018,Zemb2020,Vandeputte2017,Kleyer_2017}) .