Quantification of fungal dark matter using qPCR
Fungi are present in a wide variety of natural environments, and in the last years, various studies have shown that they are quite abundant in aquatic ecosystems. In addition, a whole new highly diverse phylum, the Cryptomycota, was discovered. Nevertheless, research on aquatic fungi and a detailed evaluation of their functions and distribution are still sparse. One of the main reasons is a limitation in reliable identification and quantification methods. To bridge part of the research gap, this study aims to implement a quantitative PCR method to detect and quantify the newly discov-ered phylum. We developed and validated a Cryptomycota-specific qPCR primer pair targeting the 5.8S region. The resulting amplicon is 102 bp long. We used different environmental samples to evaluate the primer pair, Chytrodiomycota as negative control and positive control sequences. Ob-tained amplicons were sequenced using Illumina, and the obtained ASV clustered with known Cryptomycota. The qPCR method works reliably and specifically for the quantification of Cryptomy-cota in environmental samples.