Comparative metabarcoding study performed on the mock soil nematode communities, composed of DESS-preserved and freshly extracted nematodes

Amplicon sequencing-based community analyses offer an attractive alternative to microscopy-based nematode identification approaches where expert knowledge is required. However, the potential of analysing DESS-preserved samples in metabarcoding studies remained underexplored. Moreover, previous studies often omitted certain representative groups of nematodes. To fill this gap, a nematode metabarcoding experiment was conducted on two types of mock community sample sets: DESS pretreated and freshly acquired, both of them covering taxa of various feeding strategies. Additionally, the performance of two, 18S and 28S rDNA-based (the D2A/D2 primer pair for the first time in such studies), polymerase chain reaction primer combinations, and the efficiency of two DNA isolation methods were compared. The results of this study show that the DESS preservative can be successfully used in qualitative metabarcoding studies of soil nematode communities. All 24, initially morphologically identified, nematode taxa were recovered from the DESS-treated and fresh nematode samples, using both rDNA primer combinations and both DNA isolation methods tested. Each of the two isolation methods used had stronger effect on read recovery of slightly different taxa.