Soil DNA metabarcoding: evaluating the efficiency of multiplex primer sets in recovering the soil invertebrate's community as soil quality indicators

DNA Metabarcoding was used to investigate the efficiency of two sets of primers (combinations A and B) for characterizing the soil invertebrate’s communities in different farming management systems. Soil samples were taken from three different sites in the South-West of Milan and DNA was extracted directly. PCR was applied by using 4 pairs of previously published primers targeting invertebrate’s cox1, followed by Illumina Miseq sequencing. The results showed that the presence of the most popular primer pair used in barcoding studies (LCOI490-HCO2198) has affected negatively the taxonomic assignment of OTUs, since about 67.88 % of the obtained sequences where not identified. Our analysis showed that a higher percentage of Arthropoda, Annelida, Nematoda and Rotifera &Tardigrada (41.6, 5.9, 0.8 and 1% of total reads, respectively) was obtained with primer combination B; thus this primers set can be considered a promising method to evaluate the soil arthropods community.