DNA Metabarcoding as a tool for soil’s biodiversity assessment in organic and conventional agroecosystems

Elucidating how agricultural practices affect soil invertebrate communities is of relevant importance. In the present study, using DNA metabarcoding, soil invertebrate communities of selected farms in the Po Valley (Italy) were assessed in order to address the following questions: i) is the structure of soil invertebrates’ communities different between organic and conventional farms? ii) To which extent are field use (crop vs stable meadow) and field margins affecting these communities? Soil samples were collected from organic and conventional farms in different periods of the year, covering the margins and three levels towards the centre of fields of stable meadow and barley of both farms. DNA was extracted from soil samples and a fragment of the cox1 gene amplified using three different pairs of primers; amplicons were sequenced using Illumina Miseq. Raw sequences were analysed using Qiime and ecological and statistical analyses were performed with R in order to address the above-mentioned questions. The recovered invertebrate’s communities were dominated by Arthropoda (~ 80% of the OTUs in each sample), a total of 831 OTUs (Insecta 51%, Arachnida 18% and Mollusca 14%) formed the core diversity present in all the analysed samples. α-diversity indices were not significantly different between the two farming strategies in terms of OTUs richness, Shannon index and Pielou’s evenness. β-diversity analyses showed the field margins invertebrate communities were different from the inner field communities. In conclusion, DNA metabarcoding represented a suitable method for soil invertebrates’ biodiversity estimation. The recovered communities are significantly affected by the crop and the localization in the field (margin vs center). In addition, the role of field margins as a diversity reservoir is increased in cultivated fields (barley), while in stable meadows fields, the interactions between the margins and the center of the field are lower.