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

Elucidating how agricultural practices affect the soil invertebrates communities are of relevant importance; however, the impact of agricultural strategies on soil fauna is debated. In the present study, using DNA metabarcoding, the soil invertebrate communities of selected farms in the Po Plain (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 how extend are the field use (crop vs stable meadow) and the field margins affecting these communities? Soil samples were collected from organic and conventional farms in different periods of the year, covering the margin and three levels towards the centre of fields of stable meadow and barley, in 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 by R in order to address the reported 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 analysed samples. ?-diversity indices were not significantly different between the two farming strategies in terms of OTUs richness, Shannon index and Pielou's evenness. ?-diversity analyses showed a separation of the margin from the three samples of the field. To sum up, the DNA metabarcoding represented a suitable method for soil invertebrates' biodiversity estimation. The recovered communities are significantly affected by the crop and the position in the field (margin vs center). In addition, the role of the margin of the field as a reservoir is increased in the cultivated fields (barley), while in the stable meadows the interactions between the margin and the center of the field are lower.