Raw sequences and metadata of soil multitargeted metabarcoding analyses carried out within the ReCROP project

The ReCROP project monitored soil biodiversity across 11 case studies in six countries: France, Italy, Morocco, Portugal, Spain, and Tunisia. These case studies focused on three cropping systems: aromatic plant fields, maize fields, and vineyards. For the present analysis, only paired treatments with a corresponding control differing by a single management factor were selected. The implemented practices fell into three categories: (i) organic amendments, including compost or mulch application (6 treated–control pairs); (ii) cropping pattern modifications such as crop rotations, intercropping, or cover cropping (7 treated–control pairs); and (iii) bioinoculations involving bacteria and fungi applied individually or in consortia (10 treated–control pairs). In each case study, composite soil samples consisting of 20 randomly collected cores were taken from a depth of 0–10 cm using a soil core sampler, both from the treatment plots and their respective control plots. All soil samples were stored at 4 ºC and sent to NEIKER in the next few days. Once in NEIKER, soils were sieved to < 2 mm and a DNeasy PowerSoil Pro kit (Qiagen, Hilden, Germany) was used to extract the DNA in triplicate. Following extraction, DNA quantity and quality were determined using a Qubit fluorometer (Thermo Fisher Scientific) and a NanoDrop™ One spectrophotometer (Thermo Fisher Scientific), respectively. Extracted DNA samples were stored at -20 °C. A pool of the three replicates was sent for library preparation and Illumina paired sequencing (250 bp, 30K tags per sample) to Novogene (Cambridge, UK). The regions chosen for amplicon sequencing were the following: 16S rRNA (V4) 515F-806R (5´-GTGCCAGCMGCCGCGGTAA-3´, 5´-GGACTACHVGGGTWTCTAAT-3´) for prokaryotes (Apprill et al., 2015; Parada et al., 2016), ITS (ITS1) 1FF-1FR (5´-CTTGGTCATTTAGAGGAAGTAA-3´, 5´-GCTGCGTTCTTCATCGATGC-3´) for fungi (White et al., 1990), 18S rRNA (V9) 1380F-1510R (CCCTGCCHTTTGTACACAC, CCTTCYGCAGGTTCACCTAC) for protists and metazoa (Amaral-Zettler et al., 2009), COI (5-GGWACWGGWTGAACWGTWTAYCCYCC-3´, 5´- TAAACTTCAGGGTGACCAAARAAYCA-3´) for metazoa (Leray et al., 2013) and Oligo01 (5´-CAAGAAGACCCTATAGAGCTT-3´, 5´-CCTGTTATCCCTAAGGTARCT-3´) for oligochaeta (Bloor et al., 2021).