Metagenome of soil samples from field experiment with cover crops
Amplicon-based metagenomic samples. DNA and RNA are extracted and RNA is retrotranscribed to cDNA. Field was sampled at 4 time points: T0 = during pre-crops = 4 species were grown in the field prior to the beginning of the field experiment with cover crops. Bulk and rhizosphere of these pre-crops are sampled. T1 = during cover crops growth, 2.5 months after sowing. The rhizosphere of cover crops and bulk soil from the unplanted (fallow control) is sampled. T2 = before planting the next cash crop, potato, and 4 months after the termination and incorporation of cover crops, bulk soil was collected with an auger. T3= during potato growth, 5 months after potato seedling planting. Bulk soil was collected with an auger. Each sample has sequences coming from 4 amplicons amplified with 4 primer combinations:515F/806R (Caporaso et al., 2012) targeting the V4 region of 16S (bacteria) - FW: GTGCCAGCMGCCGCGGTAA, RV: GGACTACHVGGGTWTCTAAT ,1391F/EukBr (Medlin et al., 1988; Lane, 1991) to amplify the V9 region of 18S (protists) - FW:GTACACACCGCCCGTC, RV: TGATCCTTCTGCAGGTTCACCTACFF 390.1 /FR1 (Verbruggen et al., 2012) targeting the V7-V8 region of 18S for fungi - FW: CGWTAACGAACGAGACCT, RV: AICCATTCAATCGGTAITgITS7/ITS4ngs (Tedersoo et al., 2018) targeting the ITS2 region of fungi - FW: GTGARTCATCGARTCTTTG, RV: TCCTSCGCTTATTGATATGC.