A study published in MicrobiomeJ reveals the unprecedented spatial and temporal diversity in viral community composition and activity across root, rhizosphere soil, and bulk soil compartments.
, allowing for four replicate samples of the two crop management practices. Two crop growth strategies of oilseed rape were adopted: continuous cropping, whereby oilseed rape was grown for three consecutive years; and virgin rotation, whereby oilseed rape was grown following two preceding years of winter wheat . The soil was a sandy-loam of the Wick series, with 73% sand, 12% silt, 14% clay, a pH of 6.5, and organic carbon content of 0.
DNA extractions for total metagenomes and size-fractionated metagenomes were only performed on soil samples from the second time point . For these samples, a total DNA was eluted from the same column as the RNA extractions using the RNeasy PowerSoil DNA Elution Kit , according to the manufacturer’s instructions. The DNA was quantified using Qubit DNA HS and its purity profile checked using a Nanodrop 2.
Size-fractionated DNA for DNA viromes was extracted from ~ 5 g of soil. Briefly, soil was mixed into a total volume of 50-mL of sterile PBS and shaken vigorously for ~ 5 min, before being gently agitated on a tube roller for 1 h. Following centrifugation at 500 g to pellet large material, the supernatant was removed, sequentially filtered through 0.44 μm and 0.22 μm pore size filters and concentrated using Amicon 100 kDa columns as previously described.
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