Shotgun metagenomic sequencing of pasture soil
Soil samples were collected in June, August, and October from 12 agricultural paddocks, which were equally split into four different grazing treatments---cattle, sheep, swine, or multi-species. Each sample consisted of soil cores 2.5 cm in diameter by 10 cm deep that were collected from five locations in a roughly W shape within each paddock using sterilized stainless steel soil probes. Samples were homogenized and sieved with a 2 mm sieve prior to aliquoting two 0.25 g subsamples (technical replicates) that were identically prepped for sequencing. DNA was extracted in triplicate using QIAGEN DNeasy PowerLyzer PowerSoil Kit and then pooled for each technical replicate. Libraries were prepared using Nextera XT DNA Library Preparation Kit and submitted to University of Oregon Genomics & Cell Characterization Core Facility for shallow shotgun metagenomic sequencing.