As of April 28, 2022, this is the soil viromics laboratory protocol used in the Emerson group at UC Davis to generate viral DNA from a soil sample for shotgun metagenomic sequencing. By no means did we 'invent' this protocol! It is a mash-up of several previously published protocols, influenced most substantially by Göller et al. 2020, Trubl et al. 2019, Williamson et al. 2005, and, for the ultracentrifugation step, Emerson et al. 2012 (see references below). This version of the protocol appears in Santos-Medellin et al. 2022, which would be an appropriate citation if you follow the procotol precisely, but we recommend citing at least Göller et al. 2020 as well, and for any deviations, please consult and reference the original publications as appropriate.
As part of this protocols.io page, you can find the laboratory protocol (under Steps), list of supplies and reagents (under Materials), and an extensive FAQ document (downloadable PDF under Guidelines & Warnings). Please consult the FAQ document before running the protocol. If you are inclined to deviate from the protocol, please consult the FAQ document first, as we have a number of suggestions in there, as well as info about what we have and have not tried. We will update/clarify as often as we can.