Extraction optimisation to measure viral abundance in red soils

Viruses are extremely abundant in soils and have various important ecological implications therein. The quantification and identification of soil viruses are critical for a comprehensive understanding of their abundance, diversity and ecological functions. Herein, we compared three physical dispersion methods (shaking, vortexing and sonicating) and 10 extraction buffers to determine the best protocol for virus extraction from a broad range of soils in the (sub)tropics. A 5-min sonication combined with potassium citrate (AKC) buffer (1% potassium citrate amended with 10% PBS, 5 mM EDTA and 150 mM MgSO4) treatment yielded virus-like particles (VLPs) at a yield one to two orders of magnitude greater than that achieved via other methods, as determined through epifluorescence microscopy (EFM). Using the most successful method, viral abundance in red soils ranged from 2.3 x 107 VLPs g-1 soil to 1.3 x 109 VLPs g-1 soil, with approximately two times more VLPs in paddy soils than in adjacent upland soils. VLP abundance increased with soil water content (R2 = 0.60), soil organic carbon (R2 = 0.70) and bacterial abundance (R2 = 0.69), suggesting that land use strongly affects viral abundance. This comparison clearly showed that extraction methods determine the measured viral abundance to a great extent. Based on our tests of a broad range of physical dispersion methods and chemical solutions, we concluded that a 5-min sonication combined with potassium citrate buffer treatment is the best approach for extracting VLPs from red subtropical soils.