Jane Fudyma

UC Davis

“Exploring virion, soil, and buffer physicochemical characteristics and their impacts on extractable viral DNA”

The diverse physicochemical properties of viruses and soils can control the degree of viral release from the soil matrix, potentially affecting the types of viruses recovered in viral size fraction metagenome (virome) methods. Here, I investigated how extraction buffer composition affected the types of viruses released from soil, and if this varied across three diverse soils. Results indicate that spatial distance in environment overshadows extraction buffer as the main predictor of viral community composition, implying these buffers are suitable for viral ecology interrogation.


Soils have complex physicochemical properties that vary in relative viral sorption capacities, impacting virion transport and, potentially, the types of viruses represented in viral size-fraction metagenomes. Ionic conditions, pH, and competing substrates can affect the degree of charge held by a soil and thereby the extent to which viral particles and their surface moieties sorb to soil colloids. Here I investigated how different extraction buffers (both pH adjusted and overall composition) affected the types of viruses released from the soil matrix, and if this varied across three diverse soil types. Spatial location of the collected sample (less than 1m distance), rather than extraction buffer pH, was the primary predictor of viral community composition (VCC) for all soils tested. Buffer pH did not significantly drive technical replicate VCC, yet grassland viral richness was significantly lower at pH 4.5. When testing four different buffer chemistries in wetland soil, recovered viral communities were highly similar across all buffers (89.9% vOTU similarity). Overall, results suggest that soil viral purification protocols may be surprisingly robust to differences in soil and virion chemistry.

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