Experimental evidence for viral impact on microbial community, nitrification, and denitrification in an agriculture soil

Viruses are ubiquitous, and their potential impacts on biogeochemical cycles in soil have largely been inferred from correlation evidence and virome studies. Manure has been demonstrated to affect nitrogen cycle by altering soil nutrients and microbial communities. However, the direct impacts of viruses derived from manure on microbial community, nitrification, and denitrification remained exclusive. In this study, concentrated viral extracts obtained from manure were added into an agricultural soil in varying dosages: a one-time addition of 10-fold viruses or a weekly addition of 1-fold viruses for ten weeks. The results showed that both viral extracts and manure significantly changed the microbial community compositions and structures. The effect of manure on microbial diversity was concentration-dependent, differing from the viral impact on microbial diversity in soil. Deterministic processes predominated in the assembly of microbial communities in both viral and manure treatments, with an increased contribution of deterministic processes observed after these treatments. Additionally, a high concentration (10-fold) of viruses enhanced N₂O production and reduction in soil. In the control treatment, N₂O production was driven by bacterial denitrification, fungal denitrification, and chemo-denitrification. However, bacteria became the dominant driver of N₂O production in both virus and manure treatments. Overall, experimental evidence for viral impacts on the composition and assembly of microbial community, as well as on nitrification and denitrification processes, was provided through a 70-day microcosm experiment. These findings highlight the importance of viruses in regulating the distribution and functioning of microbes in terrestrial ecosystems.