Impacts of a Simulated Precipitation Event on Active Soil Viral Communities and Extracellular DNA
Grant Gogul 1,2*, G. Michael Allen 1, Jeffrey A. Kimbrel 1, Dariia Vyshenska 3, Robert Riley 3, Simon Roux 3, Rex Malmstrom 3, Emiley Eloe-Fadrosh 3, Steven J. Blazewicz 1, Jennifer Pett-Ridge 1, Joanne B. Emerson 2+, Gareth Trubl 1+
- Lawrence Livermore National Laboratory, Livermore CA
- University of California, Davis, CA
- Joint Genome Institute, Berkeley, CA
Viruses in soils can potentially impact terrestrial nutrients cycles through auxiliary metabolic genes and by lysing their hosts, releasing nutrients into the soil. The characteristics of the Mediterranean climate found in California (dry summers and wet winters) give us the opportunity to observe how viral and microbial communities are affected by seasonal changes in soil moisture. After a dry season, a precipitation event can cause a jolt of microbial activity, reawakening soil communities, and increasing the number of viral species in grassland soils. Phosphorus concentrations can also affect the number of virus particles produced during an infection, but how phosphorus concentrations affect soil viral communities is largely unknown. Current approaches to study soil viral communities only target specific types of viruses, and the viral signal is heavily occluded by microbial DNA and environmental DNA (eDNA) derived from dead microbial cells and/or extruded from living cells that persists in soils. Here we used stable isotope probing (SIP) combined with viromics to characterize the newly replicated viruses and microbes. This was achieved by creating microcosms with dry grassland soils, simulating a precipitation event by adding natural abundance water or oxygen-heavy water, then adding potassium phosphate to half of the microcosms, and sampling the microcosms weekly for three weeks (T0, 1, 2, and 3 weeks). Using our high-throughput SIP protocol, the DNA was extracted from these microcosms and separated based on density (new viruses incorporated 18O into their DNA, making it denser), and then sequenced. To comprehensively interrogate viral communities in the soil, we also extracted and sequenced the eDNA in the < 0.02 µm size fraction. We benchmarked multiple assemblers and virus detectors to identify viruses and identified 1260 unique viral populations (vOTUs). Given that we did not detect viruses in the eDNA assemblies, we mapped the eDNA reads to vOTUs and determined that less than 0.055% of the eDNA reads mapped to a vOTU. A majority of the mapped viruses (≥ 75% of viral contig length covered) in the eDNA were detected in dry soil but not after the simulated precipitation event, suggesting that viral eDNA accumulates in the soil over the dry season and is quickly utilized upon precipitation. Interrogating soil viral communities from multiple soil DNA fractions (SIP, bulk soil, eDNA) is allowing us to better understand how viruses respond to environmental changes and how virus-host dynamics could impact the carbon cycle and other terrestrial nutrient cycles.