Evaluating viral activity and infection dynamics during wet-up of dry grassland soils
EMSL Project ID
51641
Abstract
After months of dryness, the first heavy rainfall in Mediterranean climates drives a predictable pulse of CO2 emissions and soil microbial activity each year. Responsive microbial populations begin to grow rapidly, leading to shifts in microbiome structure over hours to days for reasons that are poorly understood. Viral activity has been proposed as a contributing factor. By infecting soil microbiota, viruses likely have substantial impacts on biogeochemical cycling processes under their hosts' control, yet the composition, activity, and temporal dynamics of viruses in terrestrial ecosystems are virtually unknown. Active bacterial and archaeal viruses have the potential to alter their hosts' metabolism during infection, shunting resources towards viral replication. Subsequently, these viruses tend to kill their hosts, resulting in cessation of host metabolic processes and the release of cellular contents into the environment. Although these processes are well established in pure culture and, to some extent, in the oceans, they have yet to be comprehensively investigated in soil.Here we will leverage a laboratory simulation of wet-up (the first annual rainfall on dry soil) to drive viral activity so that we can recognize its hallmarks and to investigate the contributions of virus-host dynamics to the complex ecological responses to soil saturation after drought. Starting with dry grassland soils from the Hopland Research and Extension Center in northern California, we will apply sterile water to 21 microcosms and track virus-host dynamics through multi-omic approaches at seven time points (pre-wetting through 14 days post-wet-up). Metatranscriptomics and metaproteomics will be performed by EMSL, using the cutting-edge Illumina NextSeq550C platform and QExactive mass spectrometer, enabling identification of the specific genes, proteins, and metabolic pathways expressed by active virus and host populations during the experiment. These measurements will give essential context to our complementary metagenomic data on virus and host population abundances, revealing which viruses are actively infecting hosts and which bacteria and archaea fall prey to viral infection.
Our specific aims are to: 1) identify multi-omic signatures of active viral replication and microbial host infection in complex soil ecosystems, and 2) explore the role of virus-host dynamics in soil microbial responses to wet-up. Outcomes will include identification of the specific hallmarks of active viral infection recognizable in metagenomic (DNA), metatranscriptomic (RNA), and metaproteomic (protein) data, along with the specific microbial populations and metabolic processes impacted by viral predation during wet-up. Results will also be leveraged to interpret ongoing field studies of diverse soils, bringing us closer to a predictive understanding of viral contributions to terrestrial microbial ecology and biogeochemical cycling.
Project Details
Project type
Exploratory Research
Start Date
2020-12-01
End Date
2022-05-31
Status
Closed
Released Data Link
Team
Principal Investigator
Team Members