CAREER: Leveraging soil viromics to unravel ecological patterns in complex communities

University Of California-Davis, Davis CA

Investigators

Abstract

Soil microbes cycle nutrients that sustain plants, and these microbes are susceptible to viral infection. In the oceans, viruses kill up to 40% of microbial cells daily, impacting food webs and releasing nutrients. A teaspoon of soil can harbor thousands of viral species, but the role of viruses in soil remains a mystery. Little is known about which viruses are where, when, or why. This project will investigate how soil viral communities differ over space and time. The researchers will study how water content affects viral dynamics and how soil viral diversity is maintained. This work will require computational analyses of large datasets. A new ‘Bioinformatics for Biologists’ course will provide undergraduate students with hands-on training in these skills. The course will reach transfer students and other underrepresented groups in STEM, promoting the development of a diverse STEM workforce. This project will elucidate the spatiotemporal dynamics of soil viruses at the UC Davis Jepson Prairie Natural Reserve near Davis, CA. Using viromics (metagenomics of the viral size fraction), soil viral community biogeography and successional patterns will be compared within and across two grassland habitats that experience different amounts of mixing. The mystery of viral survival in seasonally dry soils will be explored to examine the roles of viral dormancy and seed banks in maintaining soil viral diversity. First, the researchers will establish local biogeographical patterns and evaluate the distance-decay relationship for soil viral communities in two grassland habitats. Next, they will compare intra- and inter-annual viral community successional patterns over space in dispersal-limited and well-mixed soils. Finally, they will apply a suite of DNA sequencing and experimental approaches to identify viruses in the cellular and acellular fractions of dry soils. This project will also pilot an undergraduate bioinformatics course, consisting of hands-on computational analysis modules co-led by teams of postdoctoral researchers. In addition to training and research opportunities for undergraduates, the course will facilitate pedagogical training for the postdoctoral instructors. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.