Genomics:GTL Researchers Use Metagenomics to Tap Environmental Diversity of Viruses


In a study published in the May 23rd issue of Science, researchers led by Jill Banfield at the University of California, Berkeley, used an innovative metagenomics approach to sample the diversity of viruses present in a natural microbial community inhabiting acidic mine drainage (AMD). Viruses are highly abundant in nature and have large impacts on structure and function of microbial communities, both via predation and by mediating the exchange of genetic material among species. However, relatively few genome sequences from viruses that infect bacteria and archaea are currently available. The Banfield team took advantage of a set of short virus-derived sequences, found in many bacteria and archaea, that serves as an immune system thought to confer an ability to resist viral infection. With support from DOE’s Joint Genome Institute and Genomics:GTL program, the researchers focused on these elements in AMD biofilm DNA sequences, which allowed both the identification of, and then partial reconstruction of, sequences of viral origin. This then led to the matching of specific viruses to their AMD hosts and suggested new insights into the evolutionary arms race occurring between host defense systems and viruses in these AMD populations. This is an important and novel tool for the study of community-level interactions between viruses and their bacterial (or archaeal) hosts, which will be critical to understanding how microbial communities involved in DOE mission-relevant processes change over time and how such shifts might affect community composition and function.