05/23/2008
Genomics:GTL Researchers Use Metagenomics to Tap Environmental Diversity of Viruses
The Science
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.
Summary
DNA was extracted from two biofilms collected within the Richmond Mine, Redding, CA. Researchers reconstructed virus and host bacterial and archaeal genome sequences from community genomic data from two natural acidophilic biofilms. Viruses were matched to their hosts by analyzing spacer sequences that occur among clustered regularly interspaced short palindromic repeats (CRISPRs) that are a hallmark of virus resistance. Virus population genomic analyses provided evidence that extensive recombination shuffles sequence motifs sufficiently to evade CRISPR spacers. Only the most recently acquired spacers match coexisting viruses, which suggests that community stability is achieved by rapid but compensatory shifts in host resistance levels and virus population structure.
BER Program Manager
Ramana Madupu
U.S. Department of Energy, Biological and Environmental Research (SC-33)
Biological Systems Science Division
[email protected]
References
Anderson, A. F. and J. Banfield. 2008. “Virus Population Dynamics and Acquired Virus Resistance in Natural Microbial Communities,” Science 320. DOI:10.1126/science.1157358.