Office of Biological and Environmental Research Weekly Report

June 9, 2008

Genomics:GTL Researchers Use Metagenomics to Tap Environmental Diversity of Viruses. In a study published in the May 23^rd 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.

Media Interest: None

Contact: Dan Drell, SC-23.2, (301) 903-4742

Learning from Biology: Special Issue of Geobiology Outlines the Implications of Understanding Microbial Metabolism for Environmental Applications and Bioenergy Production. Numerous researchers funded by the DOE Office of Science (SC) contributed to a special issue of Geobiology dedicated to the memory of Terry Beveridge, a world-renowned geomicrobiologist and long-time SC grantee. This special issue is a review of the current state-of-the-science in understanding microbe-metal interactions and a fitting tribute to a respected colleague whose scientific breadth spanned this entire area of science. Advances made over the last few years in understanding microbial metabolism at the microbe-mineral interface are detailed in this special issue. Several groups of bacteria are capable of respiring (breathing) solid phase materials that reside outside the cell. How cells accomplish this feat is a topic under intensive investigation within SC. Microbes with the ability to reduce inorganic materials extracellularly also reduce electrodes in microbial fuel cells, produce soluble organics with electrochemical properties, and influence mineral precipitation in novel ways. These unique traits have implications for understanding the processes that influence contaminant transport, bioenergy production, microbial biofilm formation, intercellular communication and biomineral production.

Reference: Geobiology, Vol 6(3), June 2008.

Media Interest: No

Contact: Robert T. Anderson, SC-23.4, (301) 903-5549