Interspecies Metabolic Complementation in Geothermal Microbial Mats

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This research will identify and sequence the genes responsible for anaerobic oxidation of carbon monoxide and related metabolism (e.g., hydrogen formation) within natural microbial ecosystems. Bacteria and Archaea obtain their energy and carbon from a very wide variety of sources. Some microbes can use carbon monoxide (highly toxic to humans) as both an energy source and a carbon building block for producing new biomass and cells. A subset of these microbes produces hydrogen gas in connection with consuming carbon monoxide. Very few hydrogen-producing carboxydotrophs have been isolated, but there are likely many microbes not yet cultured that have genes that encode for this metabolic capability. In this research, SIGEX (Substrate Induced Gene Expression -- a novel molecular biology technique) will be used to hunt down these genes from natural populations of microbes in a remote site, the Uzon Caldera, Kamchatka. Bulk DNA will be extracted from natural and laboratory cultures of microbial mats and sediments from hot spring environments. The DNA will then be cut into short pieces, cloned into a molecular reporter construct in E. coli, and screened for presence or absence of the genes of interest. This strategy will be based on the investigators' recently obtained genome sequence of carboxydotrophs from Yellowstone and Siberian hot springs. Genes that switch on in the presence of carbon monoxide will be sequenced, and the diversity of microbes with this metabolic activity will be assessed. Many of the genes for hydrogen production are closely associated with carbon monoxide oxidation genes and will track with this screening method. Environmental chemistry will be linked to genomic potential by using microelectrodes and scanning voltammetry to measure the chemical composition of the water bathing the microbial mats. This work will be one of the first studies to employ SIGEX for finding rare but environmentally and biotechnologically important genes. It will also broaden our understanding of hydrogen production through microbial carbon monoxide oxidation. The detection of such genes and examination of the enzymes encoded by these genes may eventually pave the way for engineered biocatalysts that would mimic the efficiency of the microbes in oxidizing carbon monoxide and producing hydrogen. If carbon monoxide sensitive genes are found to be widespread, as the investigators' hypothesis states, it could indicate that carbon monoxide is a very active component of the carbon cycle in microbial ecosystems. This research will support the interdisciplinary training of a graduate student (with a molecular biology background) and a postdoctoral fellow (with a geochemistry background). The work will be conveyed to the general public through a partnership with the San Francisco Exploratorium, a world-renowned science center that links art, science, and human perception.