and their beneficial microbial partners deal with antagonistic microbes. Lessons will have been learned from the food crops that have been successfully cultivated over the centuries. Using metagenomic approaches, we will exploit the interplay of microbes and plants more intelligently for human benefit.
Fossil fuels are a nonrenewable natural resource. It is projected that energy demand will increase by more than 50% by 2025 (US Department of Energy 2005). The US economy depends on oil imports, so there is an interest in augmenting domestic energy production. Corn serves as the major feedstock for ethanol production, and biofuel-producing companies are using specialist microbes to convert cornstarch to ethanol, a high-octane, environmentally friendly biofuel. Cellulosic ethanol—made from such agricultural wastes as corn fiber, corn stalks, and wheat straw and other biomass, such as switchgrass and miscanthus—uses as substrates products that are not usable by humans as food. Furthermore, cellulosic materials are inexpensive, renewable, and their efficient use will reduce the cost of ethanol production. Most of the known ethanol-producing microbes are incapable of using cellulose to produce ethanol, because they lack the enzymes required to break it down. In nature, however, several microbes are equipped with arrays of enzymes that act together to release glucose from cellulose. The glucose can then be fermented to ethanol. Metagenomics will enable discovery of new cellulosic enzymes and novel microbial strategies for hydrolysis of biomass. These discoveries will lead to engineering of enzyme complexes and novel pathways for enzymatic hydrolysis of cellulose and a concomitant increase in production of biofuels from cellulosic materials.
Metagenomics will shape bioremediation in many interrelated ways. First, vastly increased understanding of how microbes form “bucket brigades” for the degradation of xenobiotic compounds will allow us to distinguish contaminated sites in which the native microbiota is competent to restore environmental health from sites in which intervention in the form of in situ bioaugmentation or intensive ex situ treatment at special facilities is needed. Second, metagenomics will facilitate sensitive monitoring of remediation activities of either sort. Third, it will identify key microbial processes and keystone species and indicate how community composition could best be complemented. Fourth, it will lead to the isolation of specific strains or consortia that could be used for such complementation. Fifth, a host of novel enzymes that might be useful in cellfree treatments of specific