Sequencing the genomes of microbial ecosystems could lead to better biological machines. Scientists are sequencing the genomes of entire microbial communities in the hope of uncovering new genes and organisms that can create fuel, mine metals, or clean up superfund sites. Known as metagenomics, the field relies on studying bits of DNA from a variety of organisms that live in the same place.
The standard way to identify and study the microorganisms living in a particular community is to grow them in a lab, but this is only possible with about 1 percent of microbes. However, in the past two years, faster and cheaper gene-sequencing methods have offered microbiologists a new tool with which to study the other 99 percent. Scientists can extract the DNA from, say, a drop of seawater or a sample of sludge from a sewage-treatment plant and then sequence that DNA, deriving genomic clues to all the organisms living in that environment.
Assembling the random fragments of DNA generated during sequencing can be a challenge–even impossible in some cases. Hugenholtz likens the process to trying to put together one thousand jigsaw puzzles from a single box that holds only a few pieces from each puzzle. So rather than fully assembling these genomic puzzles, scientists try to understand the individual pieces, or genes. Identifying the genes that allow the microbes in the termite gut to digest wood, for example, could lead to better biofuels. Converting cellulose in trees and grasses into the simple sugars that can be fermented into ethanol is a very energy-intensive process. “If we had better enzymatic machinery to do that, we might be better able to make sugars into ethanol,” Bristow says. “Termites are the world’s best bioconverters.”
Metagenomic researchers have already identified a number of novel cellulases–the enzymes that break down cellulose into sugar–and are now looking at the guts of other insects that digest wood, such as an anaerobic population that eats poplar chips. The end result will be a giant parts list that synthetic biologists can put together to make an ideal energy-producing organism.