BioEd Online

A facility built to do some of the heavy-duty processing for the human genome initiative is now cracking into the genomes of microorganisms; not as individuals, but en masse.

Researchers hope that the work will uncover useful enzymes from bacteria that could be put to work in environmentally friendly applications. The bugs that help termites to digest wood, for example, could hopefully yield a formula for turning waste plants into green ethanol fuels for cars.

The US Department of Energy's Joint Genome Institute is "a factory-like setting" that runs 24 hours a day and seven days a week, says director Eddie Rubin. These days it is engaged primarily in environmental genomics, or metagenomics, where a whole world of microorganisms is sequenced at once.

The samples being probed include test tubes full of soil from a Minnesota farm, the microbial growth on deep-sea whale bones, and waters from the upper layer of the Saragossa Sea; samples from this last location were collected by science's best-known yachtsman and genome pioneer, Craig Venter.

Genomes are usually assembled by sequencing small genome sections and then pinning together overlapping portions. But environments such as soil and ocean water are so chock-a-block with microscopic life that it would take an immense amount of sequencing to piece it all together - far more than can be achieved, says Rubin.

So the units are looked at in terms of what they do, and are sorted by function rather than by which organism they belong to. They may be sorted based on whether or not they can photosynthesize, break down cellulose, or deal with sodium, for example. The result is a picture of the kinds of genes that certain environments call for.

Natural talent

Rubin is bringing this approach to the search for clean automotive fuel, he told gatherers at the American Association for the Advancement of Science meeting in St Louis, Missouri on 17 February.

Researchers are keen to make fuel from the waste portions of plants, such as corn husks or switchgrass, which President Bush mentioned in his recent 'state of the union' speech. But turning cellulose to sugar, which in turn can be fermented to fuel, is a difficult process.

Termites, however, are naturally talented in this department, thanks to the community of microbes living in their hindgut. Sequencing work on these bacteria has already turned up several promising genes that could code for wood-digesting enzymes. These could be put to work in large industrial vats, or, more intriguingly, stitched into the DNA of switchgrass to create self-digesting plants.

"These organisms have spent eons getting good at this. We are now able to take advantage of what evolution has worked on," says Rubin.

The termite gut project involves researchers at the California Institute of Technology in Pasadena and the San Diego-based biotech company Diversa. Other companies who are making cellulosic ethanol using different enzymes include Iogen, based in Ottawa, Canada, and Denmark's Novozymes in Bagsvaerd.

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