Pass the Toothpicks, Please

When it comes to digestive ability, termites have few rivals—try noshing on a two-by-four sometime. But each termite in turn depends on the 200 or so microbial species that call its digestive tract home and are found nowhere else in nature. Despite several successful attempts, the majority of these gut bugs have never been cultivated in the laboratory, so figuring out which microbe does what remains an open question. Now a group led by Caltech researchers is untangling this complex web of relationships using sophisticated “labs on a chip” that can look at a termite’s intestinal ecosystem cell by cell.

The traditional approach to this problem involves removing the gut contents of individual termites, smashing the microbial cells, extracting and pooling their DNA en masse, and analyzing the genes found in the randomized mash. Assigning relationships between any two genes or to the organisms from which they are derived is complicated at best, and often just not possible. Says Associate Professor of Environmental Microbiology Jared Leadbetter, “It was like studying the contents of several hundred books after having torn off their covers, ripped up all the pages into small pieces, and jumbled them together into a big pile. We would find sentences and paragraphs that we found extremely interesting and important, but then we were left frustrated. It was very difficult to determine what was in the rest of the book.”

The new approach uses microfluidic devices into which more than 1,000 individual cells can be distributed into separate chambers before analysis, so that each can be studied as an individual. “With this technique, we’re suddenly able to read portions of the books without having first torn off their covers,” says Leadbetter. “We are still reading with a narrow penlight, but when we identify an interesting sentence, we can quickly find the title and author, and even move on to examine the other pages. This approach can lead to a better understanding of the many microbial processes that underlie the environments in which we all live.”

In this particular instance, the researchers found that in the California dampwood termite (Zootermopsis nevadensis) a family of bacteria called spirochetes are responsible for a key step in the process of digesting wood—homoacetogenesis, which makes the acetate molecules that are the termite’s chief energy source. (As a side note, these acetate-producing microbes consume hydrogen gas, for which they compete with other gut bacteria that make methane—a potent greenhouse gas—thereby keeping many termite species from emitting as much methane as they otherwise would.) Termites are extremely abundant and active in many tropical ecosystems. Says Leadbetter, “There are 2,600 different species of termites, and it is estimated that there are at least a million billion individual termites on Earth. It is thought that they emit two and four percent of the global carbon dioxide and methane budget, respectively. And by extrapolation from numerous studies of a few dozen termite species, we think that there could be millions of novel microbial species found only in the hindguts of termites.” The work could also illuminate ways for humans to convert plant biomass into useful products, such as transforming low-value lignocellulose (that’s straw and cornstalks to you) into biofuels.

The paper appeared in the December 1 issue of Science, with Elizabeth Ottesen, a Caltech grad student in biology, as the lead author. The coauthors are Jong Wook Hong, an assistant professor of materials engineering at Auburn University; Stephen Quake, professor of bioengineering at Stanford; and Leadbetter. —RT