There just aren’t many organisms that could live in an acid mine, and that’s why Joint Genome Institute Director Eddy Rubin likes it — at least as a research starting point. Rubin, who has been at JGI for two and a half years, is guiding the DOE-funded institute full speed ahead into the area of environmental genomics, or meta-genomics.
Using genomics technologies is an increasingly popular way to study environmental communities, such as Craig Venter’s highly publicized initiative in the Sargasso Sea. “In the past we would go into the environment and take a … microbe that we could grow and culture it and sequence it,” Rubin says. That culturability requirement meant that scientists missed “much of the action,” he adds.
Taking advantage of JGI’s capacity for high-throughput shotgun sequencing has turned the old approach on its head. Scientists can sequence millions of reads taken from an environmental community and then study patterns among the genes found or even piece together some of the genomes in the sample, Rubin says.
The acid mine, which had a pH level of 0.5, was a good proving grounds for the concept of metagenomics. “It wasn’t very complex,” Rubin says. “We were able to see that there were about five predominant species present.” Studies early on showed a plethora of genes involved in iron oxidation so scientists could have learned about the site even without figuring out what each organism was. By getting clues like these, Rubin envisions this kind of research allowing scientists to “assay different environments in different time periods as a diagnostic of what’s going on.”
Metagenomics, which has been a growing field at JGI for the past two years, is expected to be a critical part of the research portfolio, Rubin says. He notes that the institute is turning away from the biomedical research it did as part of the HGP and is getting closer to its DOE roots by focusing on microbes involved in bioremediation and energy reduction, for example.
Since the acid mine research turned out so well, Rubin says the next step is to take on a really complex environment: soil. “We’re going to have to sequence hundreds of millions of base pairs before we can even think about assembling a genome,” he says, but hopes that studies of genes in the soil samples will turn up interesting results long before that.
Rubin says JGI is dutifully submitting this information to GenBank, but adds that the institute is building its own metagenomics database to better accommodate new data fields such as latitude and longitude coordinates, temperature, and pH.
As the discipline moves forward, Rubin hopes for technological advances geared toward environmental sampling. For one thing, he says, “if we have one predominant organism and we also want to see the minor organisms, we need strategies to normalize” the samples. He’s looking for improved cell-sorting technologies for this or a reliable single-cell sequencing technique to avoid the issue altogether.
— Meredith Salisbury