For most bench-bound postdocs, travelling to Italy and diving in the Mediterranean sounds like a dream holiday. But for Tanja Woyke, a fellow with Edward Rubin at the US Department of Energy Joint Genome Institute (JGI) in Walnut Creek, California, the trip marked the glamorous beginning to an arduous project in metagenomics.

The allure ended with the samples Rubin sent her to collect — a silt-dwelling gutless worm called Olavius algarvensis. Rubin became interested in this worm at a meeting in Monterey, California. He was interested in metagenomics — sequencing genomes from multiple microbes present in environmental samples. Although most environments contain thousands of microbial species, he sought a simpler problem. He found one when he heard a talk by Nicole Dubilier of the Max Planck Institute for Marine Microbiology in Bremen, Germany. He realized the marine worm she studied was ideal because only a handful of microbes were associated with it.

After visiting Dubilier in Bremen and offering the JGI's genomic sequencing clout, Rubin found that the frozen samples the German lab had collected weren't fit for sequencing, because the microbial and the worm DNA stuck together. “We tried everything we could to separate and sequence the samples, but we failed,” says Woyke.

So Woyke flew to Elba and spent two weeks searching for the worms, which are about two centimetres long, in the mud off the Capo di Sant' Andrea. She stirred up the sea bed and looked for tiny white organisms to “ball up”. Whenever she found lots of these balls, she collected buckets of sediment and carried them ashore. Every evening, she searched through 32 litres of silt, separating the worms from the dirt with a pipette. She eventually found several thousand worms, sent 300 back alive on ice, and froze the rest. “I had to pick through a lot of worms,” Woyke says. “It was very tedious.”

Tedious or not, Woyke's efforts paid off; although the frozen worms were easier to package and ship, the fresh ones proved more useful. The JGI group separated the microbial DNA from the fresh worm DNA, and sequencing the microbial DNA proved much easier than collecting the worms.

The team completed four microbial genomes. Woyke then travelled to Bremen to help identify the genes and metabolic pathways in these genomes. Dubilier suspected that this information would explain how the microbes helped the worms to digest food and excrete waste. Their genomic analysis (see page 950) showed that the worm outsources activities to the microbes that its ancestors, which had a gut and a renal system, would have done themselves.

The project helped the team understand how metagenomics can explain the biological capabilities of a simple microbial community. The JGI team is now applying these methods to larger, more complicated systems. And Rubin says that he can use pictures of Woyke's fieldwork for both public relations and recruiting. “Many of the projects we work on are connected to environments you wouldn't choose for a vacation — like looking for microbes where acid mine run-off is present,” says Rubin. “I am really pleased I can show pictures of Tania in Elba skin-diving — even if it is for worms.”