Using powerful DNA-sequencing tools developed for the Human Genome Project, scientists have sequenced partial or total genomes of hundreds of previously unknown microbes. The new research underscores the tremendous diversity of microbes in the open ocean, and it could help uncover the key roles of microbes in controlling the global environment.
To understand the workings of an ecosystem, ecologists must first identify the creatures that inhabit it. That's difficult for microbial ecologists because only about 1% of the microbes on Earth have ever been grown in the lab. Researchers have determined the species of such unculturable microbes by identifying characteristic genetic fingerprints, but these tell them little about the microbes' lifestyles--which chemicals they burn for energy, for example, and how one species lives off the waste of another.
To learn more about the ways of open-ocean bacteria, J. Craig Venter of the Institute for Biological Energy Alternatives in Rockville, Maryland, and his colleagues collected water samples from the Sargasso Sea, a region of the mid-Atlantic Ocean off the coast of Bermuda. After filtering the water to catch only bacteria or archaea, they extracted DNA. Then they smashed the DNA into smaller fragments, sequenced 1.05 billion base pairs, and used computer models to reconstruct partial genomes of different species. The effort, reported online 4 March in Science, yielded 148 entirely new types of bacteria and 1.2 million new genes, almost 10 times as many genes as all previous studies combined.
Meanwhile, Jill Banfield of the University of California, Berkeley, and her colleagues used similar sequencing methods to stitch together the genomes of microbes in highly acidic water from an abandoned California gold mine. They reconstructed the genomes of two hardy bugs and partially reconstructed those of three others, all of which lived together as a pink biofilm. According to a report in the 4 March issue of Nature, one such genome came from a bug whose likes had never been sequenced; the researchers deduced most of its metabolic pathways and figured out how it survives on a diet of iron.
The studies open up new opportunities to uncover microbial genomes from other environments, revealing how microbes alter global carbon and nitrogen cycles, how microbial metabolism evolved, and how so many different kinds of microbes can coexist, says biological oceanographer Paul Falkowski of Rutgers University in New Brunswick, New Jersey. “This is just the beginning.”