One of the most abundant types of protein identified in the study comes from proteorhodopsins, molecules that resemble light-sensing proteins in the human eye. They appear to endow microorganisms with an alternative mechanism to photosynthesis in order to generate energy from light. Researchers also found that slight changes in the protein affect the wavelength of light the organism can absorb: the particular variant an organism possesses seems to follow the predominant color of water in its environment. On the coast, for example, where the water is green, organisms can mostly absorb green light. But in the deep sea, where the water is blue, organisms can mostly absorb blue light.

In fact, every environment sampled showed high genetic diversity, both within and between samples. The findings are challenging the notion of species in microorganisms. "When you look at microbes, they don't appear to be individual species," says Douglas Rusch, also a scientist at the Venter Institute and an author of one of the papers. "It seems to be a complex mixture, which we describe as subtypes, which are adapted to a particular environment."

Venter's project is part of a new trend in genomics, enabled by new sequencing technologies, to sequence entire microbial communities rather than individual organisms. "These technologies allow massively parallel sequencing, so we can get hundreds of thousands of sequences in single runs," says George Weinstock, codirector of the Human Genome Sequencing Center at Baylor College of Medicine, in Houston. So far, scientists have sequenced the microbial inhabitants of whale carcasses, sewage-treatment plants, acid-mine drainage sites, and termite intestines, among others.

"Microbial communities are almost like a superorganism, where each microbe is contributing to community as a whole," says Weinstock. "We really need to characterize the metagenome and analyze the genes and protein products as an aggregate."

Venter and others eventually hope to find proteins that can be co-opted to create novel bacterial machines--proteins involved in hydrogen production or carbon fixation, for example, that could one day be engineered to boost the carbon-fixing capacity of the ocean or to create fuel-producing bacteria. "Genes are the design component of the future," says Venter.