ONE of the techniques that was used to unravel the human genome has been exploited to study marine microbes en masse. It has revealed over a million previously unknown genes from thousands of organisms in samples taken from the Sargasso Sea off Bermuda.
Marine microbes are hard to study because the vast majority cannot be grown in the lab. In the 1980s, biologists tried another approach 鈥� studying their DNA (快猫短视频, 27 January 2001, p 32). Such work has already helped to reveal that the number and importance of marine viruses and bacteria has been greatly underestimated.
So far, however, researchers have been sequencing only individual fragments of microbial DNA. Now a team led by Craig Venter, famous for his attempts to sequence the human genome ahead of the public project, has gone further and sequenced a large amount of DNA extracted from seawater samples. The researchers, from several institutions in the US and Bermuda, chopped the microbial DNA into fragments, sequenced some of it and then used software to fit together overlapping bits, a technique known as 鈥渟hotgun sequencing鈥�.
Advertisement
In total, the samples yielded nearly half a million genome fragments from at least 1000 different microbial species. Even with a billion base pairs sequenced, it was not possible to assemble the complete genome of every organism. In fact, the team estimates that the samples actually contained at least 1800 species, and possibly as many as 50,000 (Science, DOI: 10.1126/science.1093857).
In the fragments of genomes that could be assembled, the team found over 1.2 million new genes 鈥� the biggest haul ever made. 鈥淚n terms of sheer numbers, it鈥檚 been overwhelming to all of us,鈥� Venter told a press conference.
Studying the genes will reveal not only which species are present but what roles they play in the ecosystem. 鈥淲hat鈥檚 neat is you can start looking at the patterns of genes and their diversity as they occur in the environment,鈥� says Edward DeLong of the Monterey Bay Aquarium Research Institute in California, one of the pioneers of the genetic approach.
De Long recently found a gene for the pigment rhodopsin in a very common marine bacterium, showing it is capable of photosynthesis and could play a important role in climate. Venter and his team found no fewer than 782 versions of the rhodopsin gene, proving what DeLong suspected 鈥� that the pigment is widespread among ocean bacteria.
The team also found that the mix of species varied dramatically from site to site and from day to day. 鈥淭he ocean is not a giant homogeneous soup,鈥� concludes Venter. He plans to collect microbes from 300 sites around the world. He says, 鈥淲e think that we could end up with up to a billion new genes and maybe millions of new organisms.鈥�