to BioTechniques free email alert service to receive content updates.
Seawater Microbe’s DNA Demystified

02/02/2012
Ashley Yeager

With a new method to isolate individual genomes from millions of microorganisms in the ocean, scientists will learn about the history and evolution of these organisms.

Bookmark and Share

Microbes run the planet. A drop of ocean water holds a billion of them. So, it’s no wonder that scientists have trouble identifying the creatures in the field and culturing them in the lab.

Now, using the latest genome sequencing technology and custom computer software, scientists at the University of Washington, in Seattle, have teased apart the genetic material of a previously uncultured Euryarchaeota microbe from millions of seawater microorganisms and sequenced its genome.

This graphic shows the entangled genomes, or metagenome, of numerous bacteria, archaea and viruses found in a marine microbial community collected at Puget Sound. Of the tens of millions of bases of DNA depicted here, two million were extracted and used to reconstruct a full genome from a mysterious group of uncultured marine Archaea. Source: Vaughn Iverson, University of Washington.





Published in the February 3 issue of Science, the results demonstrate that scientists can now extract and identify individual genomes from complex microbial communities. The capability could help scientists better understand the microbes and how they will respond to human or natural changes in their environments.

Although microorganisms like Euryarchaeota are abundant, making up about 50% of the total biomass in the ocean and other environments, scientists have only know about Euryarchaeota for the past 10 years. So far, they have figured out that it is distantly related to other marine plankton. “Beyond those few tantalizing clues, the creatures have remained a mystery,” said study author Vaughn Iverson, a University of Washington graduate student in the lab of microbiologist Virginia Armbrust.

To crack the microorganism's genetic code, Iverson and colleagues collected water samples from Puget Sound in Washington. Using a sequencing technique that added an extra bit of information called “mate-pairing” to the genetic codes, the team generated a metagenome that included fragments of DNA from all the organisms in their sample.

Basically, the metagenome contained pairs of sequenced fragments that came from the same original molecule of DNA. The scientists identified these pairs and knew they were separated by some quantity of unknown sequence, which they could approximate. As a result, they had sequence data for the ends of longer DNA fragments, which could help identify 14 individual candidate genomes.

Using the mate-pairs, along with custom-designed software and assembly algorithms, the team analyzed the fragments in relationship to the marine group II type of Euryarchaeota. From this analysis, the team connected the genome fragments into longer strands, or scaffolds, and pieced together the complete sequence of the organism.

Although scientists have assembled complete or nearly complete genomes from microbes in the field in the past, this new work “appears to be somewhat unique in assembling nearly complete genomes from complex communities,” said Jonathan Eisen, a microbiologist and geneticist at the University of California, Davis, who was not involved in the research.

The new technique promises to "finally bring more of these unculturable organisms into the lab," Iverson said, allowing scientists to fill gaps in their understanding of how these microbes cooperate to stabilize their ecosystems.

For example, his team found that Euryarchaeota had the genes for proteorhodopsin, a molecule that some bacteria use to harvest energy from sunlight. The characteristics of the gene, along with other information from the genome, provides evidence that bacteria may not have evolved from the proteorhodopsin genes independently but acquired it from Euryarchaeota.

“What we need is a field guide for microbes, akin to what we have for birds, that would give us a picture of the current and past details of microbial life on the planet,” Eisen said.

References

  1. Iverson, V., R.M. Morris, C.D. Frazar, C.T. Berthiaume, R.L. Morales, and E.V. Armbrust. 2012. Untangling genomes from metagenomes: revealing an uncultured class of marine Euryarchaeota. Science 335:587-590. DOI: 10.1126/science.1212665

Keywords:  metagenomics