Microbes to the max

Credit: Courtesy of Jed Fuhrman / University of Southern California" /> Credit: Courtesy of Jed Fuhrman / University of Southern California The paper: M.L. Sogin et al., "Microbial diversity in the deep sea and the underexplored 'rare biosphere,'" Proc Nat Acad Sci, 103:12115-20, 2006. (Cited in 81 papers) The finding: In 2006, Mitchell Sogin of the Marine Biological La

Aug 1, 2008
Alla Katsnelson
<figcaption> Credit: Courtesy of Jed Fuhrman / University of Southern California</figcaption>
Credit: Courtesy of Jed Fuhrman / University of Southern California

The paper:

M.L. Sogin et al., "Microbial diversity in the deep sea and the underexplored 'rare biosphere,'" Proc Nat Acad Sci, 103:12115-20, 2006. (Cited in 81 papers)

The finding:

In 2006, Mitchell Sogin of the Marine Biological Laboratory at Woods Hole, Mass., and colleagues examined 344 water samples from the North Atlantic Deep Water. They amplified genes encoding ribosomal RNA (used to map microbial taxonomy), which they then sequenced using a new technique called "massively parallel" sequencing. They found a level of microbial diversity two orders of magnitude higher than results of earlier full-genome sequencing studies. Many of the sequences found had never before been identified, and most were very rare.

The tool:

The method used in this paper is a new way to identify rarer sequences that previous sequencing studies overlooked, says Josh Neufeld, a microbial ecologist at the University of Waterloo.

The theories:

Identifying rare gene elements of the microbial biosphere can shed light on the functioning of microbial communities overall, says Sogin. Are these rare organisms "keystone species"? Does their frequency vary in different geographic regions, or would it spike after a cataclysmic event? "Until now, we haven't had a way to prove one way or the other," he says, but now, "I think you can do the experiment."

The impact:

Researchers are applying this approach to other microbial environments, from activated sludge to the human microbiome. Tom Fenchel, a marine biologist at the University of Copenhagen, cautions that Sogin's technique might be pulling out neutral genetic variation that doesn't reflect true phenotypic diversity.

Estimates of deep-sea microbial diversity:
Venter et al. (Science, 303:66-74,2004): 1800 phenotypes
Sogin et al.: 50,000-60,000 phenotypes