Sequencing soil

The paper:

L.F.W. Roesch et al., “Pyrosequencing enumerates and contrasts soil microbial diversity,” ISME J , 1:283–90, 2007. (Cited in 57 papers)

The finding:

A team led by Eric Triplett of the University of Florida pyrosequenced four soil samples from across the Western Hemisphere, three from agricultural sites and one from forest soil, finding that each had more than 25,000 bacterial species—on par with previous estimates based on traditional sequencing approaches, but far less than some statistical predictions. “They were able to go much deeper into the soil ecosystem than anyone had been able to go before,” says Rob Knight, a microbial ecologist at the University of Colorado at Boulder.

The surprise:

Archaea made up 5–12% of all species identified in the three agricultural soils, but less than 0.01% at the forest floor. “We’re now trying to figure out why that is,” says Triplett.

The follow-up:

Last year,...

The driver:

Knight pyrosequenced 88 soil samples from ecologically diverse, nonagricultural sites across the Americas and found that pH was the best predictor of bacterial diversity, beating out soil moisture, texture, carbon:nitrogen ratio, and various other soil traits ( Appl Environ Microbiol , aop 5 Jun 2009).

Number of species per gram of soilBacteriaArchaea
Brazil corn field26,1401,259
Florida sugarcane field28,3283,546
Illinois corn field31,8184,530
Ontario boreal forest53,5335

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