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Roots and microbes: Bringing a complex underground ecology into the lab
Date:8/1/2012

al composition and a unique population of microorganisms as compared to the farm soil.

After removing native worms and insects and crushing each soil sample to produce a homogenous medium, Lundberg and the team used it to plant microbe-free seedlings from a variety of inbred genetic backgrounds. Soon, the plants were growing rapidly and the team was able to collect roots and the surrounding soil for analysis. They removed each of more than 600 plants from its pot and gently shook it to remove all but the soil in closest contact with the roots a microenvironment known as the rhizosphere. After they collected the rhizosphere soil and rinsed the roots clean, they ground the roots up so the microbes within the root cells could be sampled, as well. A few weeks later, when the plants were more mature and growth had slowed dramatically, they collected roots and soil again.

To catalog the diversity of bacteria in each sample, the scientists used a method of identification based on the sequence of the 16S ribosomal RNA (or 16S rRNA) gene, which is present in all bacteria but variable enough to distinguish between most types. For the massive sequencing effort, Dangl's team collaborated with scientists led by Susannah Green Tringe at the Department of Energy's Joint Genome Institute (JGI) in Walnut Creek, California.

Parsing the data from the sequencing required tremendous computational power and new methods of analysis. "We relied heavily on JGI's established expertise in informatics," Dangl says. "But we also realized that eventually you've got to be able to do it yourself." The two graduate students were joined by computational biology graduate student Scott Yourstone, and the team took on the analysis of 16S rRNA sequencing data for more than 1,200 different samples, each one containing a diversity of species, including devising a classification system to categorize the types of bacteria they found.

The team found that, as expec
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Contact: Jennifer Michalowski
michalow@hhmi.org
301-215-8576
Howard Hughes Medical Institute
Source:Eurekalert

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