Using computers and DNA to count bacteria

Don't call them the Dirt Doctors, or Sultans of Soil, they're just clever Lab guys. A team from Los Alamos National Laboratory has a paper in this week's Science Magazine with a new way to count bugs in dirt. Bacteria, that is, in the highly complex world beneath our feet.

"Computational Improvements Reveal Great Bacterial Diversity and High Metal Toxicity in Soil," by Jason Gans, Murray Wolinsky and John Dunbar, of Los Alamos' Bioscience Division, describes a new approach to capturing the structure of bacterial communities in soil. In addition, the study provides insight into the devastating effects of metal pollution on those bacterial populations.

Why is this important, you ask? It turns out that in our technology-driven world, with biosensors in development for homeland security, emerging diseases surprising our medical communities and lifesaving medicines being extracted from jungle plants, we still don't know what's under our feet. The bacterial communities of every day soil are intensely complex, so diverse and densely populated, that normal measurement methods are overwhelmed.

"With improved analytical methods, we show that the abundance distribution and total diversity of soil-borne bacteria can be deciphered," said Dunbar.

"More than a million distinct genomes were present in the pristine soil, exceeding previous estimates by two orders of magnitude. When we examined the populations levels in metal-contaminated soil, we found the bacterial genetic diversity was reduced more than 99.9 percent," lead author Gans added.

The Los Alamos team used a technique known as DNA re-association, separating the two strands of all the bacterial DNA in a soil sample, blending them, and measuring the time it takes for the correct halves to properly reconnect.

As often happens at Los Alamos, where thousands of scientists from every imaginable discipline are gathered, the researchers form a multidisciplinary team, with Gans (biophysicist), Wolinsky (physicist) and Dunbar (microbiologist) using their varied backgrounds to solve these types of knotty questions. Their new approach enables far more accurate measures of the contribution of microbes to global biodiversity and more importantly the impact of human activities on the organisms responsible for sustaining all higher life forms.

Source : DOE/Los Alamos National Laboratory