Using Computers And DNA To Count Bacteria, Measure Effects Of Metal Toxicity In Soil

"ComputationalImprovements Reveal Great Bacterial Diversity and High Metal Toxicityin Soil," by Jason Gans, Murray Wolinsky and John Dunbar, of LosAlamos' Bioscience Division, describes a new approach to capturing thestructure of bacterial communities in soil. In addition, the studyprovides insight into the devastating effects of metal pollution onthose bacterial populations.

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

"Withimproved analytical methods, we show that the abundance distributionand total diversity of soil-borne bacteria can be deciphered," saidDunbar.

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

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

Asoften happens at Los Alamos, where thousands of scientists from everyimaginable discipline are gathered, the researchers form amultidisciplinary team, with Gans (biophysicist), Wolinsky (physicist)and Dunbar (microbiologist) using their varied backgrounds to solvethese types of knotty questions. Their new approach enables far moreaccurate measures of the contribution of microbes to globalbiodiversity and more importantly the impact of human activities on theorganisms responsible for sustaining all higher life forms.