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DNA in Dirt Offers Ecological Clues in Species Diversity

Soil samples can reveal biological diversity.

By Amy Maxmen of Nature magazine

Ecologists have spent decades trapping and tagging species in the name of understanding biodiversity, but a far easier way may lie just beneath their feet. Soil contains fragments of DNA that can accurately reveal an area's animal diversity, according to a recent study in Molecular Ecology.

"This is the first time anyone has shown that 'dirt' DNA not only reflects what species live in an area, but how many [individuals] there are," says Eske Willerslev, an evolutionary biologist at the University of Copenhagen, Denmark, and a member of the study team. The new technique has many advantages: sampling 'dirt' DNA requires far less time, energy and zoological expertise, says Willerslev. And unlike traps and tags, it doesn't risk harming the animals.

Today's ecologists commonly identify animals by their DNA, and even by DNA the animals leave behind in flakes of skin, scales and waste. By using state-of-the-art sequencing techniques, Willerslev and his colleagues can now reveal not only unexpected species but also the number of animals of each species present.

Test run

To prove that their dirt DNA method works, Willerslev's team took samples from farms and safari parks with known numbers of large mammals, including Asian elephants and blue wildebeest. They extracted DNA from the soil and rapidly sequenced the fragments using a high-throughput DNA sequencing machine. When they compared individual sequences to the millions of sequences stored in the DNA database GenBank, they found all the animals they expected -- except for a giraffe that had only recently been introduced to one of the game parks. The quantity of a species' DNA recovered roughly reflected the number of animals of that species present, after adjusting for body weight.

The new method would be easy to apply elsewhere. Field biologists could collect the top 10 centimetres of soil from multiple sites in a territory, bring it back to a basic lab equipped with a DNA-extraction kit and a PCR machine to amplify the DNA, and then send the DNA samples elsewhere for sequencing. "It's really quite simple," says Willerslev.

Probing the past

And the technique could be used to do more than just identify the animals currently living in the area. DNA from animals that had left the test areas two months earlier was recovered in the study, indicating that genetic traces seem to stick around. Digging deeper could reveal the animals that occupied a territory several thousand years ago, says Willerslev. However, he cautions, such samples might be biased, as surface DNA can leach down through the soil, distorting the historical record, and some DNA-containing structures, such as camel hair, last longer than others.

Robert Hanner, who studies molecular biodiversity at the University of Guelph in Ontario, Canada, says that soil was already known to hold DNA but that the new work establishes a sound set of protocols for investigating its composition. "Maybe some people don't see that it's exciting, but I think it's pretty spectacular. Now we can move forward, instead of quibbling about whether or not the technique gives spurious results."

While some researchers hale the technique as a major advance, other are more cautious. "I'm not sure how well this would work in cases where we're looking for tiny and rare things like insects in a huge area," says geneticist Amy Vandergast at the US Geological Survey's San Diego Field Station in California. But she says it might work for tracking larger animals in confined areas; for example, the narrow stretches of habitat that connect one reserve to another in Southern California.

This article was reproduced with permission from Nature magazine. It was first published on September 23, 2011.

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