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Environmental DNA: Information Covers the Globe

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environmental DNA

What would you conclude if you landed on a planet and found coded information everywhere you went? That’s what we have all around us on this planet. No matter where you go, there is complex specified information. It’s under every rock. It’s in every handful of water. It’s in the soil. It’s in the air. Strings of message-bearing codes are everywhere.

It’s called environmental DNA (eDNA), and it is coming into its own as a tool for investigating the world around us. As sequencing technologies advance, reports Sandeep Ravindran in Nature, ecologists can tell what animals passed by. Insects, mammals, crustaceans, amphibians, birds — they all leave traces of their genomes behind, like bread crumbs on a trail. Scientists are finding “ecology gold” in “discarded DNA.”

Ecologists are increasingly relying on DNA shed by organisms into the environment, known as environmental DNA (eDNA), for their research. Instead of trekking into the field for weeks or months to collect and taxonomically identify creatures, these scientists are tapping sources such as shed skin cells, fish scales, urine, faeces, blood and saliva for details on rare, endangered and invasive species, and to measure biodiversity. [Emphasis added.]

A New Technology Ripens

As Ravindran says, ecology field work is becoming much easier. Before, it was hard work to catch the presence of animals in the wild, particularly small species like endangered salamanders or small insects. Your choices were hunting for insect parts in guano, or trapping birds with a net, or snapping a photo with a camera triggered by a nocturnal cat. Now, you can scoop up soil, or water, or even a sample of air, and find coded information that can prove the presence of a species of interest. 

These techniques have enabled eDNA surveys to become more innovative and ambitious in their scope, opening up a whole range of taxonomic groups across large geographical regions for study. The technology still struggles when it comes to estimating population abundance, and requires expensive lab equipment and sophisticated bioinformatics skills. And for all eDNA’s reliance on twenty-first-century technology, ecologists still need to put in the hard yards outdoors to collect the samples. But as eDNA surveys become cheaper and more accessible, it’s increasingly becoming a powerful complement to conventional field-biology techniques.

Ravindran describes how easy these techniques are becoming. Ecologists used to have to send samples to labs and wait for weeks for results. But as the technology ripens, biologists are able to take equipment with them into the field for faster results. A suitcase-sized portable “Mercury Lab” that runs qPCR (quantitative polymerase chain reaction) can be set up to process eDNA in water samples within hours. Instead of having to carry back water samples in ice chests full of bottles, the investigator can carry out the data on a thumb drive. It would not be unreasonable to expect future ecologists to head out with their smartphones and determine the biodiversity of a sample within minutes. Other techniques are also helping streamline the reading of eDNA.

In eDNA ‘metabarcoding’, DNA is amplified by PCR using short segments of DNA, called primers, that have a unique tag at one end and that target genome sequences common to organisms across an entire taxonomic group. In Bohmann’s case, she used universal primers to amplify and sequence insect eDNA from more than 100 faecal samples in parallel, which were then differentiated on the basis of their unique tags.

Kinder to Animals

Another advantage of reading the codes of a habitat is that no animal has to be killed. The new analysis techniques are also cheaper. And since anyone can collect samples, citizen scientists can get involved. In one test, volunteers with no training collected 239 samples of pond water, resulting in over 90 percent accuracy in detecting the presence of an endangered species of newt. The study authors feel that with minimal training, the scores could become more accurate.

Researchers are setting up similar projects with ecotourism companies in the Amazon. Tourists would collect eDNA samples while visiting national parks, thus contributing to long-term biodiversity monitoring. “What you’re doing is you’re taking away the bottleneck of needing expert observers, and then you can study much larger areas,” says Douglas Yu, a molecular ecologist at the University of East Anglia in Norwich, UK.

This is all possible because the biosphere is awash in information. Insect DNA can be found in flowers, showing what pollinators were present. Prey DNA can be found inside any animal that eats. And eDNA can even be snatched from the air (see “Information Storage in the Clouds,” and “Intelligent Design in the Dirt”). “The imagination is setting the limits to what sample types you can detect traces of animals and plants in,” says Kristine Bohmann, who used to pore through guano samples by hand, looking for insect remains. “I don’t know of any other method that is so broad that you can actually get information from across the taxonomic tree of life, all the way from bacteria to whales,” says Philip F. Thomsen, a molecular biologist from Denmark. 

Challenges Remain

There are still challenges to the technique. Contamination is an ever-present concern. And while eDNA can establish the presence of species, it provides little information on their abundances in the habitat. Also, “because eDNA samples are chock-full of microbial DNA,” comprehensive sequencing is necessary. But the frontier of eDNA analysis is like a curtain rising on a fantastic show: turning the lights on all the players on a stage that were previously hidden. It’s “a brand new field,” Bohmann says. 

The technology can be expected to advance toward near instantaneous identification of all species in a habitat with a smartphone app, simply by analyzing samples of their DNA left behind. In a way, this can be scary. It means that people, too, can be found by the “bread crumbs” of their genomes left in skin flakes. While this could help law enforcement, the potential for abuse becomes starkly imaginable, too.

Astounding Implications for ID

For now, the implications for intelligent design are quite astounding. Our planet is awash in codes — not just in little bits of information, but in long strings of messages containing billions of letters arranged in highly specified, non-repetitive sequences. These sequences correspond to messages that told molecular machines how to build tissues and organs, run complex metabolic processes, and construct brains. If these codes were written large on paper, it would be like walking on piles of blueprints and dictionaries at every step. 

Compare our planet with a lifeless world. A sterile robotic investigator might find lava, various liquids, and toxic gases. Even an earthlike world with the same mix of atmospheric gases and chemical compounds would be devoid of complex specified information. The closer the investigator looked, the simpler things would become, down to just 92 naturally occurring elements. Every sample would react blindly to laws of nature. As finely tuned as those laws might be, every process could be described by a few equations. Nothing would launch into the atmosphere and fly by its own power, guided by an internal compass to a purposeful destination. Nothing would swim against the current. Nobody would converse about abstract concepts. 

Lifeless, predictable worlds should be the norm. Perhaps they are. What stands apart on Earth and any other inhabited world will always be coded information: codes that can manipulate substances like tissues and organs and make them move contrary to their natural tendencies: to fly, to swim, to think. The rise of eDNA analysis teaches us that the most remarkable thing about our planet is its ubiquitous coded information. It’s what makes our world much more interesting than a sphere. It’s a biosphere.

Photo credit: NASA.