If a tree falls in the forest and no one is there to hear it, does it make a sound? This philosophical reflection on perception and reality is often loosely attributed to the Irish philosopher George Berkeley, the Bay Area town’s namesake, whose own philosophy boiled down to “to be is to be perceived”.

For much of the discipline’s history, ecological researchers studying the presence of endangered species in underwater habitats have been forced to operate by a similar axiom. If, for example, after a day of strenuous walking in ponds and raking water with dip nets, Brian Woodward, an ecology researcher at the Santa Lucia Conservancy in Carmel Valley, could not perceive with his own eyes the presence of a California Tiger Salamander or its larvae, there would be no physical evidence of its existence. The rules of detective work 101.

Yet human senses have limitations, and a relatively recent advance in scientific analysis known as eDNA (short for environmental DNA) has the potential to transcend these shortcomings. It is deployed in habitats across Monterey County, from ponds in the Santa Lucia Preserve to estuaries in Elkhorn Slough and even in the canyon depths of Monterey Bay.

Earlier this spring, with the help of a grant and partnership with the Elkhorn Slough Estuarine National Research Reserve, Woodward and a team of researchers set out to monitor the presence of the tiger salamander and frog California red-legged bird, also endangered, on the Santa Lucie Preserve. Instead of sweeping the ponds with a net and manually counting the adults and larvae they found, the team bagged pond water samples and shipped them to the University’s Goldberg Lab. of Washington State for analysis. The results, which Woodward expects to receive by September, will indicate which ponds harbor the endangered species.

The use of eDNA does for ecology what forensic laboratories have done for crime scene investigators. For tank tests in the reserve, the eDNA laboratory can capture particles as microscopic as bacteria, skin cells or feces. DNA is then extracted from these particles and analyzed using polymerase chain reaction tests (the same PCR tests used for coronavirus) to see if it matches DNA from tiger salamanders or frogs. with red legs.

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Casting a pair of waders, dragging a net across the pond, and manually counting species remains the official protocol for determining the presence of amphibians established by the US Fish and Wildlife Service. It’s also more immediate and offers more detail, including a rough cash count. However, to answer the question “Are they here?” eDNA offers a revolutionary opportunity, especially in terms of efficiency. Woodward indicates that the traditional method allows the monitoring of 10 to 12 ponds per year; eDNA allowed his team to sample 34 ponds in less time.

At the Monterey Bay Aquarium Research Institute in Moss Landing, research technician Kobun Truelove helps develop an automated eDNA system in which an autonomous underwater vehicle collects the sample, filters the water, extracts the DNA, sequence and identify species correspondence. Over the past two years, he has already helped reduce the time needed between collecting marine samples and identifying species from three months to six hours. Truelove says that beyond the science fiction of eDNA, the technology has allowed MBARI to track population changes under changing ocean conditions. Scientists have even found the presence of the rare beaked whale in the Monterey Underwater Canyon, a surprise find. If a species is detected using eDNA, it means it was likely present within five days of sample collection.

“There’s so much we’re starting to understand that we didn’t know before eDNA, and it opens up a lot of new questions,” Truelove says.

However, eDNA leaves a lot of question marks, such as population density and whether the animal was even alive or just part of a predator’s feces. Truelove says eRNA will eventually be able to answer the dead or alive question, but that method is still under development.


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