Flatwoods Salamander

Imagine that you are a field biologist exploring an
unknown area.  You come across a wetland and want to know what species are
there.  You add some of the water into a handheld gadget you have, and Presto!
Almost instantly you know what species are there.  This probably sounds like
science fiction straight out of Star Trek. However, it may not be as
far-fetched as you think.

In fact, we are already doing projects that use
water samples to tell us about species presence.  This technique is known as
using environmental DNA, or eDNA for short.  We can take advantage of the fact
that aquatic animals release a lot of DNA in their environment through
shedding, waste products, injuries and laying eggs.  We can then extract the
DNA from a filtered water sample, and if we know a small DNA sequence from our
target animal, we can identify it from the water sample.  This is exactly what
we are now doing at the Orianne Society (as well as many other researchers) to
verify presence of rare and cryptic species.

I first became aware of the possibility of eDNA from
water samples as part of a lab meeting at the University of Idaho where we
talked about a study in France that was able to isolate DNA from bullfrogs at
ponds where they occurred, even when the frogs were at really low density.  I
thought it was really neat, but was working on a rattlesnake study at the time
and so didn’t give it too much thought at that moment.  However, inspired by
this study, my colleague Dr. Caren Goldberg, a post-doctoral researcher at
University of Idaho, adapted this method to work on two species of stream
amphibians in Idaho and found it to be very successful in a river system.  This
really caught my attention, as I had recently started working on hellbender
salamanders that live in rivers. Hellbenders are declining across their range,
and when they are at low densities can be really difficult to find.  They also
can live under very large rocks that people cannot lift and can be missed that
way.  We felt, that if successful, using eDNA could be an important step to
helping to conserve important hellbender populations.

  Enlarge PhotoHellbender

With support from the Ron Goellner Conservation Fund
from the Cryptobranchid Interest Group, and in collaboration with Dr. Michael
Freake at Lee University, we did an initial survey by filtering water in
streams across Tennessee and Georgia that we either knew had hellbenders
(positive test sites) or that had historic records or strongly suspected
presence.  We took multiple samples per river to see how consistent our results
were.  It turns out that the method is highly effective for hellbenders.  We
detected hellbender DNA in all sites that had known recent populations of
hellbenders, and we even found hellbender DNA at a site where repeated visits
have only found one individual living under a bridge!  And our success is not
unique – researchers have even detected tiny New Zealand mud snails (smaller
than your fingernail) from water samples.

  Enlarge PhotoBog Turtle

Of course, so far I have just described identifying
presence with eDNA; what if we want to know the abundance of animals at a
site?  We are going to investigate that very question this summer.  We are
currently switching to a method that allows us to not only identify whether the
DNA is there, but how much of the DNA is there.  If we assume that more
individuals leave more DNA floating in the water, then we can use this to come
up with a relative measure of abundance.  For hellbenders, we might also use
this method to detect populations that are successfully reproducing.

Finally, we are currently working with Georgia Department
of Natural Resources and USGS to develop a study to use eDNA for other
threatened Georgia herps such as gopher frogs, flatwoods salamanders, striped
newts and bog turtles. We are excited to learn if eDNA can work in the highly
acidic areas these species use, as acid can degrade DNA.  If it works, then we
will have another important tool in the conservation and management of rare
species that live in bog or ephemeral wetland environments.

And this sort of eDNA work is probably just the tip
of the iceberg.  A new study just came out that found vertebrate DNA in soil
samples.  Rattlesnake and indigo snake eDNA may not be far off – Stay tuned!