Working with environmental DNA (eDNA)

>>My name is Kelly Carim, and I am
the environmental EDNA coordinator at the National Genomics Center
for Wildlife and Fish Conservation, which is a part of the Rocky Mountain
Research Station at the U.S. Forest Service. So environmental DNA is DNA that’s sloughed
off into the environment from an animal and so this could be anything from
skin cells to feces to fish slime, just any DNA that’s sloughed off
into the surrounding environment. And the great thing is that we’re able
to collect this DNA and analyze it for the presence or absence of various species. One of the big things an environmental DNA
sampling is that it’s very highly sensitive. We’re looking for often just one or
two copies of DNA from an animal. And as a result, we need to be
very concerned about contamination. I have the pump running, and I have my filter
in here, which is going to capture the DNA. And it’s in a little cup. And so what I’m going to do is
carefully put this cup onto the pump. And then I’m going to step out here
into the flowing water making sure that I am staying downstream
of where I’m sampling. And I’m just going to scoop water
and let it run through the filter. And in our protocol, we pump five
liters of water for each sample. And that allows us to collect a lot of DNA. We find that sampling more
water improves the probability that we’ll detect an animal
that’s in very low abundance. And so, again, if we’re looking for just
one or two copies of DNA from an individual, the more water we pump, the more
likely we are to get that DNA. All right. So now we’ve pumped five liters of water. And what I’m going to do is just let the pump
run for about 30 seconds to dry that filter out. Now I’m going to remove the filter from
the filter cup and place it in a little bag with silica beads and that will further
dry out the filter to preserve that DNA until we can extract it in the lab. One thing that we’ve been
looking at in our working group at the Rocky Mountain Research
Center is how we can use EDNA to determine fish distributions currently
and how that has changed with either where we found them before and where
we believe they will be in the future with changing stream temperatures. We can gain an understanding of
all the organisms in that stream, which can help managers identify areas
where there might be invasive species like, for example, pike that would potentially
come in and impact the trout populations that fly fishermen are looking for. It can also help us understand where there are
invasive species that might be in low abundance but could easily take hold and drive out some
of the native species that we’re interested in.

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