Zoo air contains enough DNA to identify the animals inside
Date:
January 6, 2022
Source:
Cell Press
Summary:
The air in a zoo is full of smells, from the fish used for feed
to the manure from the grazing herbivores, but now we know it is
also full of DNA from the animals living there. Two research groups
have each published an independent proof-of-concept study showing
that by sampling air from a local zoo, they can collect enough DNA
to identify the animals nearby. This may prove to be a valuable,
non-invasive tool to track biodiversity.
FULL STORY ==========================================================================
The air in a zoo is full of smells, from the fish used for feed to the
manure from the grazing herbivores, but now we know it is also full of
DNA from the animals living there. In the journal Current Biologyon
January 6th, two research groups have each published an independent proof-of-concept study showing that by sampling air from a local zoo,
they can collect enough DNA to identify the animals nearby. This may
prove to be a valuable, non-invasive tool to track biodiversity.
========================================================================== "Capturing airborne environmental DNA from vertebrates makes it
possible for us to detect even animals that we cannot see are there,"
says researcher Kristine Bohmann (@kristinebohmann) and head of the team
at the University of Copenhagen.
Terrestrial animals can be monitored in many ways: directly by camera
and in- person observation, or indirectly by what they leave behind,
like footprints or feces. The drawback to these methods is that they
can involve intensive fieldwork and require the animal to be physically present. For example, monitoring animals by camera requires knowledge of
where to put the cameras on the animal's path, sifting through thousands
of pictures, and usually a bit of luck.
"Earlier in my career, I went to Madagascar hoping to see lots of
lemurs. But in reality, I rarely saw them. Instead, I mostly just heard
them jumping away through the canopy." says Bohmann. "So, for many species
it can be a lot of work to detect them by direct observation, especially
if they are elusive and live in very closed or inaccessible habitats." "Compared to what people find in rivers and lakes, monitoring airborne
DNA is really, really hard, because the DNA seems super diluted in the
air," says Elizabeth Clare, lead researcher of the Queen Mary University
of London team (Clare is now at York University in Toronto). "But our
zoo studies have yet to fail for different samplers, genes, locations,
and experimental approaches. All of it worked and surprisingly well."
Bohmann and Clare draw heavily from their past research monitoring
wildlife by collecting other sample types containing DNA shed by
animals. This is referred to as "environmental DNA," or eDNA, and is
a well-established technique used most frequently to monitor aquatic
organisms by sequencing eDNA from water samples.
==========================================================================
"Air surrounds everything, and we wanted to avoid contamination in our
samples while optimizing true detection of animal DNA," says Bohmann. "Our newest work with airborne eDNA involves what we usually do when processing
eDNA samples, just tuned up a little bit." Each research group conducted
their study at a local zoo by collecting samples at various places in
the zoo, including inside walled-in enclosures like the tropical house
and indoor stables, as well as outdoor enclosures in the open air. "To
collect airborne eDNA, we used a fan, like one you would use to cool
down a computer, and attached a filter to it. We then let it run for
some time," says Christina Lynggaard (@lynggaardc), first author and postdoctoral fellow at the University of Copenhagen.
The fan draws in air from the zoo and its surroundings, which could
contain genetic material from any number of sources, like breath, saliva,
fur, or feces, though the researchers have not determined the exact
source. "It could be anything that can become airborne and is small enough
to continue floating in the air," says Lynggaard. "After air filtration,
we extracted the DNA from the filter and used PCR amplification to make a
lot of copies of the animal DNA. After DNA sequencing, we processed the millions of sequences and ultimately compared them to a DNA reference
database to identify the animal species." "There's a leap of faith
component to some of this because when you deal with regular tissue or
even aquatic DNA samples, you can measure how much DNA you have, but with
these samples we're dealing with forensically tiny amounts of DNA," says
Clare. "In many cases, when we only sample for a few minutes we can't
measure the DNA, and so we have to jump to the next stage of PCR where
we find out whether there's any in it or not. When we sample for hours
we get more but there is a tradeoff." In each study, the researchers
detected animals inside the zoo and wildlife from the nearby. Clare's
team from Queen Mary University of London detected DNA from 25 species
of mammals and birds, and even DNA belonging to the Eurasian hedgehog,
which is endangered in the UK. Bohmann's team at the University of
Copenhagen team detected 49 non-human vertebrate species, including
mammal, bird, reptile, amphibian, and fish species. These included zoo
animals like the okapi and armadillo and even the guppy in a pond in
the tropical house, locally occurring animals like squirrels, and pest
animals like the brown rat and house mouse. Further, they detected fish
species used for feed for other animals in the zoo. Both teams took
extensive measures to check that their samples were not contaminated,
including by DNA already in their labs.
By choosing a zoo for the location of their studies, the researchers
knew the position of a large collection of non-native species, so they
could tell the difference between a real signal and a contaminant. "We
had originally thought of going to a farm, but if you pick up cow DNA
you must ask 'Is that cow here or is it some cow a hundred miles away
or in someone's lunch?'" says Clare.
"But by using the zoo as a model there's no other way I would detect
DNA from a tiger, except for the zoo's tiger. It lets us really test the detection rates." "One thing both our labs do is develop and apply new
tools, so perhaps it's not so surprising that we both ended up with the
same idea at the same time," says Clare.
However, the fact that both research groups are publishing at the same
time in the journal Current Biology is far from coincidental. After seeing
each other's articles on a preprint server, the two groups decided
to submit their manuscripts to the journal together jointly. "We
decided we would rather take a bit of a gamble and say we're not
willing to compete on this," says Clare. "In fact, it's such a
crazy idea, we're better off having independent confirmations that
this works. Both teams are very eager to see this technique develop." ========================================================================== Story Source: Materials provided by Cell_Press. Note: Content may be
edited for style and length.
========================================================================== Journal References:
1. Christina Lynggaard, Mads Frost Bertelsen, Casper V. Jensen,
Matthew S.
Johnson, Tobias Guldberg Fro/slev, Morten Tange Olsen, Kristine
Bohmann.
Airborne environmental DNA for terrestrial vertebrate community
monitoring. Current Biology, 2022; DOI: 10.1016/j.cub.2021.12.014
2. Elizabeth L. Clare, Chloe K. Economou, Frances J. Bennett,
Caitlin E.
Dyer, Katherine Adams, Benjamin McRobie, Rosie Drinkwater, Joanne E.
Littlefair. Measuring biodiversity from DNA in the air. Current
Biology, 2022; DOI: 10.1016/j.cub.2021.11.064 ==========================================================================
Link to news story:
https://www.sciencedaily.com/releases/2022/01/220106111549.htm
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