How we can detect pretty much anything - Hélène Morlon and Anna Papadopoulou
For years, scientists have been staking
out this remote forest in Montana
for an animal that’s notoriously
tricky to find.
Camera traps haven’t offered
definitive evidence,
and even experts can't identify
its tracks with certainty.
But within the past decades,
researchers have developed methods that
can detect even the most elusive species.
And so, in 2018, these scientists took a
sample from some conspicuous snow tracks.
Lab tests showed conclusive results:
the Canada lynx was indeed present
in the area.
Without seeing the cat,
scientists had proof it was there
because of environmental DNA or eDNA.
Using a technique called
DNA metabarcoding,
researchers can take a sample
from the environment
and learn which organisms are in it
or have recently passed through it.
The world is covered in DNA.
It’s all around us—
on the ground, at the bottom of the ocean,
and up in the clouds.
Multicellular organisms are constantly
shedding cells.
But until recently,
eDNA wasn’t very useful to us.
Traditional scientific techniques couldn’t
parse environmental samples
containing mixed genetic material
from multiple species.
But DNA metabarcoding can.
DNA begins to degrade once it’s exposed
to the environment.
In the ocean, for example,
it may only persist for a few days.
So in many contexts, eDNA is useful
for telling us about the recent past.
The process of DNA metabarcoding starts
with an environmental sample
like a core of soil, a vial of water,
some feces, an insect trap,
or even the blood from leeches’ stomachs.
Researchers then sift out everything aside
from DNA by blending the sample up
and using enzymes that break down cellular
proteins and release DNA,
which they purify.
The result is a “soup”
of all the DNA in the sample.
Scientists then apply the polymerase
chain reaction or PCR,
which uses artificial DNA strands
called universal primers.
These primers bind to DNA sequences
that are similar across species,
then amplify genetic barcodes
that are species-specific.
High-throughput sequencing then reads
millions of these DNA fragments,
simultaneously.
And finally, researchers compare them
to reference databases
and identify how many and which species
are present—
or if they’ve found entirely new ones.
This method has led to the discovery
of tens of thousands of species
over the past decade.
While metabarcoding can detect
elusive animals like the Canada lynx,
it can also help scientists
identify invasive species.
In Yosemite, researchers used eDNA
to track and remove invasive bullfrogs.
Once no trace of these
amphibians remained,
they reintroduced a threatened native
species, California red-legged frogs,
which had disappeared from the area
some 50 years prior.
Likewise, DNA metabarcoding can be
used to monitor biodiversity.
For example, using traditional approaches,
categorizing all of the insects in a
hectare of rainforest can take decades.
But DNA from insect traps could yield
these results in just a few months.
One study compared insects
from adjacent forest and plantation sites
within China’s Yunnan province.
It quickly found that not only were
plantations less diverse,
but deforestation affected
insect groups unequally.
Grasshoppers thrived in cleared areas
while specialist forest beetles declined.
Using eDNA, scientists are able
to investigate
complex ecosystem interactions.
Tracking thousands of insects
as they visit flowers is impossible.
Instead, researchers can study
the DNA left on flowers and insects
to map pollination networks.
Before these techniques were available,
we didn’t really know how much pollination
was happening at night
because we couldn’t observe it.
Now scientists understand that moths
are important nocturnal pollinators.
eDNA can even tell stories
of long extinct species.
Cold, dry, and low oxygen conditions are
perfect for preserving genetic material.
By digging deep
into the Arctic permafrost,
researchers found 50,000 year old DNA,
which they matched
to the nutrient-rich plants
found in the stomachs of woolly mammoths.
With eDNA, they also found
that less nutritious grasses
colonized the Arctic steppe
during the last ice age,
potentially contributing
to the mammoth decline.
As we face another period
of climate change—
this time due to human activities—
understanding our planet’s rapidly
shifting biodiversity
will be crucial to protecting it.
Fortunately, eDNA and metabarcoding
give us the tools to document
rapid change in real time.
