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eDNA
TRANSFORMING FIELD SURVEYS
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TROPWATER RESEARCHERS ARE REVOLUTIONISING
HOW WE INVESTIGATE LIFE UNDERWATER USING
WATER SAMPLES AND SOME SOPHISTICATED
eDNA TECHNOLOGY.
As the pace of development increases,
there is a pressing need for ever more
information on the status of biodiversity
within our aquatic environments. Field
sampling, especially in remote locations
of northern Australia is expensive, and
poses many resourcing, safety and logisticall
challenges. This has limited our knowledge
of aquatic biodiversity in such areas. Recent
developments in DNA technology, collectively
called ‘environmental DNA’ or ‘eDNA’,
however, gives us the potential to easily
and rapidly assess species presence within
any given waterbody.
eDNA refers to DNA that can be extracted
from air, water or soil, as plants and animals
shed cellular material in their surrounding
environment. The use of eDNA technology
allows positive identification of the presence
of certain aquatic species from the collection
and analysis of DNA material in water
samples, complementing traditional field
sampling. In practice, this means surveying
an aquatic field site is as easy as collecting
a water sample. The widespread application
of eDNA technology currently under
development will revolutionise the way
field programs are conducted, and greatly
increase the flow of information about
aquatic biodiversity.
There are many potential uses of eDNA
technology in aquatic ecosystems. One of the
first applications being trialled is the detection
of introduced invasive species. These are
a major problem in Australian waterways,
especially in the tropics where warmer
water favours the many tropical species found
in the aquarium trade (the main source of
fish introductions). The Ross River, which
runs through the city of Townsville in north
Queensland, has more invasive species than
any other river in Australia. At the last count,
20 species of exotic fish had established in
this river, tilapia being the most problematic.
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Ross River eD
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Tilapia pres
Title photo: Electrofishing is
the standard method for
surveying freshwater fish.
Inset: eDNA gel picture.
Images throughout
provided by TropWATER
unless credited otherwise.
TropWATER | eDNA
Tilapia, a member of the Cichlidae family,
y,
were introduced to Australia as aquarium
fish. They have been slowly spreading in
Queensland, and are now present in 21 of
the 76 catchments. They are considered the
e,
most problematic invasive fish across the state,
ew
and have recently been found in northern New
y
South Wales. Their success lies in their highly
efficient breeding strategies, flexible habitat and
dietary preferences. They tolerate a wide range
of temperatures, high salinities and low levels
of oxygen, and are also very aggressive, easily
out-competing and displacing native Australian
fish. It is vital to prevent their further spread
into new catchments. This goal relies upon
a combination of public education (not to
spread the fish) and early detection of
any newly-created populations to guide
management responses, including eradication
attempts where feasible. Early detection, and
understanding the distribution of nascent
populations, are key to deciding on appropriate
management responses for new incursions.
At James Cook University’s TropWATER,
Drs Damien Burrows and Dean Jerry along
with PhD student Heather Robson, are
developing field and laboratory methods
for the application of eDNA to assist tilapia
management.
The first step taken by the research team
was to develop primers specific to tilapia.
Primers are very short genetic sequences from
a standard part of the genome, and distinguish
DNA in a water sample the way a supermarket
scanner distinguishes products using the black
stripes of the barcode. As no two species have
the exact same ‘code’, the primers are species
specific. The TropWATER team have been
developing cheap and rapid means of
collecting, filtering and analysing water
samples, as well as doing experimental
work to verify detection probabilities under a
range of varying conditions (e.g. temperature,
salinity, flow, time since tilapia were present).
Above left: Filtering eDNA
samples in the field. Above:
Tilapia in the hand. Below:
Tansyn Noble collecting
water samples for eDNA
at Eureka Creek. Photo
Heather Robson.
The technique has a high reliability of detection
and has been used to pinpoint the distribution
of tilapia in the Mitchell, Townsville, Fitzroy,
and Pioneer catchments in Queensland, as well
as the recent incursion into New South Wales.
The detection of invasive species is
just one application of this transformative
technology. At James Cook University, eDNA
primers have been developed and are being
used to survey for endangered frog species
and the rare freshwater sawfish. TropWATER
are currently working on developing primers
for otherwise hard to detect cryptic species, as
well as Barramundi and various turtle species.
The focus on using eDNA for other invasive
pest species also continues. Within a few years,
they plan to be able to detect most aquatic
species in northern Australia via the collection
of water samples.
FOR FURTHER INFORMATION
Damien Burrows — [email protected]
www.environmentalDNA.com.au
www.tropwater.com