A complete DNA barcode library to manage Australia’s environment

By Olly BerryApril 19th, 2021

eDNA is poised to revolutionise the way we monitor Australia’s natural environment but it relies on a complete reference library of DNA barcodes. That's where we step in. CSIRO is working with partners to create this library for Australia’s most important species.

“The cultivation of natural science cannot be efficiently carried on without reference to an extensive library.”

When Charles Darwin and his co-authors wrote these words in 1847, could they have imagined a future where nature’s library was online? That this library used just four letters in its alphabet? That it would let you scoop a bucket of seawater from a reef and read what species of fish lived there?

Could they have imagined eDNA?

Close-up shot of a Loggerhead turtle with barnacles on its shell swimming over coral reefs.

Plants and animals, like this loggerhead turtle, shed eDNA into seawater. It can be used to detect and monitor species. © Commonwealth of Australia Great Barrier Reef Marine Park Authority

A new way to detect species

In the past few years, eDNA (short for environmental DNA) has revolutionised environmental monitoring. Scientists take environmental samples like water or soil, purify the fragments of DNA present and sequence their four-letter codes. They use those sequences, known as DNA barcodes, to identify the species present.

It works because all plants, animals and microbes shed tiny invisible pieces of DNA into the environment, constantly. Every species has a unique DNA sequence. The means eDNA is a very effective way to map the distributions of species, especially aquatic species.

eDNA is poised to revolutionise the way we monitor Australia’s natural environment. But using eDNA depends on having a reference library of DNA barcodes.

In a unique and valuable natural environment

“…I had been lying on a sunny bank and was reflecting on the strange character of the animals of this country as compared with the rest of the World.” Charles Darwin’s Beagle Diary, written in NSW in January in 1836

To identify a species using eDNA, we need to know its unique DNA barcode. Yet we know the DNA barcodes for only a small fraction of Australia’s half a million plants and animals. The shelves of Australia’s DNA barcode library are almost empty.

Some groups, such as fish, are relatively well covered. Other important groups, such as insects, marine invertebrates and plants are largely missing from the library. This means that during eDNA surveys, many species go undetected because their eDNA can’t be identified.

A full library of DNA barcodes is necessary for us to make the most of eDNA’s amazing potential to provide simple, cost-effectively information on the environment.

To revolutionise biomonitoring

Honey bee pollinating a native flower.

DNA barcode libraries can be used to discover which plant species have been visited by individual bees. Photo: Liz Milla

Australia’s size, complexity and high biodiversity mean that it has been expensive and difficult to gather information to manage it effectively. eDNA can change that.

Worldwide, governments, industries and citizen scientists are adopting eDNA. It’s highly accurate and works across the tree of life. It’s also a safe and simple way to detect species without harming or disrupting wildlife.

People have used eDNA in diverse ways. They have detected pests like the crown-of-thorns starfish on the Great Barrier Reef, looked for viruses like SARS-CoV2 in wastewater, searched for cryptic species like the platypus, measured the productivity of fisheries and even hunted for the Loch Ness Monster.

A complete DNA barcode library for Australia’s most important species would create enormous national benefit. It would support multiple industries including biosecurity and agriculture, fisheries, tourism, and biodiversity management. We could detect invasive pests arriving from overseas or map the distribution of endangered or dangerous species, even if they cannot be observed. We could provide the highest assurance to consumers that the food they eat is correctly labelled.

One of the greatest potential uses of eDNA lies in monitoring biodiversity and ecosystem health in hard-to-reach places, such as Australia’s marine parks.

If we change the game

Major DNA barcode library initiatives exist overseas and, at smaller scales, within Australia. Most DNA barcodes have been generated by a very hands-on, one-at-a-time process, which is slow and expensive.

Different scientists also focus on different DNA barcodes. As a result, multiple DNA barcode reference libraries exist that can’t be easily combined.

At CSIRO we have created new technology to solve this. Our miniaturised high-throughput genome skimming platform can generate DNA barcodes for any type of organism, from microbes through fungi, to plants, insects, mammals, and birds. Not only that, our solution creates a full set of all DNA barcodes for each species. This ensures the results are compatible with existing DNA barcodes used by scientists worldwide – a DNA barcode library to rule them all.

Let’s go!

A complete DNA barcode library for Australia’s most important species would create enormous national benefit. It would support multiple industries including biosecurity and agriculture, fisheries, tourism and biodiversity management.

For the first time we have the technology to create a DNA barcode library to match the next generation needs of environmental monitoring. We propose to achieve this significant goal by 2030. We want to work with a consortium of end-users, biodiversity and biosecurity experts, state and federal governments and philanthropic organisations.

Contact us if you can help us complete this ambitious, transformational mission.

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