New technology is helping scientists to track down pests, detect endangered species, and find infectious viruses, all through the tiny bits of DNA they shed.
Speakers at the Environmental DNA Conference taking place in Wellington next week will share their stories of finding elusive pest wallabies, measuring river health, predicting algal blooms, and sieving DNA from the air.
The SMC asked conference speakers to comment.
Dr Adrian Cookson, Senior Scientist, AgResearch, comments:
“The rivers and streams of Aotearoa New Zealand are conveyor belts of genetic material from the environment. Things like slime, faeces, skin, hair, pollen, and tiny organisms release DNA into the water. This is known as environmental DNA (eDNA), and scientists use it to monitor ecosystems and check the health of our waterways.
“By analysing eDNA, they can detect a wide range of life, including insects, fish, mammals, plants, algae, and bacteria—many of which are too small or hidden to see. This groundbreaking method helps communities understand which species are present, including treasured native wildlife (taonga) and potential biosecurity threats.
“Scientists from AgResearch and Wilderlab will present recent eDNA research at this conference, conducted in collaboration with the Drysdale whānau (dairy farmers), Māori environmental groups (Taiao Ora Contracting), and Ngāi Te Rangitotohu and Ngāti Mārau hapū from Rākautātahi marae. Their work centred on freshwater sites at the headwaters of the Manawatū River near Ngā Mokopuna o Rongotautāwhi (Norsewood district) including samples taken from native bush and farmed sites.
“Subtle declines in ecosystem health were strongly correlated with changes in concentrations of nutrients, such as nitrogen and phosphorus, and contaminants, such as turbidity and E. coli, driven by increased land-use for farming. Nevertheless, almost 500 species were identified including whīo/blue duck, ruru/morepork, kōtare/kingfisher, tuna/longfin eel, kaharore bully, dwarf galaxias and freshwater crayfish/kōura.
“Community leadership was central to our methodology, enabling local stakeholders to actively participate in meaningful water monitoring and data interpretation. This approach not only fulfilled regulatory requirements but also fostered a deep connection with the river, enhancing community-led conservation efforts. By enhancing the mauri (life force) of the community through active participation and capacity building, this approach is a case-study for sustainable, collaborative efforts in environmental management and revitalisation.”
No conflict of interest.
Gracie Kroos, PhD candidate, Department of Anatomy, University of Otago, comments:
“Our team at the University of Otago is working to explore the use of environmental DNA from water and air samples to detect wallabies in New Zealand.
“Wallabies are an extremely elusive and mobile pest species that are often difficult to detect using standard methods e.g., detection dogs, thermal scopes. This issue is made even more challenging when wallabies exist at low densities across large landscapes; often many hours of search are required for a single detection.
“We are exploring proof of concept with using air eDNA, since very little research has been done so far using this technique, to see in what situations and at what distances we can detect wallabies from air samples. It’s been successful so far in a captive setting at a wallaby park, so we are now exploring natural settings around Central Otago and South Canterbury.
“I am optimistic about the future possibility of using air samples for terrestrial species detections e.g., for pest wallabies, although at this stage, important work needs to be done to understand sensitivity and accuracy of air eDNA before it can be implemented into management programmes.”
No conflict of interest.
Dr Steve Archer, Senior Scientist, Agresearch, comments:
“Airborne DNA actually originates back to Charles Darwin, who found Saharan dust on the HMS Beagle, looked under a microscope and found animalcules – or microorganisms. So the idea that stuff’s blowing around in the air is a really old concept.
“What the new concept is, and why eDNA is so so amazing, is it allows us to look at things that are completely invisible to the naked eye.
“Australia, our closest major land mass source, is a source of potential airborne pathogens blowing across in the air. These include moths and microorganisms. Atmospheric modellers can tell us when there are air bridges coming from Australia, which are like conveyor belts for biomass in the sky. It’s believed that these are associated with incursions of things like Myrtle rust or fall armyworm.
“My work is ‘ground truthing’ the atmospheric modeling by trying to determine if there is a difference in the DNA signature of the air when the wind is coming from Australia during these air bridge events, and when it’s not.
“Getting a really defined idea of how this is working is exceptionally hard, because although microorganisms are in every part of the air, the biomass is so incredibly low. Per cubic meter of air, there are maybe 10,000 cells, which sounds like a lot – but this is many, many fold less than in a single milliliter of water, which is many fold less than a single milligram of soil. The additional problem is, of course, that the weather in New Zealand changes every 10 minutes.
“There is a massive amount of increasing information in the field of airborne eDNA, and it’s one of those fields that is prime territory to make some really interesting discoveries.”
No conflict of interest declared.
Associate Professor Michael Knapp, University of Otago; and Coastal People: Southern Skies Centre of Research Excellence, comments:
“Environmental DNA is genetic material that organisms have left behind in water, soil, air or even food items. The first studies of environmental DNA go back more than 20 years, but this work has really taken off over the past 10 years. Today it is, for example, being used to detect invasive species in marine and freshwater environments, to survey biodiversity in hard-to-access places, to detect the COVID virus in wastewater and even to find out the types of pollen that are currently in the air.
“The field is rapidly developing, and we are likely only scratching the surface of its full potential. The conference will discuss exciting innovations and new applications as well as some of the challenges and limitations the field still has to overcome.
“For example, environmental DNA has demonstrated its potential to be a very cost-effective way for stakeholders such as the Department of Conservation to conduct biodiversity monitoring. However, to fully utilize this potential, it does require an initial investment in creating reference databases. Only species for which we know at least a small part of the genome can be identified in environmental samples. Great progress has been made in this field with very limited funding, but we are still a far cry from having full reference coverage for our marine and terrestrial ecosystems.
“I expect this conference to be an exciting meeting that will present plenty of real-life applications of environmental DNA technologies that will have a major impact on a broad range of fields from conservation to health sciences.”
Conflict of interest statement: I am a member of the organising committee for the 2nd Australian & New Zealand Environmental DNA conference.
Benjamín Durán-Vinet, PhD candidate in Genetics, University of Otago, comments:
“Environmental DNA is what we call traces of DNA that organisms leave behind in air, water, or on land, like an invisible fingerprint of their presence. This opens an exciting opportunity: the ability to infer the presence of organisms without needing to see them, revolutionizing conservation and biosecurity efforts.
“Now environmental DNA has teamed up with CRISPR technology – a groundbreaking gene-editing technology that has skyrocketed since its inception, and now even has its own suite of dedicated documentaries and TV shows (Unnatural Selection, Human Nature and Biohackers).
“However, rather than editing genes, we are taking advantage of a lesser-known use of CRISPR which taps into its natural ability to detect a specific genetic sequence with high sensitivity in a sample. This allows us to detect harmful species of interest from environmental DNA without costly, time-consuming and limited visual searches or capture & release surveys.
“The result? Faster, cheaper, and more effective decision-making to help protect the environment. This technology had already proven its value during the COVID pandemic when the FDA granted it emergency use authorization for detecting COVID-19-causing virus.
“Our team at the University of Otago is exploring and expanding CRISPR-based detection as an ultra-sensitive and programmable environmental DNA screening tool. Virtually capable of detecting any environmental/organism DNA combination that is targeted, either in the lab or in the field, within an hour.
“What’s more, we use artificial intelligence to accelerate and refine CRISPR to detect emerging biosecurity risks to New Zealand from the DNA fingerprints they leave behind. Potential applications include early detection of invasive species (like Undaria seaweed), searching for endangered species and early detection of toxic algae outbreaks in rivers, lakes and coastal waters.
“We are presenting promising preliminary results of our research at this prestigious eDNA conference.”
This comment is written with input from Dr Jo-Ann L. Stanton, Dr. Gert-Jan Jeunen, Dr Anastasija Zaiko, Dr. Xavier Pochon, and Distinguished Professor Neil J. Gemmell.
No conflict of interest.