Environmental DNA (eDNA)Environmental DNA (eDNA) 

eDNA research is featured in the museum's current exhibition Ultimate Depth: A Journey to the Bottom of the Sea. Dr Georgia Nester from exhibition partner Minderoo Foundation explains. 

Environmental DNA, or eDNA, is genetic material that organisms leave behind in their environment. It could be mucus, faeces, urine, skin cells, and other biological traces. Scientists can extract this DNA from samples and sequence these to detect one or more species. This makes eDNA an extremely versatile tool in ecological and conservation science. 

It is a powerful method for monitoring biodiversity, tracking endangered or invasive species and understanding how ecosystems are changing over time. Samples can also be collected remotely, eDNA is especially useful in sensitive or hard-to-reach habitats like the deep sea, alpine lakes, or caves. 

Beyond biodiversity surveys, eDNA has also been used to: 

• reconstruct animal diets and food webs,
• monitor rewilding efforts,
• detect diseases in wildlife,
• track seasonal movements like fish spawning, and
• help identify cryptic (difficult to identify on looks alone) species. 

eDNA can be collected in various ways, depending on the environment being sampled and can be collected either actively or passively.

In marine environments, eDNA is typically collected from water or sediment. 

For deep-sea sampling, we use:

• full ocean-depth landers equipped with Niskin bottles for active water collection, and/or
• sponges or filter papers mounted to the outside of the lander for passive collection. 

Once the landers are recovered, all samples are processed on board. They are preserved in a buffering solution and frozen to prevent degradation, then taken back to the lab for analysis. Looking ahead, we’re also exploring the use of automated samplers that can collect and preserve eDNA directly on the seafloor, offering exciting new possibilities for deep-sea biodiversity monitoring.

Using eDNA alongside deep-sea landers, we’ve explored some of Australia’s most remote deep-sea environments, including the Diamantina Fracture Zone and waters around Christmas Island. These regions reach depths of up to 6,000 metres and are extremely challenging to study using conventional methods alone.

What makes eDNA especially powerful in the deep sea is its ability to detect species that may never pass in front of a camera or enter a trap. It is particularly useful for deep-sea research because it can gather information and allows us to sample species from the ocean surface to the seafloor in a single go.  

By analysing eDNA collected from both the water column and seafloor, we’ve detected deep-sea fish such as snailfish, cusk eels, and sixgill sharks. These same species were also recorded by our lander cameras, showing how eDNA and visual tools can complement each other to build a fuller picture of deep-sea biodiversity. Importantly, eDNA also revealed species that our cameras and traps did not, including the elusive giant squid and Cuvier’s beaked whale, one of the deepest-diving mammals on the planet.

By combining eDNA with traditional methods, we’re building the first detailed picture of deep-sea life in these regions- vital knowledge for understanding and protecting Australia’s vast and largely unexplored deep-sea ecosystems. 

Long-term datasets from coastal and shallow-water ecosystems indicate that Australia’s marine biodiversity has experienced significant change over recent decades.  These data show significant losses and redistribution of species.  

For example, heat waves and associated coral bleaching events have become more frequent and severe. Warming ocean temperatures, habitat loss, and pollution have driven declines in habitats like coral reefs, seagrass meadows, and kelp forests in many parts of the country. Overfishing and changes in ocean chemistry have also directly affected fish populations and the broader food web. In some areas, invasive species have added further pressure to native marine life. Marine biodiversity must either adapt to accommodate, or shift where they live to avoid, these pressures. When this isn’t possible, biodiversity is lost.  

In contrast, deep-sea ecosystems remain far less studied over long timescales, meaning we don’t yet have a clear picture of how biodiversity has changed in these remote environments. What we do know is that deep-sea habitats are not immune to human impacts. Pollution, climate change, and seafloor disturbance may already be affecting species we’re only just beginning to discover and understand. 

Robust and holistic measurements of the ocean – including biodiversity discovery, monitoring of ocean conservation areas, quantifying impacts of overharvest and climate change - remain both challenging and expensive.  

DNA-based intelligence offers a scalable and affordable approach to ocean measurement that can support better decisions about restoring and safeguarding ocean health.

OceanOmics envisions a world where ocean health is routinely assessed by robust, scalable and accessible technologies, facilitating rapid adaptive responses to emerging threats. OceanOmics: 

• advocate for integration of eDNA tools and in conservation and management frameworks,  
• empower communities and stakeholders to routinely collect eDNA samples and benefit from eDNA data derived insights,  
• develop and deploy scalable eDNA-based ocean monitoring tools and  
• build the foundational genomic resources that can underpin effective and holistic conservation management of ocean biodiversity.  

OceanOmics works to ensure that healthy natural ecosystems are safeguarded for future generations. 

Robust and holistic measurements of the ocean – including biodiversity discovery, monitoring of ocean conservation areas, quantifying impacts of overharvest and climate change - remain both challenging and expensive.  

DNA-based intelligence offers a scalable and affordable approach to ocean measurement that can support better decisions about restoring and safeguarding ocean health. OceanOmics organises itself around four focal points:  

• building foundational DNA tools and resources that can support eDNA based ocean monitoring at scale,  
• increasing the resolution eDNA tools, and making eDNA data quantitative, through technological innovation,  
• getting DNA tools in the hands of those best positioned to amplify the message that we must ‘listen to nature’ more effectively, and  
• making eDNA and genomic data understandable and translating it into clear actionable insights for decision and policy makers.