Ocean Diagnostics and Minderoo Foundation scale environmental DNA technology for marine parks

Planetary and human health, food security and the economy rely on flourishing oceans with healthy biodiversity, but the Ocean is amidst a biodiversity crisis. Unsustainable fishing practices, rising seawater temperatures, ocean acidification, and other human activities have cumulatively affected the health and resilience of thousands of marine species. To meet the international goal of protecting 30 percent of the world’s oceans by 2030, governments around the globe are expanding marine conservation efforts.

While approximately 43 percent of Australia’s coastline has already been named as marine protected areas, the parks themselves have experienced varying capacity to assess and provide ongoing biodiversity conservation. To deliver a suite of scalable biodiversity monitoring tools that are accessible for marine park end users, Australia’s Minderoo Foundation partnered with Ocean Diagnostics to reconfigure the company’s automated depth sampling instrument for environmental DNA applications. From March to April of 2023, Minderoo’s OceanOmics team collected hundreds of eDNA samples across 2,000 kilometers of Australia’s southwest coastline using the device called Ascension. 

“Having Ascension that could potentially revolutionize the field was just like a beacon,” recalls OceanOmic’s Research Analyst, Marcelle Ayad. 

photo above OF minderoo's MARCELLE AYAD AND dr. ERIC RAES  with ascension, courtesY of MINDEROO FOUNDATION

Originally designed to help researchers overcome the challenges of sampling microplastics throughout the water column, Ascension is a 22-pound/10 kg instrument that collects filtered water samples directly in-situ down to 400-meter depths from the side of a small boat or fixed installation. 

“eDNA is so sensitive,” Ayad affirms. “There's DNA everywhere, so it's important to have a sterile environment and avoid contamination. That becomes quite challenging for end users to implement if they cannot go back to a molecular lab and have a sterile space. You can just go out with the Ascension device and sample quite easily on the tender itself. It opens a lot more doors for end users to implement eDNA into their (biodiversity) monitoring.” 

Ascension enabled the team to collect samples from areas typically understudied and under mapped (like Esperance to Albany) due to their remote, rocky and risky terrain. They also studied the Abrolhos Islands - a chain of 122 islands and associated coral reefs spanning over 80 kilometers along the Indian Ocean - and were joined by local marine park rangers on Christmas and Cocos. The expedition provided the first-ever eDNA biodiversity assessment of Christmas Islands. 

“There is always variability in the ocean. Always variability in biology. Having robust automated technology that allows us to capture eDNA is very powerful. The applications are really endless,” illustrates OceanOmics’ Marine Ecologist, Dr. Eric Raes. 

photo above OF OCEANOMICS TEAM DEPLOYING ASCENSION, courtesy of MINDEROO FOUNDATION

With seven independent sampling channels, Ascension collects reliable data to provide a robust snapshot of various species from microbes to jellyfish and fish and reduces both the time-consuming filtration process and sample contamination risks of existing eDNA sampling methods. 

“We don't have to sit there and pour water into little cups or filter anything. We can just do this in situ from the boat. Thinking about the number of hours and how long the days are when you're out in the field, it was really exciting for me,” explains Ayad. She continues, “Ascension was so great to have. You just throw it overboard. (With) in situ filtration and not needing to transport water back, the sample could just go straight into a preservative in the field. That was quite awesome.” 

In several tropical, sub-tropical and temperate water environments a side-by-side comparison was conducted between Ascension and Niskin bottle sampling, a method that requires collecting, transporting on ice, then filtering samples before they can be preserved for later processing. With in-situ filtration and an easy in-field preservation workflow, Ascension removes the need for these steps. 

Dr. Raes emphasizes, “What really struck us both, and everybody that used Ascension while we were out on a tender, is that suddenly you go, what else can we do now? Because the device is collecting water, already filtering and getting all the metadata, you can think about other questions like how we can enrich our data. Suddenly you have so much more time on your hands to do something else!” 

Ayad chimes in, “It just opens doors.” 

photo above of dr. eric raes  and marcelle ayad filtering water from niskin sampling device after deployment. courtesy of minderoo foundation

While research groups and governments may have access to large research vessels from which they can conduct open ocean sampling, most park rangers conduct coastline work using smaller tenders because many of these conservation zones include remote or tucked away areas like shallow lagoons or exposed rocks. 

Dr. Raes clarifies, “Society lives near the coast. While exploring the open ocean can be fascinating, ultimately, we all depend on the coast. This is where humans have the most significant impact. Trying to get some time series going by local rangers and having a device that they can trust and deploy is the way we want to go.” 

Ensuring the end users themselves could test the scalability of Ascension, several park rangers joined Ayad and Dr. Raes along the expedition to deploy the instrument first-hand. 

“They were really impressed to see how simple it is to deploy and retrieve the samples. When they think eDNA, they think molecular genomic techniques and how tricky and complicated it will be,” shares Ayad. She continues, “They were able to deploy it themselves and go, ‘oh, that was reasonable. That's something that we could implement. We could go out on our tender and we could absolutely do that.” 

photo above of oceanomics team  with edna samples, courtesy of MINDEROO FOUNDATION. 

Like human DNA, eDNA carries the genetic codes that provide information about the species living in an ecosystem. Used to detect invasive species and monitor species distribution and changes over time, eDNA has immense potential for biodiversity protection. Providing a comprehensive snapshot of an entire ecosystem's biodiversity in a single sample, without affecting any of the species it aims to protect, environmental DNA has become a powerful biodiversity monitoring method. 

“(eDNA) allows us to assess biodiversity. Often, we just do not know what is living here in the very biodiverse waters of Australia, and eDNA is a useful tool to define it,” notes Ayad.

Traditional biodiversity assessment methods include visual surveys taken by aerial video or underwater diving, net trawls or destructive sampling. These methods are time-consuming, labour intensive, harmful or prone to human error and can easily miss cryptic, well-hidden species. 

Dr. Raes reveals, “People have always been curious to explore. In the 19th century, ecologists & naturalists travelled the world using binoculars, microscopes and instruments to observe our planet. We are just observing it through a different lens with genomic technologies, and that gives us a lot more insights in how diverse life on Earth really is.” 

photo above of ascension sampling alongside dr. eric raes  in abrolhos islands courtesY of Giacomo dOrlando, 

Although eDNA methods have been around for over a decade, they were typically reserved for the academic research community mainly because there was no way to commercially process the data from sample collection through to analysis. 

“The technology that stands behind genomic techniques has dramatically increased. This has opened some doors for the technology to be used for other applications that it wouldn't have been used for before, because it wouldn't have been feasible,” says Ayad.

To date, only four percent of marine vertebrate species have had their genome sequenced. The OceanOmics team generates and releases to the public high-quality reference genome resources for marine vertebrate species and, by doing so, empowers eDNA applications and conservation science. The team collects and preserves eDNA samples, preserves then processes the samples at a dedicated high throughput molecular lab at the University of Western Australia which extracts the DNA, amplifies and sequences them all in house. They also build the genome reference library and advance research and development to scale technology and establish strong partnerships. 

“Technology allows us to get more data to paint a better picture of the world,” Dr. Raes announces. 

photo above of dr. eric raes diving alongside ascension in abrolhos islands courtesy of Giacomo dOrlando, 

Committed to making accessible the scientific data needed to protect ocean health, Ocean Diagnostics was keen to collaborate with the OceanOmics team and empower end users to access hard-to-obtain biodiversity data. 

“We have been thrilled to work with Minderoo Foundation and the OceanOmics team to develop a new enabling application in eDNA with our Ascension device. The OceanOmics program represents one of the most impactful and innovative marine genomics and conservation programs in existence today and has provided us with a strong partner to show the utility of our instrument in marine biodiversity and species monitoring. We look forward to continuing to support Minderoo Foundation in our shared vision of returning our oceans to a flourishing state," remarks Ocean Diagnostics’ Co-Founder and CEO, Ethan Edson. 

“We're all passionate about doing ocean science, scaling it up and protecting the marine environment. Working with passionate, professional people is just amazing. Having a true partnership with Ocean Diagnostics and getting feedback instantaneously is really helpful,” expresses Dr. Raes. 

Ayad concurs, “Ocean Diagnostics is one of my favourite partnerships because of the people as well as the technology. I’m really proud to see the scale and the amount of data that we’ve collected using (Ascension). Going from conversations to implementing (the tech) across remote and huge areas makes me really excited to analyze that data and see what we get from it.” 

After the data is interpreted to uncover potential species of interest, the OceanOmics team will build and publish accessible reference libraries of marine vertebrates which are necessary to accurately detect, monitor and determine the health of these species ongoing. 

The graph above is a statistical analysis showing edna samples collected with a niskin (circles) and ascension (triangles) and shows consistent site fidelity with no significant differences observed between the two methods. the Colours denote different comparative sites where edna was collected along the southwest Australian coastline (top figure; green polygons on the map show marine parks). graph courtesy of dr. eric raes. these findings demonstrate the immediate ability to scale eDNA sample collection by the incorporation of automated sampling devices. High-throughput eDNA sampling devices offer significant advantages for marine monitoring, including increased efficiency, cost-effectiveness, automation, standardization, and scalability.

Ayad describes, “A lot of genomic data can be presented in a challenging way to interpret. Developing systems so (stakeholders) can look at the data in a format that they want would make them keener to implement that kind of method into their bio monitoring toolbox.” She continues, “eDNA tools can really give us insights to the diversity that is present in those marine protected area across space and time.” 

Both Ayad and Dr. Raes convey that biodiversity monitoring requires a multidisciplinary approach involving the people at sea, rangers on the ground who can monitor changes over time, people in the lab analyzing the data, computational biologists and policy makers. They plan to work with marine park stakeholders to implement technological advancements into daily operations and use the data for policy decisions, all while navigating international law and respecting Indigenous rights to DNA data sharing. 

Through the synergetic collaboration, both Minderoo and Ocean Diagnostics are keen to see the technology applied in marine parks to help discover biodiversity hotspots and inform evidence-based management solutions that protect these habitats and measure their impacts. 

“I think that there are a lot of applications for it.” says Dr. Raes. He concludes, “Ascension can be integrated into normal monitoring of (marine parks) to give them a vast amount of information that they wouldn't be able to get with other methods.” 

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