Deciphering sea genomes

Marine ecologist Dr Eric Raes is a scientist with the Minderoo OceanOmics team and works aboard the 184-foot (58.22-metre) research vessel Pangaea Ocean Explorer.

As he explains, the cumulative effects of unsustainable fishing practices, rising seawater temperatures, ocean acidification, the expansion of oxygen minimum zones, pollution and eutrophication of coastal habitats have caused a rapid decline in ocean biodiversity.

“Thousands of marine species are considered endangered and extinction rates have accelerated in the past century,” he asserts. “Addressing this crisis is one of the most challenging tasks of our time.

“Nucleic acids (DNA and RNA) are the architectural blueprints for all life on earth. Capturing and analysing these blueprints from cells found in the environment with genomic tools is the study of environmental DNA,” he adds.

Collecting environmental DNA or eDNA from seawater is an efficient, relatively cost- effective means of gathering data that will be useful for governments and organisations involved in ocean conservation.

A partnership through the Australian government’s Ocean Discovery and Restoration Program is leveraging Minderoo’s OceanOmics experience to develop and scale the use of eDNA as a non-invasive, robust biomonitoring tool for management and conservation in Australia’s marine ecosystems. So far, the Australian Government has contributed AU$3.4 million and Minderoo has invested another AU$8.4 million toward the program.

Twenty-five Minderoo in-house researchers and dozens of other contributors are engaged in the project, which is focused on the waters off Australia’s west coast. “The aim is to provide proof of concept as to how the Australian government can apply eDNA as the tool for biodiversity monitoring, and in biosecurity and conservation.

“Knowing what’s in the ocean will allow us to protect it,” explains Dr Raes. “We believe that eDNA-based marine genomics and AI can form the technological basis for innovations that will revolutionise how we measure, understand and ultimately protect life in the ocean.

“By developing and deploying these technologies we will characterise and monitor marine wildlife at a pace and level of precision that traditional survey methods can’t achieve.”

He continues, “We’ve equipped Pangaea Ocean Explorer with shipboard laboratories containing cutting-edge cellular and molecular biology equipment, including high throughput DNA sequencing instruments and bioinformatics workstations.”

The partnership includes a series of oceanographic expeditions from the tropics, Cocos (Keeling) and Christmas Islands, all the way to the Southern Ocean, Tasmania.

The west coast of Australia is the chosen location for its sampling and research, primarily because of the alliance with the University of Western Australia, and for other compelling reasons, as Dr Raes outlines.

“The west coast is a biodiversity hotspot yet remains under-sampled and understudied compared to the east coast and other ocean basins such as the Atlantic and Pacific,” he says. “The technology can be applied to any marine ecosystem.

“Our aim is to showcase how genomics tools can be integrated into the day-to-day operations of conservation and fisheries managers. The ultimate goal of this endeavour is to gather data that can advance genomics research and ocean conservation by using innovative molecular methods to characterise and monitor marine wildlife.”

Pangaea Ocean Explorer is the state-of-the-art deep-water marine research vessel that has supported OceanOmics voyages on the east coast of Australia around the Great Barrier Reef, forays in waters off the Western Australian coast and expeditions to the Cocos (Keeling) and Christmas Islands.

Pangaea and her specially trained crew are equipped to support the research team. Her lazarette workspace was renovated in 2019–20 to provide adequate space, shelter and ready access to seawater collection and processing for cellular and molecular analyses.

There are purpose-built freezers for storing samples at ultra-low temperatures and a containerised custom laboratory where automated (robotic) extraction equipment will be operated and trialled in future missions.

Poised to set off on the next phase of the expedition to the Abrolhos Islands, 122 islands about 60 kilometres off the coast of Geraldton on Western Australia’s Coral Coast, Dr Raes describes eDNA collection and analysis as the natural next step in conservation science.

“Cataloguing marine biodiversity and describing the ecological patterns that shape our understanding of species’ distribution and evolution is fundamental to conservation,” he states.

“Ocean-scale, high-quality data generated by high-tech technologies, integrated by multi-disciplinary thinkers and well communicated to policymakers is required to arrest marine biodiversity loss before it’s too late.

“Genomics and AI are technologies that have the potential to transform ocean conservation,” he concludes. “Minderoo Foundation’s OceanOmics division is advancing marine genomics and computational technologies and approaches with the aim to improve knowledge through monitoring programs that inform how we combat threats to ocean health.”

Data and results can be found on the Minderoo OceanOmics Dashboard.

edna.minderoo.org