The ocean is in the midst of a biodiversity crisis
We’ve seen a rapid decline in ocean biodiversity from the cumulative effects of unsustainable fishing practices, rising seawater temperatures, ocean acidification, the expansion of oxygen minimum zones, pollution and eutrophication of coastal habitats.
As a result, thousands of marine species are considered endangered and extinction rates have accelerated in the past century. Addressing this crisis is one of the most challenging tasks of our time.
Cataloguing marine biodiversity and describing ecological patterns that shape our understanding of species’ distribution and evolution is fundamental to conservation. Ocean-scale, high-quality data generated by ground-breaking technologies, integrated by multi-disciplinary thinkers, and well communicated to policymakers, are required to arrest marine biodiversity loss before it is too late.
Genomics and artificial intelligence (AI) are technologies that have the potential to transform ocean conservation. Minderoo Foundation’s OceanOmics program 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.
Research using eDNA, marine genomics and AI
Nucleic acids (DNA and RNA) are the architectural blueprints for all life on Earth. Capturing and analysing these blueprints from pieces of DNA or cells found in the environment with genomic tools is the study of environmental DNA (eDNA).
We believe 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 cannot achieve.
We have equipped the research vessel, Pangaea Ocean Explorer, with shipboard laboratories containing cutting-edge cellular and molecular biology equipment, including high throughput DNA sequencing instruments and bioinformatics workstations.
We are investing in building and openly publishing the reference libraries for marine vertebrates which are necessary to accurately detect, monitor and determine the health of these species.
Marine expeditions
Our goal is to use eDNA approaches to more accurately monitor life in the global ocean. With an initial focus on the continental Australian Commonwealth marine estate, the Pangaea Ocean Explorer has already embarked on eight voyages, enabling sample collection and onboard genomic analyses for population-scale monitoring of the health of Australia’s ocean wildlife.
Samples of eDNA were collected and analysed from Australia’s Great Barrier Reef and Ningaloo Reef, as well as from the unique marine ecosystems of the Abrolhos Islands, the underwater canyon system of the Perth Canyon, and the nearshore waters off the south-west coast of Western Australia.
Contributing valuable evidence to support conservation and protection
The OceanOmics program supports the goal of conserving 30 per cent of the world’s ocean by 2030 by fostering novel methods for monitoring and combating threats to marine wildlife and ecosystems; quantifying the health status of current marine protected areas (MPAs); and assisting governments and management agencies in identifying new biodiversity hotspots and ecosystems in need of protection.
Generating reference genomes for thousands of marine species
To characterise marine biodiversity based on eDNA we require a library of references. That way, we can look up the snippets of DNA found in seawater and identify all the species present in our samples, similar to a dictionary. Unfortunately, to date only one per cent of the 20,000 known species of marine fish have had their genome sequenced. In collaboration with our global partners, one of OceanOmics’ ambitious goals is to generate and release to the public the reference genomic resources for thousands of marine species; and by doing so empower conservation science.
- Dr Philipp Bayer, Research Officer, Computational Biology
- Dr Sebastian Rauschert, Research Officer, Bioinformatics
- Dr Eric Raes, Research Officer, Field Operations & Ocean Health
- Dr Matt Fraser, Research Officer, Biodiversity & Ecology
- Dr Shannon Corrigan, Research Officer, Vertebrate Genomics
- Marcelle Ayad, Research Assistant
- Dr Priscila Goncalves, Head of Operations, OceanOmics
- Yvette Mordini, Strategic Portfolio Manager
- Jemma Rowe, Manager, Partnerships, OceanOmics
- Dr Steve Burnell, Director, OceanOmics
- Dr Richard Edwards, Laboratory Lead, Ocean Genomes
- Dr Rachel Jamieson, Laboratory Manager
- Dr Lara Parata, Postdoctoral Research Fellow
- Dr Emma de Jong, Postdoctoral Research Fellow
To support and steer this important work, Minderoo Foundation collaborates with leading experts in an array of marine genomics, AI and conservation fields from the USA, Europe, New Zealand, and Australia through the OceanOmics Scientific Advisory Panel.
- Professor Barbara Block, Hopkins Marine Station, Stanford University, United States
- Professor Michael Bunce, Institute of Environment Science and Research (ESR), New Zealand Crown Research Institute, New Zealand
- Professor Tom Gilbert, Centre for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Associate Professor Siavash Mirarab, Department of Electrical and Computer Engineering, University of California San Diego, United States
- Dr Ramunas Stepanauskas, Single Cell Genomics Center, Bigelow Laboratory for Ocean Sciences, United States
eDNA sequencing datasets
Raw reads
The raw DNA sequencing reads of our expeditions are continuously uploaded to the Sequence Read Archive (SRA).
When using this data, please acknowledge the Minderoo Foundation by including this text in your Acknowledgments section: We would like to thank Minderoo Foundation for sequencing reads deposited in [use sequence IDs or DOIs here].
Rowley Shoals Expedition – BioProject PRJNA930913
