Genomic-monitoring
We here choose to focus our eDNA sampling on iconic Sydney Harbour, which has more than 240 kilometres of shoreline including beaches, coves, bays, commercial ports, naval bases, and reclaimed land. Sydney Harbour also has a rich fish fauna, quantified at nearly 600 resident/transient species based on the Australian Museum’s historical collection records dating back to the 1870’s. By sampling seawater from our AM vessel at several locations in North Harbour, Middle Harbour, Sydney Harbour, and Darling Harbour, as well as at varying distances up the Lane Cove and Parramatta Rivers, we aim to deliver on the following by sequencing the eDNA free-floating in these samples: (i) Species discovery, with a focus on fish and crustaceans. In short, detecting unexpected fauna and fauna for the first time. (ii) Refining distributions. In short, fish and crustacea found in new locations and where one might not expect within the harbour. (iii) Invasive species. In short, detecting taxa that are not meant to be in Sydney Harbour and ones that might have damaging effects on the ecosystem and infrastructure. (iv) Anthropogenic effects. In short, examining how the diversity of species may change with distance from the open ocean, but also with varying levels of urban impacts ‘up river’.
Area of science
Biology
Systems used
Nimbus
Applications used
AdapterRemoval; OBITools; USEARCH; BLASTN; LULUThe Challenge
Australia governs the earth’s third largest ocean territory and protection of its biodiversity, ecosystem functioning, productivity and resilience is key to protecting the $47.2 billion that Australians derive per annum from its ‘blue economy’. Environmental DNA (or eDNA) technologies provide a new and exciting alternative to traditional monitoring techniques in order to better manage these precious resources.
The Solution
By combining next-generation sequencing with the powerful bioinformatic pipelines implemented on NIMBUS, we can now harness the sensitive approach to monitor large portions of Sydney Harbour and the east Australian coastline.
The Outcome
The Pawsey NIMBUS platform has provided the processing power required for this project. We have the following publication currently in review:
Hobbs, J.-P.A., Sinclair-Taylor, T.H., and DiBattista, J.D. (in review) Ecological versatility aids adaption to climate change: coral reef fishes expand their range by colonising a new habitat. Biology Letters.
With the following in advanced stages of preparation:
DiBattista, J.D., Fowler, A.M., Reader, S., Hay, A.C., Parkinson, K., Riley, I.J., and Hobbs, J.-P.A. (in preparation) The use of environmental DNA to monitor impacted coastal estuaries: A case study of Manly Lagoon in New South Wales. Biological Conservation.
