Miss Laura Missen1, Miss Marcelle Ayad2, Dr Sang Huynh1, Mr John Blinco1, Dr Eric Raes2, Miss Anna Depiazzi1, Dr Shannon Corrigan2, NA OceanOmics Division1,2, Dr Priscila Goncalves2
1The University of Western Australia, Crawley, Australia, 2The Minderoo Foundation, Perth, Australia
Biography:
Laura Missen has a background in marine biology and molecular ecology. She is currently a Scientific Officer at the Minderoo OceanOmics Centre at The University of Western Australia where she focuses on the optimisation and automation of laboratory techniques for environmental DNA metabarcoding of marine vertebrates.
Marcelle Ayad is a Research Analyst at The Minderoo Foundation. She has a background in trophic and behavioural ecology focusing on landscape-scale effects of predator-prey interactions.
Her current interests are in developing and optimising field and laboratory techniques of environmental DNA to enhance marine monitoring and conservation.
Abstract:
Environmental DNA (eDNA) metabarcoding is an increasingly valuable tool for marine biodiversity monitoring, but large-scale implementation is challenging due to costs, processing times and the labour-intensive nature of eDNA collection and laboratory processing. Here we present the integration of automated technologies in the metabarcoding workflow to address these challenges, enhancing scalability and reproducibility, as well as reducing human error and contamination.
The Ascension device by Ocean Diagnostics is an in-situ sampler that can filter water at depth with minimal human intervention, reducing contamination risk. We have deployed this instrument across multiple sites in Western Australia, demonstrating considerably reduced sampling times compared to a Niskin-based approach, while maintaining consistent taxonomic outcomes. For extractions, we have implemented the Promega Maxwell RSC© 48, an automated system capable of processing 48 samples simultaneously, which has quadrupled our extraction capacity while consistently yielding high-quality DNA. We have established a fully automated qPCR setup using the Biomek i7 Workstation and Echo 525. The Biomek i7, a high-precision liquid handler, efficiently plates master mix and eDNA extracts, while the Echo 525 uses acoustic waves for precise transfer of indexed primers. Evaluation against manual methods showed no significant differences in qPCR metrics. Additionally, post-PCR pooling and clean-up procedures have been validated on the Biomek i7, with Next Generation Sequencing revealing no significant differences in community composition between manual and automated methods.
These advancements demonstrate the potential of automation to scale-up biodiversity monitoring, improve operational efficiency and reproducibility, and enable comprehensive, real-time assessments to inform marine conservation efforts.