Dr Haylea Power1, Dr Darren Korbie2, Dr Mitchell O’Brien3, Dr Miwa Takahashi1, Dr Henry Hui4, Dr Kathy Fuller4, Dr Oliver Berry1, Dr Simon Jarman5
1Environomics Future Science Platform, Indian Ocean Marine Research Centre, Commonwealth Scientific and Industrial Research Organization, Perth, Australia, 2The Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology at The University of Queensland, Brisbane, Australia, 3Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organisation, Sydney, Australia, 4Translational Cancer Pathology Laboratory, School of Biomedical Sciences, The University of Western Australia, Perth, Australia, 5School of Molecular and Life Sciences, Curtin University, Perth, Australia
Biography:
Dr Haylea Power is a researcher at CSIRO’s Environomics Future Science Platform (FSP), where they focus on pioneering single-cell sequencing techniques as the future of population genetics in marine environments. Their work centres on isolating and analysing individual cells from aquatic ecosystems to unlock detailed genomic information that was previously inaccessible. By advancing methods like "emCell-Seq," they are at the forefront of transforming how we study and manage marine populations, moving beyond traditional approaches to enable precise, non-invasive genetic analyses.
Abstract:
Environmental DNA (eDNA) metabarcoding has revolutionized ecological research, enabling rapid species detection without physical capture. However, mitochondrial DNA barcodes used in typical eDNA studies often lack the resolution to distinguish individuals. To address this, we explored the potential of isolating genetic material more selectively from marine samples to enhance species-specific or individual-level targeting.
Our research reveals that eDNA exists as a physical spectrum in aquatic environments, from extracellular DNA fragments to whole cells, some embedded within microbial biofilms. By optimizing collection strategies, we successfully enriched specific taxa, including bony and cartilaginous fish. Using a novel multi-factor gating strategy and custom Fluorescence-activated cell sorting (FACS) protocol, we isolated environmental metazoan cells (emCells) from a complex marine mesocosm containing over 50 metazoan species. Subsequent 16S rRNA and 18S nDNA metabarcoding confirmed these cells’ identity as known species within the mesocosm.
The analysis of whole metazoan cells offers a new approach to obtaining intact, linked, multi-locus nuclear targets. "emCell-Seq" is a cutting-edge technique enabling nuclear genotyping from isolated emCells. Through emCell-Seq, we identified individual zebrafish with over 90% accuracy using single nucleotide polymorphism (SNP) analysis. This method allows for consistent acquisition of linked nuclear targets, enabling population-level analyses like Capture-Mark-Recapture (CMR) and Close-Kin Mark-Recapture (CKMR) without needing tissue samples.
Our findings represent a significant advancement in non-invasive genomic analysis, providing new opportunities for detailed population genetic studies beyond traditional presence-absence data.