Abstract – Environmental DNA for mapping biodiversity, detecting pests and characterising food-webs

The primary objective of the environmental DNA (eDNA) project was to showcase the application of eDNA methods across three case studies, involving freshwater and marine ecosystems, and evaluate eDNA’s capacity to provide meaningful biological information to support practical decisions. eDNA has the potential to examine environments based on the DNA present in samples, thus identifiying the presence of organisms without having to see or capture them. The project sought to establish eDNA molecular analysis capabilities for aquatic system within each of respective business unit (Oceans and Atmosphere, Land and Water and National Collections and Marine Infrastructure), to collaborate across business units (Data61) and disciplines to optimize project outcomes.

The major goal of the Tropical eDNA Component was to advance eDNA methods and to extend scientific capabilty beyond detecting species presence/absence data to generating semi-quantitative abundance estimates in tropical marine systems. The Temperate eDNA Component sought to develop user friendly methods to sample water, develop and optimise eDNA methods to detect fishes and sharks (for presence/absence knowledge) from temperate marine waters. The goal of Freshwater eDNA Component was to develop and apply eDNA methods to determine diets of freshwater fish and in doing so, develop food web structures.

The combined efforts developed and applied eDNA-based methods across tropical and temperate marine systems and within native freshwater fish. This included from the very way samples need to be collected, methods to extract DNA and amplify targeted sequences of DNA, developing pipelines to examine sequence information and final statistical analysis.

This work continues and the tropical team are currently processing data collected at Ashmore Reef to evaluate the potential for a semi-quantitative approach to species abundance when large volumes of water (~600 L) are sampled throughout a study site. Fish gut analysis also generated the first fish gut microbiome data set, (a map of the bacteria present in the fish guts), for a native fish species and the freshwater team are now examining fish microbiome to determine if a healthy gut microbiome equates to healthy fish. The temperate team developed a Sterivex filter extraction method for vertebrate DNA and tested four eDNA molecular assays for the detection of fishes and sharks. The validation of these assays and taxonomy assignments from two different sequence databases has resulted in optimised methods and bioinformatic pipelines for the detection of fishes and sharks from smaller spatial and temporal 2 L water volumes.

If you would to know more about this work, please contact Gavin Rees.