Robust survey design enables monitoring of key values in Melbourne’s waterways

Melbourne Water’s Healthy Waterways Strategy 2018-28 sets a medium-term vision for managing the health of rivers, wetlands and estuaries in the Port Phillip and Westernport region, to protect and improve their value to the community.

Underpinning this strategy is the implementation of a monitoring, evaluation, reporting and improvement (MERI) framework for ‘key values’ throughout the three ecosystem types (rivers, wetlands and estuaries) in Melbourne Water’s 69 sub-catchments.

Melbourne Water has engaged EnviroDNA to undertake an extensive eDNA monitoring program as part of the MERI framework to monitor key biological values, including native fish, birds, frogs and platypuses.

eDNA sampling offers an approach for gathering broadscale data using techniques that are efficient, cost-effective and safe for field work operators. To ensure the highest quality outcomes, the project team implemented a robust eDNA survey design that is tailored to the large spatial scale required for this survey.

Key values in all 69 river sub-catchments, all 29 estuaries and a sub-set of high priority wetlands (n=233) that are representative of the more than 1400 wetlands that occur across Melbourne’s catchments, will be assessed as part of the Melbourne Water MERI eDNA Monitoring Program.

Importance of survey design

eDNA metabarcoding presents an exciting opportunity to monitor key values across space and time as part of the MERI program. Delivering such a program, however, requires a monitoring framework that considers a survey’s ability to determine the distribution of key values, and importantly, to detect changes in the distributions of those values over time.

EnviroDNA drew upon their expertise in survey design, spatial data and site occupancy detection modelling. Using the proportion of sites occupied by each species as a monitoring variable, we aimed to allocate eDNA sampling effort in each monitoring period to watercourses within each of Melbourne’s 69 sub-catchments.

By combining habitat suitability models that depict the likelihood of species occurrence in each watercourse with statistical power analyses that account for imperfect species detection, EnviroDNA was able to identify sampling designs that achieved enough statistical power to detect changes in the site occupancy of target species between monitoring periods.

This exercise highlights how advances in spatial and quantitative ecology can be usefully applied to eDNA monitoring programs, increasing the likelihood that programs fit the diverse needs of eDNA practitioners.

Advances in sampling equipment

Initially the Melbourne Water MERI eDNA monitoring program was developed with EnviroDNA’s syringe-filter manual sampling system in mind. However, data collected through a Melbourne Water eDNA research project investigating the detection of frogs in wetlands across the Melbourne catchment highlighted the increased sensitivity achieved by using the Smith-Root backpack sampling system (Weeks et al. 2021).

The backpack sampling system has been designed to allow continuous, mobile eDNA sampling in the field. It’s computer-controlled pump logs sampling data including sample volume, flow rate and GPS locations.

The Backpack Sampler was paired with the telescoping sampling pole, which allows extended reach when taking samples. All samples collected in the field are stored at room temperature due to the self-preserving filters being used by the field team.

Timing for impact

An important aspect of survey design is timing because there can be temporal and seasonal variability in the detectability of species. For instance, for the Melbourne Water’s MERI eDNA sampling program, platypuses are active in spring, autumn and winter, but less active in summer (due to having young in burrows). Many fish species are more likely to be detected after breeding, when juveniles are present in waterways.

Similarly, many frog species are more likely to be active in water during breeding season or when tadpoles are present. Many waterbird species (particularly migratory species) may not be present within wetlands at all times of the year.

Therefore, it’s very important to take these aspects of species biology into consideration when developing and implementing an eDNA sampling program.

Sampling, sampling, sampling

Our field team are experts at undertaking eDNA sampling and bring a wealth of ecological knowledge to field surveying. Sampling for the MERI program is currently being undertaken for Spring and sites are being logged in a field app to track the sampling progress.

EnviroDNA will soon be processing the samples and will undertake laboratory analysis of key values. When finalised, Melbourne Water will make the data available through their platforms. We look forward to sharing the results of this extensive survey.

Acknowledgments 

Thank you to the project team from Melbourne Water (Al Danger, Dr Rhys Coleman, William Steele, Sharyn Rossrakesh, Trish Grant and Belinda Lovell) for discussions and support throughout this project and the EnviroDNA project team (Dr Reid Tingley, Sarah Hale, William Webster, Emma Walker and Dr Taylor Gundry) for contributions to this article.

Questions about survey design?

We are experts at designing robust eDNA surveys tailored for your objectives. Contact us for more information.