eDNA monitoring in a lake that fills once a decade

[Reading time: 2 minutes 25 seconds].

Chris Hofmeester is a Principal Aquatic Ecologist who has been with Biologic since 2022. He recently contributed his expertise to an eDNA research project, published in Ecology and Evolution, collecting the sediment samples the study was built on.

You’ve probably heard of eDNA and its power to assess biodiversity in wetlands. The catch? Sampling usually means passing large volumes of water through filters to capture eDNA. In arid central Australia, water is in short supply.

Chris explains how the team got around that.

Salt lakes, such as Lake Way, located in the remote central Murchison region of WA, can go years, or even decades, empty. It may seem odd that we monitor lake beds with no water in them, but this is most of inland Australia. If you only survey when there is water, you almost never survey, and approvals, compliance monitoring, and impact assessment still need to happen.

It is also important to continue to monitor the biodiversity of these salt lakes, as they support abundant invertebrate communities whose conservation can only be prioritised when they are studied.

Between filling events, these communities persist as resting eggs buried in the lakebed. These can remain viable for years, waiting for water. We call this the “egg bank”.

So, we work with the egg bank using rehydration trials. This involves collecting sediment samples from the lake and taking them back to our headquarters in Osborne Park, Perth. Here, our Aquatic Ecology team will attempt to hatch specimens in aquariums and examine them under the microscope.

This method comes with its own set of limitations. The most notable being that it is impossible to replicate all the conditions that can contribute to hatching, making it possible that the resulting data misses a portion of macroinvertebrate taxa in the study area.

We put our heads together with Dr Angus Lawrie from TrEnD Lab, Curtin University, and our own Molecular Systematics team head up by Dr Joel Huey, to trial an eDNA approach; metabarcoding DNA extractions of the same sediment samples we use in rehydrate trials. Perplexingly, this initial approach failed to return dependable results, only recovering target species in one of the eighteen samples. However, scientific progress rarely moves in a straight line.

The breakthrough came when we combined sugar floatation with metabarcoding. Sugar flotation works on density. Mixed into a concentrated sugar solution, the sediment grains sink while the eggs lift and can be filtered out. And each egg acts as its own DNA repository, sitting right in the dry sediment. With sugar flotation applied, nearly every sample returned a detection. Flotation works on density. Mixed into a concentrated sugar solution, the grains sink while the eggs lift and can be filtered out. And each egg acts as its own DNA repository, sitting right in the dry sediment. 

The volume of sediment processed played a key role too, with species richness rising sharply between 50 and 250 grams. Across all sites and volumes, the method recovered 27 invertebrate taxa. Compared directly against rehydration trials on the same sediment, it picked up seven taxa that the trials did not. 

This makes metabarcoding paired with sugar flotation a valuable addition to any monitoring program. The two are best read together: rehydration tells us a lot about the abundance of the common, “keystone” species, while eDNA reveals a more comprehensive list of taxa. 

The project was made possible by the melting pot of scientific disciplines that exist under the one roof at Biologic, as well as our strong relationships with research institutions like TrEnD Lab, and our clients, who regularly entrust us with their data to advance scientific research.

Citation: Angus D’Arcy Lawrie, Pia Dethlefsen, et al. (2026) Desiccation to DNA: Bulk DNA Metabarcoding of Macroinvertebrate Egg Banks via Sugar-Flotation Enhances Biodiversity Surveys of Dry Salt Lakes