The South Australian Museum has opened a new genomics laboratory dedicated to DNA-based biodiversity monitoring, enabling researchers to detect hundreds of species from environmental samples in ways that would be impossible with traditional survey methods.

The facility uses environmental DNA (eDNA) analysis, where genetic material shed by organisms into water, soil, or air is extracted and sequenced to identify which species are present in an environment without directly observing or catching them.

Dr. Steve Cooper, who directs the museum’s evolutionary biology unit, said eDNA is transforming how biodiversity is assessed. “You can take a litre of river water, sequence the DNA in it, and identify every fish, frog, and invertebrate species that’s been in that stretch of river recently. That would take weeks of traditional surveying and you’d still miss rare or cryptic species.”

The technology works because all organisms constantly shed DNA through skin cells, mucus, faeces, and other sources. That DNA degrades relatively quickly, usually within days or weeks, but while intact it provides a record of recent biological activity.

Environmental DNA has been used for research for over a decade, but costs have dropped dramatically with improvements in DNA sequencing technology. What once cost thousands of dollars per sample now costs under $100, making routine monitoring economically feasible.

The South Australian Museum facility includes automated DNA extraction equipment, next-generation sequencing platforms, and bioinformatics systems that match DNA sequences to reference databases containing genetic signatures of known species.

Building those reference databases is a major challenge. Many Australian species lack genetic reference data, making it impossible to identify them from eDNA. The museum is systematically sequencing specimens from its collections to fill those gaps.

The museum holds over 4 million specimens collected over 160 years, representing much of South Australia’s biodiversity. Extracting and sequencing DNA from preserved specimens creates reference data for species identification without collecting new specimens.

This connects traditional museum collections to cutting-edge genomics, demonstrating that natural history museums remain relevant for contemporary biodiversity research. Museums worldwide are digitising and genomically characterising their collections for similar reasons.

The new facility is being used for several applications. State environmental agencies are using eDNA to monitor threatened species in rivers and wetlands. The method detects rare fish and frogs that are difficult to survey using conventional methods.

Agricultural agencies are using eDNA to monitor soil biodiversity, which influences soil health and crop productivity. Understanding which microbial and invertebrate species are present in agricultural soils helps evaluate management practices.

Biosecurity is another application. Environmental DNA can detect invasive species before they establish widespread populations, enabling early intervention. The lab is monitoring for several high-risk invasive species including European carp, red foxes, and various aquatic weeds.

One limitation of eDNA is that it provides presence/absence information but doesn’t directly estimate abundance. Finding DNA from a species tells you it’s present but not how many individuals there are or whether they’re breeding locally.

Researchers are developing quantitative eDNA methods that estimate abundance from DNA concentrations, but these require careful calibration and validation. For most applications, knowing presence is sufficient for conservation and management decisions.

The facility also supports ancient DNA research, extracting and analysing DNA from archaeological and paleontological specimens. This connects to work on megafauna extinctions, Aboriginal land management history, and environmental change over millennia.

Environmental DNA from sediment cores provides records of ecosystem composition going back thousands of years. By analysing DNA at different depths in lake or ocean sediments, researchers can track how biodiversity changed in response to climate shifts or human activities.

The lab is equipped with contamination control systems essential for ancient DNA work. When working with degraded DNA, tiny amounts of contamination from modern DNA can swamp the ancient signal. Clean rooms and specialised extraction protocols minimise contamination risks.

The facility cost $2.8 million to establish, funded by the South Australian government, CSIRO, and several conservation organisations. Operating costs are roughly $600,000 annually, covered by research grants and commercial service contracts.

Other Australian museums and universities are establishing similar facilities. Collectively these labs are building national capacity for DNA-based biodiversity monitoring that complements traditional ecological survey methods.

Whether eDNA becomes a standard tool for environmental monitoring and conservation depends partly on regulatory acceptance. Environmental assessments and management plans traditionally rely on visual surveys and expert species identification. Incorporating eDNA data requires regulatory agencies to accept the methodology and understand its limitations.

Standards for eDNA sampling, analysis, and interpretation are being developed by the Australian Government’s Environmental DNA Working Group. These standards help ensure consistency and quality across studies and build confidence in eDNA as an assessment tool.

The technology has limitations. It works well for aquatic environments where DNA disperses in water, but terrestrial applications are more challenging. DNA in soil is abundant but highly degraded, making species identification harder.

Air sampling for eDNA is emerging as a method for detecting flying organisms or wind-dispersed spores, but technology is less developed than for water or soil samples.

Despite limitations, eDNA provides capabilities that traditional methods can’t match, particularly for detecting rare or elusive species in difficult environments. It’s becoming an important tool for conservation biology and environmental management.

The South Australian Museum facility will process thousands of samples annually for research and management applications. Researchers expect eDNA methods to become routine components of environmental assessments within five years, complementing but not replacing traditional survey methods.

Combining eDNA with other monitoring technologies like acoustic sensors, camera traps, and satellite imagery provides comprehensive pictures of biodiversity that inform conservation priorities and management decisions. The museum’s new facility represents important infrastructure enabling this integrated approach to biodiversity monitoring.