Researchers develop new eDNA techniques to detect the rare Australian endemic Blind Cave Eel

University of Adelaide researchers have designed a new way to locate the Blind Cave Eel, paving the way to locate fauna in future.

Groundwater is the largest source of unfrozen freshwater on Earth and can be extremely vulnerable due to overexploitation. Far from being a sterile habitat, groundwater is home to a wide variety of subterranean life including microbes, worms, arthropods and some vertebrates (i.e. fish and salamanders).

The Blind Cave Eel, Ophisternon candidum is the largest of three cavefish species known from Australia (average length, 34.0 cm). The species exists entirely in subterranean groundwater systems of the northern Carnarvon Basin (Cape Range and Barrow Island) and the Robe River catchment in the Pilbara region, north-western Australia. It lacks eyes and has unpigmented skin. This species is notoriously difficult to sample during bio-monitoring surveys. This might be because the species is rare or it might be that they can avoid capture.

In Australia, under the Commonwealth Environmental Protection and Biodiversity Conservation Act 1999 (EPBC Act), Ophisternon candidum, has equal conservation status to the eastern koala (vulnerable). This listing is based on O. candidum being endemic to a restricted area in the north-western corner of Australia.

In this study, researchers at the University of Adelaide designed new species-specific PCR assays, which can be performed directly on genomic DNA samples for O. candidum. They were able to sequence its mitochondrial genome. This new technique enabled detection of the Blind Cave Eel from environmental DNA (eDNA) in groundwater, without physically catching the animals. Water samples were taken from 31 groundwater monitoring bores and two surface locations at the Robe River (Pilbara, Western Australia) and samples were processed in the laboratory.

The Blind Cave Eel was detected at eight separate locations at our study area; three sites where it has previously been physically detected and, more significantly, at five sites from which the species has never been recorded. Dr Michelle Guzik said

“The study is of importance because it has been demonstrated that eDNA species-specific PCR assays, can successfully be used to detect species from groundwater, without physically catching individuals. This can be performed at known sites as well as potentially expanding known distributional range in a very short timeframe (as little as three months).”

“With this information, researchers have demonstrated the implementation of new technologies to innovate bio-monitoring of subterranean fauna” she said.

In 2017, WA’s mineral and petroleum industry was worth approximately $108.8 billion. The mining industry’s compliance with Environmental Protection Authority (EPA) regulation is of the highest priority for resource exploration and developments. Therefore, there is an urgent requirement to develop methodologies and a knowledge base that increases both the speed and scientific rigour of biological surveys for monitoring the impact of resource developments, including groundwater extraction, on the fauna over time.

“In the future we aim to broaden eDNA techniques to subterranean fauna generally, with a view to Improving the efficiency and accuracy of sampling to characterise the complete ecological community assemblages of subterranean fauna in Pilbara locations. The team aim to have these methods included into future EPA guidelines for improved efficiency and accuracy of bio-monitoring surveys and better definition of species distributions for end-users” said Dr Guzik.


For more information contact:

  • Dr Michelle Guzik, School of Biological Sciences, The University of Adelaide. Mobile +61 (0)411 443 702 Email:
  • Professor Andrew Austin, School of Biological Sciences, The University of Adelaide. Mobile +61 (0)438 378 151, Email:

Head image: blind cave eel photo by Glenn Moore, Western Australian Museum

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