Looking for ‘needles in a haystack’: using eDNA to detect endangered sturgeon populations

Sturgeons are some of the most iconic fish species in the Danube River. However, their populations are in significant decline as a result of decades of pollution, habitat loss, overfishing and the fragmentation of migratory routes.

Often termed ‘living fossils’ due to their ancient lineages, sturgeons are often large and long-lived. Their migratory lifespans between freshwater and saltwater environments makes sturgeons particularly vulnerable to human pressures. The Danube River supports six native species of sturgeons, all of which are threatened by human activities.

Given the Danube’s vast length – spanning more than 2800km – it is vital that conservationists can monitor the size and location of sturgeon populations along the river in order to protect them. Two recently-published studies suggest that new environmental DNA (or eDNA) techniques offer significant potential for detecting sturgeon populations across large rivers like the Danube.

When an organism moves through an environment it constantly sheds tiny pieces of organic material such as dead skin cells, mucus and faeces. Scientists can test water samples for the DNA in this organic material. Such environmental DNA can point to the recent presence of a species, even if it cannot be otherwise detected or seen. As a result, eDNA approaches are increasingly valuable to scientists seeking to detect a host of elusive and tiny species across different ecosystems.

“Despite the need for a better understanding of the distribution and population status for many fish species in large rivers, the use of traditional sampling methods failed in the past, thereby hampering reliable assessments,” says Dr. Paul Meulenbroek, senior author of both studies, based at BOKU, Vienna. “Water samples can be used to identify those species that have recently been present in a local environment, with genetic material such as skin cells, intestinal cells, scales, or mucus being obtained directly from environmental samples.”

One study, published in Biodiversity and Conservation, developed an eDNA reference database for five native Danube sturgeons, and two non-native species. This allowed researchers to use eDNA techniques to search for the “needles in a haystack” sturgeon populations along the entire length of the Danube. This work provided the first large-scale snapshot of threatened sterlet populations along the river, with the species found in around half of all surveyed sites.

The partner study, published in Molecular Ecology Resources, explored the potential of eDNA techniques to estimate the abundance of sturgeon species. Researchers found that total fish eDNA concentrations and total fish abundance were highly correlated.

Together, the two studies suggest that sifting river water for microscopic pieces of organic eDNA material can help scientists determine both the location and abundance of sturgeon species along the vast Danube catchment.

“An in-depth understanding of species distribution and population dynamics is essential for developing adaptive conservation management plans, and in this regard, the benefits of an eDNA approach for conservation efforts, fisheries management, and scientific studies are numerous,” outlines Dr. Meulenbroek.

“eDNA metabarcoding is potentially more sensitive than traditional survey methods, as well as being more cost effective and non-invasive,” Dr. Meulenbroek continues. “It facilitates time-limited coverage of large geographical areas, thereby enabling the implementation of conservation measures within an ecologically and politically-actionable time scale.”

As the new studies suggest, eDNA approaches hold significant promise for conservationists seeking to strengthen their existing attempts to protect sturgeon populations across the Danube basin. “To facilitate sustainable conservation initiatives, it is of the utmost importance to gain a reliable understanding of the present status and development of remnant populations and sound study results providing evidence-based data for making water management decisions,” concludes Dr. Meulenbroek.

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This post is supported by the MEASURES project.