eDNA surveys for aquatic wildlife
eDNA is a powerful tool for surveying aquatic vertebrate communities without the need to catch the animals themselves. It has been shown to be effective in a wide variety of aquatic ecosystems (ponds, lakes, streams, rivers, estuaries and oceans) and can be used either to detect the presence of particular species, or to survey whole communities of organisms.
NatureMetrics provides kits and instructions for collecting eDNA samples from various types of waterbodies. Our sampling kits are based on manual on-site filtration of water, and the filters can be sent to the laboratory using non-specialist postage.
Analysis services we currently offer are listed below. Please contact us for pricing and to discuss your requirements. Note that multiple tests can be performed on a single eDNA sample.
Our Fish service uses metabarcoding of the 12S gene to characterise the fish diversity in an eDNA sample. We have applied it to samples collected in ponds, lakes, streams, rivers and oceans, detecting hundreds of species of fish. Analysis typically takes 6-8 weeks. Read more about our fish service here.
Our Vertebrates service is similar to the Fish Survey but detects fish, amphibians, mammals and birds (currently not reptiles). In addition to aquatic and semi-aquatic animals, a surprising number of terrestrial species are also detected, but these should be considered incidental detections. Previous analyses have detected species such as water voles and otters in the UK, beavers and moose in Scandinavia, and river dolphins and tapirs in the South America. Over 400 vertebrate species were detected in just 43 water samples from the Peruvian Amazon. Contact us to find out more about this service.
Native freshwater mussels
We have recently developed a test to detect and identify native freshwater mussels in the family Unionidae. This includes the endangered freshwater pearl mussel as well as the duck mussel, swan mussel, depressed mussel and painted mussel. The analysis has been tested on freshwater pearl mussels in several rivers in the West of England through a pilot project with Natural England
This very sensitive qPCR test detects the presence of zebra mussels even at low population levels. It is being extensively piloted in a collaboration with Yorkshire Water and the University of Leeds and has detected zebra mussels in reservoirs, rivers and pipe systems during the early summer. Zebra mussels are ideal for eDNA detection because they produce a lot of mucous and have free-floating veligers. We are now undertaking tests to understand seasonal variation in detectability. Results are returned within 2 weeks.
We run a well-validated qPCR test for the presence of signal crayfish, which we have detected in streams rivers and lakes. The test can also be combined with a test for the presence of crayfish plague. Crayfish give off plenty of DNA when they are active, growing and breeding, but the presence of a small number of non-breeding adults may be harder to detect, so a negative result should never be interpreted as proof of absence.
Key considerations and limitations
It’s important to be aware of the inherent uncertainties in the use of eDNA for monitoring, particularly in terms of the distance that eDNA can travel from the source organism while still remaining detectable. This means that in flowing water the eDNA signal should be regarded as characteristic of the diversity in the wider upstream catchment rather than only reflecting the species present at the sampling site itself.
In still water, eDNA moves much less far from source and can be patchily distributed. Our sampling protocols take account of waterbody type in order to account for the different levels of expected mixing.
Detection probability is strongly influenced by species ecology. For instance, species can be more easily detected when they are highly active in the water and when they are breeding. It is therefore important to take the species lifecycle into account when planning a sampling campaign.