The dynamics of environmental DNA in subtropical waterholes

Humanity is currently altering ecosystems globally on an unprecedented scale. Due to anthropogenic impacts, animal and plant species are drastically changing their geographic distribution and whole species are getting extinct at an alarming rate. In order counteract these negative impacts we need efficient biomonitoring methods. Such methods assess which species are present in a given habitat or area. Examples of such methods are camera trapping (for terrestrial mammals) or electrofishing (for fishes). In the last two decades, the utilization of environmental DNA (or eDNA) has evolved into a new, powerful tool for such assessments. Environmental DNA is genetic material that any organism drops into the environment through for example lost hair, scales or skin cells or through body excretions. This DNA stays in the environment for a while until it gets broken down through degradation. While still being in a relatively intact state, eDNA can be captured from a given substrate of the environment (such as water, soil or air) and used for genetic analysis in order to assess which species have been in the area. Most of the eDNA-based research has focused on aquatic systems, and within these, on fishes. For these, it is best understood how long eDNA persists in the environment before it gets too degraded for detection. However, eDNA might also be a great tool for biomonitoring in other systems, such as for monitoring mammals in African savannahs. In these very dry habitats, terrestrial mammals have to regularly visit waterholes for drinking. When drinking or bathing in these waterholes, they shed their DNA into the water which might be used to for eDNA-based monitoring. However, currently very little is known about how much DNA is shed from terrestrial mammals into the water while interacting with it (through drinking, crossing through or wallowing) and how fast this DNA degrades in waterholes to a point that it is not detectable any more. This project will assess how much DNA is shed from terrestrial mammals into water when during certain interactions (drinking, walking through, wallowing or defecating), and how long this DNA stays detectable in subtropical waterholes. Thereby, the influence of certain environmental factors (such as UV radiation, pH or bacterial activity) on eDNA degradation will be evaluated. Finally, a field study will compare the performance of eDNA-based biomonitoring of South African mammals to camera trapping at waterholes. We will evaluate whether the eDNA-based monitoring can detect mammal species with higher sensitivity and efficiency than camera trapping and how long after an animal visited a waterhole it can still be detected using the eDNA extracted from water samples of that waterhole. If this method proves to be effective in these subtropical systems, it could be applied on a large scale for the monitoring terrestrial mammals in Southern Africa.