New approaches for the application of species-specific environmental DNA assays in aquatic species monitoring and conservation
Authors:   , Riaz Maria 
Published: November 2024

Biodiversity is threatened globally and its decline is being accelerated mainly due to human activities. Halting the current rate of biodiversity loss requires protection and conservation of species at local as well as at global scales. Biological conservation strategies heavily rely upon the availability of good quality and real-time information about species distribution. Information on species distribution can also be utilized to address crucial ecological challenges including estimation of reintroduction success and biotic interactions. Traditionally, species distribution data is mainly collected through invasive monitoring approaches that relied upon capturing the species or observing them closely. While these invasive monitoring approaches are well-established, they may cause harm to rare and endangered species. Also, these monitoring approaches may not be efficient for certain cases, e.g., early detection of biological invasions by pathogenic or predatory species. Hence, there is a dire need for a non-invasive and robust monitoring technique to map species distributions. One potential solution is the establishment of environmental DNA (eDNA) techniques based on molecular species detection from DNA shed by organisms naturally in the environment. This non-invasive and robust monitoring technique is being increasingly applied in biodiversity conservation and applied ecology. In this thesis, I aimed to develop eDNA based TaqMan assays for several species including one locally endangered and reintroduced fish species, Alburnoides bipunctatus. My main goal was to assess the reintroduction success of A. bipunctatus across the Federal German state of Hessen by integrating eDNA and species distribution modeling (SDM) in an iterative format. In addition to Global Biodiversity Information Facility (GBIF) data, I built SDM models with high-quality presence/absence data retrieved through eDNA to evaluate the improvement in the predictive power of SDM and used SDM predictions for an effective eDNA sampling design. I also utilized eDNA in a multi-species context to understand the dynamics of predator and prey interactions in a protected area. For this, I designed and established eDNA based TaqMan assays for two invasive predatory fish species, Pseudorasbora parva and Lepomis gibbosus. I related the presence of both predator and prey species to test for potential effects of predators on prey species occurrences. My results highlight the potential of eDNA techniques beyond simple species detection for efficient biodiversity assessment and conservation. I successfully developed and validated highly specific and sensitive TaqMan assays for A. bipunctatus, P. parva and L. gibbosus. By using these TaqMan assays, I found that (i) eDNA can be utilized for the assessment of reintroduction success, to provide fast and reliable feedback to conservation management. Moreover, the combination of eDNA and SDM in an iterative approach can be useful to guide future reintroduction actions, (ii) eDNA can serve as an effective technique to explore biotic interactions between predator and prey species. Overall, the results of my study underpin the usefulness of eDNA-based detection methods for biodiversity management and conservation. The great flexibility of eDNA to integrate with other techniques can give a tremendous boost to species monitoring and conservation. For example, I showed that the integration of eDNA and SDM can enhance the predictive accuracy of SDM. This enhancement facilitates the probability of species presence, serving as a tool for exploring the spread of reintroduced species. Moreover, this combined approach holds the potential to discover unrecognised populations of rare species. Furthermore, eDNA can be used for the assessment of biotic interactions, especially the effects of predator-prey interactions, which are considered as a crucial driver for shaping community structure. For future research, I suggest implementing the combined eDNA-SDM approach to estimate the reintroduction success of other naturally extinct species, early detection, and monitoring of invasive or pathogenic species to guide conservation management actions. Also, the application of eDNA techniques can be extended to more complex systems to assess biotic interactions between species for long periods. In addition to these, several other scientific questions such as, exploring ancient community structure, niche separation, delineating pollinator networks, and also biosecurity issues including monitoring water quality and biological vectors of deadly pathogenic species can be addressed. In conclusion, eDNA-based species detection is a robust and cost-effective tool for applied ecology and biodiversity conservation.