Monitoring Aquatic Biodiversity in the Gulf using Environmental DNA
Authors: Thomsen Philip Francis , Bach Steffen Sanvig , Sigsgaard Eva , Moeller Peter Rask 
Published: July 2019

Aquatic ecosystems across the globe are under significant threat, suffering from various forms of anthropogenic disturbances, which is greatly impacting global biodiversity, economy and human health. Reliable monitoring of species is crucial for data-driven management actions in this context, but remains a challenge owing to non-standardized and selective methods relaying on physical identification of species by visual surveys and counting of individuals. However, traditional monitoring techniques remain problematic due to difficulties associated with correct identification of cryptic species or juvenile life stages, These traditional methods depend on practical and taxonomic expertise, which is steadily declining. In an attempt to come up with new objective solutions for monitoring biodiversity, recent and ongoing studies in Qatari waters, uses and further develops novel environmental DNA (eDNA) methods for Monitoring aquatic biodiversity in the Gulf and elsewhere.

Previous studies have shown that diversity of rare and threatened European freshwater animals - representing amphibians, fish, mammals, insects and crustaceans - can be detected and quantified based on environmental DNA (eDNA) obtained directly from small water samples of lakes, ponds and streams (Thomsen et al. 2012a).

Subsequently, for the first time, we investigated the potential of using metabarcoding of eDNA obtained directly from seawater samples to account for marine fish and mammal biodiversity. We show that such marine eDNA can account for fish biodiversity using high-throughput sequencing. Promisingly, eDNA covered the fish diversity better than any of 9 methods, conventionally used in marine fish surveys. Additionally, we show that even short fish eDNA sequences in seawater degrades beyond detectable levels within days, in accordance with results obtained from freshwater eDNA (Thomsen et al. 2012b). Controlled mesocosm experiments have also shown that eDNA becomes undetectable within 2 weeks after removal of animals, indicating that eDNA traces are near contemporary with species presence. Our findings underpin the ubiquitous nature of eDNA traces in the environment and support the use of eDNA as a tool for monitoring rare, threatened and economically important species across a wide range of taxonomic groups.

A particularly interesting study focuses on the large whale shark aggregation at the Al Shaheen Oil Field, located in the offshore area called “Block 5”, in the NE of the Exclusive Economic Zone (EEZ) of Qatar. Maersk Oil Qatar is currently operating several oil and gas production platforms within this field, and also take active part in a large whale shark research project studying many aspect about the aggregation. Quantitative PCR (qPCR) and high-throughput sequencing of sea water from the area have successfully been employed to gain new information about the occurrence, abundance and biology of the aggregation. More specifically, data from 2013 and 2014 showed that whale shark eDNA concentrations follows visual observations of abundance, and that degradation of eDNA occur rapidly, supporting that the obtained genetic material is of local origin. Our findings confirm that seawater samples can contain key information on populations of oceanic species, and demonstrate a general potential of eDNA for studying populations of marine organisms.

Although further studies are needed to validate the eDNA approach under varying environmental conditions, our findings provide a strong proof-of-concept with great perspectives for future monitoring of aquatic biodiversity and resources in the Gulf.

References

Thomsen PF, Kielgast J, Iversen LL, Wiuf C, Rasmussen M, Gilbert MTP, Orlando L, Willerslev E (2012a). Monitoring Endangered Freshwater Biodiversity using Environmental DNA. Molecular Ecology 21, 2565–2573.

Thomsen PF, Kielgast J, Iversen LL, Møller PR, Rasmussen M, Willerslev E (2012b). Detection of a Diverse Marine Fish Fauna using Environmental DNA from Seawater Samples. PLOS ONE 7(8), e41732.