The application of DNA metabarcoding to explore shark ecology on micro and macro scales

Elasmobranchs (sharks, skates and rays) play a pivotal role within marine ecosystems, yet fishing exploitation and by-catch have driven down population numbers to the extent that one third of all shark and ray species are now threatened with extinction. Therefore, harnessing the power of technological advancements to implement novel approaches to tackle elasmobranch conservation presents an urgent research priority. Marker gene amplicon sequencing (MGAS) is an emerging next generation sequencing (NGS) technique that allows the characterisation of whole communities of target organisms simultaneously. Here, I endeavoured to showcase the utility of MGAS in targeting two distinct aspects of shark ecology, through consideration of the fungal microbiome and environmental DNA (eDNA). For the first time in published literature, I investigate the fungal communities within the microbiome of healthy and injured sharks, and report upon the efficacy of a novel primer in detecting wild shark species in the Amirante Islands, Seychelles. Firstly, I characterised the shark skin fungal microbiome (or mycobiome) from the skin of healthy and injured black tip reef sharks (Carcharhinus melanopterus), and one sickle fin lemon shark (Negaprion acutidens), through amplicon sequencing of the fungal communities colonising the skin of line-caught sharks in the Amirantes islands, Seychelles. My findings show that the microbial consortia did not exhibit any shifts in correspondence with wound status. Additionally, there was a notable absence of a ‘core’ commensal fungal community shared by the sharks, and rare taxa made up the majority of shark skin communities. As emerging research points to the importance of microbial functionality over the identity of specific members, I recommended that future mycobiome studies take into account microbial co-occurrence patterns and the role of rare taxa. Secondly, I employed eDNA techniques to explore the diversity of elasmobranch communities across D’Aross Island and St Joseph Atoll, Southern Seychelles. Here I recovered ten elasmobranch species from nine sites around the study area. All ten species were faced with some level of extinction risk, highlighting the utility of eDNA as a tool to detect and monitor threatened species. However, there were instances where species encountered at the time of sampling were not detected in the corresponding environmental sample, highlighting the necessity for stringent optimisation of eDNA methods before it can be used as a routine biodiversity monitoring method in and of itself. Overall, the findings from this work demonstrate the broad scope of MGAS in targeting different aspects of shark ecology and highlights areas requiring further attention in order to provide valuable and impactful information that can be used to enhance shark conservation.