Environmental DNA (eDNA) is a cutting-edge and cost-effective tool for biodiversity monitoring. This study integrated eDNA analysis with photo-ID surveys of bottlenose dolphins (Tursiops truncatus) off the southwest of Ireland (Kilrush to Dingle) to evaluate protocols and explore marine mammals and fish co-occurrence. Seawater samples were collected aboard RV Celtic Mist in May 2024 during the Shannon Dolphin Project monitoring program (SDP). Upon sighting dolphins or other species of interest, 5L of surface water was filtered (0.45 μm) in triplicate, and a passive sampler (“metaprobe”, Maiello et al., 2023) was deployed. The DNA extracted from filters and metaprobes with DNeasy Blood&Tissue and Powerwater kits (Qiagen) were pooled, and the DNA library was prepared by amplifying with primers targeting the 12s rRNA gene for fish (tele02, MiFish) and marine mammals (MarVer1) (Taberlet et al., 2018; Miya et al., 2015; Valsecchi et al., 2019). Sequencing was conducted on Illumina Next2000 (600 cycles), and data were analyzed with Vsearch. T. truncatus was detected with tele02 primer confirming the 12 sightings (10/12 filters, and all metaprobes). Unexpectedly, during the sighting of four common dolphins (Delphinus delphis), only T. truncatus was detected (filter RRA 10.29%, metaprobe RRA 3.84%), suggesting a potential species assignment mismatch. In the case of three basking sharks (Cetorhinus maximus), DNA was detected only via metaprobe (RRA 0.16%), highlighting its potential as an alternative to traditional filtering. Surprisingly, the tele02 outperformed MiFish and MarVer1 in detecting fish (Sardina pilchardus and Scomber scombrus in 50% of the sightings) and marine mammals. This study confirms the reliability of our eDNA protocols in natural conditions. The data could also provide insights into local metacommunity ecology and interspecific interactions, which remain poorly explored in the area.
On the trail of bottlenose dolphins: active and passive eDNA monitoring give insights into metacommunity ecology in Southwest Ireland
Mariani Giulia;Di Domenico Marco;Di Renzo Ludovica;
2025-01-01
Abstract
Environmental DNA (eDNA) is a cutting-edge and cost-effective tool for biodiversity monitoring. This study integrated eDNA analysis with photo-ID surveys of bottlenose dolphins (Tursiops truncatus) off the southwest of Ireland (Kilrush to Dingle) to evaluate protocols and explore marine mammals and fish co-occurrence. Seawater samples were collected aboard RV Celtic Mist in May 2024 during the Shannon Dolphin Project monitoring program (SDP). Upon sighting dolphins or other species of interest, 5L of surface water was filtered (0.45 μm) in triplicate, and a passive sampler (“metaprobe”, Maiello et al., 2023) was deployed. The DNA extracted from filters and metaprobes with DNeasy Blood&Tissue and Powerwater kits (Qiagen) were pooled, and the DNA library was prepared by amplifying with primers targeting the 12s rRNA gene for fish (tele02, MiFish) and marine mammals (MarVer1) (Taberlet et al., 2018; Miya et al., 2015; Valsecchi et al., 2019). Sequencing was conducted on Illumina Next2000 (600 cycles), and data were analyzed with Vsearch. T. truncatus was detected with tele02 primer confirming the 12 sightings (10/12 filters, and all metaprobes). Unexpectedly, during the sighting of four common dolphins (Delphinus delphis), only T. truncatus was detected (filter RRA 10.29%, metaprobe RRA 3.84%), suggesting a potential species assignment mismatch. In the case of three basking sharks (Cetorhinus maximus), DNA was detected only via metaprobe (RRA 0.16%), highlighting its potential as an alternative to traditional filtering. Surprisingly, the tele02 outperformed MiFish and MarVer1 in detecting fish (Sardina pilchardus and Scomber scombrus in 50% of the sightings) and marine mammals. This study confirms the reliability of our eDNA protocols in natural conditions. The data could also provide insights into local metacommunity ecology and interspecific interactions, which remain poorly explored in the area.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
