Detecting Marine Vertebrates in the Red Sea

Summary

Applied Genomics has completed an extensive assessment of fish and vertebrate detection using environmental DNA (eDNA) from water samples collected in the Red Sea during the winter and summer seasons of 2024. This project was in collaboration with KAUST Beacon Development to review the ecological status of marine fishes within the Red Sea.

Sampling Methodology

The study utilised Applied Genomics’ inDepth Water Sampler, which sampled water for one hour at each location. With a 50-liter filtering capacity, the inDepth sampler enabled the collection of large water volumes, surpassing the typical 4-liter capacity of standard spot sampling methods.

Sample Collection

• Winter (March): Water samples were collected from 13 locations, each sampled at three depths, totalling 39 samples.
• Summer (May-June): Water samples were collected from 11 locations, each sampled at three depths, plus an additional two control locations sampled at one depth, totalling 35 samples.

Species Detection

All samples were amplified using two fish and vertebrate specific markers targeting the 12S and 16S genes of the mitochondrion. Table 1 displays the number of unique species detected at species-level across all samples, in winter and summer samples, separately. 

Table 1. Unique species detected in each season and combined (identified to species-level)

Endangered Species

The study identified four endangered species:

• Honeycomb Stingray (Himantura uarnak)
• Napoleon Wrasse (Cheilinus undulatus)
• Spotted Eagle Ray (Aetobatus narinari)
• Green Sea Turtle (Chelonia mydas)

These identifications highlight the power and effectiveness of eDNA and importantly large volume sampling to be able to capture as much DNA as possible to give the most representative data. 

Client Specific Findings

Our client was interested in detection of 14 economically and commercially significant fishes. The detection results are summarised in Table 2. 

Table 2. Detection of significant fish species

Across seasons and sites we identified all but 4 of the target commercial species. Based on geographic data, as expected, European seabass and Greater Amberjack were not identified in any samples. Sobaity and Gilthead seabream were only found at the same control site, which is suspected to be a fish farm. 

We identified Cobia the most frequently in both seasons, which is a fish that has been historically reported as escaping from aquaculture farms in the 1970's. Napoleon Wrasse and Najil was also frequently identified in both seasons.

Conclusion

The Red Sea is renowned for its unique and diverse marine habitats, including coral reefs, seagrass beds, mangroves, salt pans, and salt marshes¹. These habitats support a wide array of marine life, making the Red Sea a biodiversity hotspot. The significant size and depth of the Red Sea contribute to the complexity of its ecosystems, providing niches for various species².

This study underscores the power of eDNA and large-volume sampling in capturing comprehensive and representative data on marine biodiversity. The detection of numerous species, including endangered ones, highlight the effectiveness of large-volume eDNA sampling. The identification of multiple haplotypes further emphasizes the genetic diversity within fish populations in the Red Sea.

By leveraging advanced eDNA techniques, Applied Genomics has demonstrated the potential to monitor and protect the unique marine ecosystems of the Red Sea. This research not only contributes to our understanding of marine biodiversity but also aids in the conservation efforts of this ecologically significant region.

References

1. https://www.redsea-project.com/Education/red-sea-marine-ecosystems-project

2. https://www.egyptinsights.com/the-red-sea-facts/

What species of interest? rare? groups captured? Haplotype numbers? Kronaplot and genetic diversity