Assessing the utility of eDNA as a tool to survey reef-fish communities in the Red Sea
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Relatively small volumes of water may contain sufficient environmental DNA (eDNA) to detect target aquatic organisms via genetic sequencing. We therefore assessed the utility of eDNA to document the diversity of coral reef fishes in the central Red Sea. DNA from seawater samples was extracted, amplified using fish-specific 16S mitochondrial DNA primers, and sequenced using a metabarcoding workflow. DNA sequences were assigned to taxa using available genetic repositories or custom genetic databases generated from reference fishes. Our approach revealed a diversity of conspicuous, cryptobenthic, and commercially relevant reef fish at the genus level, with select genera in the family Labridae over-represented. Our approach, however, failed to capture a significant fraction of the fish fauna known to inhabit the Red Sea, which we attribute to limited spatial sampling, amplification stochasticity, and an apparent lack of sequencing depth. Given an increase in fish species descriptions, completeness of taxonomic checklists, and improvement in species-level assignment with custom genetic databases as shown here, we suggest that the Red Sea region may be ideal for further testing of the eDNA approach.
KeywordsBiodiversity Coral reef Environmental DNA Metabarcoding Next-generation sequencing
This study was funded by KAUST Award No. CRG-1-2012-BER-002 and baseline research funds to M.L.B., as well as a Curtin University Early Career Research Fellowship to J.D.D., M.S., and M.B. acknowledge the support of ARC Linkage Project (LP160100839) to explore marine metabarcoding applications. The authors would also like to acknowledge KAUST’s Coastal and Marine Resources Core Lab for logistical support, as well as Matthew Power, Megan Coghlan, and Brendan Chapman for DNA sequencing assistance.
- DiBattista JD, Roberts M, Bouwmeester J, Bowen BW, Coker DF, Lozano-Cortés DF, Choat JH, Gaither MR, Hobbs JP, Khalil M, Kochzius M, Myers R, Paulay G, Robitzch V, Saenz-Agudelo P, Salas E, Sinclair-Taylor TH, Toonen RJ, Westneat M, Williams S, Berumen ML (2016b) A review of contemporary patterns of endemism for shallow water reef fauna in the Red Sea. J Biogeogr 43:423–439CrossRefGoogle Scholar
- DiBattista JD, Bowen BW, Gaither MR, Hobbs J-PA, Saenz-Agudelo P, Piatek M, Rocha LA, Choat JH, McIlwain J, Priest MA, Sinclair-Taylor TH, Berumen ML (2017) Comparative phylogeography of reef fishes from the Gulf of Aden to the Arabian Sea reveals two cryptic lineages. Coral Reefs 36:625–638CrossRefGoogle Scholar
- Drummond AJ, Ashton B, Cheung M, Heled J, Kearse M, Moir R, Stones-Havas S, Thierer T, Wilson A (2009) Geneious v 4.8. www.geneious.com/
- Miya M, Sato Y, Fukunaga T, Sado T, Poulsen JY, Sato K, Minamoto T, Yamamoto S, Yamanaka H, Araki H, Kondoh M (2015) MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species. R Soc Open Sci 2:150088CrossRefPubMedPubMedCentralGoogle Scholar
- Spalding MD, Ravilious C, Green EP (2001) World atlas of coral reefs. University of California Press, BerkeleyGoogle Scholar