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DNA metabarcoding confirms primary targets and breadth of diet for coral reef butterflyfishes

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Abstract

Understanding species-specific resource requirements is paramount in managing and protecting biodiversity in a world where environmental quality is in decline. Dietary data can inform predator–prey relationships and how changes in prey availability impact different species. However, for many coral reef fishes, prey and predatory events can be difficult to observe and identify, both in situ and within examined stomach samples. Here we applied DNA metabarcoding of stomach content samples for 11 Red Sea butterflyfish species to identify the diversity of dietary components that these primarily benthic feeding fish consume across coral reefs. Detections based on 18S and COI sequences from partially digested stomach contents significantly increased the resolution and diversity of the known diet for this group of fish, which included cryptic prey that are difficult to visually document due to soft parts or morphological ambiguity. In addition to scleractinian corals and other Cnidaria, the obligate corallivore species fed on a wide range of benthic organisms, whereas facultative species displayed a broader diet with crustaceans, tunicates, and worms contributing to samples. While a number of individuals contained DNA that could not be confidently identified using this method, the proportion of unidentifiable sequences was relatively low across butterflyfish species. The COI marker identified the importance of soft corals in the diet for two hard coral specialists; Chaetodon melannotus and Chaetodon semilarvatus, with soft coral detected in over half of the individuals and contributing significantly to the number of DNA sequence reads within their gut. Notably, five prey items identified to the species level were detected that are currently not documented in the Red Sea. Our analysis revealed that the diet of different species of butterflyfish significantly overlaps, with all species deriving most of their diet from the phylum Cnidaria (hard and soft coral, anemones) and symbiotic Symbiodiniaceae algae. Furthermore, accumulation curves suggest that all study species may feed on an even greater fraction of the benthos, likely driven by the availability and diversity of each individual/pair’s territory. This approach increases the known dietary resolution and diversity of these key reef fishes and further enhances our understanding of the relationship between butterflyfish and benthic organisms.

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Data availability

All data are provided within the manuscript and supporting tables. Raw sequencing data are available from the Dryad Digital Repository: TBA. https://doi.org/10.5061/dryad.4b8gthtdb

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Acknowledgements

We would like to acknowledge the field support of Malek Amr Gusti, Dream Divers, KAUST Coastal and Marine Resources Core Lab, and all the fish that were sampled for this project. This study was funded by baseline research funds to M.L.B, ARC Linkage Project (LP160100839) to J.D.D., M.S., and M.B., as well as a Curtin University Early Career Research Fellowship (ECRF) to J.D.D. This work was also supported by the Pawsey Supercomputing Centre with funding from the Australian Government and the Government of Western Australia. The authors would like to acknowledge Matthew Power and Megan Coghlan for DNA sequencing assistance, as well as Mahsa Mousavi-Derazmahalleh for assistance with the eDNAFlow pipeline.

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Authors and Affiliations

  1. Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia

    Darren J. Coker, Roberto Arrigoni, Tullia I. Terraneo, Rodrigo Villalobos & Michael L. Berumen

  2. Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, WA, 6102, Australia

    Joseph D. DiBattista & Michael Bunce

  3. Australian Museum Research Institute, Australian Museum, 1 William St, Sydney, NSW, 2010, Australia

    Joseph D. DiBattista

  4. School of Environmental and Life Sciences, The University of Newcastle, Callaghan, 2308, Australia

    Michael Stat

  5. Department of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn–National Institute of Marine Biology, Ecology and Biotechnology, Genoa Marine Centre, 16126, Genoa, Italy

    Roberto Arrigoni

  6. Molecular Invertebrate Systematics and Ecology Laboratory, Department of Biology, Chemistry and Marine Sciences, University of the Ryukyus Nishihara, Nishihara, 903-0213, Japan

    James Reimer

  7. Tropical Biosphere Research Center, University of the Ryukyus Nishihara, Nishihara, 903-0213, Japan

    James Reimer

  8. Biology Department, Stanford University, Stanford, CA, 94305, USA

    Jessica P. Nowicki

  9. Institute of Environmental Science and Research (ESR), Kenepuru, Porirua, 5022, New Zealand

    Michael Bunce

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  1. Darren J. Coker
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Correspondence to Darren J. Coker.

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This research was undertaken in accordance with the policies and procedures of the King Abdullah University of Science and Technology (KAUST) Institutional Animal Care and Use Committee (IACUC#17-04-006, IACUC#17-04-007). Permissions relevant for KAUST to undertake the research was obtained from the applicable governmental agencies (Government Affairs, Regional Coastguard) in the Kingdom of Saudi Arabia.

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Coker, D.J., DiBattista, J.D., Stat, M. et al. DNA metabarcoding confirms primary targets and breadth of diet for coral reef butterflyfishes. Coral Reefs 42, 1–15 (2023). https://doi.org/10.1007/s00338-022-02302-2

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