Cross-ocean patterns and processes in fish biodiversity on coral reefs through the lens of eDNA metabarcoding

Laetitia Mathon; Virginie Marques; David Mouillot; Camille Albouy; Marco Andrello; Florian Baletaud; Giomar H. Borrero-Pérez; Tony Dejean; Graham J. Edgar; Jonathan Grondin; Pierre Edouard Guerin; Régis Hocdé; Jean Baptiste Juhel; Kadarusman; Eva Maire; Gael Mariani; Matthew McLean; Andrea Polanco F.; Laurent Pouyaud; Rick D. Stuart-Smith; Hagi Yulia Sugeha; Alice Valentini; Laurent Vigliola; Indra B. Vimono; Loïc Pellissier; Stéphanie Manel

doi:10.1098/rspb.2022.0162

Cross-ocean patterns and processes in fish biodiversity on coral reefs through the lens of eDNA metabarcoding

Laetitia Mathon, Virginie Marques, David Mouillot, Camille Albouy, Marco Andrello, Florian Baletaud, Giomar H. Borrero-Pérez, Tony Dejean, Graham J. Edgar, Jonathan Grondin, Pierre Edouard Guerin, Régis Hocdé, Jean Baptiste Juhel, Kadarusman, Eva Maire, Gael Mariani, Matthew McLean, Andrea Polanco F., Laurent Pouyaud, Rick D. Stuart-SmithHagi Yulia Sugeha, Alice Valentini, Laurent Vigliola, Indra B. Vimono, Loïc Pellissier, Stéphanie Manel

Medicine

Producción científica: Contribución a una revista › Artículo › revisión exhaustiva

49 Citas (Scopus)

Resumen

Increasing speed and magnitude of global change threaten the world's biodiversity and particularly coral reef fishes. A better understanding of large-scale patterns and processes on coral reefs is essential to prevent fish biodiversity decline but it requires new monitoring approaches. Here, we use environmental DNA metabarcoding to reconstruct well-known patterns of fish biodiversity on coral reefs and uncover hidden patterns on these highly diverse and threatened ecosystems. We analysed 226 environmental DNA (eDNA) seawater samples from 100 stations in five tropical regions (Caribbean, Central and Southwest Pacific, Coral Triangle and Western Indian Ocean) and compared those to 2047 underwater visual censuses from the Reef Life Survey in 1224 stations. Environmental DNA reveals a higher (16%) fish biodiversity, with 2650 taxa, and 25% more families than underwater visual surveys. By identifying more pelagic, reef-associated and crypto-benthic species, eDNA offers a fresh view on assembly rules across spatial scales. Nevertheless, the reef life survey identified more species than eDNA in 47 shared families, which can be due to incomplete sequence assignment, possibly combined with incomplete detection in the environment, for some species. Combining eDNA metabarcoding and extensive visual census offers novel insights on the spatial organization of the richest marine ecosystems.

Idioma original	English
Número de artículo	20220162
Publicación	Proceedings of the Royal Society B: Biological Sciences
Volumen	289
N.º	1973
DOI	https://doi.org/10.1098/rspb.2022.0162
Estado	Published - 2022

Nota bibliográfica

Funding Information:
The sampling in the Caribbean, Indian Ocean and Polynesia and the sequencing were funded by Monaco Explorations. Fieldwork in Indonesia and laboratory activities were supported by the Lengguru 2017 Project ( www.lengguru.org ), conducted by the French National Research Institute for Sustainable Development (IRD), National Research and Innovation Agency (BRIN) with the Research Center for Oceanography (RCO), the Politeknik Kelautan dan Perikanan Sorong), the University of Papua (UNIPA) with the help of the Institut Français in Indonesia (IFI), funding from Monaco Explorations, and corporate sponsorship from the Total Foundation and TIPCO company. Fieldwork and laboratory activities in New-Caledonia were supported by the projects ANR SEAMOUNTS and CIFRE REEF 3.0 conducted by the French National Institute for Sustainable Development (IRD) and GINGER-BURGEAP-SOPRONER company with funding from Monaco Explorations. Fieldwork and laboratory activities in Colombia were supported by Monaco Explorations, ETH Global grant and the project Reefish, conducted in collaboration with the Instituto de Investigaciones Marinas y Costeras – INVEMAR. Monaco Explorations supported also sampling and sequencing in the Caribbean. Fieldwork in the French Scattered islands was supported by the Terres Australes et Antartiques Françaises (TAAF). Acknowledgements

Publisher Copyright:
© 2022 Royal Society Publishing. All rights reserved.

ASJC Scopus Subject Areas

General Immunology and Microbiology
General Biochemistry,Genetics and Molecular Biology
General Environmental Science
General Agricultural and Biological Sciences

PubMed: MeSH publication types

Journal Article
Research Support, Non-U.S. Gov't

ODS de las Naciones Unidas

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Mathon, L., Marques, V., Mouillot, D., Albouy, C., Andrello, M., Baletaud, F., Borrero-Pérez, G. H., Dejean, T., Edgar, G. J., Grondin, J., Guerin, P. E., Hocdé, R., Juhel, J. B., Kadarusman, Maire, E., Mariani, G., McLean, M., Polanco F., A., Pouyaud, L., ... Manel, S. (2022). Cross-ocean patterns and processes in fish biodiversity on coral reefs through the lens of eDNA metabarcoding. Proceedings of the Royal Society B: Biological Sciences, 289(1973), Artículo 20220162. https://doi.org/10.1098/rspb.2022.0162

Mathon, L, Marques, V, Mouillot, D, Albouy, C, Andrello, M, Baletaud, F, Borrero-Pérez, GH, Dejean, T, Edgar, GJ, Grondin, J, Guerin, PE, Hocdé, R, Juhel, JB, Kadarusman, Maire, E, Mariani, G, McLean, M, Polanco F., A, Pouyaud, L, Stuart-Smith, RD, Sugeha, HY, Valentini, A, Vigliola, L, Vimono, IB, Pellissier, L & Manel, S 2022, 'Cross-ocean patterns and processes in fish biodiversity on coral reefs through the lens of eDNA metabarcoding', Proceedings of the Royal Society B: Biological Sciences, vol. 289, n.º 1973, 20220162. https://doi.org/10.1098/rspb.2022.0162

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abstract = "Increasing speed and magnitude of global change threaten the world's biodiversity and particularly coral reef fishes. A better understanding of large-scale patterns and processes on coral reefs is essential to prevent fish biodiversity decline but it requires new monitoring approaches. Here, we use environmental DNA metabarcoding to reconstruct well-known patterns of fish biodiversity on coral reefs and uncover hidden patterns on these highly diverse and threatened ecosystems. We analysed 226 environmental DNA (eDNA) seawater samples from 100 stations in five tropical regions (Caribbean, Central and Southwest Pacific, Coral Triangle and Western Indian Ocean) and compared those to 2047 underwater visual censuses from the Reef Life Survey in 1224 stations. Environmental DNA reveals a higher (16%) fish biodiversity, with 2650 taxa, and 25% more families than underwater visual surveys. By identifying more pelagic, reef-associated and crypto-benthic species, eDNA offers a fresh view on assembly rules across spatial scales. Nevertheless, the reef life survey identified more species than eDNA in 47 shared families, which can be due to incomplete sequence assignment, possibly combined with incomplete detection in the environment, for some species. Combining eDNA metabarcoding and extensive visual census offers novel insights on the spatial organization of the richest marine ecosystems.",

author = "Laetitia Mathon and Virginie Marques and David Mouillot and Camille Albouy and Marco Andrello and Florian Baletaud and Borrero-P{\'e}rez, {Giomar H.} and Tony Dejean and Edgar, {Graham J.} and Jonathan Grondin and Guerin, {Pierre Edouard} and R{\'e}gis Hocd{\'e} and Juhel, {Jean Baptiste} and Kadarusman and Eva Maire and Gael Mariani and Matthew McLean and {Polanco F.}, Andrea and Laurent Pouyaud and Stuart-Smith, {Rick D.} and Sugeha, {Hagi Yulia} and Alice Valentini and Laurent Vigliola and Vimono, {Indra B.} and Lo{\"i}c Pellissier and St{\'e}phanie Manel",

note = "Funding Information: The sampling in the Caribbean, Indian Ocean and Polynesia and the sequencing were funded by Monaco Explorations. Fieldwork in Indonesia and laboratory activities were supported by the Lengguru 2017 Project ( www.lengguru.org ), conducted by the French National Research Institute for Sustainable Development (IRD), National Research and Innovation Agency (BRIN) with the Research Center for Oceanography (RCO), the Politeknik Kelautan dan Perikanan Sorong), the University of Papua (UNIPA) with the help of the Institut Fran{\c c}ais in Indonesia (IFI), funding from Monaco Explorations, and corporate sponsorship from the Total Foundation and TIPCO company. Fieldwork and laboratory activities in New-Caledonia were supported by the projects ANR SEAMOUNTS and CIFRE REEF 3.0 conducted by the French National Institute for Sustainable Development (IRD) and GINGER-BURGEAP-SOPRONER company with funding from Monaco Explorations. Fieldwork and laboratory activities in Colombia were supported by Monaco Explorations, ETH Global grant and the project Reefish, conducted in collaboration with the Instituto de Investigaciones Marinas y Costeras – INVEMAR. Monaco Explorations supported also sampling and sequencing in the Caribbean. Fieldwork in the French Scattered islands was supported by the Terres Australes et Antartiques Fran{\c c}aises (TAAF). Acknowledgements Publisher Copyright: {\textcopyright} 2022 Royal Society Publishing. All rights reserved.",

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AU - Mathon, Laetitia

AU - Marques, Virginie

AU - Mouillot, David

AU - Albouy, Camille

AU - Andrello, Marco

AU - Baletaud, Florian

AU - Borrero-Pérez, Giomar H.

AU - Dejean, Tony

AU - Edgar, Graham J.

AU - Grondin, Jonathan

AU - Guerin, Pierre Edouard

AU - Hocdé, Régis

AU - Juhel, Jean Baptiste

AU - Kadarusman,

AU - Maire, Eva

AU - Mariani, Gael

AU - McLean, Matthew

AU - Polanco F., Andrea

AU - Pouyaud, Laurent

AU - Stuart-Smith, Rick D.

AU - Sugeha, Hagi Yulia

AU - Valentini, Alice

AU - Vigliola, Laurent

AU - Vimono, Indra B.

AU - Pellissier, Loïc

AU - Manel, Stéphanie

N1 - Funding Information: The sampling in the Caribbean, Indian Ocean and Polynesia and the sequencing were funded by Monaco Explorations. Fieldwork in Indonesia and laboratory activities were supported by the Lengguru 2017 Project ( www.lengguru.org ), conducted by the French National Research Institute for Sustainable Development (IRD), National Research and Innovation Agency (BRIN) with the Research Center for Oceanography (RCO), the Politeknik Kelautan dan Perikanan Sorong), the University of Papua (UNIPA) with the help of the Institut Français in Indonesia (IFI), funding from Monaco Explorations, and corporate sponsorship from the Total Foundation and TIPCO company. Fieldwork and laboratory activities in New-Caledonia were supported by the projects ANR SEAMOUNTS and CIFRE REEF 3.0 conducted by the French National Institute for Sustainable Development (IRD) and GINGER-BURGEAP-SOPRONER company with funding from Monaco Explorations. Fieldwork and laboratory activities in Colombia were supported by Monaco Explorations, ETH Global grant and the project Reefish, conducted in collaboration with the Instituto de Investigaciones Marinas y Costeras – INVEMAR. Monaco Explorations supported also sampling and sequencing in the Caribbean. Fieldwork in the French Scattered islands was supported by the Terres Australes et Antartiques Françaises (TAAF). Acknowledgements Publisher Copyright: © 2022 Royal Society Publishing. All rights reserved.

PY - 2022

Y1 - 2022

N2 - Increasing speed and magnitude of global change threaten the world's biodiversity and particularly coral reef fishes. A better understanding of large-scale patterns and processes on coral reefs is essential to prevent fish biodiversity decline but it requires new monitoring approaches. Here, we use environmental DNA metabarcoding to reconstruct well-known patterns of fish biodiversity on coral reefs and uncover hidden patterns on these highly diverse and threatened ecosystems. We analysed 226 environmental DNA (eDNA) seawater samples from 100 stations in five tropical regions (Caribbean, Central and Southwest Pacific, Coral Triangle and Western Indian Ocean) and compared those to 2047 underwater visual censuses from the Reef Life Survey in 1224 stations. Environmental DNA reveals a higher (16%) fish biodiversity, with 2650 taxa, and 25% more families than underwater visual surveys. By identifying more pelagic, reef-associated and crypto-benthic species, eDNA offers a fresh view on assembly rules across spatial scales. Nevertheless, the reef life survey identified more species than eDNA in 47 shared families, which can be due to incomplete sequence assignment, possibly combined with incomplete detection in the environment, for some species. Combining eDNA metabarcoding and extensive visual census offers novel insights on the spatial organization of the richest marine ecosystems.

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Cross-ocean patterns and processes in fish biodiversity on coral reefs through the lens of eDNA metabarcoding

Resumen

Nota bibliográfica

ASJC Scopus Subject Areas

PubMed: MeSH publication types

ODS de las Naciones Unidas

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