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Galand PE, Ruscheweyh HJ, Salazar G, Hochart C, Henry N, Hume BCC, Oliveira PH, Perdereau A, Labadie K, Belser C, Boissin E, Romac S, Poulain J, Bourdin G, Iwankow G, Moulin C, Armstrong EJ, Paz-García DA, Ziegler M, Agostini S, Banaigs B, Boss E, Bowler C, de Vargas C, Douville E, Flores M, Forcioli D, Furla P, Gilson E, Lombard F, Pesant S, Reynaud S, Thomas OP, Troublé R, Zoccola D, Voolstra CR, Thurber RV, Sunagawa S, Wincker P, Allemand D, Planes S. Diversity of the Pacific Ocean coral reef microbiome. Nat Commun 2023; 14:3039. [PMID: 37264002 DOI: 10.1038/s41467-023-38500-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 04/26/2023] [Indexed: 06/03/2023] Open
Abstract
Coral reefs are among the most diverse ecosystems on Earth. They support high biodiversity of multicellular organisms that strongly rely on associated microorganisms for health and nutrition. However, the extent of the coral reef microbiome diversity and its distribution at the oceanic basin-scale remains to be explored. Here, we systematically sampled 3 coral morphotypes, 2 fish species, and planktonic communities in 99 reefs from 32 islands across the Pacific Ocean, to assess reef microbiome composition and biogeography. We show a very large richness of reef microorganisms compared to other environments, which extrapolated to all fishes and corals of the Pacific, approximates the current estimated total prokaryotic diversity for the entire Earth. Microbial communities vary among and within the 3 animal biomes (coral, fish, plankton), and geographically. For corals, the cross-ocean patterns of diversity are different from those known for other multicellular organisms. Within each coral morphotype, community composition is always determined by geographic distance first, both at the island and across ocean scale, and then by environment. Our unprecedented sampling effort of coral reef microbiomes, as part of the Tara Pacific expedition, provides new insight into the global microbial diversity, the factors driving their distribution, and the biocomplexity of reef ecosystems.
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Affiliation(s)
- Pierre E Galand
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, Banyuls sur Mer, France.
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022 GOSEE, Paris, France.
| | - Hans-Joachim Ruscheweyh
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland
| | - Guillem Salazar
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland
| | - Corentin Hochart
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, Banyuls sur Mer, France
| | - Nicolas Henry
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022 GOSEE, Paris, France
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, Roscoff, France
| | | | - Pedro H Oliveira
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022 GOSEE, Paris, France
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Aude Perdereau
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022 GOSEE, Paris, France
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Karine Labadie
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022 GOSEE, Paris, France
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Caroline Belser
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022 GOSEE, Paris, France
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Emilie Boissin
- PSL Research University: EPHE-UPVD-CNRS, UAR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, Perpignan, Cedex, France
| | - Sarah Romac
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, Roscoff, France
| | - Julie Poulain
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022 GOSEE, Paris, France
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | | | - Guillaume Iwankow
- PSL Research University: EPHE-UPVD-CNRS, UAR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, Perpignan, Cedex, France
| | | | - Eric J Armstrong
- PSL Research University: EPHE-UPVD-CNRS, UAR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, Perpignan, Cedex, France
| | - David A Paz-García
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), La Paz, BCS, México
| | - Maren Ziegler
- Department of Animal Ecology & Systematics, Justus Liebig University Giessen, Giessen, Germany
| | - Sylvain Agostini
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Japan
| | - Bernard Banaigs
- PSL Research University: EPHE-UPVD-CNRS, UAR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, Perpignan, Cedex, France
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, USA
| | - Chris Bowler
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022 GOSEE, Paris, France
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Colomban de Vargas
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022 GOSEE, Paris, France
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, Roscoff, France
| | - Eric Douville
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Michel Flores
- Weizmann Institute of Science, Department of Earth and Planetary Sciences, Rehovot, Israel
| | - Didier Forcioli
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Medical School, Nice, France
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco, Monaco, Principality of Monaco
| | - Paola Furla
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Medical School, Nice, France
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco, Monaco, Principality of Monaco
| | - Eric Gilson
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Medical School, Nice, France
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco, Monaco, Principality of Monaco
- Department of Medical Genetics, CHU of Nice, Nice, France
| | - Fabien Lombard
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022 GOSEE, Paris, France
- Sorbonne Université, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, Villefranche-sur-Mer, France
- Institut Universitaire de France, Paris, France
| | - Stéphane Pesant
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Stéphanie Reynaud
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco, Monaco, Principality of Monaco
- Centre Scientifique de Monaco, Monaco, Principality of Monaco
| | - Olivier P Thomas
- School of Biological and Chemical Sciences, Ryan Institute, University of Galway, Galway, Ireland
| | - Romain Troublé
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022 GOSEE, Paris, France
- Fondation Tara Océan, Paris, France
| | - Didier Zoccola
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco, Monaco, Principality of Monaco
- Centre Scientifique de Monaco, Monaco, Principality of Monaco
| | | | | | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland
| | - Patrick Wincker
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022 GOSEE, Paris, France
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Denis Allemand
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco, Monaco, Principality of Monaco
- Centre Scientifique de Monaco, Monaco, Principality of Monaco
| | - Serge Planes
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022 GOSEE, Paris, France
- PSL Research University: EPHE-UPVD-CNRS, UAR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, Perpignan, Cedex, France
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Cheutin MC, Villéger S, Hicks CC, Robinson JPW, Graham NAJ, Marconnet C, Restrepo CXO, Bettarel Y, Bouvier T, Auguet JC. Microbial Shift in the Enteric Bacteriome of Coral Reef Fish Following Climate-Driven Regime Shifts. Microorganisms 2021; 9:microorganisms9081711. [PMID: 34442789 PMCID: PMC8398123 DOI: 10.3390/microorganisms9081711] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/03/2021] [Accepted: 08/06/2021] [Indexed: 01/04/2023] Open
Abstract
Replacement of coral by macroalgae in post-disturbance reefs, also called a “coral-macroalgal regime shift”, is increasing in response to climate-driven ocean warming. Such ecosystem change is known to impact planktonic and benthic reef microbial communities but few studies have examined the effect on animal microbiota. In order to understand the consequence of coral-macroalgal shifts on the coral reef fish enteric bacteriome, we used a metabarcoding approach to examine the gut bacteriomes of 99 individual fish representing 36 species collected on reefs of the Inner Seychelles islands that, following bleaching, had either recovered to coral domination, or shifted to macroalgae. While the coral-macroalgal shift did not influence the diversity, richness or variability of fish gut bacteriomes, we observed a significant effect on the composition (R2 = 0.02; p = 0.001), especially in herbivorous fishes (R2 = 0.07; p = 0.001). This change is accompanied by a significant increase in the proportion of fermentative bacteria (Rikenella, Akkermensia, Desulfovibrio, Brachyspira) and associated metabolisms (carbohydrates metabolism, DNA replication, and nitrogen metabolism) in relation to the strong turnover of Scarinae and Siganidae fishes. Predominance of fermentative metabolisms in fish found on macroalgal dominated reefs indicates that regime shifts not only affect the taxonomic composition of fish bacteriomes, but also have the potential to affect ecosystem functioning through microbial functions.
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Affiliation(s)
- Marie-Charlotte Cheutin
- UMR MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, 34095 Montpellier, France; (S.V.); (C.M.); (C.X.O.R.); (Y.B.); (T.B.); (J.-C.A.)
- Correspondence:
| | - Sébastien Villéger
- UMR MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, 34095 Montpellier, France; (S.V.); (C.M.); (C.X.O.R.); (Y.B.); (T.B.); (J.-C.A.)
| | - Christina C. Hicks
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK; (C.C.H.); (J.P.W.R.); (N.A.J.G.)
| | - James P. W. Robinson
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK; (C.C.H.); (J.P.W.R.); (N.A.J.G.)
| | - Nicholas A. J. Graham
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK; (C.C.H.); (J.P.W.R.); (N.A.J.G.)
| | - Clémence Marconnet
- UMR MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, 34095 Montpellier, France; (S.V.); (C.M.); (C.X.O.R.); (Y.B.); (T.B.); (J.-C.A.)
| | - Claudia Ximena Ortiz Restrepo
- UMR MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, 34095 Montpellier, France; (S.V.); (C.M.); (C.X.O.R.); (Y.B.); (T.B.); (J.-C.A.)
| | - Yvan Bettarel
- UMR MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, 34095 Montpellier, France; (S.V.); (C.M.); (C.X.O.R.); (Y.B.); (T.B.); (J.-C.A.)
| | - Thierry Bouvier
- UMR MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, 34095 Montpellier, France; (S.V.); (C.M.); (C.X.O.R.); (Y.B.); (T.B.); (J.-C.A.)
| | - Jean-Christophe Auguet
- UMR MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, 34095 Montpellier, France; (S.V.); (C.M.); (C.X.O.R.); (Y.B.); (T.B.); (J.-C.A.)
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Feng L, He L, Jiang S, Chen J, Zhou C, Qian ZJ, Hong P, Sun S, Li C. Investigating the composition and distribution of microplastics surface biofilms in coral areas. CHEMOSPHERE 2020; 252:126565. [PMID: 32220722 DOI: 10.1016/j.chemosphere.2020.126565] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 03/16/2020] [Accepted: 03/18/2020] [Indexed: 06/10/2023]
Abstract
In recent years, global climate change and pollution of the marine environment have caused large-scale coral deaths and severe damages to coral reef ecosystems. Numerous studies have shown that coral diseases are closely related to microorganisms. And microplastics (MPs) are a potential threat to corals. In marine ecosystems, MPs are an emerging contaminant. MPs have a strong adsorption effect on pollutants in the water environment, and they are very easily colonized by microorganisms to form biofilms. Biofilms may accumulate many pathogens, increasing the probability of coral disease. However, there is no report about the composition of biofilms on the surface of microplastics in coral growth areas. In this study, nine kinds of MPs were chosen in the experiments, which are commonly found in the ocean. Four stakeout points were selected in the coral area. Biofilms were cultivated in natural environment. The composition and distribution of biofilms on the surface of the MPs were analyzed by 16 S rRNA sequencing. The characteristics of biofilms were observed by scanning electron microscopy (SEM). The experimental results show that the species composition and abundance distribution of the biofilm on the MP surface are significantly different from the surrounding seawater. The type of MPs and the stake out point are important factors affecting the structure of the biofilm bacterial community. Compared to seawater samples, MPs are enriched with certain dominant bacteria such as Vibrionaceae, Rhodobacteraceae, Flavobacteraceae, Microtrichaceae and Sphingomonadaceae. Among them, Vibrionaceae, Rhodobacteraceae and Flavobacteraceae are closely related to the tissue damage of stony corals, and Vibrios are also the main pathogens of coral albinism. In addition, Pseudomonas and Bbellvibrio cholerae are also detected on the MPs biofilm. SEM graphs of the MPs after culture could clearly observe rod-shaped bacteria and Streptococci. This study can provide a new direction for the study of coral toxicology by MPs and provide basic data for the toxicology research of MPs.
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Affiliation(s)
- Limin Feng
- School of Chemistry and Environment, Guangdong Ocean University, Zhanjiang, 524088, China; Shenzhen Institute of Guangdong Ocean University, Shenzhen, 518108, China
| | - Lei He
- School of Chemistry and Environment, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Shiqi Jiang
- School of Chemistry and Environment, Guangdong Ocean University, Zhanjiang, 524088, China; Shenzhen Institute of Guangdong Ocean University, Shenzhen, 518108, China
| | - Jinjun Chen
- College of Agriculture, Guangdong Ocean University, Zhanjiang, 524088, China.
| | - Chunxia Zhou
- Shenzhen Institute of Guangdong Ocean University, Shenzhen, 518108, China; Southern Marine Science and Engineering Guangdong Laboratory, Zhanjiang, 524088, China
| | - Zhong-Ji Qian
- School of Chemistry and Environment, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Pengzhi Hong
- Shenzhen Institute of Guangdong Ocean University, Shenzhen, 518108, China; Southern Marine Science and Engineering Guangdong Laboratory, Zhanjiang, 524088, China
| | - Shengli Sun
- School of Chemistry and Environment, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Chengyong Li
- School of Chemistry and Environment, Guangdong Ocean University, Zhanjiang, 524088, China; Shenzhen Institute of Guangdong Ocean University, Shenzhen, 518108, China; Southern Marine Science and Engineering Guangdong Laboratory, Zhanjiang, 524088, China.
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