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Dubé CE, Ziegler M, Mercière A, Boissin E, Planes S, Bourmaud CAF, Voolstra CR. Naturally occurring fire coral clones demonstrate a genetic and environmental basis of microbiome composition. Nat Commun 2021; 12:6402. [PMID: 34737272 PMCID: PMC8568919 DOI: 10.1038/s41467-021-26543-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 10/04/2021] [Indexed: 02/07/2023] Open
Abstract
Coral microbiomes are critical to holobiont functioning, but much remains to be understood about how prevailing environment and host genotype affect microbial communities in ecosystems. Resembling human identical twin studies, we examined bacterial community differences of naturally occurring fire coral clones within and between contrasting reef habitats to assess the relative contribution of host genotype and environment to microbiome structure. Bacterial community composition of coral clones differed between reef habitats, highlighting the contribution of the environment. Similarly, but to a lesser extent, microbiomes varied across different genotypes in identical habitats, denoting the influence of host genotype. Predictions of genomic function based on taxonomic profiles suggest that environmentally determined taxa supported a functional restructuring of the microbial metabolic network. In contrast, bacteria determined by host genotype seemed to be functionally redundant. Our study suggests microbiome flexibility as a mechanism of environmental adaptation with association of different bacterial taxa partially dependent on host genotype.
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Affiliation(s)
- C. E. Dubé
- grid.11642.300000 0001 2111 2608UMR 9220 ENTROPIE, UR-IRD-CNRS-UNC-IFREMER, Université de La Réunion, 15 Avenue René Cassin, CS 92003, 97744 Saint-Denis Cedex, La Réunion France ,grid.11136.340000 0001 2192 5916PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860 Perpignan, France ,Laboratoire d’Excellence “CORAIL”, 98729 Papetoai, Moorea French Polynesia ,grid.23856.3a0000 0004 1936 8390Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, G1V 0A6 Canada
| | - M. Ziegler
- grid.8664.c0000 0001 2165 8627Department of Animal Ecology and Systematics, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32 IFZ, 35392 Giessen, Germany ,grid.45672.320000 0001 1926 5090Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, 23955 Saudi Arabia
| | - A. Mercière
- grid.11136.340000 0001 2192 5916PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860 Perpignan, France ,Laboratoire d’Excellence “CORAIL”, 98729 Papetoai, Moorea French Polynesia
| | - E. Boissin
- grid.11136.340000 0001 2192 5916PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860 Perpignan, France ,Laboratoire d’Excellence “CORAIL”, 98729 Papetoai, Moorea French Polynesia
| | - S. Planes
- grid.11136.340000 0001 2192 5916PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860 Perpignan, France ,Laboratoire d’Excellence “CORAIL”, 98729 Papetoai, Moorea French Polynesia
| | - C. A. -F. Bourmaud
- grid.11642.300000 0001 2111 2608UMR 9220 ENTROPIE, UR-IRD-CNRS-UNC-IFREMER, Université de La Réunion, 15 Avenue René Cassin, CS 92003, 97744 Saint-Denis Cedex, La Réunion France ,Laboratoire d’Excellence “CORAIL”, 98729 Papetoai, Moorea French Polynesia
| | - C. R. Voolstra
- grid.45672.320000 0001 1926 5090Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, 23955 Saudi Arabia ,grid.9811.10000 0001 0658 7699Department of Biology, University of Konstanz, 78457 Konstanz, Germany
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Grottoli AG, Toonen RJ, Woesik R, Vega Thurber R, Warner ME, McLachlan RH, Price JT, Bahr KD, Baums IB, Castillo KD, Coffroth MA, Cunning R, Dobson KL, Donahue MJ, Hench JL, Iglesias‐Prieto R, Kemp DW, Kenkel CD, Kline DI, Kuffner IB, Matthews JL, Mayfield AB, Padilla‐Gamiño JL, Palumbi S, Voolstra CR, Weis VM, Wu HC. Increasing comparability among coral bleaching experiments. Ecol Appl 2021; 31:e02262. [PMID: 33222325 PMCID: PMC8243963 DOI: 10.1002/eap.2262] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 09/09/2020] [Indexed: 05/14/2023]
Affiliation(s)
- A. G. Grottoli
- School of Earth Sciences The Ohio State University Columbus Ohio43210USA
| | - R. J. Toonen
- Hawaiʻi Institute of Marine Biology University of Hawaiʻi at Mānoa Kāneʻohe Hawaii96744USA
| | - R. Woesik
- Department of Ocean Engineering and Marine Sciences Florida Institute of Technology Melbourne Florida32901USA
| | - R. Vega Thurber
- Department of Microbiology Oregon State University Corvallis Oregon97331USA
| | - M. E. Warner
- School of Marine Science and Policy University of Delaware Lewes Delaware19958USA
| | - R. H. McLachlan
- School of Earth Sciences The Ohio State University Columbus Ohio43210USA
| | - J. T. Price
- School of Earth Sciences The Ohio State University Columbus Ohio43210USA
| | - K. D. Bahr
- Department of Life Sciences Texas A&M University–Corpus Christi Corpus Christi Texas78412USA
| | - I. B. Baums
- Department of Biology Pennsylvania State University University Park Pennsylvania16802USA
| | - K. D. Castillo
- Department of Marine Sciences University of North Carolina at Chapel Hill Chapel Hill North Carolina27599USA
| | - M. A. Coffroth
- Department of Geology State University of New York at Buffalo Buffalo New York14260USA
| | - R. Cunning
- Daniel P. Hearther Center for Conservation and Research John G. Shedd Aquarium Chicago Illinois60605USA
| | - K. L. Dobson
- School of Earth Sciences The Ohio State University Columbus Ohio43210USA
| | - M. J. Donahue
- Hawaiʻi Institute of Marine Biology University of Hawaiʻi at Mānoa Kāneʻohe Hawaii96744USA
| | - J. L. Hench
- Nicholas School of the Environment Duke University Beaufort North Carolina28516USA
| | - R. Iglesias‐Prieto
- Department of Biology Pennsylvania State University University Park Pennsylvania16802USA
| | - D. W. Kemp
- Department of Biology University of Alabama at Birmingham Birmingham Alabama35233USA
| | - C. D. Kenkel
- Department of Biological Sciences University of Southern California Los Angeles California90089USA
| | - D. I. Kline
- Smithsonian Tropical Research Institute Washington D.C.20013USA
| | - I. B. Kuffner
- St Petersburg Coastal & Marine Science Center United States Geological Survey St Petersburg Florida33701USA
| | - J. L. Matthews
- Faculty of Science Climate Change Cluster University of Technology Sydney Broadway, Sydney New South Wales2007Australia
| | - A. B. Mayfield
- Oceanographic and Meteorological Laboratory Atlantic National Oceanic and Atmospheric Administration Miami Florida33149USA
- Cooperative Institute for Marine & Atmospheric Studies University of Miami Miami Florida33149USA
| | - J. L. Padilla‐Gamiño
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington98117USA
| | - S. Palumbi
- Hopkins Marine Station Stanford University Pacific Grove California93950USA
| | - C. R. Voolstra
- Department of Biology University of Konstanz Konstanz78457Germany
| | - V. M. Weis
- Department of Integrative Biology Oregon State University Corvallis Oregon97331USA
| | - H. C. Wu
- Leibniz Centre for Tropical Marine Research Bremen28359Germany
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Mies M, Voolstra CR, Castro CB, Pires DO, Calderon EN, Sumida PYG. Expression of a symbiosis-specific gene in Symbiodinium type A1 associated with coral, nudibranch and giant clam larvae. R Soc Open Sci 2017; 4:170253. [PMID: 28573035 PMCID: PMC5451836 DOI: 10.1098/rsos.170253] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 04/27/2017] [Indexed: 06/07/2023]
Abstract
Symbiodinium are responsible for the majority of primary production in coral reefs and found in a mutualistic symbiosis with multiple animal phyla. However, little is known about the molecular signals involved in the establishment of this symbiosis and whether it initiates during host larval development. To address this question, we monitored the expression of a putative symbiosis-specific gene (H+-ATPase) in Symbiodinium A1 ex hospite and in association with larvae of a scleractinian coral (Mussismilia hispida), a nudibranch (Berghia stephanieae) and a giant clam (Tridacna crocea). We acquired broodstock for each host, induced spawning and cultured the larvae. Symbiodinium cells were offered and larval samples taken for each host during the first 72 h after symbiont addition. In addition, control samples including free-living Symbiodinium and broodstock tissue containing symbionts for each host were collected. RNA extraction and RT-PCR were performed and amplified products cloned and sequenced. Our results show that H+-ATPase was expressed in Symbiodinium associated with coral and giant clam larvae, but not with nudibranch larvae, which digested the symbionts. Broodstock tissue for coral and giant clam also expressed H+-ATPase, but not the nudibranch tissue sample. Our results of the expression of H+-ATPase as a marker gene suggest that symbiosis between Symbiodinium and M. hispida and T. crocea is established during host larval development. Conversely, in the case of B. stephanieae larvae, evidence does not support a mutualistic relationship. Our study supports the utilization of H+-ATPase expression as a marker for assessing Symbiodinium-invertebrate relationships with applications for the differentiation of symbiotic and non-symbiotic associations. At the same time, insights from a single marker gene approach are limited and future studies should direct the identification of additional symbiosis-specific genes, ideally from both symbiont and host.
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Affiliation(s)
- M. Mies
- Oceanographic Institute, University of São Paulo, Praça do Oceanográfico 191, 05508-120 São Paulo, SP, Brazil
| | - C. R. Voolstra
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, 23955-6900 Thuwal, Saudi Arabia
| | - C. B. Castro
- Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista, s/n, 20940-040 Rio de Janeiro, RJ, Brazil
- Instituto Coral Vivo, Rua dos Coqueiros, 87-45807-000 Santa Cruz Cabrália, BA, Brazil
| | - D. O. Pires
- Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista, s/n, 20940-040 Rio de Janeiro, RJ, Brazil
- Instituto Coral Vivo, Rua dos Coqueiros, 87-45807-000 Santa Cruz Cabrália, BA, Brazil
| | - E. N. Calderon
- Instituto Coral Vivo, Rua dos Coqueiros, 87-45807-000 Santa Cruz Cabrália, BA, Brazil
- Núcleo em Ecologia e Desenvolvimento Socioambiental de Macaé, Universidade Federal do Rio de Janeiro, Av São José do Barreto, 764-27965-045 Macaé, RJ, Brazil
| | - P. Y. G. Sumida
- Oceanographic Institute, University of São Paulo, Praça do Oceanográfico 191, 05508-120 São Paulo, SP, Brazil
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Roder C, Berumen ML, Bouwmeester J, Papathanassiou E, Al-Suwailem A, Voolstra CR. First biological measurements of deep-sea corals from the Red Sea. Sci Rep 2013; 3:2802. [PMID: 24091830 PMCID: PMC3789407 DOI: 10.1038/srep02802] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Accepted: 09/11/2013] [Indexed: 12/01/2022] Open
Abstract
It is usually assumed that metabolic constraints restrict deep-sea corals to cold-water habitats, with 'deep-sea' and 'cold-water' corals often used as synonymous. Here we report on the first measurements of biological characters of deep-sea corals from the central Red Sea, where they occur at temperatures exceeding 20°C in highly oligotrophic and oxygen-limited waters. Low respiration rates, low calcification rates, and minimized tissue cover indicate that a reduced metabolism is one of the key adaptations to prevailing environmental conditions. We investigated four sites and encountered six species of which at least two appear to be undescribed. One species is previously reported from the Red Sea but occurs in deep cold waters outside the Red Sea raising interesting questions about presumed environmental constraints for other deep-sea corals. Our findings suggest that the present understanding of deep-sea coral persistence and resilience needs to be revisited.
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Affiliation(s)
- C. Roder
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - M. L. Berumen
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, USA
| | - J. Bouwmeester
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | | | - A. Al-Suwailem
- Coastal and Marine Resources Core Lab, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - C. R. Voolstra
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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DeSalvo MK, Sunagawa S, Fisher PL, Voolstra CR, Iglesias-Prieto R, Medina M. Coral host transcriptomic states are correlated with Symbiodinium genotypes. Mol Ecol 2010; 19:1174-86. [PMID: 20149089 DOI: 10.1111/j.1365-294x.2010.04534.x] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
A mutualistic relationship between reef-building corals and endosymbiotic dinoflagellates (Symbiodinium spp.) forms the basis for the existence of coral reefs. Genotyping tools for Symbiodinium spp. have added a new level of complexity to studies concerning cnidarian growth, nutrient acquisition, and stress. For example, the response of the coral holobiont to thermal stress is connected to the host-Symbiodinium genotypic combination, as different partnerships can have different bleaching susceptibilities. In this study, we monitored Symbiodinium physiological parameters and profiled the coral host transcriptional responses in acclimated, thermally stressed, and recovered fragments of the coral Montastraea faveolata using a custom cDNA gene expression microarray. Interestingly, gene expression was more similar among samples with the same Symbiodinium content rather than the same experimental condition. In order to discount for host-genotypic effects, we sampled fragments from a single colony of M. faveolata containing different symbiont types, and found that the host transcriptomic states grouped according to Symbiodinium genotype rather than thermal stress. As the first study that links coral host transcriptomic patterns to the clade content of their Symbiodinium community, our results provide a critical step to elucidating the molecular basis of the apparent variability seen among different coral-Symbiodinium partnerships.
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Affiliation(s)
- M K DeSalvo
- School of Natural Sciences, University of California, Merced, 5200 N. Lake Road, Merced, CA 95343 USA
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DeSalvo MK, Voolstra CR, Sunagawa S, Schwarz JA, Stillman JH, Coffroth MA, Szmant AM, Medina M. Differential gene expression during thermal stress and bleaching in the Caribbean coralMontastraea faveolata. Mol Ecol 2008; 17:3952-71. [PMID: 18662230 DOI: 10.1111/j.1365-294x.2008.03879.x] [Citation(s) in RCA: 244] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- M K DeSalvo
- School of Natural Sciences, University of California, Merced, PO Box 2039, Merced, CA 95344, USA
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