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Delgadillo-Ordoñez N, Garcias-Bonet N, Raimundo I, García FC, Villela H, Osman EO, Santoro EP, Curdia J, Rosado JGD, Cardoso P, Alsaggaf A, Barno A, Antony CP, Bocanegra C, Berumen ML, Voolstra CR, Benzoni F, Carvalho S, Peixoto RS. Probiotics reshape the coral microbiome in situ without detectable off-target effects in the surrounding environment. Commun Biol 2024; 7:434. [PMID: 38594357 PMCID: PMC11004148 DOI: 10.1038/s42003-024-06135-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 04/02/2024] [Indexed: 04/11/2024] Open
Abstract
Beneficial microorganisms for corals (BMCs), or probiotics, can enhance coral resilience against stressors in laboratory trials. However, the ability of probiotics to restructure the coral microbiome in situ is yet to be determined. As a first step to elucidate this, we inoculated putative probiotic bacteria (pBMCs) on healthy colonies of Pocillopora verrucosa in situ in the Red Sea, three times per week, during 3 months. pBMCs significantly influenced the coral microbiome, while bacteria of the surrounding seawater and sediment remained unchanged. The inoculated genera Halomonas, Pseudoalteromonas, and Bacillus were significantly enriched in probiotic-treated corals. Furthermore, the probiotic treatment also correlated with an increase in other beneficial groups (e.g., Ruegeria and Limosilactobacillus), and a decrease in potential coral pathogens, such as Vibrio. As all corals (treated and non-treated) remained healthy throughout the experiment, we could not track health improvements or protection against stress. Our data indicate that healthy, and therefore stable, coral microbiomes can be restructured in situ, although repeated and continuous inoculations may be required in these cases. Further, our study provides supporting evidence that, at the studied scale, pBMCs have no detectable off-target effects on the surrounding microbiomes of seawater and sediment near inoculated corals.
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Affiliation(s)
- Nathalia Delgadillo-Ordoñez
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Marine Science and Bioscience Programs, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Neus Garcias-Bonet
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Inês Raimundo
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Marine Science and Bioscience Programs, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Francisca C García
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Helena Villela
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Eslam O Osman
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Erika P Santoro
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Joao Curdia
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Joao G D Rosado
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Marine Science and Bioscience Programs, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Pedro Cardoso
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Marine Science and Bioscience Programs, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Ahmed Alsaggaf
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Marine Science and Bioscience Programs, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Adam Barno
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Marine Science and Bioscience Programs, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Chakkiath Paul Antony
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Carolina Bocanegra
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Michael L Berumen
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Marine Science and Bioscience Programs, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | | | - Francesca Benzoni
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Marine Science and Bioscience Programs, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Susana Carvalho
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Marine Science and Bioscience Programs, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Raquel S Peixoto
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.
- Marine Science and Bioscience Programs, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.
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Voolstra CR, Raina JB, Dörr M, Cárdenas A, Pogoreutz C, Silveira CB, Mohamed AR, Bourne DG, Luo H, Amin SA, Peixoto RS. The coral microbiome in sickness, in health and in a changing world. Nat Rev Microbiol 2024:10.1038/s41579-024-01015-3. [PMID: 38438489 DOI: 10.1038/s41579-024-01015-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2024] [Indexed: 03/06/2024]
Abstract
Stony corals, the engines and engineers of reef ecosystems, face unprecedented threats from anthropogenic environmental change. Corals are holobionts that comprise the cnidarian animal host and a diverse community of bacteria, archaea, viruses and eukaryotic microorganisms. Recent research shows that the bacterial microbiome has a pivotal role in coral biology. A healthy bacterial assemblage contributes to nutrient cycling and stress resilience, but pollution, overfishing and climate change can break down these symbiotic relationships, which results in disease, bleaching and, ultimately, coral death. Although progress has been made in characterizing the spatial-temporal diversity of bacteria, we are only beginning to appreciate their functional contribution. In this Review, we summarize the ecological and metabolic interactions between bacteria and other holobiont members, highlight the biotic and abiotic factors influencing the structure of bacterial communities and discuss the impact of climate change on these communities and their coral hosts. We emphasize how microbiome-based interventions can help to decipher key mechanisms underpinning coral health and promote reef resilience. Finally, we explore how recent technological developments may be harnessed to address some of the most pressing challenges in coral microbiology, providing a road map for future research in this field.
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Affiliation(s)
| | - Jean-Baptiste Raina
- Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales, Australia.
| | - Melanie Dörr
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Anny Cárdenas
- Department of Biology, American University, Washington, DC, USA
| | - Claudia Pogoreutz
- PSL Université Paris: EPHE-UPVD-CNRS, UAR 3278 CRIOBE, Université de Perpignan, Perpignan, France
| | | | - Amin R Mohamed
- Marine Microbiomics Laboratory, Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - David G Bourne
- Australian Institute of Marine Science, Townsville, Queensland, Australia
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - Haiwei Luo
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, State Key Laboratory of Agrobiotechnology and Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Shady A Amin
- Marine Microbiomics Laboratory, Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
- Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Raquel S Peixoto
- Red Sea Research Center (RSRC) and Computational Biology Research Center (CBRC), Biological, Environmental Sciences, and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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3
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Garcias-Bonet N, Roik A, Tierney B, García FC, Villela HDM, Dungan AM, Quigley KM, Sweet M, Berg G, Gram L, Bourne DG, Ushijima B, Sogin M, Hoj L, Duarte G, Hirt H, Smalla K, Rosado AS, Carvalho S, Thurber RV, Ziegler M, Mason CE, van Oppen MJH, Voolstra CR, Peixoto RS. Horizon scanning the application of probiotics for wildlife. Trends Microbiol 2024; 32:252-269. [PMID: 37758552 DOI: 10.1016/j.tim.2023.08.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/24/2023] [Accepted: 08/28/2023] [Indexed: 09/29/2023]
Abstract
The provision of probiotics benefits the health of a wide range of organisms, from humans to animals and plants. Probiotics can enhance stress resilience of endangered organisms, many of which are critically threatened by anthropogenic impacts. The use of so-called 'probiotics for wildlife' is a nascent application, and the field needs to reflect on standards for its development, testing, validation, risk assessment, and deployment. Here, we identify the main challenges of this emerging intervention and provide a roadmap to validate the effectiveness of wildlife probiotics. We cover the essential use of inert negative controls in trials and the investigation of the probiotic mechanisms of action. We also suggest alternative microbial therapies that could be tested in parallel with the probiotic application. Our recommendations align approaches used for humans, aquaculture, and plants to the emerging concept and use of probiotics for wildlife.
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Affiliation(s)
- Neus Garcias-Bonet
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Anna Roik
- Helmholtz Institute for Functional Marine Biodiversity (HIFMB), Oldenburg, Germany; Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research (AWI), Bremerhaven, Germany
| | - Braden Tierney
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Francisca C García
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Helena D M Villela
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Ashley M Dungan
- School of Biosciences, The University of Melbourne, Parkville, VIC, Australia
| | - Kate M Quigley
- Minderoo Foundation, Perth, WA, Australia; James Cook University, Townsville, Australia
| | - Michael Sweet
- Aquatic Research Facility, Nature-based Solutions Research Centre, University of Derby, Derby, UK
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria; University of Potsdam and Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany
| | - Lone Gram
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs., Lyngby, Denmark
| | - David G Bourne
- College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia; Australian Institute of Marine Science, PMB 3, Townsville MC, Townsville, QLD 4810, Australia
| | - Blake Ushijima
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, USA
| | - Maggie Sogin
- Molecular Cell Biology, University of California, Merced, CA, USA
| | - Lone Hoj
- Australian Institute of Marine Science, PMB 3, Townsville MC, Townsville, QLD 4810, Australia
| | - Gustavo Duarte
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; IMPG, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Heribert Hirt
- Center for Desert Agriculture (CDA), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | | | - Alexandre S Rosado
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; Computational Bioscience Research Center (CBRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Susana Carvalho
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | | | - Maren Ziegler
- Department of Animal Ecology and Systematics, Justus Liebig University Giessen, Giessen, Germany
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA; WorldQuant Initiative on Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
| | - Madeleine J H van Oppen
- School of Biosciences, The University of Melbourne, Parkville, VIC, Australia; Australian Institute of Marine Science, PMB 3, Townsville MC, Townsville, QLD 4810, Australia
| | | | - Raquel S Peixoto
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; Computational Bioscience Research Center (CBRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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Staab S, Cardénas A, Peixoto RS, Schreiber F, Voolstra CR. Coracle-a machine learning framework to identify bacteria associated with continuous variables. Bioinformatics 2024; 40:btad749. [PMID: 38123508 PMCID: PMC10766586 DOI: 10.1093/bioinformatics/btad749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 11/06/2023] [Accepted: 12/19/2023] [Indexed: 12/23/2023] Open
Abstract
SUMMARY We present Coracle, an artificial intelligence (AI) framework that can identify associations between bacterial communities and continuous variables. Coracle uses an ensemble approach of prominent feature selection methods and machine learning (ML) models to identify features, i.e. bacteria, associated with a continuous variable, e.g. host thermal tolerance. The results are aggregated into a score that incorporates the performances of the different ML models and the respective feature importance, while also considering the robustness of feature selection. Additionally, regression coefficients provide first insights into the direction of the association. We show the utility of Coracle by analyzing associations between bacterial composition data (i.e. 16S rRNA Amplicon Sequence Variants, ASVs) and coral thermal tolerance (i.e. standardized short-term heat stress-derived diagnostics). This analysis identified high-scoring bacterial taxa that were previously found associated with coral thermal tolerance. Coracle scales with feature number and performs well with hundreds to thousands of features, corresponding to the typical size of current datasets. Coracle performs best if run at a higher taxonomic level first (e.g. order or family) to identify groups of interest that can subsequently be run at the ASV level. AVAILABILITY AND IMPLEMENTATION Coracle can be accessed via a dedicated web server that allows free and simple access: http://www.micportal.org/coracle/index. The underlying code is open-source and available via GitHub https://github.com/SebastianStaab/coracle.git.
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Affiliation(s)
- Sebastian Staab
- Department of Biology, University of Konstanz, Konstanz 78457, Germany
| | - Anny Cardénas
- Department of Biology, University of Konstanz, Konstanz 78457, Germany
- Department of Biology, American University, Washington, DC, 20016, USA
| | - Raquel S Peixoto
- Computational Biology Research Center (CBRC) and Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Falk Schreiber
- Department of Computer and Information Science, University of Konstanz, Konstanz 78457, Germany
- Faculty of Information Technology, Monash University, 3168, Australia
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Rädecker N, Escrig S, Spangenberg JE, Voolstra CR, Meibom A. Coupled carbon and nitrogen cycling regulates the cnidarian-algal symbiosis. Nat Commun 2023; 14:6948. [PMID: 37914705 PMCID: PMC10620199 DOI: 10.1038/s41467-023-42579-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 10/16/2023] [Indexed: 11/03/2023] Open
Abstract
Efficient nutrient recycling underpins the ecological success of cnidarian-algal symbioses in oligotrophic waters. In these symbioses, nitrogen limitation restricts the growth of algal endosymbionts in hospite and stimulates their release of photosynthates to the cnidarian host. However, the mechanisms controlling nitrogen availability and their role in symbiosis regulation remain poorly understood. Here, we studied the metabolic regulation of symbiotic nitrogen cycling in the sea anemone Aiptasia by experimentally altering labile carbon availability in a series of experiments. Combining 13C and 15N stable isotope labeling experiments with physiological analyses and NanoSIMS imaging, we show that the competition for environmental ammonium between the host and its algal symbionts is regulated by labile carbon availability. Light regimes optimal for algal photosynthesis increase carbon availability in the holobiont and stimulate nitrogen assimilation in the host metabolism. Consequently, algal symbiont densities are lowest under optimal environmental conditions and increase toward the lower and upper light tolerance limits of the symbiosis. This metabolic regulation promotes efficient carbon recycling in a stable symbiosis across a wide range of environmental conditions. Yet, the dependence on resource competition may favor parasitic interactions, explaining the instability of the cnidarian-algal symbiosis as environmental conditions in the Anthropocene shift towards its tolerance limits.
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Affiliation(s)
- Nils Rädecker
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
| | - Stéphane Escrig
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Jorge E Spangenberg
- Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, Switzerland
| | | | - Anders Meibom
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Center for Advanced Surface Analysis, Institute of Earth Sciences, University of Lausanne, Lausanne, Switzerland
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Röthig T, Trevathan-Tackett SM, Voolstra CR, Ross C, Chaffron S, Durack PJ, Warmuth LM, Sweet M. Human-induced salinity changes impact marine organisms and ecosystems. Glob Chang Biol 2023; 29:4731-4749. [PMID: 37435759 DOI: 10.1111/gcb.16859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 06/06/2023] [Accepted: 06/11/2023] [Indexed: 07/13/2023]
Abstract
Climate change is fundamentally altering marine and coastal ecosystems on a global scale. While the effects of ocean warming and acidification on ecology and ecosystem functions and services are being comprehensively researched, less attention is directed toward understanding the impacts of human-driven ocean salinity changes. The global water cycle operates through water fluxes expressed as precipitation, evaporation, and freshwater runoff from land. Changes to these in turn modulate ocean salinity and shape the marine and coastal environment by affecting ocean currents, stratification, oxygen saturation, and sea level rise. Besides the direct impact on ocean physical processes, salinity changes impact ocean biological functions with the ecophysiological consequences are being poorly understood. This is surprising as salinity changes may impact diversity, ecosystem and habitat structure loss, and community shifts including trophic cascades. Climate model future projections (of end of the century salinity changes) indicate magnitudes that lead to modification of open ocean plankton community structure and habitat suitability of coral reef communities. Such salinity changes are also capable of affecting the diversity and metabolic capacity of coastal microorganisms and impairing the photosynthetic capacity of (coastal and open ocean) phytoplankton, macroalgae, and seagrass, with downstream ramifications on global biogeochemical cycling. The scarcity of comprehensive salinity data in dynamic coastal regions warrants additional attention. Such datasets are crucial to quantify salinity-based ecosystem function relationships and project such changes that ultimately link into carbon sequestration and freshwater as well as food availability to human populations around the globe. It is critical to integrate vigorous high-quality salinity data with interacting key environmental parameters (e.g., temperature, nutrients, oxygen) for a comprehensive understanding of anthropogenically induced marine changes and its impact on human health and the global economy.
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Affiliation(s)
- Till Röthig
- Department of Biology, University of Konstanz, Konstanz, Germany
- Branch of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
- Aquatic Research Facility, Nature-Based Solutions Research Centre, University of Derby, Derby, UK
| | - Stacey M Trevathan-Tackett
- School of Life and Environmental Science, Centre for Integrative Ecology, Deakin University, Geelong, Victoria, Australia
- Deakin Marine Research and Innovation Centre, Deakin University, Geelong, Victoria, Australia
| | | | - Cliff Ross
- Department of Biology, University of North Florida, Jacksonville, Florida, USA
| | - Samuel Chaffron
- Nantes Université, École Centrale Nantes, CNRS, LS2N, UMR 6004, F-44000, Nantes, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, F-75016, Paris, France
| | - Paul J Durack
- Program for Climate Model Diagnosis and Intercomparison, Lawrence Livermore National Laboratory, Livermore, California, USA
| | | | - Michael Sweet
- Aquatic Research Facility, Nature-Based Solutions Research Centre, University of Derby, Derby, UK
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Alderdice R, Perna G, Cárdenas A, Hume BCC, Wolf M, Kühl M, Pernice M, Suggett DJ, Voolstra CR. Author Correction: Deoxygenation lowers the thermal threshold of coral bleaching. Sci Rep 2023; 13:13254. [PMID: 37582837 PMCID: PMC10427604 DOI: 10.1038/s41598-023-40318-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2023] Open
Affiliation(s)
- Rachel Alderdice
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Ultimo, NSW, 2007, Australia.
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany.
| | - Gabriela Perna
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Anny Cárdenas
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Benjamin C C Hume
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Martin Wolf
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Michael Kühl
- Marine Biology Section, Department of Biology, University of Copenhagen, Strandpromenaden 5, 3000, Helsingør, Denmark
| | - Mathieu Pernice
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - David J Suggett
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Ultimo, NSW, 2007, Australia
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Canesi M, Douville E, Montagna P, Taviani M, Stolarski J, Bordier L, Dapoigny A, Coulibaly GEH, Simon AC, Agelou M, Fin J, Metzl N, Iwankow G, Allemand D, Planes S, Moulin C, Lombard F, Bourdin G, Troublé R, Agostini S, Banaigs B, Boissin E, Boss E, Bowler C, de Vargas C, Flores M, Forcioli D, Furla P, Gilson E, Galand PE, Pesant S, Sunagawa S, Thomas OP, Vega Thurber R, Voolstra CR, Wincker P, Zoccola D, Reynaud S. Differences in carbonate chemistry up-regulation of long-lived reef-building corals. Sci Rep 2023; 13:11589. [PMID: 37463961 DOI: 10.1038/s41598-023-37598-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 06/23/2023] [Indexed: 07/20/2023] Open
Abstract
With climate projections questioning the future survival of stony corals and their dominance as tropical reef builders, it is critical to understand the adaptive capacity of corals to ongoing climate change. Biological mediation of the carbonate chemistry of the coral calcifying fluid is a fundamental component for assessing the response of corals to global threats. The Tara Pacific expedition (2016-2018) provided an opportunity to investigate calcification patterns in extant corals throughout the Pacific Ocean. Cores from colonies of the massive Porites and Diploastrea genera were collected from different environments to assess calcification parameters of long-lived reef-building corals. At the basin scale of the Pacific Ocean, we show that both genera systematically up-regulate their calcifying fluid pH and dissolved inorganic carbon to achieve efficient skeletal precipitation. However, while Porites corals increase the aragonite saturation state of the calcifying fluid (Ωcf) at higher temperatures to enhance their calcification capacity, Diploastrea show a steady homeostatic Ωcf across the Pacific temperature gradient. Thus, the extent to which Diploastrea responds to ocean warming and/or acidification is unclear, and it deserves further attention whether this is beneficial or detrimental to future survival of this coral genus.
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Affiliation(s)
- Marine Canesi
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, UMR 8212 CEA-CNRS-UVSQ, Université Paris-Saclay, 91191, Gif-Sur-Yvette, France.
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, 98000, Monaco City, Monaco.
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco - U FR, Monaco City, Monaco.
| | - Eric Douville
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, UMR 8212 CEA-CNRS-UVSQ, Université Paris-Saclay, 91191, Gif-Sur-Yvette, France
| | - Paolo Montagna
- Institute of Polar Sciences (ISP), CNR, Via Gobetti 101, 40129, Bologna, Italy
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy
| | - Marco Taviani
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy
- Institute of Marine Sciences (ISMAR), CNR, Via Gobetti 101, 40129, Bologna, Italy
| | - Jarosław Stolarski
- Institute of Paleobiology, Polish Academy of Sciences, 00818, Warsaw, Poland
| | - Louise Bordier
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, UMR 8212 CEA-CNRS-UVSQ, Université Paris-Saclay, 91191, Gif-Sur-Yvette, France
| | - Arnaud Dapoigny
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, UMR 8212 CEA-CNRS-UVSQ, Université Paris-Saclay, 91191, Gif-Sur-Yvette, France
| | - Gninwoyo Eric Hermann Coulibaly
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, UMR 8212 CEA-CNRS-UVSQ, Université Paris-Saclay, 91191, Gif-Sur-Yvette, France
| | | | | | - Jonathan Fin
- Laboratoire LOCEAN/IPSL, Sorbonne Université-CNRS-IRD-MNHN, 75005, Paris, France
| | - Nicolas Metzl
- Laboratoire LOCEAN/IPSL, Sorbonne Université-CNRS-IRD-MNHN, 75005, Paris, France
| | - Guillaume Iwankow
- Laboratoire d'Excellence "CORAIL," PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 66100, Perpignan, France
| | - Denis Allemand
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, 98000, Monaco City, Monaco
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco - U FR, Monaco City, Monaco
| | - Serge Planes
- Laboratoire d'Excellence "CORAIL," PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 66100, Perpignan, France
| | | | - Fabien Lombard
- Institut de la Mer de Villefranche Sur Mer, Laboratoire d'Océanographie de Villefranche, Sorbonne Université, 06230, Villefranche-sur-Mer, France
| | | | | | - Sylvain Agostini
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka, Japan
| | - Bernard Banaigs
- Laboratoire d'Excellence "CORAIL," PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 66100, Perpignan, France
| | - Emilie Boissin
- Laboratoire d'Excellence "CORAIL," PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 66100, Perpignan, France
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, ME, USA
| | - Chris Bowler
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Colomban de Vargas
- CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, Sorbonne Université, 29680, Roscoff, France
| | - Michel Flores
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, 76100, Rehovot, Israel
| | - Didier Forcioli
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco - U FR, Monaco City, Monaco
- Institute for Research on Cancer and Aging (IRCAN), Nice, France
| | - Paola Furla
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco - U FR, Monaco City, Monaco
- Institute for Research on Cancer and Aging (IRCAN), Nice, France
| | - Eric Gilson
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco - U FR, Monaco City, Monaco
- Institute for Research on Cancer and Aging (IRCAN), Nice, France
- Department of Medical Genetics, CHU, Nice, France
| | - Pierre E Galand
- CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, Sorbonne Université, 66650, Banyuls sur Mer, France
| | - Stéphane Pesant
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Olivier P Thomas
- School of Biological and Chemical Sciences, Ryan Institute, University of Galway, University Road, H91 TK33, Galway, Ireland
| | - Rebecca Vega Thurber
- Department of Microbiology, Oregon State University, 220 Nash Hall, Corvallis, OR, 97331, USA
| | | | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Didier Zoccola
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, 98000, Monaco City, Monaco
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco - U FR, Monaco City, Monaco
| | - Stéphanie Reynaud
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, 98000, Monaco City, Monaco
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco - U FR, Monaco City, Monaco
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9
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Hochart C, Paoli L, Ruscheweyh HJ, Salazar G, Boissin E, Romac S, Poulain J, Bourdin G, Iwankow G, Moulin C, Ziegler M, Porro B, Armstrong EJ, Hume BCC, Aury JM, Pogoreutz C, Paz-García DA, Nugues MM, 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, Wincker P, Zoccola D, Allemand D, Planes S, Thurber RV, Voolstra CR, Sunagawa S, Galand PE. Ecology of Endozoicomonadaceae in three coral genera across the Pacific Ocean. Nat Commun 2023; 14:3037. [PMID: 37264015 DOI: 10.1038/s41467-023-38502-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 04/26/2023] [Indexed: 06/03/2023] Open
Abstract
Health and resilience of the coral holobiont depend on diverse bacterial communities often dominated by key marine symbionts of the Endozoicomonadaceae family. The factors controlling their distribution and their functional diversity remain, however, poorly known. Here, we study the ecology of Endozoicomonadaceae at an ocean basin-scale by sampling specimens from three coral genera (Pocillopora, Porites, Millepora) on 99 reefs from 32 islands across the Pacific Ocean. The analysis of 2447 metabarcoding and 270 metagenomic samples reveals that each coral genus harbored a distinct new species of Endozoicomonadaceae. These species are composed of nine lineages that have distinct biogeographic patterns. The most common one, found in Pocillopora, appears to be a globally distributed symbiont with distinct metabolic capabilities, including the synthesis of amino acids and vitamins not produced by the host. The other lineages are structured partly by the host genetic lineage in Pocillopora and mainly by the geographic location in Porites. Millepora is more rarely associated to Endozoicomonadaceae. Our results show that different coral genera exhibit distinct strategies of host-Endozoicomonadaceae associations that are defined at the bacteria lineage level.
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Affiliation(s)
- Corentin Hochart
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, 66650, Banyuls sur Mer, France
| | - Lucas Paoli
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, 8093, Zürich, Switzerland
| | - Hans-Joachim Ruscheweyh
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, 8093, Zürich, Switzerland
| | - Guillem Salazar
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, 8093, Zürich, Switzerland
| | - Emilie Boissin
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Sarah Romac
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, Roscoff, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France
| | | | - Guillaume Iwankow
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | | | - Maren Ziegler
- Department of Animal Ecology & Systematics, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32 (IFZ), 35392, Giessen, Germany
| | - Barbara Porro
- CNRS, INSERM, Institute for Research on Cancer and Aging (IRCAN), Université Côte d'Azur, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Principality of Monaco
| | - Eric J Armstrong
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Benjamin C C Hume
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France
| | - Claudia Pogoreutz
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - David A Paz-García
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), La Paz, Baja California Sur, 23096, México
| | - Maggy M Nugues
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Sylvain Agostini
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1, Shimoda, Shizuoka, Japan
| | - Bernard Banaigs
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, ME, 04469, USA
| | - Chris Bowler
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Colomban de Vargas
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, Roscoff, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France
| | - Eric Douville
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, 91191, Gif-sur-Yvette, France
| | - Michel Flores
- Weizmann Institute of Science, Department of Earth and Planetary Sciences, 76100, Rehovot, Israel
| | - Didier Forcioli
- CNRS, INSERM, Institute for Research on Cancer and Aging (IRCAN), Université Côte d'Azur, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Principality of Monaco
| | - Paola Furla
- CNRS, INSERM, Institute for Research on Cancer and Aging (IRCAN), Université Côte d'Azur, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Principality of Monaco
| | - Eric Gilson
- CNRS, INSERM, Institute for Research on Cancer and Aging (IRCAN), Université Côte d'Azur, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Principality of Monaco
- Department of Medical Genetics, CHU Nice, Nice, France
| | - Fabien Lombard
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France
- Sorbonne Université, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, 06230, Villefranche-sur-Mer, France
- Institut Universitaire de France, 75231, Paris, France
| | - Stéphane Pesant
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Stéphanie Reynaud
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), 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
- Fondation Tara Océan, 8 rue de Prague, 75012, Paris, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France
| | - Didier Zoccola
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Principality of Monaco
- Centre Scientifique de Monaco, Monaco, Principality of Monaco
| | - Denis Allemand
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Principality of Monaco
- Centre Scientifique de Monaco, Monaco, Principality of Monaco
| | - Serge Planes
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France
| | | | | | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, 8093, Zürich, Switzerland
| | - Pierre E Galand
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, 66650, Banyuls sur Mer, France.
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France.
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10
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Rouan A, Pousse M, Djerbi N, Porro B, Bourdin G, Carradec Q, Hume BC, Poulain J, Lê-Hoang J, Armstrong E, Agostini S, Salazar G, Ruscheweyh HJ, Aury JM, Paz-García DA, McMinds R, Giraud-Panis MJ, Deshuraud R, Ottaviani A, Morini LD, Leone C, Wurzer L, Tran J, Zoccola D, Pey A, Moulin C, Boissin E, Iwankow G, Romac S, de Vargas C, Banaigs B, Boss E, Bowler C, Douville E, Flores M, Reynaud S, Thomas OP, Troublé R, Thurber RV, Planes S, Allemand D, Pesant S, Galand PE, Wincker P, Sunagawa S, Röttinger E, Furla P, Voolstra CR, Forcioli D, Lombard F, Gilson E. Telomere DNA length regulation is influenced by seasonal temperature differences in short-lived but not in long-lived reef-building corals. Nat Commun 2023; 14:3038. [PMID: 37263999 DOI: 10.1038/s41467-023-38499-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 04/26/2023] [Indexed: 06/03/2023] Open
Abstract
Telomeres are environment-sensitive regulators of health and aging. Here,we present telomere DNA length analysis of two reef-building coral genera revealing that the long- and short-term water thermal regime is a key driver of between-colony variation across the Pacific Ocean. Notably, there are differences between the two studied genera. The telomere DNA lengths of the short-lived, more stress-sensitive Pocillopora spp. colonies were largely determined by seasonal temperature variation, whereas those of the long-lived, more stress-resistant Porites spp. colonies were insensitive to seasonal patterns, but rather influenced by past thermal anomalies. These results reveal marked differences in telomere DNA length regulation between two evolutionary distant coral genera exhibiting specific life-history traits. We propose that environmentally regulated mechanisms of telomere maintenance are linked to organismal performances, a matter of paramount importance considering the effects of climate change on health.
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Affiliation(s)
- Alice Rouan
- Université Côte d'Azur-CNRS-Inserm-Institute for Research on Cancer and Ageing, Nice (IRCAN), Medical School, Nice, France.
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Nice, France.
| | - Melanie Pousse
- Université Côte d'Azur-CNRS-Inserm-Institute for Research on Cancer and Ageing, Nice (IRCAN), Medical School, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Nice, France
- Institut Fédératif de Recherche-Ressources Marines (IFR MARRES), Université Côte d'Azur, Nice, France
| | - Nadir Djerbi
- Université Côte d'Azur-CNRS-Inserm-Institute for Research on Cancer and Ageing, Nice (IRCAN), Medical School, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Nice, France
- Institut Fédératif de Recherche-Ressources Marines (IFR MARRES), Université Côte d'Azur, Nice, France
| | - Barbara Porro
- Université Côte d'Azur-CNRS-Inserm-Institute for Research on Cancer and Ageing, Nice (IRCAN), Medical School, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Nice, France
- Institut Fédératif de Recherche-Ressources Marines (IFR MARRES), Université Côte d'Azur, Nice, France
| | | | - Quentin Carradec
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GO-SEE, 75016, Paris, France
| | - Benjamin Cc Hume
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GO-SEE, 75016, Paris, France
| | - Julie Lê-Hoang
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GO-SEE, 75016, Paris, France
| | - Eric Armstrong
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GO-SEE, 75016, Paris, France
| | - Sylvain Agostini
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Japan
| | - Guillem Salazar
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, 8092, Zurich, Switzerland
| | - Hans-Joachim Ruscheweyh
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, 8092, Zurich, Switzerland
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GO-SEE, 75016, Paris, France
| | - David A Paz-García
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Av. IPN 195, La Paz, Baja California Sur, 23096, La Paz, México
| | - Ryan McMinds
- Université Côte d'Azur-CNRS-Inserm-Institute for Research on Cancer and Ageing, Nice (IRCAN), Medical School, Nice, France
- University of South Florida Center for Global Health and Infectious Diseases Research, Tampa, FL, USA
- Maison de la Modélisation, de la Simulation et des Interactions (MSI),, Université Côte d'Azur, Nice, France
| | - Marie-Josèphe Giraud-Panis
- Université Côte d'Azur-CNRS-Inserm-Institute for Research on Cancer and Ageing, Nice (IRCAN), Medical School, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Nice, France
- Institut Fédératif de Recherche-Ressources Marines (IFR MARRES), Université Côte d'Azur, Nice, France
| | - Romane Deshuraud
- Université Côte d'Azur-CNRS-Inserm-Institute for Research on Cancer and Ageing, Nice (IRCAN), Medical School, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Nice, France
- Institut Fédératif de Recherche-Ressources Marines (IFR MARRES), Université Côte d'Azur, Nice, France
| | - Alexandre Ottaviani
- Université Côte d'Azur-CNRS-Inserm-Institute for Research on Cancer and Ageing, Nice (IRCAN), Medical School, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Nice, France
- Institut Fédératif de Recherche-Ressources Marines (IFR MARRES), Université Côte d'Azur, Nice, France
| | - Lycia Die Morini
- Université Côte d'Azur-CNRS-Inserm-Institute for Research on Cancer and Ageing, Nice (IRCAN), Medical School, Nice, France
| | - Camille Leone
- Université Côte d'Azur-CNRS-Inserm-Institute for Research on Cancer and Ageing, Nice (IRCAN), Medical School, Nice, France
| | - Lia Wurzer
- Université Côte d'Azur-CNRS-Inserm-Institute for Research on Cancer and Ageing, Nice (IRCAN), Medical School, Nice, France
| | - Jessica Tran
- Université Côte d'Azur-CNRS-Inserm-Institute for Research on Cancer and Ageing, Nice (IRCAN), Medical School, Nice, France
| | - Didier Zoccola
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Nice, France
- Centre Scientifique de Monaco, Principality of Monaco, Monaco, Monaco
| | - Alexis Pey
- Université Côte d'Azur-CNRS-Inserm-Institute for Research on Cancer and Ageing, Nice (IRCAN), Medical School, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Nice, France
- Institut Fédératif de Recherche-Ressources Marines (IFR MARRES), Université Côte d'Azur, Nice, France
| | - Clémentine Moulin
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GO-SEE, 75016, Paris, France
- Tara Ocean Foundation, 8 rue de Prague, 75012, Paris, France
| | - Emilie Boissin
- Laboratoire d'Excellence "CORAIL," PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan Cedex, France
| | - Guillaume Iwankow
- Laboratoire d'Excellence "CORAIL," PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan Cedex, France
| | - Sarah Romac
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, Roscoff, France
| | - Colomban de Vargas
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GO-SEE, 75016, Paris, France
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, Roscoff, France
| | - Bernard Banaigs
- Laboratoire d'Excellence "CORAIL," PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan Cedex, France
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, ME, USA
| | - Chris Bowler
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GO-SEE, 75016, Paris, France
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Eric Douville
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, 91191, Gif-sur-Yvette, France
| | - Michel Flores
- Weizmann Institute of Science, Department of Earth, and Planetary Sciences, 76100, Rehovot, Israel
| | - Stéphanie Reynaud
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Nice, France
- Centre Scientifique de Monaco, Principality of Monaco, Monaco, Monaco
| | - Olivier P Thomas
- School of Biological and Chemical Sciences, Ryan Institute, University of Galway, University Road, H91TK33, Galway, Ireland
| | - Romain Troublé
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GO-SEE, 75016, Paris, France
- Tara Ocean Foundation, 8 rue de Prague, 75012, Paris, France
| | - Rebecca Vega Thurber
- Oregon State University, Department of Microbiology, 220 Nash Hall, Corvallis, OR, 97331, USA
| | - Serge Planes
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GO-SEE, 75016, Paris, France
- Laboratoire d'Excellence "CORAIL," PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan Cedex, France
| | - Denis Allemand
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Nice, France
- Centre Scientifique de Monaco, Principality of Monaco, Monaco, Monaco
| | - Stephane Pesant
- European Bioinformatics Institute, Wellcome Genome Campus, European Molecular Biology Laboratory, Wellcome Genome Campus, Cambridge CB10 1SD, UK, UK
| | - Pierre E Galand
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GO-SEE, 75016, Paris, France
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, Banyuls-sur-Mer, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GO-SEE, 75016, Paris, France
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, 8092, Zurich, Switzerland
| | - Eric Röttinger
- Université Côte d'Azur-CNRS-Inserm-Institute for Research on Cancer and Ageing, Nice (IRCAN), Medical School, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Nice, France
- Institut Fédératif de Recherche-Ressources Marines (IFR MARRES), Université Côte d'Azur, Nice, France
| | - Paola Furla
- Université Côte d'Azur-CNRS-Inserm-Institute for Research on Cancer and Ageing, Nice (IRCAN), Medical School, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Nice, France
- Institut Fédératif de Recherche-Ressources Marines (IFR MARRES), Université Côte d'Azur, Nice, France
| | | | - Didier Forcioli
- Université Côte d'Azur-CNRS-Inserm-Institute for Research on Cancer and Ageing, Nice (IRCAN), Medical School, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Nice, France
- Institut Fédératif de Recherche-Ressources Marines (IFR MARRES), Université Côte d'Azur, Nice, France
| | - Fabien Lombard
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GO-SEE, 75016, 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, Ministère chargé de l'enseignement supérieur, Paris, France
| | - Eric Gilson
- Université Côte d'Azur-CNRS-Inserm-Institute for Research on Cancer and Ageing, Nice (IRCAN), Medical School, Nice, France.
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Nice, France.
- Institut Fédératif de Recherche-Ressources Marines (IFR MARRES), Université Côte d'Azur, Nice, France.
- Department of Medical Genetics, CHU, Nice, France.
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11
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Lombard F, Bourdin G, Pesant S, Agostini S, Baudena A, Boissin E, Cassar N, Clampitt M, Conan P, Da Silva O, Dimier C, Douville E, Elineau A, Fin J, Flores JM, Ghiglione JF, Hume BCC, Jalabert L, John SG, Kelly RL, Koren I, Lin Y, Marie D, McMinds R, Mériguet Z, Metzl N, Paz-García DA, Pedrotti ML, Poulain J, Pujo-Pay M, Ras J, Reverdin G, Romac S, Rouan A, Röttinger E, Vardi A, Voolstra CR, Moulin C, Iwankow G, Banaigs B, Bowler C, de Vargas C, Forcioli D, Furla P, Galand PE, Gilson E, Reynaud S, Sunagawa S, Sullivan MB, Thomas OP, Troublé R, Thurber RV, Wincker P, Zoccola D, Allemand D, Planes S, Boss E, Gorsky G. Open science resources from the Tara Pacific expedition across coral reef and surface ocean ecosystems. Sci Data 2023; 10:324. [PMID: 37264023 DOI: 10.1038/s41597-022-01757-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 10/10/2022] [Indexed: 06/03/2023] Open
Abstract
The Tara Pacific expedition (2016-2018) sampled coral ecosystems around 32 islands in the Pacific Ocean and the ocean surface waters at 249 locations, resulting in the collection of nearly 58 000 samples. The expedition was designed to systematically study warm-water coral reefs and included the collection of corals, fish, plankton, and seawater samples for advanced biogeochemical, molecular, and imaging analysis. Here we provide a complete description of the sampling methodology, and we explain how to explore and access the different datasets generated by the expedition. Environmental context data were obtained from taxonomic registries, gazetteers, almanacs, climatologies, operational biogeochemical models, and satellite observations. The quality of the different environmental measures has been validated not only by various quality control steps, but also through a global analysis allowing the comparison with known environmental large-scale structures. Such publicly released datasets open the perspective to address a wide range of scientific questions.
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Affiliation(s)
- Fabien Lombard
- Sorbonne Université, Laboratoire d'Océanographie de Villefranche, UMR 7093, CNRS, Institut de la Mer de Villefranche, 06230, Villefranche sur mer, France.
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France.
- Institut Universitaire de France, 75231, Paris, France.
| | - Guillaume Bourdin
- Sorbonne Université, Laboratoire d'Océanographie de Villefranche, UMR 7093, CNRS, Institut de la Mer de Villefranche, 06230, Villefranche sur mer, France
- School of Marine Sciences, University of Maine, Orono, Maine, 04469, USA
| | - Stéphane Pesant
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Sylvain Agostini
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1, Shimoda, Shizuoka, Japan
| | - Alberto Baudena
- Sorbonne Université, Laboratoire d'Océanographie de Villefranche, UMR 7093, CNRS, Institut de la Mer de Villefranche, 06230, Villefranche sur mer, France
| | - Emilie Boissin
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Nicolas Cassar
- Nicholas School of the Environment, Duke University, Durham, NC, USA
- Laboratoire des Sciences de l'Environnement Marin, UMR 6539 UBO/CNRS/IRD/IFREMER, Institut Universitaire Européen de la Mer, Brest, France
| | - Megan Clampitt
- Université Côte d'Azur, CNRS, INSERM, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France
- Université Côte d'Azur, Institut Fédératif de Recherche - Ressources Marines (IFR MARRES), Nice, France
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco, Nice, Monaco
| | - Pascal Conan
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne, LOMIC, 66650, Banyuls Sur Mer, France
- Sorbonne Université, CNRS, OSU STAMAR - UAR2017, 75252 Paris, France
| | - Ophélie Da Silva
- Sorbonne Université, Laboratoire d'Océanographie de Villefranche, UMR 7093, CNRS, Institut de la Mer de Villefranche, 06230, Villefranche sur mer, France
| | - Céline Dimier
- Sorbonne Université, Laboratoire d'Océanographie de Villefranche, UMR 7093, CNRS, Institut de la Mer de Villefranche, 06230, Villefranche sur mer, France
| | - Eric Douville
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Amanda Elineau
- Sorbonne Université, Laboratoire d'Océanographie de Villefranche, UMR 7093, CNRS, Institut de la Mer de Villefranche, 06230, Villefranche sur mer, France
| | - Jonathan Fin
- Laboratoire LOCEAN/IPSL, Sorbonne Université-CNRS-IRD-MNHN, Paris, 75005, France
| | - J Michel Flores
- Weizmann Institute of Science, Department of Earth and Planetary Sciences, Rehovot, Israel
| | - Jean-François Ghiglione
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne, LOMIC, 66650, Banyuls Sur Mer, France
| | | | - Laetitia Jalabert
- Sorbonne Université, Laboratoire d'Océanographie de Villefranche, UMR 7093, CNRS, Institut de la Mer de Villefranche, 06230, Villefranche sur mer, France
| | - Seth G John
- Department of Earth Science, University of Southern California, Los Angeles, CA, USA
| | - Rachel L Kelly
- Department of Earth Science, University of Southern California, Los Angeles, CA, USA
| | - Ilan Koren
- Weizmann Institute of Science, Department of Earth and Planetary Sciences, Rehovot, Israel
| | - Yajuan Lin
- Nicholas School of the Environment, Duke University, Durham, NC, USA
- Laboratoire des Sciences de l'Environnement Marin, UMR 6539 UBO/CNRS/IRD/IFREMER, Institut Universitaire Européen de la Mer, Brest, France
- Environmental Research Center, Duke Kunshan University, Kunshan, China
| | - Dominique Marie
- Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR 7144, AD2M, Roscoff, France
| | - Ryan McMinds
- Université Côte d'Azur, CNRS, INSERM, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France
- Université Côte d'Azur, Maison de la Modélisation, de la Simulation et des Interactions (MSI), Nice, France
- Department of Microbiology, Oregon State University, Corvallis, OR, USA
| | - Zoé Mériguet
- Sorbonne Université, Laboratoire d'Océanographie de Villefranche, UMR 7093, CNRS, Institut de la Mer de Villefranche, 06230, Villefranche sur mer, France
| | - Nicolas Metzl
- Laboratoire LOCEAN/IPSL, Sorbonne Université-CNRS-IRD-MNHN, Paris, 75005, France
| | - David A Paz-García
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), La Paz, Baja California Sur, 23096, México
| | - Maria Luiza Pedrotti
- Sorbonne Université, Laboratoire d'Océanographie de Villefranche, UMR 7093, CNRS, Institut de la Mer de Villefranche, 06230, Villefranche sur mer, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Mireille Pujo-Pay
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne, LOMIC, 66650, Banyuls Sur Mer, France
| | - Joséphine Ras
- Sorbonne Université, Laboratoire d'Océanographie de Villefranche, UMR 7093, CNRS, Institut de la Mer de Villefranche, 06230, Villefranche sur mer, France
| | - Gilles Reverdin
- Laboratoire LOCEAN/IPSL, Sorbonne Université-CNRS-IRD-MNHN, Paris, 75005, France
| | - Sarah Romac
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France
- Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR 7144, AD2M, Roscoff, France
| | - Alice Rouan
- Université Côte d'Azur, CNRS, INSERM, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France
- Université Côte d'Azur, Institut Fédératif de Recherche - Ressources Marines (IFR MARRES), Nice, France
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco, Nice, Monaco
| | - Eric Röttinger
- Université Côte d'Azur, CNRS, INSERM, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France
- Université Côte d'Azur, Institut Fédératif de Recherche - Ressources Marines (IFR MARRES), Nice, France
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco, Nice, Monaco
| | - Assaf Vardi
- Weizmann Institute of Science, Department of Plant and Environmental Science, Rehovot, Israel
| | | | | | - Guillaume Iwankow
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Bernard Banaigs
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Chris Bowler
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France
- Institut de Biologie de l'Ecole Normale Supérieure, 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/Tara GOSEE, 75000, Paris, France
- Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR 7144, AD2M, Roscoff, France
| | - Didier Forcioli
- Université Côte d'Azur, CNRS, INSERM, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France
- Université Côte d'Azur, Institut Fédératif de Recherche - Ressources Marines (IFR MARRES), Nice, France
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco, Nice, Monaco
| | - Paola Furla
- Université Côte d'Azur, CNRS, INSERM, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France
- Université Côte d'Azur, Institut Fédératif de Recherche - Ressources Marines (IFR MARRES), Nice, France
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco, Nice, Monaco
| | - Pierre E Galand
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques, UMR 8222, LECOB, Banyuls-sur-Mer, France
| | - Eric Gilson
- Université Côte d'Azur, CNRS, INSERM, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France
- Université Côte d'Azur, Institut Fédératif de Recherche - Ressources Marines (IFR MARRES), Nice, France
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco, Nice, Monaco
- Department of Medical Genetics, CHU, Nice, France
| | - Stéphanie Reynaud
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco, Nice, Monaco
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, MC-98000, Antoine, Monaco
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zurich, Switzerland
| | - Matthew B Sullivan
- Department of Microbiology and Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH, USA
| | - Olivier P Thomas
- School of Biological and Chemical Sciences, Ryan Institute, University of Galway, University Road, Galway, Ireland
| | | | | | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Didier Zoccola
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco, Nice, Monaco
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, MC-98000, Antoine, Monaco
| | - Denis Allemand
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco, Nice, Monaco
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, MC-98000, Antoine, Monaco
| | - Serge Planes
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, Maine, 04469, USA
| | - Gaby Gorsky
- Sorbonne Université, Laboratoire d'Océanographie de Villefranche, UMR 7093, CNRS, Institut de la Mer de Villefranche, 06230, Villefranche sur mer, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France
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12
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Veglia AJ, Bistolas KSI, Voolstra CR, Hume BCC, Ruscheweyh HJ, Planes S, Allemand D, Boissin E, Wincker P, Poulain J, Moulin C, Bourdin G, Iwankow G, Romac S, Agostini S, Banaigs B, Boss E, Bowler C, de Vargas C, Douville E, Flores M, Forcioli D, Furla P, Galand PE, Gilson E, Lombard F, Pesant S, Reynaud S, Sunagawa S, Thomas OP, Troublé R, Zoccola D, Correa AMS, Vega Thurber RL. Endogenous viral elements reveal associations between a non-retroviral RNA virus and symbiotic dinoflagellate genomes. Commun Biol 2023; 6:566. [PMID: 37264063 DOI: 10.1038/s42003-023-04917-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 04/24/2023] [Indexed: 06/03/2023] Open
Abstract
Endogenous viral elements (EVEs) offer insight into the evolutionary histories and hosts of contemporary viruses. This study leveraged DNA metagenomics and genomics to detect and infer the host of a non-retroviral dinoflagellate-infecting +ssRNA virus (dinoRNAV) common in coral reefs. As part of the Tara Pacific Expedition, this study surveyed 269 newly sequenced cnidarians and their resident symbiotic dinoflagellates (Symbiodiniaceae), associated metabarcodes, and publicly available metagenomes, revealing 178 dinoRNAV EVEs, predominantly among hydrocoral-dinoflagellate metagenomes. Putative associations between Symbiodiniaceae and dinoRNAV EVEs were corroborated by the characterization of dinoRNAV-like sequences in 17 of 18 scaffold-scale and one chromosome-scale dinoflagellate genome assembly, flanked by characteristically cellular sequences and in proximity to retroelements, suggesting potential mechanisms of integration. EVEs were not detected in dinoflagellate-free (aposymbiotic) cnidarian genome assemblies, including stony corals, hydrocorals, jellyfish, or seawater. The pervasive nature of dinoRNAV EVEs within dinoflagellate genomes (especially Symbiodinium), as well as their inconsistent within-genome distribution and fragmented nature, suggest ancestral or recurrent integration of this virus with variable conservation. Broadly, these findings illustrate how +ssRNA viruses may obscure their genomes as members of nested symbioses, with implications for host evolution, exaptation, and immunity in the context of reef health and disease.
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Affiliation(s)
- Alex J Veglia
- BioSciences Department, Rice University, Houston, TX, USA
| | | | | | | | - Hans-Joachim Ruscheweyh
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, Vladimir-Prelog-Weg 4, ETH Zürich, CH-8093, Zürich, Switzerland
| | - Serge Planes
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Denis Allemand
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, Monaco, MC-98000, Principality of Monaco
| | - Emilie Boissin
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Clémentine Moulin
- Fondation Tara Océan, Base Tara, 8 rue de Prague, 75012, Paris, France
| | | | - Guillaume Iwankow
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Sarah Romac
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, Roscoff, France
| | - Sylvain Agostini
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1, Shimoda, Shizuoka, Japan
| | - Bernard Banaigs
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, ME, USA
| | - Chris Bowler
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Colomban de Vargas
- 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, F-91191, Gif-sur-Yvette, France
| | - Michel Flores
- Weizmann Institute of Science, Department of Earth and Planetary Sciences, 76100, Rehovot, Israel
| | - Didier Forcioli
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Medical School, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco, LIA ROPSE, Monaco, France
| | - Paola Furla
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Medical School, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco, LIA ROPSE, Monaco, France
| | - Pierre E Galand
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, 66650, Banyuls sur mer, France
| | - Eric Gilson
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Medical School, Nice, France
- Department of Medical Genetics, CHU of Nice, Nice, France
| | - Fabien Lombard
- Sorbonne Université, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, F-06230, Villefranche-sur-Mer, France
| | - Stéphane Pesant
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Stéphanie Reynaud
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, Monaco, MC-98000, Principality of Monaco
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, Vladimir-Prelog-Weg 4, ETH Zürich, CH-8093, Zürich, Switzerland
| | - Olivier P Thomas
- School of Biological and Chemical Sciences, Ryan Institute, University of Galway, University Road H91 TK33, Galway, Ireland
| | - Romain Troublé
- Fondation Tara Océan, Base Tara, 8 rue de Prague, 75012, Paris, France
| | - Didier Zoccola
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, Monaco, MC-98000, Principality of Monaco
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13
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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14
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Belser C, Poulain J, Labadie K, Gavory F, Alberti A, Guy J, Carradec Q, Cruaud C, Da Silva C, Engelen S, Mielle P, Perdereau A, Samson G, Gas S, Voolstra CR, Galand PE, Flores JM, Hume BCC, Perna G, Ziegler M, Ruscheweyh HJ, Boissin E, Romac S, Bourdin G, Iwankow G, Moulin C, Paz García DA, Agostini S, Banaigs B, Boss E, Bowler C, de Vargas C, Douville E, Forcioli D, Furla P, Gilson E, Lombard F, Pesant S, Reynaud S, Sunagawa S, Thomas OP, Troublé R, Thurber RV, Zoccola D, Scarpelli C, Jacoby EK, Oliveira PH, Aury JM, Allemand D, Planes S, Wincker P. Integrative omics framework for characterization of coral reef ecosystems from the Tara Pacific expedition. Sci Data 2023; 10:326. [PMID: 37264047 DOI: 10.1038/s41597-023-02204-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 09/14/2022] [Indexed: 06/03/2023] Open
Abstract
Coral reef science is a fast-growing field propelled by the need to better understand coral health and resilience to devise strategies to slow reef loss resulting from environmental stresses. Key to coral resilience are the symbiotic interactions established within a complex holobiont, i.e. the multipartite assemblages comprising the coral host organism, endosymbiotic dinoflagellates, bacteria, archaea, fungi, and viruses. Tara Pacific is an ambitious project built upon the experience of previous Tara Oceans expeditions, and leveraging state-of-the-art sequencing technologies and analyses to dissect the biodiversity and biocomplexity of the coral holobiont screened across most archipelagos spread throughout the entire Pacific Ocean. Here we detail the Tara Pacific workflow for multi-omics data generation, from sample handling to nucleotide sequence data generation and deposition. This unique multidimensional framework also includes a large amount of concomitant metadata collected side-by-side that provide new assessments of coral reef biodiversity including micro-biodiversity and shape future investigations of coral reef dynamics and their fate in the Anthropocene.
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Affiliation(s)
- Caroline Belser
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France.
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France.
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Karine Labadie
- Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057, Evry, France
| | - Frederick Gavory
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Adriana Alberti
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Julie Guy
- Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057, Evry, France
| | - Quentin Carradec
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Corinne Cruaud
- Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057, Evry, France
| | - Corinne Da Silva
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Stefan Engelen
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Paul Mielle
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, 91000, Evry, France
| | - Aude Perdereau
- Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057, Evry, France
| | - Gaelle Samson
- Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057, Evry, France
| | - Shahinaz Gas
- Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057, Evry, France
| | | | - Pierre E Galand
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
- Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, Banyuls/Mer, France
| | - J Michel Flores
- Weizmann Institute of Science, Dept. Earth and Planetary Science, Rehovot, Israel
| | - Benjamin C C Hume
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Gabriela Perna
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Maren Ziegler
- Department of Animal Ecology & Systematics, Justus Liebig University Giessen, 35392, Giessen, Germany
| | - Hans-Joachim Ruscheweyh
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, 8093, Switzerland
| | - Emilie Boissin
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan Cedex, France
| | - Sarah Romac
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, Roscoff, France
| | | | - Guillaume Iwankow
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan Cedex, France
| | - Clémentine Moulin
- Fondation Tara Océan, Base Tara, 8 rue de Prague, 75 012, Paris, France
| | - David A Paz García
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Av. IPN 195, Col. Playa Palo de Santa Rita Sur, La Paz, 23096, Baja California Sur, México
| | - Sylvain Agostini
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1, Shimoda, Shizuoka, Japan
| | - Bernard Banaigs
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, 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/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Colomban de Vargas
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, 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, F-91191, Gif-sur-Yvette, France
| | - Didier Forcioli
- Université Côte d'Azur, CNRS, Inserm, IRCAN, Nice, France
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco, Monaco, France
| | - Paola Furla
- Université Côte d'Azur, CNRS, Inserm, IRCAN, Nice, France
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco, Monaco, France
| | - Eric Gilson
- Université Côte d'Azur, CNRS, Inserm, IRCAN, Nice, France
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco, Monaco, France
- Department of Medical Genetics, CHU of Nice, Nice, France
| | - Fabien Lombard
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
- Sorbonne Université, Institut de la Mer de Villefranche sur mer, Laboratoire d' Océanographie de Villefranche, F-06230, Villefranche-sur-Mer, France
- Institut Universitaire de France, 75231, Paris, France
| | - Stéphane Pesant
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Stéphanie Reynaud
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco, Monaco, France
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, MC-98000, Monaco, Principality of Monaco
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, 8093, Switzerland
| | - Olivier P Thomas
- School of Biological and Chemical Sciences, Ryan Institute, University of Galway, University Road, H91 TK33, Galway, Ireland
| | - Romain Troublé
- Fondation Tara Océan, Base Tara, 8 rue de Prague, 75 012, Paris, France
| | - Rebecca Vega Thurber
- Oregon State University, Department of Microbiology, 220 Nash Hall, 97331, Corvallis, OR, USA
| | - Didier Zoccola
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco, Monaco, France
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, MC-98000, Monaco, Principality of Monaco
| | - Claude Scarpelli
- Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057, Evry, France
| | - E' Krame Jacoby
- Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057, Evry, France
| | - Pedro H Oliveira
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Denis Allemand
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco, Monaco, France
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, MC-98000, Monaco, Principality of Monaco
| | - Serge Planes
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan Cedex, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
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15
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Noel B, Denoeud F, Rouan A, Buitrago-López C, Capasso L, Poulain J, Boissin E, Pousse M, Da Silva C, Couloux A, Armstrong E, Carradec Q, Cruaud C, Labadie K, Lê-Hoang J, Tambutté S, Barbe V, Moulin C, Bourdin G, Iwankow G, Romac S, Agostini S, Banaigs B, Boss E, Bowler C, de Vargas C, Douville E, Flores JM, Forcioli D, Furla P, Galand PE, Lombard F, Pesant S, Reynaud S, Sullivan MB, Sunagawa S, Thomas OP, Troublé R, Thurber RV, Allemand D, Planes S, Gilson E, Zoccola D, Wincker P, Voolstra CR, Aury JM. Pervasive tandem duplications and convergent evolution shape coral genomes. Genome Biol 2023; 24:123. [PMID: 37264421 DOI: 10.1186/s13059-023-02960-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/05/2023] [Indexed: 06/03/2023] Open
Abstract
BACKGROUND Over the last decade, several coral genomes have been sequenced allowing a better understanding of these symbiotic organisms threatened by climate change. Scleractinian corals are reef builders and are central to coral reef ecosystems, providing habitat to a great diversity of species. RESULTS In the frame of the Tara Pacific expedition, we assemble two coral genomes, Porites lobata and Pocillopora cf. effusa, with vastly improved contiguity that allows us to study the functional organization of these genomes. We annotate their gene catalog and report a relatively higher gene number than that found in other public coral genome sequences, 43,000 and 32,000 genes, respectively. This finding is explained by a high number of tandemly duplicated genes, accounting for almost a third of the predicted genes. We show that these duplicated genes originate from multiple and distinct duplication events throughout the coral lineage. They contribute to the amplification of gene families, mostly related to the immune system and disease resistance, which we suggest to be functionally linked to coral host resilience. CONCLUSIONS At large, we show the importance of duplicated genes to inform the biology of reef-building corals and provide novel avenues to understand and screen for differences in stress resilience.
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Affiliation(s)
- Benjamin Noel
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
| | - France Denoeud
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
| | - Alice Rouan
- Université Côte d'Azur, CNRS, Inserm, IRCAN, Nice, France
- LIA ROPSE, Laboratoire International Associé, Université Côte d'Azur - Centre Scientifique de Monaco, France
| | | | - Laura Capasso
- LIA ROPSE, Laboratoire International Associé, Université Côte d'Azur - Centre Scientifique de Monaco, France
- Centre Scientifique de Monaco, Marine Biology Department, Monaco City, 98000, Monaco
- Sorbonne Université, Collège Doctoral, 75005, Paris, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
| | - Emilie Boissin
- Laboratoire d'Excellence CORAIL, PSL Research University, EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Cedex, Perpignan, France
| | - Mélanie Pousse
- Université Côte d'Azur, CNRS, Inserm, IRCAN, Nice, France
- LIA ROPSE, Laboratoire International Associé, Université Côte d'Azur - Centre Scientifique de Monaco, France
| | - Corinne Da Silva
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
| | - Arnaud Couloux
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
| | - Eric Armstrong
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
| | - Quentin Carradec
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
| | - Corinne Cruaud
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
- Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
| | - Karine Labadie
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
- Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
| | - Julie Lê-Hoang
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
| | - Sylvie Tambutté
- LIA ROPSE, Laboratoire International Associé, Université Côte d'Azur - Centre Scientifique de Monaco, France
- Centre Scientifique de Monaco, Marine Biology Department, Monaco City, 98000, Monaco
| | - Valérie Barbe
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
| | - Clémentine Moulin
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
- Fondation Tara Océan, Base Tara, 8 Rue de Prague, 75 012, Paris, France
| | | | - Guillaume Iwankow
- Laboratoire d'Excellence CORAIL, PSL Research University, EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Cedex, Perpignan, France
| | - Sarah Romac
- AD2M, UMR 7144, Sorbonne Université, CNRS, Station Biologique de Roscoff, ECOMAP, Roscoff, France
| | - Sylvain Agostini
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1, Shimoda, Shizuoka, Japan
| | - Bernard Banaigs
- Laboratoire d'Excellence CORAIL, PSL Research University, EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Cedex, Perpignan, 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, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
- Institut de Biologie de L'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Colomban de Vargas
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
- AD2M, UMR 7144, Sorbonne Université, CNRS, Station Biologique de Roscoff, 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, 91191, France
| | - J Michel Flores
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, 76100, Rehovot, Israel
| | - Didier Forcioli
- Université Côte d'Azur, CNRS, Inserm, IRCAN, Nice, France
- LIA ROPSE, Laboratoire International Associé, Université Côte d'Azur - Centre Scientifique de Monaco, France
| | - Paola Furla
- Université Côte d'Azur, CNRS, Inserm, IRCAN, Nice, France
- LIA ROPSE, Laboratoire International Associé, Université Côte d'Azur - Centre Scientifique de Monaco, France
| | - Pierre E Galand
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, Banyuls Sur Mer, France
| | - Fabien Lombard
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
- Institut de La Mer de Villefranche Sur Mer, Sorbonne Université, Laboratoire d'Océanographie de Villefranche, Villefranche-Sur-Mer, 06230, France
- Institut Universitaire de France, Paris, 75231, France
| | - Stéphane Pesant
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Stéphanie Reynaud
- LIA ROPSE, Laboratoire International Associé, Université Côte d'Azur - Centre Scientifique de Monaco, France
- Centre Scientifique de Monaco, Marine Biology Department, Monaco City, 98000, Monaco
| | - Matthew B Sullivan
- Departments of Microbiology and Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Vladimir-Prelog-Weg 4, CH-8093, Zurich, Switzerland
| | - Olivier P Thomas
- School of Biological and Chemical Sciences, Ryan Institute, University of Galway, University Road H91 TK33, Galway, Ireland
| | - Romain Troublé
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
- Fondation Tara Océan, Base Tara, 8 Rue de Prague, 75 012, Paris, France
| | - Rebecca Vega Thurber
- Department of Microbiology, Oregon State University, 220 Nash Hall, Corvallis, OR, 97331, USA
| | - Denis Allemand
- LIA ROPSE, Laboratoire International Associé, Université Côte d'Azur - Centre Scientifique de Monaco, France
- Centre Scientifique de Monaco, Marine Biology Department, Monaco City, 98000, Monaco
| | - Serge Planes
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
- Laboratoire d'Excellence CORAIL, PSL Research University, EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Cedex, Perpignan, France
| | - Eric Gilson
- Université Côte d'Azur, CNRS, Inserm, IRCAN, Nice, France
- LIA ROPSE, Laboratoire International Associé, Université Côte d'Azur - Centre Scientifique de Monaco, France
- Department of Human Genetics, CHU Nice, Nice, France
| | - Didier Zoccola
- LIA ROPSE, Laboratoire International Associé, Université Côte d'Azur - Centre Scientifique de Monaco, France
- Centre Scientifique de Monaco, Marine Biology Department, Monaco City, 98000, Monaco
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
| | | | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France.
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France.
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16
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Armstrong EJ, Lê-Hoang J, Carradec Q, Aury JM, Noel B, Hume BCC, Voolstra CR, Poulain J, Belser C, Paz-García DA, Cruaud C, Labadie K, Da Silva C, Moulin C, Boissin E, Bourdin G, Iwankow G, Romac S, Agostini S, Banaigs B, Boss E, Bowler C, de Vargas C, Douville E, Flores M, Forcioli D, Furla P, Galand PE, Gilson E, Lombard F, Pesant S, Reynaud S, Sullivan MB, Sunagawa S, Thomas OP, Troublé R, Thurber RV, Zoccola D, Planes S, Allemand D, Wincker P. Host transcriptomic plasticity and photosymbiotic fidelity underpin Pocillopora acclimatization across thermal regimes in the Pacific Ocean. Nat Commun 2023; 14:3056. [PMID: 37264036 DOI: 10.1038/s41467-023-38610-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 05/10/2023] [Indexed: 06/03/2023] Open
Abstract
Heat waves are causing declines in coral reefs globally. Coral thermal responses depend on multiple, interacting drivers, such as past thermal exposure, endosymbiont community composition, and host genotype. This makes the understanding of their relative roles in adaptive and/or plastic responses crucial for anticipating impacts of future warming. Here, we extracted DNA and RNA from 102 Pocillopora colonies collected from 32 sites on 11 islands across the Pacific Ocean to characterize host-photosymbiont fidelity and to investigate patterns of gene expression across a historical thermal gradient. We report high host-photosymbiont fidelity and show that coral and microalgal gene expression respond to different drivers. Differences in photosymbiotic association had only weak impacts on host gene expression, which was more strongly correlated with the historical thermal environment, whereas, photosymbiont gene expression was largely determined by microalgal lineage. Overall, our results reveal a three-tiered strategy of thermal acclimatization in Pocillopora underpinned by host-photosymbiont specificity, host transcriptomic plasticity, and differential photosymbiotic association under extreme warming.
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Affiliation(s)
- Eric J Armstrong
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France.
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France.
- PSL Université Paris: EPHE-UPVD-CNRS, UAR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan Cedex, France.
| | - Julie Lê-Hoang
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Quentin Carradec
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France.
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France.
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Benjamin Noel
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Benjamin C C Hume
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | | | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Caroline Belser
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - David A Paz-García
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Av. IPN 195, La Paz, Baja California Sur, 23096, México
| | - Corinne Cruaud
- Genoscope, Institut François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Karine Labadie
- Genoscope, Institut François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Corinne Da Silva
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Clémentine Moulin
- Fondation Tara Océan, Base Tara, 8 rue de Prague, 75 012, Paris, France
| | - Emilie Boissin
- PSL Université Paris: EPHE-UPVD-CNRS, UAR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan Cedex, France
| | - Guillaume Bourdin
- School of Marine Sciences, University of Maine, Orono, 04469, ME, USA
| | - Guillaume Iwankow
- PSL Université Paris: EPHE-UPVD-CNRS, UAR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan Cedex, France
| | - Sarah Romac
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, 29680, Roscoff, France
| | - Sylvain Agostini
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1, Shimoda, Shizuoka, Japan
| | - Bernard Banaigs
- PSL Université Paris: EPHE-UPVD-CNRS, UAR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan Cedex, France
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, 04469, ME, USA
| | - Chris Bowler
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
- Ecole Normale Supérieure, PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, 46 rue d'Ulm, F-75005, Paris, France
| | - Colomban de Vargas
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, 29680, Roscoff, France
| | - Eric Douville
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, F-91191, Gif-sur-Yvette, France
| | - Michel Flores
- Weizmann Institute of Science, Department of Earth and Planetary Sciences, 76100, 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, Principality of Monaco, 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, Principality of Monaco, Monaco
| | - Pierre E Galand
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, 66650, Banyuls sur mer, France
| | - 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, Principality of Monaco, Monaco
- Department of Medical Genetics, CHU, Nice, France
| | - Fabien Lombard
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
- Sorbonne Université, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, F-06230, Villefranche-sur-Mer, France
| | - Stéphane Pesant
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Stéphanie Reynaud
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco, Principality of Monaco, Monaco
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, MC-98000, Principality of Monaco, Monaco
| | - Matthew B Sullivan
- Departments of Microbiology and Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH, 43210, USA
| | - Shinichi Sunagawa
- Institute of Microbiology, Department of Biology, Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
| | - Olivier P Thomas
- School of Biological and Chemical Sciences, Ryan institute, University of Galway, University Road H91TK33, Galway, Ireland
| | - Romain Troublé
- Fondation Tara Océan, Base Tara, 8 rue de Prague, 75 012, Paris, France
| | - Rebecca Vega Thurber
- Oregon State University, Department of Microbiology, 220 Nash Hall, 97331, Corvallis, OR, USA
| | - Didier Zoccola
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco, Principality of Monaco, Monaco
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, MC-98000, Principality of Monaco, Monaco
| | - Serge Planes
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 66860, Perpignan Cedex, France
| | - Denis Allemand
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco, Principality of Monaco, Monaco
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, MC-98000, Principality of Monaco, Monaco
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
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17
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Cui G, Konciute MK, Ling L, Esau L, Raina JB, Han B, Salazar OR, Presnell JS, Rädecker N, Zhong H, Menzies J, Cleves PA, Liew YJ, Krediet CJ, Sawiccy V, Cziesielski MJ, Guagliardo P, Bougoure J, Pernice M, Hirt H, Voolstra CR, Weis VM, Pringle JR, Aranda M. Molecular insights into the Darwin paradox of coral reefs from the sea anemone Aiptasia. Sci Adv 2023; 9:eadf7108. [PMID: 36921053 PMCID: PMC10017044 DOI: 10.1126/sciadv.adf7108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
Symbiotic cnidarians such as corals and anemones form highly productive and biodiverse coral reef ecosystems in nutrient-poor ocean environments, a phenomenon known as Darwin's paradox. Resolving this paradox requires elucidating the molecular bases of efficient nutrient distribution and recycling in the cnidarian-dinoflagellate symbiosis. Using the sea anemone Aiptasia, we show that during symbiosis, the increased availability of glucose and the presence of the algae jointly induce the coordinated up-regulation and relocalization of glucose and ammonium transporters. These molecular responses are critical to support symbiont functioning and organism-wide nitrogen assimilation through glutamine synthetase/glutamate synthase-mediated amino acid biosynthesis. Our results reveal crucial aspects of the molecular mechanisms underlying nitrogen conservation and recycling in these organisms that allow them to thrive in the nitrogen-poor ocean environments.
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Affiliation(s)
- Guoxin Cui
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Migle K. Konciute
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Lorraine Ling
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Luke Esau
- Core Labs, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Jean-Baptiste Raina
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Baoda Han
- DARWIN21, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Octavio R. Salazar
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Jason S. Presnell
- Department of Integrative Biology, Oregon State University, Corvallis, OR 97331, USA
| | - Nils Rädecker
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Department of Biology, University of Konstanz, Konstanz 78457, Germany
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Huawen Zhong
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Jessica Menzies
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Phillip A. Cleves
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218, USA
| | - Yi Jin Liew
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Cory J. Krediet
- Department of Marine Science, Eckerd College, St. Petersburg, FL 33711, USA
| | - Val Sawiccy
- Department of Integrative Biology, Oregon State University, Corvallis, OR 97331, USA
| | - Maha J. Cziesielski
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Paul Guagliardo
- Centre for Microscopy Characterisation and Analysis, The University of Western Australia, Perth, WA, Australia
| | - Jeremy Bougoure
- Centre for Microscopy Characterisation and Analysis, The University of Western Australia, Perth, WA, Australia
| | - Mathieu Pernice
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Heribert Hirt
- DARWIN21, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Christian R. Voolstra
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Department of Biology, University of Konstanz, Konstanz 78457, Germany
| | - Virginia M. Weis
- Department of Integrative Biology, Oregon State University, Corvallis, OR 97331, USA
| | - John R. Pringle
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Manuel Aranda
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
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18
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Buitrago-López C, Cárdenas A, Hume BCC, Gosselin T, Staubach F, Aranda M, Barshis DJ, Sawall Y, Voolstra CR. Disparate population and holobiont structure of pocilloporid corals across the Red Sea gradient demonstrate species-specific evolutionary trajectories. Mol Ecol 2023; 32:2151-2173. [PMID: 36869609 DOI: 10.1111/mec.16871] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 01/25/2023] [Accepted: 01/30/2023] [Indexed: 03/05/2023]
Abstract
Global habitat degradation heightens the need to better understand patterns of genetic connectivity and diversity of marine biota across geographical ranges to guide conservation efforts. Corals across the Red Sea are subject to pronounced environmental differences, but studies so far suggest that animal populations are largely connected, excepting evidence for a genetic break between the northern-central and southern regions. Here, we investigated population structure and holobiont assemblage of two common pocilloporid corals, Pocillopora verrucosa and Stylophora pistillata, across the Red Sea. We found little evidence for population differentiation in P. verrucosa, except for the southernmost site. Conversely, S. pistillata exhibited a complex population structure with evidence for within-reef and regional genetic differentiation, in line with differences in their reproductive mode (P. verrucosa is a broadcast spawner and S. pistillata is a brooder). Analysis for genomic loci under positive selection identified 85 sites (18 of which were in coding sequences) that distinguished the southern P. verrucosa population from the remainder of the Red Sea population. By comparison, we found 128 loci (24 of which were residing in coding sequences) in S. pistillata with evidence for local adaptation at various sites. Functional annotation of the underlying proteins revealed putative roles in the response to stress, lipid metabolism, transport, cytoskeletal rearrangement, and ciliary function (among others). Microbial assemblages of both coral species showed pervasive association with microalgal symbionts from the genus Symbiodinium (former clade A) and bacteria from the genus Endozoicomonas that exhibited significant differences according to host genotype and environment. The disparity of population genetic and holobiont assemblage patterns even between closely related species (family Pocilloporidae) highlights the need for multispecies investigations to better understand the role of the environment in shaping evolutionary trajectories. It further emphasizes the importance of networks of reef reserves to achieve conservation of genetic variants critical to the future survival of coral ecosystems.
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Affiliation(s)
- Carol Buitrago-López
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,Department of Environment and Sustainability, Red Sea Global, Riyadh, Saudi Arabia
| | - Anny Cárdenas
- Department of Biology, University of Konstanz, Konstanz, Germany.,Department of Biology, American University, Washington, DC, USA
| | | | - Thierry Gosselin
- CSIRO Marine and Atmospheric Research, Tasmania, Hobart, Australia
| | - Fabian Staubach
- Institute of Biology I, Department of Evolutionary Biology and Ecology, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Manuel Aranda
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Daniel J Barshis
- Department of Biological Sciences, Old Dominion University, Norfolk, Virginia, USA
| | - Yvonne Sawall
- Bermuda Institute of Ocean Sciences (BIOS), St. George's, Bermuda
| | - Christian R Voolstra
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,Department of Biology, University of Konstanz, Konstanz, Germany
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19
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Voolstra CR, Peixoto RS, Ferrier-Pagès C. Mitigating the ecological collapse of coral reef ecosystems: Effective strategies to preserve coral reef ecosystems: Effective strategies to preserve coral reef ecosystems. EMBO Rep 2023; 24:e56826. [PMID: 36862379 PMCID: PMC10074092 DOI: 10.15252/embr.202356826] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 01/25/2023] [Accepted: 02/09/2023] [Indexed: 03/03/2023] Open
Abstract
Global warming is decimating coral reefs. We need to implement mitigation and restoration strategies now to prevent coral reefs from disappearing altogether.
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Affiliation(s)
| | - Raquel S Peixoto
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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20
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Xiang N, Meyer A, Pogoreutz C, Rädecker N, Voolstra CR, Wild C, Gärdes A. Excess labile carbon promotes diazotroph abundance in heat-stressed octocorals. R Soc Open Sci 2023; 10:221268. [PMID: 36938541 PMCID: PMC10014249 DOI: 10.1098/rsos.221268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 10/08/2022] [Accepted: 02/22/2023] [Indexed: 06/18/2023]
Abstract
Nitrogen limitation is the foundation of stable coral-algal symbioses. Diazotrophs, prokaryotes capable of fixing N2 into ammonia, support the productivity of corals in oligotrophic waters, but could contribute to the destabilization of holobiont functioning when overstimulated. Recent studies on reef-building corals have shown that labile dissolved organic carbon (DOC) enrichment or heat stress increases diazotroph abundance and activity, thereby increasing nitrogen availability and destabilizing the coral-algal symbiosis. However, the (a)biotic drivers of diazotrophs in octocorals are still poorly understood. We investigated diazotroph abundance (via relative quantification of nifH gene copy numbers) in two symbiotic octocorals, the more mixotrophic soft coral Xenia umbellata and the more autotrophic gorgonian Pinnigorgia flava, under (i) labile DOC enrichment for 21 days, followed by (ii) combined labile DOC enrichment and heat stress for 24 days. Without heat stress, relative diazotroph abundances in X. umbellata and P. flava were unaffected by DOC enrichment. During heat stress, DOC enrichment (20 and 40 mg glucose l-1) increased the relative abundances of diazotrophs by sixfold in X. umbellata and fourfold in P. flava, compared with their counterparts without excess DOC. Our data suggest that labile DOC enrichment and concomitant heat stress could disrupt the nitrogen limitation in octocorals by stimulating diazotroph proliferation. Ultimately, the disruption of nitrogen cycling may further compromise octocoral fitness by destabilizing symbiotic nutrient cycling. Therefore, improving local wastewater facilities to reduce labile DOC input into vulnerable coastal ecosystems may help octocorals cope with ocean warming.
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Affiliation(s)
- Nan Xiang
- Marine Ecology Department, Faculty of Biology and Chemistry, University of Bremen Bremen 28359, Germany
- Section of Polar Biological Oceanography, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven 27570, Germany
- Leibniz Center for Tropical Marine Research (ZMT), Bremen 28359, Germany
| | - Achim Meyer
- Leibniz Center for Tropical Marine Research (ZMT), Bremen 28359, Germany
| | - Claudia Pogoreutz
- Department of Biology, University of Konstanz, Konstanz 78457, Germany
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Nils Rädecker
- Department of Biology, University of Konstanz, Konstanz 78457, Germany
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | | | - Christian Wild
- Marine Ecology Department, Faculty of Biology and Chemistry, University of Bremen Bremen 28359, Germany
| | - Astrid Gärdes
- Section of Polar Biological Oceanography, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven 27570, Germany
- Leibniz Center for Tropical Marine Research (ZMT), Bremen 28359, Germany
- Hochschule Bremerhaven, Fachbereich 1, An der Karlstadt 8, Bremerhaven 27568, Germany
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21
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Islas-Morales PF, Cárdenas A, Mosqueira MJ, Jiménez-García LF, Voolstra CR. Ultrastructural and proteomic evidence for the presence of a putative nucleolus in an Archaeon. Front Microbiol 2023; 14:1075071. [PMID: 36819014 PMCID: PMC9932318 DOI: 10.3389/fmicb.2023.1075071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 01/02/2023] [Indexed: 02/05/2023] Open
Abstract
Nucleoli are subcellular compartments where transcription and maturation of pre-ribosomal RNAs occur. While the transcription of ribosomal RNAs is common to all living cells, the presence and ultrastructure of nucleoli has been only documented in eukaryotes. Asgard-Archaea, the closest prokaryotic relatives of eukaryotes, and their near relatives TACK-Archaea have homologs of nucleolar proteins and RNAs in their genome, but the cellular organization of both is largely unexplored. Here we provide ultrastructural and molecular evidence for the presence of putative nucleolus-like subcellular domains in the TACK crenarchaeon Saccharolobus solfataricus (formerly known as Sulfolobus solfataricus). Transmission electron microscopy (TEM) revealed consistent electron-dense fibro-granular compartments, also positive to the specific silver staining for nucleolar organizer regions (AgNOR). TEM also confirmed that ribosomal DNA (rDNA) is spatially distributed in non-random, clustered arrays underlying fine structures, as observed by ultrastructural in situ hybridization (UISH). To further explore these observations, proteomic sequencing of isolated bands from AgNOR-stained protein gels was conducted and compared against a compiled inventory of putative nucleolar homologs from the S. solfataricus P1 genome. Sequenced AgNOR-sensitive peptides encoded homologs of eukaryotic nucleoli proteins, enriched for nucleolus-related functions. Our results provide first evidence that subcellular domains of nucleolar-like nature are not exclusive to eukaryotes. Based on our data, we propose a model for a putative nucleolus in S. solfataricus. Whereas technical limitations and further aspects remain a matter for future functional studies, our data supports the origin of nucleoli within the common ancestor of Eukarya and TACK-Archaea, based on a two-domain tree of life.
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Affiliation(s)
- Parsifal F. Islas-Morales
- Programa de Doctorado en Ciencias Biomédicas, Facultad de Medicina, UNAM, Mexico City, Mexico,UNESCO Chair on Science Diplomacy and Scientific Heritage, Instituto de Biología, UNAM, Mexico City, Mexico,Red Sea Research Center (RSRC), Biological, Environmental Sciences, and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Anny Cárdenas
- Red Sea Research Center (RSRC), Biological, Environmental Sciences, and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia,Department of Biology, University of Konstanz, Konstanz, Germany,Department of Biology, American University, Washington, DC, United States
| | - María J. Mosqueira
- Red Sea Research Center (RSRC), Biological, Environmental Sciences, and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia,NEOM, Saudi Arabia
| | - Luis Felipe Jiménez-García
- Programa de Doctorado en Ciencias Biomédicas, Facultad de Medicina, UNAM, Mexico City, Mexico,Department of Cell Biology, Faculty of Sciences, UNAM, Mexico City, Mexico,*Correspondence: Luis Felipe Jiménez-García, ✉
| | - Christian R. Voolstra
- Red Sea Research Center (RSRC), Biological, Environmental Sciences, and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia,Department of Biology, University of Konstanz, Konstanz, Germany,Christian R. Voolstra, ✉
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22
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Davies SW, Gamache MH, Howe-Kerr LI, Kriefall NG, Baker AC, Banaszak AT, Bay LK, Bellantuono AJ, Bhattacharya D, Chan CX, Claar DC, Coffroth MA, Cunning R, Davy SK, del Campo J, Díaz-Almeyda EM, Frommlet JC, Fuess LE, González-Pech RA, Goulet TL, Hoadley KD, Howells EJ, Hume BCC, Kemp DW, Kenkel CD, Kitchen SA, LaJeunesse TC, Lin S, McIlroy SE, McMinds R, Nitschke MR, Oakley CA, Peixoto RS, Prada C, Putnam HM, Quigley K, Reich HG, Reimer JD, Rodriguez-Lanetty M, Rosales SM, Saad OS, Sampayo EM, Santos SR, Shoguchi E, Smith EG, Stat M, Stephens TG, Strader ME, Suggett DJ, Swain TD, Tran C, Traylor-Knowles N, Voolstra CR, Warner ME, Weis VM, Wright RM, Xiang T, Yamashita H, Ziegler M, Correa AMS, Parkinson JE. Building consensus around the assessment and interpretation of Symbiodiniaceae diversity. PeerJ 2023; 11:e15023. [PMID: 37151292 PMCID: PMC10162043 DOI: 10.7717/peerj.15023] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 02/17/2023] [Indexed: 05/09/2023] Open
Abstract
Within microeukaryotes, genetic variation and functional variation sometimes accumulate more quickly than morphological differences. To understand the evolutionary history and ecology of such lineages, it is key to examine diversity at multiple levels of organization. In the dinoflagellate family Symbiodiniaceae, which can form endosymbioses with cnidarians (e.g., corals, octocorals, sea anemones, jellyfish), other marine invertebrates (e.g., sponges, molluscs, flatworms), and protists (e.g., foraminifera), molecular data have been used extensively over the past three decades to describe phenotypes and to make evolutionary and ecological inferences. Despite advances in Symbiodiniaceae genomics, a lack of consensus among researchers with respect to interpreting genetic data has slowed progress in the field and acted as a barrier to reconciling observations. Here, we identify key challenges regarding the assessment and interpretation of Symbiodiniaceae genetic diversity across three levels: species, populations, and communities. We summarize areas of agreement and highlight techniques and approaches that are broadly accepted. In areas where debate remains, we identify unresolved issues and discuss technologies and approaches that can help to fill knowledge gaps related to genetic and phenotypic diversity. We also discuss ways to stimulate progress, in particular by fostering a more inclusive and collaborative research community. We hope that this perspective will inspire and accelerate coral reef science by serving as a resource to those designing experiments, publishing research, and applying for funding related to Symbiodiniaceae and their symbiotic partnerships.
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Affiliation(s)
- Sarah W. Davies
- Department of Biology, Boston University, Boston, MA, United States
| | - Matthew H. Gamache
- Department of Integrative Biology, University of South Florida, Tampa, FL, United States
| | | | | | - Andrew C. Baker
- Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL, United States
| | - Anastazia T. Banaszak
- Unidad Académica de Sistemas Arrecifales, Universidad Nacional Autónoma de México, Puerto Morelos, Mexico
| | - Line Kolind Bay
- Australian Institute of Marine Science, Townsville, Australia
| | - Anthony J. Bellantuono
- Department of Biological Sciences, Florida International University, Miami, FL, United States
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, United States
| | - Cheong Xin Chan
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Danielle C. Claar
- Nearshore Habitat Program, Washington State Department of Natural Resources, Olympia, WA, USA
| | | | - Ross Cunning
- Daniel P. Haerther Center for Conservation and Research, John G. Shedd Aquarium, Chicago, IL, United States
| | - Simon K. Davy
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Javier del Campo
- Institut de Biologia Evolutiva (CSIC - Universitat Pompeu Fabra), Barcelona, Catalonia, Spain
| | | | - Jörg C. Frommlet
- Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
| | - Lauren E. Fuess
- Department of Biology, Texas State University, San Marcos, TX, United States
| | - Raúl A. González-Pech
- Department of Integrative Biology, University of South Florida, Tampa, FL, United States
- Department of Biology, Pennsylvania State University, State College, PA, United States
| | - Tamar L. Goulet
- Department of Biology, University of Mississippi, University, MS, United States
| | - Kenneth D. Hoadley
- Department of Biological Sciences, University of Alabama—Tuscaloosa, Tuscaloosa, AL, United States
| | - Emily J. Howells
- National Marine Science Centre, Faculty of Science and Engineering, Southern Cross University, Coffs Harbour, NSW, Australia
| | | | - Dustin W. Kemp
- Department of Biology, University of Alabama—Birmingham, Birmingham, Al, United States
| | - Carly D. Kenkel
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Sheila A. Kitchen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
| | - Todd C. LaJeunesse
- Department of Biology, Pennsylvania State University, University Park, PA, United States
| | - Senjie Lin
- Department of Marine Sciences, University of Connecticut, Mansfield, CT, United States
| | - Shelby E. McIlroy
- Swire Institute of Marine Science, School of Biological Sciences, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Ryan McMinds
- Center for Global Health and Infectious Disease Research, University of South Florida, Tampa, FL, United States
| | | | - Clinton A. Oakley
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Raquel S. Peixoto
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Carlos Prada
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, United States
| | - Hollie M. Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, United States
| | | | - Hannah G. Reich
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, United States
| | - James Davis Reimer
- Department of Biology, Chemistry and Marine Sciences, Faculty of Science, University of the Ryukyus, Nishihara, Okinawa, Japan
| | | | - Stephanie M. Rosales
- The Cooperative Institute For Marine and Atmospheric Studies, Miami, FL, United States
| | - Osama S. Saad
- Department of Biological Oceanography, Red Sea University, Port-Sudan, Sudan
| | - Eugenia M. Sampayo
- School of Biological Sciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Scott R. Santos
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, United States
| | - Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Edward G. Smith
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Michael Stat
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, Australia
| | - Timothy G. Stephens
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, United States
| | - Marie E. Strader
- Department of Biology, Texas A&M University, College Station, TX, United States
| | - David J. Suggett
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Timothy D. Swain
- Department of Marine and Environmental Science, Nova Southeastern University, Dania Beach, FL, United States
| | - Cawa Tran
- Department of Biology, University of San Diego, San Diego, CA, United States
| | - Nikki Traylor-Knowles
- Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL, United States
| | | | - Mark E. Warner
- School of Marine Science and Policy, University of Delaware, Lewes, DE, United States
| | - Virginia M. Weis
- Department of Integrative Biology, Oregon State University, Corvallis, OR, United States
| | - Rachel M. Wright
- Department of Biological Sciences, Southern Methodist University, Dallas, TX, United States
| | - Tingting Xiang
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Hiroshi Yamashita
- Fisheries Technology Institute, Japan Fisheries Research and Education Agency, Ishigaki, Okinawa, Japan
| | - Maren Ziegler
- Department of Animal Ecology & Systematics, Justus Liebig University Giessen (Germany), Giessen, Germany
| | | | - John Everett Parkinson
- Department of Integrative Biology, University of South Florida, Tampa, FL, United States
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23
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Delgadillo-Ordoñez N, Raimundo I, Barno AR, Osman EO, Villela H, Bennett-Smith M, Voolstra CR, Benzoni F, Peixoto RS. Red Sea Atlas of Coral-Associated Bacteria Highlights Common Microbiome Members and Their Distribution across Environmental Gradients-A Systematic Review. Microorganisms 2022; 10:microorganisms10122340. [PMID: 36557593 PMCID: PMC9787610 DOI: 10.3390/microorganisms10122340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 10/12/2022] [Accepted: 11/18/2022] [Indexed: 11/29/2022] Open
Abstract
The Red Sea is a suitable model for studying coral reefs under climate change due to its strong environmental gradient that provides a window into future global warming scenarios. For instance, corals in the southern Red Sea thrive at temperatures predicted to occur at the end of the century in other biogeographic regions. Corals in the Red Sea thrive under contrasting thermal and environmental regimes along their latitudinal gradient. Because microbial communities associated with corals contribute to host physiology, we conducted a systematic review of the known diversity of Red Sea coral-associated bacteria, considering geographic location and host species. Our assessment comprises 54 studies of 67 coral host species employing cultivation-dependent and cultivation-independent techniques. Most studies have been conducted in the central and northern Red Sea, while the southern and western regions remain largely unexplored. Our data also show that, despite the high diversity of corals in the Red Sea, the most studied corals were Pocillopora verrucosa, Dipsastraea spp., Pleuractis granulosa, and Stylophora pistillata. Microbial diversity was dominated by bacteria from the class Gammaproteobacteria, while the most frequently occurring bacterial families included Rhodobacteraceae and Vibrionaceae. We also identified bacterial families exclusively associated with each of the studied coral orders: Scleractinia (n = 125), Alcyonacea (n = 7), and Capitata (n = 2). This review encompasses 20 years of research in the Red Sea, providing a baseline compendium for coral-associated bacterial diversity.
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Affiliation(s)
- Nathalia Delgadillo-Ordoñez
- Marine Microbiomes Laboratory, Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Inês Raimundo
- Marine Microbiomes Laboratory, Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Adam R. Barno
- Marine Microbiomes Laboratory, Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Eslam O. Osman
- Marine Microbiomes Laboratory, Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Helena Villela
- Marine Microbiomes Laboratory, Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Morgan Bennett-Smith
- Marine Microbiomes Laboratory, Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Christian R. Voolstra
- Marine Microbiomes Laboratory, Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Francesca Benzoni
- Marine Microbiomes Laboratory, Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Raquel S. Peixoto
- Marine Microbiomes Laboratory, Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
- Correspondence:
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24
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Alderdice R, Perna G, Cárdenas A, Hume BCC, Wolf M, Kühl M, Pernice M, Suggett DJ, Voolstra CR. Deoxygenation lowers the thermal threshold of coral bleaching. Sci Rep 2022; 12:18273. [PMID: 36316371 PMCID: PMC9622859 DOI: 10.1038/s41598-022-22604-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 10/17/2022] [Indexed: 12/02/2022] Open
Abstract
Exposure to deoxygenation from climate warming and pollution is emerging as a contributing factor of coral bleaching and mortality. However, the combined effects of heating and deoxygenation on bleaching susceptibility remain unknown. Here, we employed short-term thermal stress assays to show that deoxygenated seawater can lower the thermal limit of an Acropora coral by as much as 1 °C or 0.4 °C based on bleaching index scores or dark-acclimated photosynthetic efficiencies, respectively. Using RNA-Seq, we show similar stress responses to heat with and without deoxygenated seawater, both activating putative key genes of the hypoxia-inducible factor response system indicative of cellular hypoxia. We also detect distinct deoxygenation responses, including a disruption of O2-dependent photo-reception/-protection, redox status, and activation of an immune response prior to the onset of bleaching. Thus, corals are even more vulnerable when faced with heat stress in deoxygenated waters. This highlights the need to integrate dissolved O2 measurements into global monitoring programs of coral reefs.
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Affiliation(s)
- Rachel Alderdice
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Ultimo, NSW, 2007, Australia.
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany.
| | - Gabriela Perna
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Anny Cárdenas
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Benjamin C C Hume
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Martin Wolf
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Michael Kühl
- Marine Biology Section, Department of Biology, University of Copenhagen, Strandpromenaden 5, 3000, Helsingør, Denmark
| | - Mathieu Pernice
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - David J Suggett
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Ultimo, NSW, 2007, Australia
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25
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Xiang N, Rädecker N, Pogoreutz C, Cárdenas A, Meibom A, Wild C, Gärdes A, Voolstra CR. Presence of algal symbionts affects denitrifying bacterial communities in the sea anemone Aiptasia coral model. ISME Commun 2022; 2:105. [PMID: 37938763 PMCID: PMC9723753 DOI: 10.1038/s43705-022-00190-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 09/28/2022] [Accepted: 10/10/2022] [Indexed: 11/09/2023]
Abstract
The coral-algal symbiosis is maintained by a constant and limited nitrogen availability in the holobiont. Denitrifiers, i.e., prokaryotes reducing nitrate/nitrite to dinitrogen, could contribute to maintaining the nitrogen limitation in the coral holobiont, however the effect of host and algal identity on their community is still unknown. Using the coral model Aiptasia, we quantified and characterized the denitrifier community in a full-factorial design combining two hosts (CC7 and H2) and two strains of algal symbionts of the family Symbiodiniaceae (SSA01 and SSB01). Strikingly, relative abundance of denitrifiers increased by up to 22-fold in photosymbiotic Aiptasia compared to their aposymbiotic (i.e., algal-depleted) counterparts. In line with this, while the denitrifier community in aposymbiotic Aiptasia was largely dominated by diet-associated Halomonas, we observed an increasing relative abundance of an unclassified bacterium in photosymbiotic CC7, and Ketobacter in photosymbiotic H2, respectively. Pronounced changes in denitrifier communities of Aiptasia with Symbiodinium linucheae strain SSA01 aligned with the higher photosynthetic carbon availability of these holobionts compared to Aiptasia with Breviolum minutum strain SSB01. Our results reveal that the presence of algal symbionts increases abundance and alters community structure of denitrifiers in Aiptasia. Thereby, patterns in denitrifier community likely reflect the nutritional status of aposymbiotic vs. symbiotic holobionts. Such a passive regulation of denitrifiers may contribute to maintaining the nitrogen limitation required for the functioning of the cnidarian-algal symbiosis.
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Affiliation(s)
- Nan Xiang
- Marine Ecology Department, Faculty of Biology and Chemistry, University of Bremen, 28359, Bremen, Germany.
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, 27570, Bremerhaven, Germany.
| | - Nils Rädecker
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Claudia Pogoreutz
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Anny Cárdenas
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Anders Meibom
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
- Center for Advanced Surface Analysis (CASA), Institute of Earth Science, University of Lausanne, 1015, Lausanne, Switzerland
| | - Christian Wild
- Marine Ecology Department, Faculty of Biology and Chemistry, University of Bremen, 28359, Bremen, Germany
| | - Astrid Gärdes
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, 27570, Bremerhaven, Germany
- Hochschule Bremerhaven, Fachbereich 1, An der Karlstadt 8, 27568, Bremerhaven, Germany
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26
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Cárdenas A, Raina JB, Pogoreutz C, Rädecker N, Bougoure J, Guagliardo P, Pernice M, Voolstra CR. Greater functional diversity and redundancy of coral endolithic microbiomes align with lower coral bleaching susceptibility. ISME J 2022; 16:2406-2420. [PMID: 35840731 PMCID: PMC9478130 DOI: 10.1038/s41396-022-01283-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 06/14/2022] [Accepted: 06/28/2022] [Indexed: 04/14/2023]
Abstract
The skeleton of reef-building coral harbors diverse microbial communities that could compensate for metabolic deficiencies caused by the loss of algal endosymbionts, i.e., coral bleaching. However, it is unknown to what extent endolith taxonomic diversity and functional potential might contribute to thermal resilience. Here we exposed Goniastrea edwardsi and Porites lutea, two common reef-building corals from the central Red Sea to a 17-day long heat stress. Using hyperspectral imaging, marker gene/metagenomic sequencing, and NanoSIMS, we characterized their endolithic microbiomes together with 15N and 13C assimilation of two skeletal compartments: the endolithic band directly below the coral tissue and the deep skeleton. The bleaching-resistant G. edwardsi was associated with endolithic microbiomes of greater functional diversity and redundancy that exhibited lower N and C assimilation than endoliths in the bleaching-sensitive P. lutea. We propose that the lower endolithic primary productivity in G. edwardsi can be attributed to the dominance of chemolithotrophs. Lower primary production within the skeleton may prevent unbalanced nutrient fluxes to coral tissues under heat stress, thereby preserving nutrient-limiting conditions characteristic of a stable coral-algal symbiosis. Our findings link coral endolithic microbiome structure and function to bleaching susceptibility, providing new avenues for understanding and eventually mitigating reef loss.
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Affiliation(s)
- Anny Cárdenas
- Department of Biology, University of Konstanz, Konstanz, 78457, Germany.
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.
| | - Jean-Baptiste Raina
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, 2007, Australia.
| | - Claudia Pogoreutz
- Department of Biology, University of Konstanz, Konstanz, 78457, Germany
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, 1015, Switzerland
| | - Nils Rädecker
- Department of Biology, University of Konstanz, Konstanz, 78457, Germany
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, 1015, Switzerland
| | - Jeremy Bougoure
- Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, Perth, WA, 6009, Australia
| | - Paul Guagliardo
- Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, Perth, WA, 6009, Australia
| | - Mathieu Pernice
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Christian R Voolstra
- Department of Biology, University of Konstanz, Konstanz, 78457, Germany.
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.
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27
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Scott CB, Cárdenas A, Mah M, Narasimhan VM, Rohland N, Toth LT, Voolstra CR, Reich D, Matz MV. Millennia-old coral holobiont DNA provides insight into future adaptive trajectories. Mol Ecol 2022; 31:4979-4990. [PMID: 35943423 DOI: 10.1111/mec.16642] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 07/26/2022] [Accepted: 08/03/2022] [Indexed: 11/28/2022]
Abstract
Ancient DNA (aDNA) has been applied to evolutionary questions across a wide variety of taxa. Here, for the first time, we leverage aDNA from millennia-old fossil coral fragments to gain new insights into a rapidly declining western Atlantic reef ecosystem. We sampled four Acropora palmata fragments (dated 4215 BCE - 1099 CE) obtained from two Florida Keys reef cores. From these samples, we established that it is possible both to sequence ancient DNA from reef cores and place the data in the context of modern-day genetic variation. We recovered varying amounts of nuclear DNA exhibiting the characteristic signatures of aDNA from the A. palmata fragments. To describe the holobiont sensu lato, which plays a crucial role in reef health, we utilized metagenome-assembled genomes as a reference to identify a large additional proportion of ancient microbial DNA from the samples. The samples shared many common microbes with modern-day coral holobionts from the same region, suggesting remarkable holobiont stability over time. Despite efforts, we were unable to recover ancient Symbiodiniaceae reads from the samples. Comparing the ancient A. palmata data to whole-genome sequencing data from living acroporids, we found that while slightly distinct, ancient samples were most closely related to individuals of their own species. Together, these results provide a proof-of-principle showing that it is possible to carry out direct analysis of coral holobiont change over time, which lays a foundation for studying the impacts of environmental stress and evolutionary constraints.
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Affiliation(s)
- Carly B Scott
- Department of Integrative Biology, University of Texas, Austin, TX, USA
| | - Anny Cárdenas
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA, Austin, TX, USA
| | | | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Lauren T Toth
- U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center, St. Petersburg, FL
| | | | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA, Austin, TX, USA.,Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Mikhail V Matz
- Department of Integrative Biology, University of Texas, Austin, TX, USA
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28
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Peixoto RS, Voolstra CR, Sweet M, Duarte CM, Carvalho S, Villela H, Lunshof JE, Gram L, Woodhams DC, Walter J, Roik A, Hentschel U, Thurber RV, Daisley B, Ushijima B, Daffonchio D, Costa R, Keller-Costa T, Bowman JS, Rosado AS, Reid G, Mason CE, Walke JB, Thomas T, Berg G. Harnessing the microbiome to prevent global biodiversity loss. Nat Microbiol 2022; 7:1726-1735. [PMID: 35864220 DOI: 10.1038/s41564-022-01173-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 06/14/2022] [Indexed: 01/21/2023]
Abstract
Global biodiversity loss and mass extinction of species are two of the most critical environmental issues the world is currently facing, resulting in the disruption of various ecosystems central to environmental functions and human health. Microbiome-targeted interventions, such as probiotics and microbiome transplants, are emerging as potential options to reverse deterioration of biodiversity and increase the resilience of wildlife and ecosystems. However, the implementation of these interventions is urgently needed. We summarize the current concepts, bottlenecks and ethical aspects encompassing the careful and responsible management of ecosystem resources using the microbiome (termed microbiome stewardship) to rehabilitate organisms and ecosystem functions. We propose a real-world application framework to guide environmental and wildlife probiotic applications. This framework details steps that must be taken in the upscaling process while weighing risks against the high toll of inaction. In doing so, we draw parallels with other aspects of contemporary science moving swiftly in the face of urgent global challenges.
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Affiliation(s)
- Raquel S Peixoto
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
| | - Christian R Voolstra
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,Department of Biology, University of Konstanz, Konstanz, Germany
| | - Michael Sweet
- Aquatic Research Facility, Environmental Sustainability Research Centre, University of Derby, Derby, UK
| | - Carlos M Duarte
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,Computational Bioscience Research Center (CBRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Susana Carvalho
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Helena Villela
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Jeantine E Lunshof
- Department of Global Health and Social Medicine, Center for Bioethics, Harvard Medical School, Boston, MA, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Lone Gram
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Douglas C Woodhams
- Department of Biology, University of Massachusetts Boston, Boston, MA, USA.,Smithsonian Tropical Research Institute, Panama City, Panama
| | - Jens Walter
- APC Microbiome Ireland, School of Microbiology, and Department of Medicine, University College Cork, Cork, Ireland
| | - Anna Roik
- Helmholtz Institute for Functional Marine Biodiversity (HIFMB), Oldenburg, Germany
| | - Ute Hentschel
- RD3 Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | | | - Brendan Daisley
- Lawson Health Research Institute, University of Western Ontario, London, Ontario, Canada
| | - Blake Ushijima
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, USA
| | - Daniele Daffonchio
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Rodrigo Costa
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
| | - Tina Keller-Costa
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
| | - Jeff S Bowman
- Scripps Institution of Oceanography, University of California San Diego, San Diego, CA, USA
| | - Alexandre S Rosado
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Gregor Reid
- Lawson Health Research Institute, University of Western Ontario, London, Ontario, Canada
| | | | - Jenifer B Walke
- Department of Biology, Eastern Washington University, Cheney, WA, USA
| | - Torsten Thomas
- Centre for Marine Science and Innovation and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria.,University of Postdam and Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany
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29
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van Woesik R, Shlesinger T, Grottoli AG, Toonen RJ, Vega Thurber R, Warner ME, Marie Hulver A, Chapron L, McLachlan RH, Albright R, Crandall E, DeCarlo TM, Donovan MK, Eirin‐Lopez J, Harrison HB, Heron SF, Huang D, Humanes A, Krueger T, Madin JS, Manzello D, McManus LC, Matz M, Muller EM, Rodriguez‐Lanetty M, Vega‐Rodriguez M, Voolstra CR, Zaneveld J. Coral-bleaching responses to climate change across biological scales. Glob Chang Biol 2022; 28:4229-4250. [PMID: 35475552 PMCID: PMC9545801 DOI: 10.1111/gcb.16192] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/28/2022] [Accepted: 03/29/2022] [Indexed: 05/26/2023]
Abstract
The global impacts of climate change are evident in every marine ecosystem. On coral reefs, mass coral bleaching and mortality have emerged as ubiquitous responses to ocean warming, yet one of the greatest challenges of this epiphenomenon is linking information across scientific disciplines and spatial and temporal scales. Here we review some of the seminal and recent coral-bleaching discoveries from an ecological, physiological, and molecular perspective. We also evaluate which data and processes can improve predictive models and provide a conceptual framework that integrates measurements across biological scales. Taking an integrative approach across biological and spatial scales, using for example hierarchical models to estimate major coral-reef processes, will not only rapidly advance coral-reef science but will also provide necessary information to guide decision-making and conservation efforts. To conserve reefs, we encourage implementing mesoscale sanctuaries (thousands of km2 ) that transcend national boundaries. Such networks of protected reefs will provide reef connectivity, through larval dispersal that transverse thermal environments, and genotypic repositories that may become essential units of selection for environmentally diverse locations. Together, multinational networks may be the best chance corals have to persist through climate change, while humanity struggles to reduce emissions of greenhouse gases to net zero.
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Affiliation(s)
- Robert van Woesik
- Institute for Global EcologyFlorida Institute of TechnologyMelbourneFloridaUSA
| | - Tom Shlesinger
- Institute for Global EcologyFlorida Institute of TechnologyMelbourneFloridaUSA
| | | | - Rob J. Toonen
- Hawai'i Institute of Marine Biology, KāneʻoheUniversity of Hawaiʻi at MānoaHonoluluHawaiiUSA
| | | | - Mark E. Warner
- School of Marine Science and PolicyUniversity of DelawareLewesDelawareUSA
| | - Ann Marie Hulver
- School of Earth SciencesThe Ohio State UniversityColumbusOhioUSA
| | - Leila Chapron
- School of Earth SciencesThe Ohio State UniversityColumbusOhioUSA
| | - Rowan H. McLachlan
- School of Earth SciencesThe Ohio State UniversityColumbusOhioUSA
- Department of MicrobiologyOregon State UniversityCorvallisOregonUSA
| | | | - Eric Crandall
- Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | | | - Mary K. Donovan
- Center for Global Discovery and Conservation Science and School of Geographical Sciences and Urban PlanningArizona State UniversityTempeArizonaUSA
| | - Jose Eirin‐Lopez
- Institute of EnvironmentFlorida International UniversityMiamiFloridaUSA
| | - Hugo B. Harrison
- ARC Centre of Excellence for Coral Reef StudiesJames Cook UniversityTownsvilleQueenslandAustralia
- Australian Institute of Marine ScienceTownsvilleQueenslandAustralia
| | - Scott F. Heron
- ARC Centre of Excellence for Coral Reef StudiesJames Cook UniversityTownsvilleQueenslandAustralia
- Physics and Marine Geophysical LaboratoryJames Cook UniversityTownsvilleQueenslandAustralia
| | - Danwei Huang
- Department of Biological SciencesNational University of SingaporeSingapore
| | - Adriana Humanes
- School of Natural and Environmental SciencesNewcastle UniversityNewcastle upon TyneUnited Kingdom
| | - Thomas Krueger
- Department of BiochemistryUniversity of CambridgeCambridgeUnited Kingdom
| | - Joshua S. Madin
- Hawai'i Institute of Marine Biology, KāneʻoheUniversity of Hawaiʻi at MānoaHonoluluHawaiiUSA
| | - Derek Manzello
- Center for Satellite Applications and ResearchSatellite Oceanography & Climate DivisionNational Oceanic and Atmospheric AdministrationCollege ParkMarylandUSA
| | - Lisa C. McManus
- Hawai'i Institute of Marine Biology, KāneʻoheUniversity of Hawaiʻi at MānoaHonoluluHawaiiUSA
| | - Mikhail Matz
- Department of Integrative BiologyUniversity of Texas at AustinAustinTexasUSA
| | | | | | | | | | - Jesse Zaneveld
- Division of Biological SciencesUniversity of WashingtonBothellWashingtonUSA
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30
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Hughes DJ, Alexander J, Cobbs G, Kühl M, Cooney C, Pernice M, Varkey D, Voolstra CR, Suggett DJ. Widespread oxyregulation in tropical corals under hypoxia. Mar Pollut Bull 2022; 179:113722. [PMID: 35537305 DOI: 10.1016/j.marpolbul.2022.113722] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 04/12/2022] [Accepted: 04/30/2022] [Indexed: 06/14/2023]
Abstract
Hypoxia (low oxygen stress) is increasingly reported on coral reefs, caused by ocean deoxygenation linked to coastal nutrient pollution and ocean warming. While the ability to regulate respiration is a key driver of hypoxia tolerance in many other aquatic taxa, corals' oxyregulatory capabilities remain virtually unexplored. Here, we examine O2-consumption patterns across 17 coral species under declining O2 partial pressure (pO2). All corals showed ability to oxyregulate, but total positive regulation (Tpos) varied between species, ranging from 0.41 (Pocillopora damicornis) to 2.42 (P. acuta). On average, corals performed maximum regulation effort (Pcmax) at low pO2 (30% air saturation, corresponding to lower O2 levels measured on natural reef systems), and exhibited detectable regulation down to as low as <10% air saturation. Our study shows that corals are not oxyconformers as previously thought, suggesting oxyregulation is likely important for survival in dynamic O2 environments of shallow coral reefs subjected to hypoxic events.
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Affiliation(s)
- David J Hughes
- University of Technology Sydney, Climate Change Cluster, Ultimo, NSW 2007, Australia.
| | - James Alexander
- Department of Biology, University of Louisville, Louisville, KY 40292, USA
| | - Gary Cobbs
- Department of Biology, University of Louisville, Louisville, KY 40292, USA
| | - Michael Kühl
- Marine Biology Section, Department of Biology, University of Copenhagen, Strandpromenaden 5, DK 3000 Helsingør, Denmark
| | - Chris Cooney
- University of Technology Sydney, Climate Change Cluster, Ultimo, NSW 2007, Australia
| | - Mathieu Pernice
- University of Technology Sydney, Climate Change Cluster, Ultimo, NSW 2007, Australia
| | - Deepa Varkey
- Department of Molecular Sciences, Macquarie University, NSW 2109, Australia
| | | | - David J Suggett
- University of Technology Sydney, Climate Change Cluster, Ultimo, NSW 2007, Australia
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31
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Rosenberg Y, Simon‐Blecher N, Lalzar M, Yam R, Shemesh A, Alon S, Perna G, Cárdenas A, Voolstra CR, Miller DJ, Levy O. Urbanization comprehensively impairs biological rhythms in coral holobionts. Glob Chang Biol 2022; 28:3349-3364. [PMID: 35218086 PMCID: PMC9311646 DOI: 10.1111/gcb.16144] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 02/08/2022] [Accepted: 02/09/2022] [Indexed: 05/28/2023]
Abstract
Coral reefs are in global decline due to climate change and anthropogenic influences (Hughes et al., Conservation Biology, 27: 261-269, 2013). Near coastal cities or other densely populated areas, coral reefs face a range of additional challenges. While considerable progress has been made in understanding coral responses to acute individual stressors (Dominoni et al., Nature Ecology & Evolution, 4: 502-511, 2020), the impacts of chronic exposure to varying combinations of sensory pollutants are largely unknown. To investigate the impacts of urban proximity on corals, we conducted a year-long in-natura study-incorporating sampling at diel, monthly, and seasonal time points-in which we compared corals from an urban area to corals from a proximal non-urban area. Here we reveal that despite appearing relatively healthy, natural biorhythms and environmental sensory systems were extensively disturbed in corals from the urban environment. Transcriptomic data indicated poor symbiont performance, disturbance to gametogenic cycles, and loss or shifted seasonality of vital biological processes. Altered seasonality patterns were also observed in the microbiomes of the urban coral population, signifying the impact of urbanization on the holobiont, rather than the coral host alone. These results should raise alarm regarding the largely unknown long-term impacts of sensory pollution on the resilience and survival of coral reefs close to coastal communities.
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Affiliation(s)
- Yaeli Rosenberg
- Mina and Everard Goodman Faculty of Life SciencesBar‐Ilan UniversityRamat GanIsrael
| | - Noa Simon‐Blecher
- Mina and Everard Goodman Faculty of Life SciencesBar‐Ilan UniversityRamat GanIsrael
| | - Maya Lalzar
- Bioinformatics Service UnitUniversity of HaifaHaifaIsrael
| | - Ruth Yam
- Department of Earth and Planetary SciencesWeizmann Institute of ScienceRehovotIsrael
| | - Aldo Shemesh
- Department of Earth and Planetary SciencesWeizmann Institute of ScienceRehovotIsrael
| | - Shahar Alon
- Faculty of EngineeringBar‐Ilan UniversityRamat GanIsrael
| | - Gabriela Perna
- Department of BiologyUniversity of KonstanzKonstanzGermany
| | - Anny Cárdenas
- Department of BiologyUniversity of KonstanzKonstanzGermany
| | | | - David J. Miller
- ARC Centre of Excellence for Coral Reef Studies and School of Pharmacy and Molecular SciencesJames Cook UniversityTownsvilleQueenslandAustralia
| | - Oren Levy
- Mina and Everard Goodman Faculty of Life SciencesBar‐Ilan UniversityRamat GanIsrael
- The H. Steinitz Marine Biology LaboratoryThe Interuniversity Institute for Marine Sciences of EilatEilatIsrael
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32
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Klein SG, Geraldi NR, Anton A, Schmidt‐Roach S, Ziegler M, Cziesielski MJ, Martin C, Rädecker N, Frölicher TL, Mumby PJ, Pandolfi JM, Suggett DJ, Voolstra CR, Aranda M, Duarte CM. Projecting coral responses to intensifying marine heatwaves under ocean acidification. Glob Chang Biol 2022; 28:1753-1765. [PMID: 34343392 PMCID: PMC9291544 DOI: 10.1111/gcb.15818] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 05/05/2021] [Accepted: 07/12/2021] [Indexed: 05/12/2023]
Abstract
Over this century, coral reefs will run the gauntlet of climate change, as marine heatwaves (MHWs) become more intense and frequent, and ocean acidification (OA) progresses. However, we still lack a quantitative assessment of how, and to what degree, OA will moderate the responses of corals to MHWs as they intensify throughout this century. Here, we first projected future MHW intensities for tropical regions under three future greenhouse gas emissions scenario (representative concentration pathways, RCP2.6, RCP4.5 and RCP8.5) for the near-term (2021-2040), mid-century (2041-2060) and late-century (2081-2100). We then combined these MHW intensity projections with a global data set of 1,788 experiments to assess coral attribute performance and survival under the three emissions scenarios for the near-term, mid-century and late-century in the presence and absence of OA. Although warming and OA had predominately additive impacts on the coral responses, the contribution of OA in affecting most coral attributes was minor relative to the dominant role of intensifying MHWs. However, the addition of OA led to greater decreases in photosynthesis and survival under intermediate and unrestricted emissions scenario for the mid- and late-century than if intensifying MHWs were considered as the only driver. These results show that role of OA in modulating coral responses to intensifying MHWs depended on the focal coral attribute and extremity of the scenario examined. Specifically, intensifying MHWs and OA will cause increasing instances of coral bleaching and substantial declines in coral productivity, calcification and survival within the next two decades under the low and intermediate emissions scenario. These projections suggest that corals must rapidly adapt or acclimatize to projected ocean conditions to persist, which is far more likely under a low emissions scenario and with increasing efforts to manage reefs to enhance resilience.
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Affiliation(s)
- Shannon G. Klein
- Red Sea Research Center (RSRC) and Computational Bioscience Research Center (CBRC)King Abdullah University of Science and Technology (KAUST)ThuwalKingdom of Saudi Arabia
| | - Nathan R. Geraldi
- Red Sea Research Center (RSRC) and Computational Bioscience Research Center (CBRC)King Abdullah University of Science and Technology (KAUST)ThuwalKingdom of Saudi Arabia
| | - Andrea Anton
- Red Sea Research Center (RSRC) and Computational Bioscience Research Center (CBRC)King Abdullah University of Science and Technology (KAUST)ThuwalKingdom of Saudi Arabia
| | - Sebastian Schmidt‐Roach
- Red Sea Research Center (RSRC)King Abdullah University of Science and Technology (KAUST)ThuwalKingdom of Saudi Arabia
| | - Maren Ziegler
- Red Sea Research Center (RSRC)King Abdullah University of Science and Technology (KAUST)ThuwalKingdom of Saudi Arabia
- Department of Animal Ecology & SystematicsJustus Liebig UniversityGiessenGermany
| | - Maha J. Cziesielski
- Red Sea Research Center (RSRC)King Abdullah University of Science and Technology (KAUST)ThuwalKingdom of Saudi Arabia
| | - Cecilia Martin
- Red Sea Research Center (RSRC) and Computational Bioscience Research Center (CBRC)King Abdullah University of Science and Technology (KAUST)ThuwalKingdom of Saudi Arabia
| | - Nils Rädecker
- Red Sea Research Center (RSRC)King Abdullah University of Science and Technology (KAUST)ThuwalKingdom of Saudi Arabia
| | - Thomas L. Frölicher
- Climate and Environmental PhysicsPhysics InstituteUniversity of BernBernSwitzerland
- Oeschger Centre for Climate Change ResearchUniversity of BernBernSwitzerland
| | - Peter J. Mumby
- Marine Spatial Ecology LabSchool of Biological SciencesThe University of QueenslandBrisbaneQueenslandAustralia
| | - John M. Pandolfi
- Australian Research Council Centre of Excellence for Coral Reef StudiesSchool of Biological SciencesThe University of QueenslandBrisbaneQueenslandAustralia
| | - David J. Suggett
- Climate Change ClusterFaculty of ScienceUniversity of Technology SydneySydneyNew South WalesAustralia
| | - Christian R. Voolstra
- Red Sea Research Center (RSRC)King Abdullah University of Science and Technology (KAUST)ThuwalKingdom of Saudi Arabia
- Department of BiologyUniversity of KonstanzKonstanzGermany
| | - Manuel Aranda
- Red Sea Research Center (RSRC)King Abdullah University of Science and Technology (KAUST)ThuwalKingdom of Saudi Arabia
| | - Carlos. M. Duarte
- Red Sea Research Center (RSRC) and Computational Bioscience Research Center (CBRC)King Abdullah University of Science and Technology (KAUST)ThuwalKingdom of Saudi Arabia
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33
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Robert NSM, Sarigol F, Zimmermann B, Meyer A, Voolstra CR, Simakov O. Emergence of distinct syntenic density regimes is associated with early metazoan genomic transitions. BMC Genomics 2022; 23:143. [PMID: 35177000 PMCID: PMC8851819 DOI: 10.1186/s12864-022-08304-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 01/10/2022] [Indexed: 12/03/2022] Open
Abstract
Background Animal genomes are strikingly conserved in terms of local gene order (microsynteny). While some of these microsyntenies have been shown to be coregulated or to form gene regulatory blocks, the diversity of their genomic and regulatory properties across the metazoan tree of life remains largely unknown. Results Our comparative analyses of 49 animal genomes reveal that the largest gains of synteny occurred in the last common ancestor of bilaterians and cnidarians and in that of bilaterians. Depending on their node of emergence, we further show that novel syntenic blocks are characterized by distinct functional compositions (Gene Ontology terms enrichment) and gene density properties, such as high, average and low gene density regimes. This is particularly pronounced among bilaterian novel microsyntenies, most of which fall into high gene density regime associated with higher gene coexpression levels. Conversely, a majority of vertebrate novel microsyntenies display a low gene density regime associated with lower gene coexpression levels. Conclusions Our study provides first evidence for evolutionary transitions between different modes of microsyntenic block regulation that coincide with key events of metazoan evolution. Moreover, the microsyntenic profiling strategy and interactive online application (Syntenic Density Browser, available at: http://synteny.csb.univie.ac.at/) we present here can be used to explore regulatory properties of microsyntenic blocks and predict their coexpression in a wide-range of animal genomes. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08304-2.
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Affiliation(s)
- Nicolas S M Robert
- Department of Neurosciences and Developmental Biology, University of Vienna, Althanstrasse 14, 1090, Wien, Austria.
| | - Fatih Sarigol
- Department of Neurosciences and Developmental Biology, University of Vienna, Althanstrasse 14, 1090, Wien, Austria
| | - Bob Zimmermann
- Department of Neurosciences and Developmental Biology, University of Vienna, Althanstrasse 14, 1090, Wien, Austria
| | - Axel Meyer
- Department of Biology, University of Konstanz, 78457, Constance, Germany
| | | | - Oleg Simakov
- Department of Neurosciences and Developmental Biology, University of Vienna, Althanstrasse 14, 1090, Wien, Austria.
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34
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Barreto MM, Ziegler M, Venn A, Tambutté E, Zoccola D, Tambutté S, Allemand D, Antony CP, Voolstra CR, Aranda M. Effects of Ocean Acidification on Resident and Active Microbial Communities of Stylophora pistillata. Front Microbiol 2021; 12:707674. [PMID: 34899619 PMCID: PMC8656159 DOI: 10.3389/fmicb.2021.707674] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 05/10/2021] [Accepted: 10/28/2021] [Indexed: 12/12/2022] Open
Abstract
Ocean warming and ocean acidification (OA) are direct consequences of climate change and affect coral reefs worldwide. While the effect of ocean warming manifests itself in increased frequency and severity of coral bleaching, the effects of ocean acidification on corals are less clear. In particular, long-term effects of OA on the bacterial communities associated with corals are largely unknown. In this study, we investigated the effects of ocean acidification on the resident and active microbiome of long-term aquaria-maintained Stylophora pistillata colonies by assessing 16S rRNA gene diversity on the DNA (resident community) and RNA level (active community). Coral colony fragments of S. pistillata were kept in aquaria for 2 years at four different pCO2 levels ranging from current pH conditions to increased acidification scenarios (i.e., pH 7.2, 7.4, 7.8, and 8). We identified 154 bacterial families encompassing 2,047 taxa (OTUs) in the resident and 89 bacterial families including 1,659 OTUs in the active communities. Resident communities were dominated by members of Alteromonadaceae, Flavobacteriaceae, and Colwelliaceae, while active communities were dominated by families Cyclobacteriacea and Amoebophilaceae. Besides the overall differences between resident and active community composition, significant differences were seen between the control (pH 8) and the two lower pH treatments (7.2 and 7.4) in the active community, but only between pH 8 and 7.2 in the resident community. Our analyses revealed profound differences between the resident and active microbial communities, and we found that OA exerted stronger effects on the active community. Further, our results suggest that rDNA- and rRNA-based sequencing should be considered complementary tools to investigate the effects of environmental change on microbial assemblage structure and activity.
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Affiliation(s)
- Marcelle Muniz Barreto
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Maren Ziegler
- Department of Animal Ecology and Systematics, Justus Liebig University Giessen, Giessen, Germany
| | | | | | | | | | | | - Chakkiath Paul Antony
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Christian R Voolstra
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,Department of Biology, University of Konstanz, Konstanz, Germany
| | - Manuel Aranda
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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35
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Rädecker N, Pogoreutz C, Gegner HM, Cárdenas A, Perna G, Geißler L, Roth F, Bougoure J, Guagliardo P, Struck U, Wild C, Pernice M, Raina JB, Meibom A, Voolstra CR. Heat stress reduces the contribution of diazotrophs to coral holobiont nitrogen cycling. ISME J 2021; 16:1110-1118. [PMID: 34857934 PMCID: PMC8941099 DOI: 10.1038/s41396-021-01158-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 11/11/2021] [Accepted: 11/16/2021] [Indexed: 12/22/2022]
Abstract
Efficient nutrient cycling in the coral-algal symbiosis requires constant but limited nitrogen availability. Coral-associated diazotrophs, i.e., prokaryotes capable of fixing dinitrogen, may thus support productivity in a stable coral-algal symbiosis but could contribute to its breakdown when overstimulated. However, the effects of environmental conditions on diazotroph communities and their interaction with other members of the coral holobiont remain poorly understood. Here we assessed the effects of heat stress on diazotroph diversity and their contribution to holobiont nutrient cycling in the reef-building coral Stylophora pistillata from the central Red Sea. In a stable symbiotic state, we found that nitrogen fixation by coral-associated diazotrophs constitutes a source of nitrogen to the algal symbionts. Heat stress caused an increase in nitrogen fixation concomitant with a change in diazotroph communities. Yet, this additional fixed nitrogen was not assimilated by the coral tissue or the algal symbionts. We conclude that although diazotrophs may support coral holobiont functioning under low nitrogen availability, altered nutrient cycling during heat stress abates the dependence of the coral host and its algal symbionts on diazotroph-derived nitrogen. Consequently, the role of nitrogen fixation in the coral holobiont is strongly dependent on its nutritional status and varies dynamically with environmental conditions.
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Affiliation(s)
- Nils Rädecker
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia. .,Department of Biology, University of Konstanz, Konstanz, Germany. .,Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
| | - Claudia Pogoreutz
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,Department of Biology, University of Konstanz, Konstanz, Germany
| | - Hagen M Gegner
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,Metabolomics Core Technology Platform, Centre for Organismal Studies, University of Heidelberg, Heidelberg, Germany
| | - Anny Cárdenas
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,Department of Biology, University of Konstanz, Konstanz, Germany
| | - Gabriela Perna
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,Department of Biology, University of Konstanz, Konstanz, Germany
| | - Laura Geißler
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Florian Roth
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,Baltic Sea Centre, Stockholm University, Stockholm, Sweden.,Faculty of Biological and Environmental Sciences, Tvärminne Zoological Station, University of Helsinki, Helsinki, Finland
| | - Jeremy Bougoure
- Centre for Microscopy, Characterisation and Analysis, University of Western Australia, Perth, WA, Australia
| | - Paul Guagliardo
- Centre for Microscopy, Characterisation and Analysis, University of Western Australia, Perth, WA, Australia
| | - Ulrich Struck
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany.,Department of Earth Sciences, Freie Universität Berlin, Berlin, Germany
| | - Christian Wild
- Faculty of Biology and Chemistry, Marine Ecology Department, University of Bremen, Bremen, Germany
| | - Mathieu Pernice
- Climate Change Cluster, University of Technology Sydney, Sydney, NSW, Australia
| | - Jean-Baptiste Raina
- Climate Change Cluster, University of Technology Sydney, Sydney, NSW, Australia
| | - Anders Meibom
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Center for Advanced Surface Analysis, Institute of Earth Sciences, Université de Lausanne, Lausanne, Switzerland
| | - Christian R Voolstra
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,Department of Biology, University of Konstanz, Konstanz, Germany
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36
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Ziegler M, Anton A, Klein SG, Rädecker N, Geraldi NR, Schmidt-Roach S, Saderne V, Mumby PJ, Cziesielski MJ, Martin C, Frölicher TL, Pandolfi JM, Suggett DJ, Aranda M, Duarte CM, Voolstra CR. Integrating environmental variability to broaden the research on coral responses to future ocean conditions. Glob Chang Biol 2021; 27:5532-5546. [PMID: 34391212 DOI: 10.1111/gcb.15840] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 06/19/2021] [Accepted: 06/25/2021] [Indexed: 06/13/2023]
Abstract
Our understanding of the response of reef-building corals to changes in their physical environment is largely based on laboratory experiments, analysis of long-term field data, and model projections. Experimental data provide unique insights into how organisms respond to variation of environmental drivers. However, an assessment of how well experimental conditions cover the breadth of environmental conditions and variability where corals live successfully is missing. Here, we compiled and analyzed a globally distributed dataset of in-situ seasonal and diurnal variability of key environmental drivers (temperature, pCO2 , and O2 ) critical for the growth and livelihood of reef-building corals. Using a meta-analysis approach, we compared the variability of environmental conditions assayed in coral experimental studies to current and projected conditions in their natural habitats. We found that annual temperature profiles projected for the end of the 21st century were characterized by distributional shifts in temperatures with warmer winters and longer warm periods in the summer, not just peak temperatures. Furthermore, short-term hourly fluctuations of temperature and pCO2 may regularly expose corals to conditions beyond the projected average increases for the end of the 21st century. Coral reef sites varied in the degree of coupling between temperature, pCO2 , and dissolved O2 , which warrants site-specific, differentiated experimental approaches depending on the local hydrography and influence of biological processes on the carbonate system and O2 availability. Our analysis highlights that a large portion of the natural environmental variability at short and long timescales is underexplored in experimental designs, which may provide a path to extend our understanding on the response of corals to global climate change.
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Affiliation(s)
- Maren Ziegler
- Department of Animal Ecology & Systematics, Justus Liebig University Giessen, Giessen, Germany
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Andrea Anton
- Red Sea Research Center (RSRC) and Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
- Global Change Research Group, IMEDEA (CSIC-UIB), Mediterranean Institute for Advanced Studies, Esporles (Illes Balears), Spain
| | - Shannon G Klein
- Red Sea Research Center (RSRC) and Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Nils Rädecker
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
- Department of Biology, University of Konstanz, Konstanz, Germany
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Nathan R Geraldi
- Red Sea Research Center (RSRC) and Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Sebastian Schmidt-Roach
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Vincent Saderne
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Peter J Mumby
- Marine Spatial Ecology Lab, School of Biological Sciences, The University of Queensland, St. Lucia, Qld, Australia
| | - Maha J Cziesielski
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Cecilia Martin
- Red Sea Research Center (RSRC) and Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Thomas L Frölicher
- Climate and Environmental Physics, Physics Institute, University of Bern, Bern, Switzerland
- Oeschger Centre for Climate Change Research, University of Bern, Bern, Switzerland
| | - John M Pandolfi
- Australian Research Council Centre of Excellence for Coral Reef Studies, School of Biological Sciences, The University of Queensland, Brisbane, Qld, Australia
| | - David J Suggett
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
| | - Manuel Aranda
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Carlos M Duarte
- Red Sea Research Center (RSRC) and Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Christian R Voolstra
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
- Department of Biology, University of Konstanz, Konstanz, Germany
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37
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Alderdice R, Pernice M, Cárdenas A, Hughes DJ, Harrison PL, Boulotte N, Chartrand K, Kühl M, Suggett DJ, Voolstra CR. Hypoxia as a physiological cue and pathological stress for coral larvae. Mol Ecol 2021; 31:571-587. [PMID: 34716959 DOI: 10.1111/mec.16259] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 10/15/2021] [Accepted: 10/20/2021] [Indexed: 11/30/2022]
Abstract
Ocean deoxygenation events are intensifying worldwide and can rapidly drive adult corals into a state of metabolic crisis and bleaching-induced mortality, but whether coral larvae are subject to similar stress remains untested. We experimentally exposed apo-symbiotic coral larvae of Acropora selago to deoxygenation stress with subsequent reoxygenation aligned to their night-day light cycle, and followed their gene expression using RNA-Seq. After 12 h of deoxygenation stress (~2 mg O2 /L), coral planulae demonstrated a low expression of HIF-targeted hypoxia response genes concomitant with a significantly high expression of PHD2 (a promoter of HIFα proteasomal degradation), similar to corresponding adult corals. Despite exhibiting a consistent swimming phenotype compared to control samples, the differential gene expression observed in planulae exposed to deoxygenation-reoxygenation suggests a disruption of pathways involved in developmental regulation, mitochondrial activity, lipid metabolism, and O2 -sensitive epigenetic regulators. Importantly, we found that treated larvae exhibited a disruption in the expression of conserved HIF-targeted developmental regulators, for example, Homeobox (HOX) genes, corroborating how changes in external oxygen levels can affect animal development. We discuss how the observed deoxygenation responses may be indicative of a possible acclimation response or alternatively may imply negative latent impacts for coral larval fitness.
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Affiliation(s)
- Rachel Alderdice
- Faculty of Science, Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Mathieu Pernice
- Faculty of Science, Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Anny Cárdenas
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - David J Hughes
- Faculty of Science, Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Peter L Harrison
- Marine Ecology Research Centre, Southern Cross University, Lismore, NSW, Australia
| | - Nadine Boulotte
- Marine Ecology Research Centre, Southern Cross University, Lismore, NSW, Australia
| | - Katie Chartrand
- Centre of Tropical Water and Aquatic Ecosystem Research, James Cook University, Townsville, Qld, Australia
| | - Michael Kühl
- Faculty of Science, Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia.,Marine Biology Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - David J Suggett
- Faculty of Science, Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
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38
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Buitrago-López C, Mariappan KG, Cárdenas A, Gegner HM, Voolstra CR. The Genome of the Cauliflower Coral Pocillopora verrucosa. Genome Biol Evol 2021; 12:1911-1917. [PMID: 32857844 PMCID: PMC7594246 DOI: 10.1093/gbe/evaa184] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2020] [Indexed: 02/06/2023] Open
Abstract
Climate change and ocean warming threaten the persistence of corals worldwide. Genomic resources are critical to study the evolutionary trajectory, adaptive potential, and genetic distinctiveness of coral species. Here, we provide a reference genome of the cauliflower coral Pocillopora verrucosa, a broadly prevalent reef-building coral with important ecological roles in the maintenance of reefs across the Red Sea, the Indian Ocean, and the Pacific Ocean. The genome has an assembly size of 380,505,698 bp with a scaffold N50 of 333,696 bp and a contig N50 of 75,704 bp. The annotation of the assembled genome returned 27,439 gene models of which 89.88% have evidence of transcription from RNA-Seq data and 97.87% show homology to known genes. A high proportion of the genome (41.22%) comprised repetitive elements in comparison to other cnidarian genomes, in particular in relation to the small genome size of P. verrucosa.
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Affiliation(s)
- Carol Buitrago-López
- Red Sea Research Center, Division of Biological BESE, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Kiruthiga G Mariappan
- Red Sea Research Center, Division of Biological BESE, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Anny Cárdenas
- Department of Biology, University of Konstanz, Germany
| | - Hagen M Gegner
- Red Sea Research Center, Division of Biological BESE, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,Centre for Organismal Studies (COS), University of Heidelberg, Germany
| | - Christian R Voolstra
- Red Sea Research Center, Division of Biological BESE, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,Department of Biology, University of Konstanz, Germany
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39
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Meunier V, Geissler L, Bonnet S, Rädecker N, Perna G, Grosso O, Lambert C, Rodolfo-Metalpa R, Voolstra CR, Houlbrèque F. Microbes support enhanced nitrogen requirements of coral holobionts in a high CO 2 environment. Mol Ecol 2021; 30:5888-5899. [PMID: 34473860 DOI: 10.1111/mec.16163] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 08/24/2021] [Accepted: 08/27/2021] [Indexed: 12/24/2022]
Abstract
Ocean acidification is posing a threat to calcifying organisms due to the increased energy requirements of calcification under high CO2 conditions. The ability of scleractinian corals to cope with future ocean conditions will thus depend on their ability to fulfil their carbon requirement. However, the primary productivity of coral holobionts is limited by low nitrogen (N) availability in coral reef waters. Here, we employed CO2 seeps of Tutum Bay (Papua New Guinea) as a natural laboratory to understand how coral holobionts offset their increased energy requirements under high CO2 conditions. Our results demonstrate for the first time that under high pCO2 conditions, N assimilation pathways of Pocillopora damicornis are jointly modified. We found that diazotroph-derived N assimilation rates in the Symbiodiniaceae were significantly higher in comparison to an ambient CO2 control site, concomitant with a restructured diazotroph community and the specific prevalence of an alpha-proteobacterium. Further, corals at the high CO2 site also had increased feeding rates on picoplankton and in particular exhibited selective feeding on Synechococcus sp., known to be rich in N. Given the high abundance of picoplankton in oligotrophic waters at large, our results suggest that corals exhibiting flexible diazotrophic communities and capable of exploiting N-rich picoplankton sources to offset their increased N requirements may be able to cope better in a high pCO2 world.
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Affiliation(s)
- Valentine Meunier
- Centre IRD Nouméa, UMR ENTROPIE (IRD, Université de La Réunion, CNRS, Université de La Nouvelle-Calédonie, Ifremer), Nouméa, New Caledonia
| | - Laura Geissler
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Sophie Bonnet
- Aix-Marseille Université, Université de Toulon, CNRS, IRD, Marseille, France
| | - Nils Rädecker
- Department of Biology, University of Konstanz, Konstanz, Germany.,Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Gabriela Perna
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Olivier Grosso
- Aix-Marseille Université, Université de Toulon, CNRS, IRD, Marseille, France
| | | | - Riccardo Rodolfo-Metalpa
- Centre IRD Nouméa, UMR ENTROPIE (IRD, Université de La Réunion, CNRS, Université de La Nouvelle-Calédonie, Ifremer), Nouméa, New Caledonia
| | | | - Fanny Houlbrèque
- Centre IRD Nouméa, UMR ENTROPIE (IRD, Université de La Réunion, CNRS, Université de La Nouvelle-Calédonie, Ifremer), Nouméa, New Caledonia
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40
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Voolstra CR, Valenzuela JJ, Turkarslan S, Cárdenas A, Hume BCC, Perna G, Buitrago-López C, Rowe K, Orellana MV, Baliga NS, Paranjape S, Banc-Prandi G, Bellworthy J, Fine M, Frias-Torres S, Barshis DJ. Contrasting heat stress response patterns of coral holobionts across the Red Sea suggest distinct mechanisms of thermal tolerance. Mol Ecol 2021; 30:4466-4480. [PMID: 34342082 DOI: 10.1111/mec.16064] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 06/04/2021] [Accepted: 06/30/2021] [Indexed: 12/18/2022]
Abstract
Corals from the northern Red Sea, in particular the Gulf of Aqaba (GoA), have exceptionally high bleaching thresholds approaching >5℃ above their maximum monthly mean (MMM) temperatures. These elevated thresholds are thought to be due to historical selection, as corals passed through the warmer Southern Red Sea during recolonization from the Arabian Sea. To test this hypothesis, we determined thermal tolerance thresholds of GoA versus central Red Sea (CRS) Stylophora pistillata corals using multi-temperature acute thermal stress assays to determine thermal thresholds. Relative thermal thresholds of GoA and CRS corals were indeed similar and exceptionally high (~7℃ above MMM). However, absolute thermal thresholds of CRS corals were on average 3℃ above those of GoA corals. To explore the molecular underpinnings, we determined gene expression and microbiome response of the coral holobiont. Transcriptomic responses differed markedly, with a strong response to the thermal stress in GoA corals and their symbiotic algae versus a remarkably muted response in CRS colonies. Concomitant to this, coral and algal genes showed temperature-induced expression in GoA corals, while exhibiting fixed high expression (front-loading) in CRS corals. Bacterial community composition of GoA corals changed dramatically under heat stress, whereas CRS corals displayed stable assemblages. We interpret the response of GoA corals as that of a resilient population approaching a tipping point in contrast to a pattern of consistently elevated thermal resistance in CRS corals that cannot further attune. Such response differences suggest distinct thermal tolerance mechanisms that may affect the response of coral populations to ocean warming.
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Affiliation(s)
| | | | | | - Anny Cárdenas
- Department of Biology, University of Konstanz, Konstanz, Germany
| | | | - Gabriela Perna
- Department of Biology, University of Konstanz, Konstanz, Germany
| | | | - Katherine Rowe
- School of Science, The University of Waikato, Hamilton, New Zealand
| | - Monica V Orellana
- Institute for Systems Biology, Seattle, USA.,Polar Science Center, University of Washington, Seattle, USA
| | - Nitin S Baliga
- Institute for Systems Biology, Seattle, USA.,Departments of Biology and Microbiology, University of Washington, Seattle, USA.,Molecular and Cellular Biology Program, University of Washington, Seattle, USA.,Lawrence Berkeley National Laboratory, Berkeley, USA
| | | | - Guilhem Banc-Prandi
- The Interuniversity Institute for Marine Sciences (IUI), Eilat, Israel.,The Goodman Faculty of Life Sciences, Bar Ilan University, Ramat-Gan, Israel
| | - Jessica Bellworthy
- The Interuniversity Institute for Marine Sciences (IUI), Eilat, Israel.,The Goodman Faculty of Life Sciences, Bar Ilan University, Ramat-Gan, Israel
| | - Maoz Fine
- The Interuniversity Institute for Marine Sciences (IUI), Eilat, Israel.,The Goodman Faculty of Life Sciences, Bar Ilan University, Ramat-Gan, Israel
| | | | - Daniel J Barshis
- Department of Biological Sciences, Old Dominion University, Norfolk, USA
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41
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Santoro EP, Borges RM, Espinoza JL, Freire M, Messias CSMA, Villela HDM, Pereira LM, Vilela CLS, Rosado JG, Cardoso PM, Rosado PM, Assis JM, Duarte GAS, Perna G, Rosado AS, Macrae A, Dupont CL, Nelson KE, Sweet MJ, Voolstra CR, Peixoto RS. Coral microbiome manipulation elicits metabolic and genetic restructuring to mitigate heat stress and evade mortality. Sci Adv 2021; 7:7/33/eabg3088. [PMID: 34389536 PMCID: PMC8363143 DOI: 10.1126/sciadv.abg3088] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 06/24/2021] [Indexed: 05/03/2023]
Abstract
Beneficial microorganisms for corals (BMCs) ameliorate environmental stress, but whether they can prevent mortality and the underlying host response mechanisms remains elusive. Here, we conducted omics analyses on the coral Mussismilia hispida exposed to bleaching conditions in a long-term mesocosm experiment and inoculated with a selected BMC consortium or a saline solution placebo. All corals were affected by heat stress, but the observed "post-heat stress disorder" was mitigated by BMCs, signified by patterns of dimethylsulfoniopropionate degradation, lipid maintenance, and coral host transcriptional reprogramming of cellular restructuration, repair, stress protection, and immune genes, concomitant with a 40% survival rate increase and stable photosynthetic performance by the endosymbiotic algae. This study provides insights into the responses that underlie probiotic host manipulation. We demonstrate that BMCs trigger a dynamic microbiome restructuring process that instigates genetic and metabolic alterations in the coral host that eventually mitigate coral bleaching and mortality.
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Affiliation(s)
- Erika P Santoro
- Institute of Microbiology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Ricardo M Borges
- Walter Mors Institute of Research on Natural Products, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Josh L Espinoza
- Department of Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA, USA
- Applied Sciences, Durban University of Technology, Durban, South Africa
| | - Marcelo Freire
- Department of Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA, USA
- Department of Infectious Diseases and Global Health, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Camila S M A Messias
- Institute of Microbiology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Helena D M Villela
- Institute of Microbiology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Leandro M Pereira
- Institute of Microbiology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Caren L S Vilela
- Institute of Microbiology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - João G Rosado
- Institute of Microbiology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Pedro M Cardoso
- Institute of Microbiology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Phillipe M Rosado
- Institute of Microbiology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Juliana M Assis
- Institute of Microbiology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Gustavo A S Duarte
- Institute of Microbiology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Gabriela Perna
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Department of Biology, University of Konstanz, Konstanz 78457, Germany
| | - Alexandre S Rosado
- Institute of Microbiology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Andrew Macrae
- Institute of Microbiology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Christopher L Dupont
- Department of Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA, USA
| | - Karen E Nelson
- Department of Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA, USA
| | - Michael J Sweet
- Aquatic Research Facility, Environmental Sustainability Research Centre, University of Derby, Derby, UK
| | - Christian R Voolstra
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Department of Biology, University of Konstanz, Konstanz 78457, Germany
| | - Raquel S Peixoto
- Institute of Microbiology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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Aeby GS, Shore A, Jensen T, Ziegler M, Work T, Voolstra CR. A comparative baseline of coral disease in three regions along the Saudi Arabian coast of the central Red Sea. PLoS One 2021; 16:e0246854. [PMID: 34242223 PMCID: PMC8270217 DOI: 10.1371/journal.pone.0246854] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 01/25/2021] [Accepted: 06/27/2021] [Indexed: 01/10/2023] Open
Abstract
Coral disease is a growing problem for coral reefs globally and diseases have been linked to thermal stress, excess nutrients, overfishing and other human impacts. The Red Sea is a unique environment for corals with a strong environmental gradient characterized by temperature extremes and high salinities, but minimal terrestrial runoff or riverine input and their associated pollution. Yet, relatively little is known about coral diseases in this region. Disease surveys were conducted at 22 reefs within three regions (Yanbu, Thuwal, Al Lith) in the central Red Sea along the Saudi Arabian coast. Surveys occurred in October 2015, which coincided with a hyperthermal-induced bleaching event. Our objectives were to 1) document types, prevalence, and distribution of coral diseases in a region with minimal terrestrial input, 2) compare regional differences in diseases and bleaching along a latitudinal gradient of environmental conditions, and 3) use histopathology to characterize disease lesions at the cellular level. Coral reefs of the central Red Sea had a widespread but a surprisingly low prevalence of disease (<0.5%), based on the examination of >75,750 colonies. Twenty diseases were recorded affecting 16 coral taxa and included black band disease, white syndromes, endolithic hypermycosis, skeletal eroding band, growth anomalies and focal bleached patches. The three most common diseases were Acropora white syndrome (59.1% of the survey sites), Porites growth anomalies (40.9%), and Porites white syndrome (31.8%). Sixteen out of 30 coral genera within transects had lesions and Acropora, Millepora and Lobophyllia were the most commonly affected. Cell-associated microbial aggregates were found in four coral genera including a first report in Stylophora. Differences in disease prevalence, coral cover, amount of heat stress as measured by degree heating weeks (DHW) and extent of bleaching was evident among sites. Disease prevalence was not explained by coral cover or DHW, and a negative relationship between coral bleaching and disease prevalence was found. The northern-most sites off the coast of Yanbu had the highest average disease prevalence and highest average DHW values but no bleaching. Our study provides a foundation and baseline data for coral disease prevalence in the central Red Sea, which is projected to increase as a consequence of increased frequency and severity of ocean warming.
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Affiliation(s)
- Greta Smith Aeby
- Department of Biological and Environmental Sciences, Qatar University, Doha, Qatar
| | - Amanda Shore
- Department of Biology, Farmingdale State College, Farmingdale, NY, United States of America
| | - Thor Jensen
- Division of Biological and Environmental Science and Engineering, Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, SaudiArabia
| | - Maren Ziegler
- Division of Biological and Environmental Science and Engineering, Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, SaudiArabia
- Department of Animal Ecology & Systematics, Justus Liebig University Giessen, Giessen, Germany
| | - Thierry Work
- US Geological Survey, Wildlife Health Center, Honolulu Field Station, Honolulu, Hawaii, United States of America
| | - Christian R. Voolstra
- Division of Biological and Environmental Science and Engineering, Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, SaudiArabia
- Department of Biology, University of Konstanz, Konstanz, Germany
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El-Khaled YC, Nafeh R, Roth F, Rädecker N, Karcher DB, Jones BH, Voolstra CR, Wild C. High plasticity of nitrogen fixation and denitrification of common coral reef substrates in response to nitrate availability. Mar Pollut Bull 2021; 168:112430. [PMID: 34000709 DOI: 10.1016/j.marpolbul.2021.112430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/19/2021] [Accepted: 04/21/2021] [Indexed: 06/12/2023]
Abstract
Nitrogen cycling in coral reefs may be affected by nutrient availability, but knowledge about concentration-dependent thresholds that modulate dinitrogen fixation and denitrification is missing. We determined the effects of different nitrate concentrations (ambient, 1, 5, 10 μM nitrate addition) on both processes under two light scenarios (i.e., light and dark) using a combined acetylene assay for two common benthic reef substrates, i.e., turf algae and coral rubble. For both substrates, dinitrogen fixation rates peaked at 5 μM nitrate addition in light, whereas denitrification was highest at 10 μM nitrate addition in the dark. At 10 μm nitrate addition in the dark, a near-complete collapse of dinitrogen fixation concurrent with a 76-fold increase in denitrification observed for coral rubble, suggesting potential threshold responses linked to the nutritional state of the community. We conclude that dynamic nitrogen cycling activity may help stabilise nitrogen availability in microbial communities associated with coral reef substrates.
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Affiliation(s)
- Yusuf C El-Khaled
- Marine Ecology Department, Faculty of Biology and Chemistry, University of Bremen, 28359 Bremen, Germany.
| | - Rassil Nafeh
- Marine Ecology Department, Faculty of Biology and Chemistry, University of Bremen, 28359 Bremen, Germany
| | - Florian Roth
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), 23995 Thuwal, Saudi Arabia; Baltic Sea Centre, Stockholm University, 10691 Stockholm, Sweden; Faculty of Biological and Environmental Sciences, Tvärminne Zoological Station, University of Helsinki, 00014 Helsinki, Finland
| | - Nils Rädecker
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), 23995 Thuwal, Saudi Arabia; Department of Biology, University of Konstanz, 78457 Konstanz, Germany; Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Denis B Karcher
- Marine Ecology Department, Faculty of Biology and Chemistry, University of Bremen, 28359 Bremen, Germany; Australian National Centre for the Public Awareness of Science, Australian National University, ACT 2601 Canberra, Australia
| | - Burton H Jones
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), 23995 Thuwal, Saudi Arabia
| | - Christian R Voolstra
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), 23995 Thuwal, Saudi Arabia; Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Christian Wild
- Marine Ecology Department, Faculty of Biology and Chemistry, University of Bremen, 28359 Bremen, Germany
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Roth F, El-Khaled YC, Karcher DB, Rädecker N, Carvalho S, Duarte CM, Silva L, Calleja ML, Morán XAG, Jones BH, Voolstra CR, Wild C. Nutrient pollution enhances productivity and framework dissolution in algae- but not in coral-dominated reef communities. Mar Pollut Bull 2021; 168:112444. [PMID: 33984578 DOI: 10.1016/j.marpolbul.2021.112444] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/26/2021] [Accepted: 04/28/2021] [Indexed: 06/12/2023]
Abstract
Ecosystem services provided by coral reefs may be susceptible to the combined effects of benthic species shifts and anthropogenic nutrient pollution, but related field studies are scarce. We thus investigated in situ how dissolved inorganic nutrient enrichment, maintained for two months, affected community-wide biogeochemical functions of intact coral- and degraded algae-dominated reef patches in the central Red Sea. Results from benthic chamber incubations revealed 87% increased gross productivity and a shift from net calcification to dissolution in algae-dominated communities after nutrient enrichment, but the same processes were unaffected by nutrients in neighboring coral communities. Both community types changed from net dissolved organic nitrogen sinks to sources, but the increase in net release was 56% higher in algae-dominated communities. Nutrient pollution may, thus, amplify the effects of community shifts on key ecosystem services of coral reefs, possibly leading to a loss of structurally complex habitats with carbonate dissolution and altered nutrient recycling.
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Affiliation(s)
- Florian Roth
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; Baltic Sea Centre, Stockholm University, Stockholm, Sweden; Tvärminne Zoological Station, University of Helsinki, Helsinki, Finland.
| | - Yusuf C El-Khaled
- Marine Ecology, Faculty of Biology and Chemistry, University of Bremen, Bremen, Germany
| | - Denis B Karcher
- Marine Ecology, Faculty of Biology and Chemistry, University of Bremen, Bremen, Germany; Australian National Centre for the Public Awareness of Science, Australian National University, Canberra, Australia
| | - Nils Rädecker
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland; Department of Biology, University of Konstanz, Konstanz, Germany
| | - Susana Carvalho
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Carlos M Duarte
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; Computational Biology Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Luis Silva
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Maria Ll Calleja
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; Department of Climate Geochemistry, Max Planck Institute for Chemistry (MPIC), Mainz, Germany
| | - Xosé Anxelu G Morán
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Burton H Jones
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Christian R Voolstra
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; Department of Biology, University of Konstanz, Konstanz, Germany
| | - Christian Wild
- Marine Ecology, Faculty of Biology and Chemistry, University of Bremen, Bremen, Germany
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Sweet M, Villela H, Keller-Costa T, Costa R, Romano S, Bourne DG, Cárdenas A, Huggett MJ, Kerwin AH, Kuek F, Medina M, Meyer JL, Müller M, Pollock FJ, Rappé MS, Sere M, Sharp KH, Voolstra CR, Zaccardi N, Ziegler M, Peixoto R. Insights into the Cultured Bacterial Fraction of Corals. mSystems 2021; 6:e0124920. [PMID: 34156291 PMCID: PMC8269258 DOI: 10.1128/msystems.01249-20] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 05/13/2021] [Indexed: 02/06/2023] Open
Abstract
Bacteria associated with coral hosts are diverse and abundant, with recent studies suggesting involvement of these symbionts in host resilience to anthropogenic stress. Despite their putative importance, the work dedicated to culturing coral-associated bacteria has received little attention. Combining published and unpublished data, here we report a comprehensive overview of the diversity and function of culturable bacteria isolated from corals originating from tropical, temperate, and cold-water habitats. A total of 3,055 isolates from 52 studies were considered by our metasurvey. Of these, 1,045 had full-length 16S rRNA gene sequences, spanning 138 formally described and 12 putatively novel bacterial genera across the Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria phyla. We performed comparative genomic analysis using the available genomes of 74 strains and identified potential signatures of beneficial bacterium-coral symbioses among the strains. Our analysis revealed >400 biosynthetic gene clusters that underlie the biosynthesis of antioxidant, antimicrobial, cytotoxic, and other secondary metabolites. Moreover, we uncovered genomic features-not previously described for coral-bacterium symbioses-potentially involved in host colonization and host-symbiont recognition, antiviral defense mechanisms, and/or integrated metabolic interactions, which we suggest as novel targets for the screening of coral probiotics. Our results highlight the importance of bacterial cultures to elucidate coral holobiont functioning and guide the selection of probiotic candidates to promote coral resilience and improve holistic and customized reef restoration and rehabilitation efforts. IMPORTANCE Our paper is the first study to synthesize currently available but decentralized data of cultured microbes associated with corals. We were able to collate 3,055 isolates across a number of published studies and unpublished collections from various laboratories and researchers around the world. This equated to 1,045 individual isolates which had full-length 16S rRNA gene sequences, after filtering of the original 3,055. We also explored which of these had genomes available. Originally, only 36 were available, and as part of this study, we added a further 38-equating to 74 in total. From this, we investigated potential genetic signatures that may facilitate a host-associated lifestyle. Further, such a resource is an important step in the selection of probiotic candidates, which are being investigated for promoting coral resilience and potentially applied as a novel strategy in reef restoration and rehabilitation efforts. In the spirit of open access, we have ensured this collection is available to the wider research community through the web site http://isolates.reefgenomics.org/ with the hope many scientists across the globe will ask for access to these cultures for future studies.
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Affiliation(s)
- Michael Sweet
- Aquatic Research Facility, Environmental Sustainability Research Centre, University of Derby, Derby, United Kingdom
| | - Helena Villela
- Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Tina Keller-Costa
- Institute for Bioengineering and Biosciences (iBB), University of Lisbon, Lisbon, Portugal
- Instituto Superior Técnico (IST), University of Lisbon, Lisbon, Portugal
| | - Rodrigo Costa
- Institute for Bioengineering and Biosciences (iBB), University of Lisbon, Lisbon, Portugal
- Instituto Superior Técnico (IST), University of Lisbon, Lisbon, Portugal
- Department of Energy, Joint Genome Institute and Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Stefano Romano
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, United Kingdom
| | - David G. Bourne
- College of Science and Engineering, James Cook University, Townsville, Australia
- Australian Institute of Marine Science, Townsville, Australia
| | - Anny Cárdenas
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Megan J. Huggett
- School of Environmental and Life Sciences, The University of Newcastle, Ourimbah, NSW, Australia
- Centre for Marine Ecosystems Research, Edith Cowan University, Joondalup, WA, Australia
| | | | - Felicity Kuek
- Australian Institute of Marine Science, Townsville, Australia
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Australia
| | - Mónica Medina
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Julie L. Meyer
- Soil and Water Sciences Department, Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Moritz Müller
- Faculty of Engineering, Computing and Science, Swinburne University of Technology Sarawak Campus, Kuching, Sarawak, Malaysia
| | - F. Joseph Pollock
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA
- Hawaii and Palmyra Programs, The Nature Conservancy, Honolulu, Hawaii, USA
| | - Michael S. Rappé
- Hawaii Institute of Marine Biology, University of Hawaii, Kaneohe, Hawaii, USA
| | - Mathieu Sere
- Aquatic Research Facility, Environmental Sustainability Research Centre, University of Derby, Derby, United Kingdom
| | - Koty H. Sharp
- Department of Biology and Marine Biology, Roger Williams University, Bristol, Rhode Island, USA
| | | | - Nathan Zaccardi
- Department of Biology and Marine Biology, Roger Williams University, Bristol, Rhode Island, USA
| | - Maren Ziegler
- Department of Animal Ecology and Systematics, Justus Liebig University Giessen, Giessen, Germany
| | - Raquel Peixoto
- Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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El-Khaled YC, Roth F, Rädecker N, Tilstra A, Karcher DB, Kürten B, Jones BH, Voolstra CR, Wild C. Nitrogen fixation and denitrification activity differ between coral- and algae-dominated Red Sea reefs. Sci Rep 2021; 11:11820. [PMID: 34083565 PMCID: PMC8175748 DOI: 10.1038/s41598-021-90204-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 05/07/2021] [Indexed: 11/18/2022] Open
Abstract
Coral reefs experience phase shifts from coral- to algae-dominated benthic communities, which could affect the interplay between processes introducing and removing bioavailable nitrogen. However, the magnitude of such processes, i.e., dinitrogen (N2) fixation and denitrification levels, and their responses to phase shifts remain unknown in coral reefs. We assessed both processes for the dominant species of six benthic categories (hard corals, soft corals, turf algae, coral rubble, biogenic rock, and reef sands) accounting for > 98% of the benthic cover of a central Red Sea coral reef. Rates were extrapolated to the relative benthic cover of the studied organisms in co-occurring coral- and algae-dominated areas of the same reef. In general, benthic categories with high N2 fixation exhibited low denitrification activity. Extrapolated to the respective reef area, turf algae and coral rubble accounted for > 90% of overall N2 fixation, whereas corals contributed to more than half of reef denitrification. Total N2 fixation was twice as high in algae- compared to coral-dominated areas, whereas denitrification levels were similar. We conclude that algae-dominated reefs promote new nitrogen input through enhanced N2 fixation and comparatively low denitrification. The subsequent increased nitrogen availability could support net productivity, resulting in a positive feedback loop that increases the competitive advantage of algae over corals in reefs that experienced a phase shift.
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Affiliation(s)
- Yusuf C El-Khaled
- Marine Ecology Department, Faculty of Biology and Chemistry, University of Bremen, 28359, Bremen, Germany.
| | - Florian Roth
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23995, Saudi Arabia
- Baltic Sea Centre, Stockholm University, 10691, Stockholm, Sweden
- Faculty of Biological and Environmental Sciences, Tvärminne Zoological Station, University of Helsinki, 00014, Helsinki, Finland
| | - Nils Rädecker
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23995, Saudi Arabia
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Arjen Tilstra
- Marine Ecology Department, Faculty of Biology and Chemistry, University of Bremen, 28359, Bremen, Germany
| | - Denis B Karcher
- Marine Ecology Department, Faculty of Biology and Chemistry, University of Bremen, 28359, Bremen, Germany
- Australian National Centre for the Public Awareness of Science, Australian National University, ACT, Canberra, 2601, Australia
| | - Benjamin Kürten
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23995, Saudi Arabia
- Project Management Jülich, Jülich Research Centre GmbH, 18069, Rostock, Germany
| | - Burton H Jones
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23995, Saudi Arabia
| | - Christian R Voolstra
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23995, Saudi Arabia
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Christian Wild
- Marine Ecology Department, Faculty of Biology and Chemistry, University of Bremen, 28359, Bremen, Germany
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Tilstra A, Roth F, El-Khaled YC, Pogoreutz C, Rädecker N, Voolstra CR, Wild C. Relative abundance of nitrogen cycling microbes in coral holobionts reflects environmental nitrate availability. R Soc Open Sci 2021; 8:201835. [PMID: 34109033 PMCID: PMC8170195 DOI: 10.1098/rsos.201835] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 10/15/2020] [Accepted: 05/14/2021] [Indexed: 06/12/2023]
Abstract
Recent research suggests that nitrogen (N) cycling microbes are important for coral holobiont functioning. In particular, coral holobionts may acquire bioavailable N via prokaryotic dinitrogen (N2) fixation or remove excess N via denitrification activity. However, our understanding of environmental drivers on these processes in hospite remains limited. Employing the strong seasonality of the central Red Sea, this study assessed the effects of environmental parameters on the proportional abundances of N cycling microbes associated with the hard corals Acropora hemprichii and Stylophora pistillata. Specifically, we quantified changes in the relative ratio between nirS and nifH gene copy numbers, as a proxy for seasonal shifts in denitrification and N2 fixation potential in corals, respectively. In addition, we assessed coral tissue-associated Symbiodiniaceae cell densities and monitored environmental parameters to provide a holobiont and environmental context, respectively. While ratios of nirS to nifH gene copy numbers varied between seasons, they revealed similar seasonal patterns in both coral species, with ratios closely following patterns in environmental nitrate availability. Symbiodiniaceae cell densities aligned with environmental nitrate availability, suggesting that the seasonal shifts in nirS to nifH gene abundance ratios were probably driven by nitrate availability in the coral holobiont. Thereby, our results suggest that N cycling in coral holobionts probably adjusts to environmental conditions by increasing and/or decreasing denitrification and N2 fixation potential according to environmental nitrate availability. Microbial N cycling may, thus, extenuate the effects of changes in environmental nitrate availability on coral holobionts to support the maintenance of the coral-Symbiodiniaceae symbiosis.
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Affiliation(s)
- Arjen Tilstra
- Marine Ecology Department, Faculty of Biology and Chemistry, University of Bremen, Bremen, Germany
| | - Florian Roth
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
- Baltic Sea Centre, Stockholm University, Stockholm, Sweden
- Tvärminne Zoological Station, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Yusuf C. El-Khaled
- Marine Ecology Department, Faculty of Biology and Chemistry, University of Bremen, Bremen, Germany
| | - Claudia Pogoreutz
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Nils Rädecker
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
- Department of Biology, University of Konstanz, Konstanz, Germany
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Christian R. Voolstra
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Christian Wild
- Marine Ecology Department, Faculty of Biology and Chemistry, University of Bremen, Bremen, Germany
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48
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Savary R, Barshis DJ, Voolstra CR, Cárdenas A, Evensen NR, Banc-Prandi G, Fine M, Meibom A. Fast and pervasive transcriptomic resilience and acclimation of extremely heat-tolerant coral holobionts from the northern Red Sea. Proc Natl Acad Sci U S A 2021; 118:e2023298118. [PMID: 33941698 PMCID: PMC8126839 DOI: 10.1073/pnas.2023298118] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Corals from the northern Red Sea and Gulf of Aqaba exhibit extreme thermal tolerance. To examine the underlying gene expression dynamics, we exposed Stylophora pistillata from the Gulf of Aqaba to short-term (hours) and long-term (weeks) heat stress with peak seawater temperatures ranging from their maximum monthly mean of 27 °C (baseline) to 29.5 °C, 32 °C, and 34.5 °C. Corals were sampled at the end of the heat stress as well as after a recovery period at baseline temperature. Changes in coral host and symbiotic algal gene expression were determined via RNA-sequencing (RNA-Seq). Shifts in coral microbiome composition were detected by complementary DNA (cDNA)-based 16S ribosomal RNA (rRNA) gene sequencing. In all experiments up to 32 °C, RNA-Seq revealed fast and pervasive changes in gene expression, primarily in the coral host, followed by a return to baseline gene expression for the majority of coral (>94%) and algal (>71%) genes during recovery. At 34.5 °C, large differences in gene expression were observed with minimal recovery, high coral mortality, and a microbiome dominated by opportunistic bacteria (including Vibrio species), indicating that a lethal temperature threshold had been crossed. Our results show that the S. pistillata holobiont can mount a rapid and pervasive gene expression response contingent on the amplitude and duration of the thermal stress. We propose that the transcriptomic resilience and transcriptomic acclimation observed are key to the extraordinary thermal tolerance of this holobiont and, by inference, of other northern Red Sea coral holobionts, up to seawater temperatures of at least 32 °C, that is, 5 °C above their current maximum monthly mean.
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Affiliation(s)
- Romain Savary
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland;
| | - Daniel J Barshis
- Department of Biological Sciences, Old Dominion University, Norfolk, VA 23529
| | | | - Anny Cárdenas
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Nicolas R Evensen
- Department of Biological Sciences, Old Dominion University, Norfolk, VA 23529
| | - Guilhem Banc-Prandi
- The Goodman Faculty of Life Sciences, Bar-Ilan University, 52900 Ramat-Gan, Israel
- Laboratory for Coral Reef Ecology, Interuniversity Institute for Marine Sciences, 88103 Eilat, Israel
| | - Maoz Fine
- The Goodman Faculty of Life Sciences, Bar-Ilan University, 52900 Ramat-Gan, Israel
- Laboratory for Coral Reef Ecology, Interuniversity Institute for Marine Sciences, 88103 Eilat, Israel
| | - Anders Meibom
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
- Center for Advanced Surface Analysis, Institute of Earth Sciences, University of Lausanne, CH-1015 Lausanne, Switzerland
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49
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Costa RM, Cárdenas A, Loussert-Fonta C, Toullec G, Meibom A, Voolstra CR. Surface Topography, Bacterial Carrying Capacity, and the Prospect of Microbiome Manipulation in the Sea Anemone Coral Model Aiptasia. Front Microbiol 2021; 12:637834. [PMID: 33897642 PMCID: PMC8060496 DOI: 10.3389/fmicb.2021.637834] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 12/04/2020] [Accepted: 02/19/2021] [Indexed: 11/13/2022] Open
Abstract
Aiptasia is an emerging model organism to study cnidarian symbioses due to its taxonomic relatedness to other anthozoans such as stony corals and similarities of its microalgal and bacterial partners, complementing the existing Hydra (Hydrozoa) and Nematostella (Anthozoa) model systems. Despite the availability of studies characterizing the microbiomes of several natural Aiptasia populations and laboratory strains, knowledge on basic information, such as surface topography, bacterial carrying capacity, or the prospect of microbiome manipulation is lacking. Here we address these knowledge gaps. Our results show that the surface topographies of the model hydrozoan Hydra and anthozoans differ substantially, whereas the ultrastructural surface architecture of Aiptasia and stony corals is highly similar. Further, we determined a bacterial carrying capacity of ∼104 and ∼105 bacteria (i.e., colony forming units, CFUs) per polyp for aposymbiotic and symbiotic Aiptasia anemones, respectively, suggesting that the symbiotic status changes bacterial association/density. Microbiome transplants from Acropora humilis and Porites sp. to gnotobiotic Aiptasia showed that only a few foreign bacterial taxa were effective colonizers. Our results shed light on the putative difficulties of transplanting microbiomes between cnidarians in a manner that consistently changes microbial host association at large. At the same time, our study provides an avenue to identify bacterial taxa that exhibit broad ability to colonize different hosts as a starting point for cross-species microbiome manipulation. Our work is relevant in the context of microbial therapy (probiotics) and microbiome manipulation in corals and answers to the need of having cnidarian model systems to test the function of bacteria and their effect on holobiont biology. Taken together, we provide important foundation data to extend Aiptasia as a coral model for bacterial functional studies.
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Affiliation(s)
- Rúben M Costa
- Division of Biological and Environmental Science and Engineering, Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Anny Cárdenas
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Céline Loussert-Fonta
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Gaëlle Toullec
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Anders Meibom
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Center for Advanced Surface Analysis, Institute of Earth Sciences, University of Lausanne, Lausanne, Switzerland
| | - Christian R Voolstra
- Division of Biological and Environmental Science and Engineering, Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,Department of Biology, University of Konstanz, Konstanz, Germany
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Rossbach S, Hume BCC, Cárdenas A, Perna G, Voolstra CR, Duarte CM. Flexibility in Red Sea Tridacna maxima-Symbiodiniaceae associations supports environmental niche adaptation. Ecol Evol 2021; 11:3393-3406. [PMID: 33841792 PMCID: PMC8019035 DOI: 10.1002/ece3.7299] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 09/25/2020] [Revised: 01/13/2021] [Accepted: 02/02/2021] [Indexed: 12/20/2022] Open
Abstract
Giant clams (Tridacninae) are important members of Indo-Pacific coral reefs and among the few bivalve groups that live in symbiosis with unicellular algae (Symbiodiniaceae). Despite the importance of these endosymbiotic dinoflagellates for clam ecology, the diversity and specificity of these associations remain relatively poorly studied, especially in the Red Sea. Here, we used the internal transcribed spacer 2 (ITS2) rDNA gene region to investigate Symbiodiniaceae communities associated with Red Sea Tridacna maxima clams. We sampled five sites spanning 1,300 km (10° of latitude, from the Gulf of Aqaba, 29°N, to the Farasan Banks, 18°N) along the Red Sea's North-South environmental gradient. We detected a diverse and structured assembly of host-associated algae with communities demonstrating region and site-specificity. Specimens from the Gulf of Aqaba harbored three genera of Symbiodiniaceae, Cladocopium, Durusdinium, and Symbiodinium, while at all other sites clams associated exclusively with algae from the Symbiodinium genus. Of these exclusively Symbiodinium-associating sites, the more northern (27° and 22°) and more southern sites (20° and 18°) formed two separate groupings despite site-specific algal genotypes being resolved at each site. These groupings were congruent with the genetic break seen across multiple marine taxa in the Red Sea at approximately 19°, and along with our documented site-specificity of algal communities, contrasted the panmictic distribution of the T. maxima host. As such, our findings indicate flexibility in T. maxima-Symbiodiniaceae associations that may explain its relatively high environmental plasticity and offers a mechanism for environmental niche adaptation.
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Affiliation(s)
- Susann Rossbach
- Biological and Environmental Science and Engineering DivisionRed Sea Research Center (RSRC) and Computational Bioscience Research Center (CBRC)King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
| | - Benjamin C. C. Hume
- Biological and Environmental Science and Engineering DivisionRed Sea Research Center (RSRC)King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
- Department of BiologyUniversity of KonstanzKonstanzGermany
| | - Anny Cárdenas
- Department of BiologyUniversity of KonstanzKonstanzGermany
| | - Gabriela Perna
- Department of BiologyUniversity of KonstanzKonstanzGermany
| | - Christian R. Voolstra
- Biological and Environmental Science and Engineering DivisionRed Sea Research Center (RSRC)King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
- Department of BiologyUniversity of KonstanzKonstanzGermany
| | - Carlos M. Duarte
- Biological and Environmental Science and Engineering DivisionRed Sea Research Center (RSRC) and Computational Bioscience Research Center (CBRC)King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
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