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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; 22:460-475. [PMID: 38438489 DOI: 10.1038/s41579-024-01015-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [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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2
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Chuang PS, Wang TH, Lu CY, Tandon K, Shikina S, Tang SL. Microbiome heterogeneity in tissues of the coral, Fimbriaphyllia (Euphyllia) ancora. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13310. [PMID: 38982629 PMCID: PMC11233273 DOI: 10.1111/1758-2229.13310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 06/25/2024] [Indexed: 07/11/2024]
Abstract
Coral microbiomes differ in the mucus, soft tissue and skeleton of a coral colony, but whether variations exist in different tissues of a single polyp is unknown. In the stony coral, Fimbriaphyllia ancora, we identified 8,994 amplicon sequencing variants (ASVs) in functionally differentiated polyp tissues, i.e., tentacles, body wall, mouth and pharynx, mesenterial filaments, and gonads (testes and ovaries), with a large proportion of ASVs specific to individual tissues. However, shared ASVs comprised the majority of microbiomes from all tissues in terms of relative abundance. No tissue-specific ASVs were found, except in testes, for which there were only two samples. At the generic level, Endozoicomonas was significantly less abundant in the body wall, where calicoblastic cells reside. On the other hand, several bacterial taxa presented significantly higher abundances in the mouth. Interestingly, although without statistical confirmation, gonadal tissues showed lower ASV richness and relatively high abundances of Endozoicomonas (in ovaries) and Pseudomonas (in testes). These findings provide evidence for microbiome heterogeneity between tissues within coral polyps, suggesting a promising field for future studies of functional interactions between corals and their bacterial symbionts.
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Affiliation(s)
- Po-Shun Chuang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Tzu-Haw Wang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan
| | - Chih-Ying Lu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei, Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Kshitij Tandon
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Shinya Shikina
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung, Taiwan
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan
| | - Sen-Lin Tang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Taiwan Ocean Genome Center, National Taiwan Ocean University, Keelung, Taiwan
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Raimundo I, Rosado PM, Barno AR, Antony CP, Peixoto RS. Unlocking the genomic potential of Red Sea coral probiotics. Sci Rep 2024; 14:14514. [PMID: 38914624 PMCID: PMC11196684 DOI: 10.1038/s41598-024-65152-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 06/17/2024] [Indexed: 06/26/2024] Open
Abstract
The application of beneficial microorganisms for corals (BMC) decreases the bleaching susceptibility and mortality rate of corals. BMC selection is typically performed via molecular and biochemical assays, followed by genomic screening for BMC traits. Herein, we present a comprehensive in silico framework to explore a set of six putative BMC strains. We extracted high-quality DNA from coral samples collected from the Red Sea and performed PacBio sequencing. We identified BMC traits and mechanisms associated with each strain as well as proposed new traits and mechanisms, such as chemotaxis and the presence of phages and bioactive secondary metabolites. The presence of prophages in two of the six studied BMC strains suggests their possible distribution within beneficial bacteria. We also detected various secondary metabolites, such as terpenes, ectoines, lanthipeptides, and lasso peptides. These metabolites possess antimicrobial, antifungal, antiviral, anti-inflammatory, and antioxidant activities and play key roles in coral health by reducing the effects of heat stress, high salinity, reactive oxygen species, and radiation. Corals are currently facing unprecedented challenges, and our revised framework can help select more efficient BMC for use in studies on coral microbiome rehabilitation, coral resilience, and coral restoration.
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Affiliation(s)
- Inês Raimundo
- Biological and Environmental Science and Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology, Biological and Environmental Science and Engineering Division, Thuwal, Saudi Arabia
| | - Phillipe M Rosado
- Biological and Environmental Science and Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology, Biological and Environmental Science and Engineering Division, Thuwal, Saudi Arabia
| | - Adam R Barno
- Biological and Environmental Science and Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology, Biological and Environmental Science and Engineering Division, Thuwal, Saudi Arabia
| | - Chakkiath P Antony
- Biological and Environmental Science and Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology, Biological and Environmental Science and Engineering Division, Thuwal, Saudi Arabia
| | - Raquel S Peixoto
- Biological and Environmental Science and Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology, Biological and Environmental Science and Engineering Division, Thuwal, Saudi Arabia.
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4
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Vohsen SA, Herrera S. Coral microbiomes are structured by environmental gradients in deep waters. ENVIRONMENTAL MICROBIOME 2024; 19:38. [PMID: 38858739 PMCID: PMC11165896 DOI: 10.1186/s40793-024-00579-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 06/02/2024] [Indexed: 06/12/2024]
Abstract
BACKGROUND Coral-associated microbiomes vary greatly between colonies and localities with functional consequences on the host. However, the full extent of variability across the ranges of most coral species remains unknown, especially for corals living in deep waters which span greater ranges. Here, we characterized the microbiomes of four octocoral species from mesophotic and bathyal deep-sea habitats in the northern Gulf of Mexico, Muricea pendula, Swiftia exserta, Callogorgia delta, and Paramuricea biscaya, using 16S rRNA gene metabarcoding. We sampled extensively across their ranges to test for microbiome differentiation between and within species, examining the influence of environmental factors that vary with depth (53-2224 m) and geographic location (over 680 m) as well as the host coral's genotype using RAD-sequencing. RESULTS Coral microbiomes were often dominated by amplicon sequence variants whose abundances varied across their hosts' ranges, including symbiotic taxa: corallicolids, Endozoicomonas, members of the Mollicutes, and the BD1-7 clade. Coral species, depth, and geographic location significantly affected diversity, microbial community composition, and the relative abundance of individual microbes. Depth was the strongest environmental factor determining microbiome structure within species, which influenced the abundance of most dominant symbiotic taxa. Differences in host genotype, bottom temperature, and surface primary productivity could explain a significant part of the microbiome variation associated with depth and geographic location. CONCLUSIONS Altogether, this work demonstrates that the microbiomes of corals in deep waters vary substantially across their ranges in accordance with depth and other environmental conditions. It reveals that the influence of depth on the ecology of mesophotic and deep-sea corals extends to its effects on their microbiomes which may have functional consequences. This work also identifies the distributions of microbes including potential parasites which can be used to inform restoration plans in response to the Deepwater Horizon oil spill.
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Affiliation(s)
- Samuel A Vohsen
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA.
- Lehigh Oceans Research Center, Lehigh University, Bethlehem, PA, USA.
| | - Santiago Herrera
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA.
- Lehigh Oceans Research Center, Lehigh University, Bethlehem, PA, USA.
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Galià-Camps C, Junkin L, Borrallo X, Carreras C, Pascual M, Turon X. Navigating spatio-temporal microbiome dynamics: Environmental factors and trace elements shape the symbiont community of an invasive marine species. MARINE POLLUTION BULLETIN 2024; 203:116477. [PMID: 38759466 DOI: 10.1016/j.marpolbul.2024.116477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 04/30/2024] [Accepted: 05/06/2024] [Indexed: 05/19/2024]
Abstract
The proliferation of marine invasive species is a mounting concern. While the role of microbial communities in invasive ascidian species is recognized, the role of seasonal shifts in microbiome composition remains largely unexplored. We sampled five individuals of the invasive ascidian Styela plicata quarterly from January 2020 to October 2021 in two harbours, examining gills, tunics, and surrounding water. By analysing Amplicon Sequence Variants (ASVs) and seawater trace elements, we found that compartment (seawater, tunic, or gills) was the primary differentiating factor, followed by harbour. Clear seasonal patterns were evident in seawater bacteria, less so in gills, and absent in tunics. We identified compartment-specific bacteria, as well as seasonal indicator ASVs and ASVs correlated with trace element concentrations. Among these bacteria, we found that Endozoicomonas, Hepatoplasma and Rhodobacteraceae species had reported functions which might be necessary for overcoming seasonality and trace element shifts. This study contributes to understanding microbiome dynamics in invasive holobiont systems, and the patterns found indicate a potential role in adaptation and invasiveness.
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Affiliation(s)
- Carles Galià-Camps
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Avinguda Diagonal 643, 08028 Barcelona, Spain; Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain; Department of Marine Ecology, Centre d'Estudis Avançats de Blanes (CEAB-CSIC), Accés Cala Sant Francesc 14, 17300 Blanes, Spain.
| | - Liam Junkin
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Avinguda Diagonal 643, 08028 Barcelona, Spain.
| | - Xavier Borrallo
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Avinguda Diagonal 643, 08028 Barcelona, Spain
| | - Carlos Carreras
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Avinguda Diagonal 643, 08028 Barcelona, Spain; Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain.
| | - Marta Pascual
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Avinguda Diagonal 643, 08028 Barcelona, Spain; Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain.
| | - Xavier Turon
- Department of Marine Ecology, Centre d'Estudis Avançats de Blanes (CEAB-CSIC), Accés Cala Sant Francesc 14, 17300 Blanes, Spain.
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6
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Pogoreutz C, Ziegler M. Frenemies on the reef? Resolving the coral-Endozoicomonas association. Trends Microbiol 2024; 32:422-434. [PMID: 38216372 DOI: 10.1016/j.tim.2023.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/09/2023] [Accepted: 11/13/2023] [Indexed: 01/14/2024]
Abstract
Stony corals are poster child holobionts due to their intimate association with diverse microorganisms from all domains of life. We are only beginning to understand the diverse functions of most of these microbial associates, including potential main contributors to holobiont health and resilience. Among these, bacteria of the elusive genus Endozoicomonas are widely perceived as beneficial symbionts based on their genomic potential and their high prevalence and ubiquitous presence in coral tissues. Simultaneously, evidence of pathogenic and parasitic Endozoicomonas lineages in other marine animals is emerging. Synthesizing the current knowledge on the association of Endozoicomonas with marine holobionts, we challenge the perception of a purely mutualistic coral-Endozoicomonas relationship and propose directions to elucidate its role along the symbiotic spectrum.
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Affiliation(s)
- Claudia Pogoreutz
- EPHE-UPVD-CNRS, UAR 3278 CRIOBE, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy, 66860 Perpignan Cedex, France.
| | - Maren Ziegler
- Department of Animal Ecology and Systematics, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32 (IFZ), 35392, Giessen, Germany.
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7
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Williams A. Multiomics data integration, limitations, and prospects to reveal the metabolic activity of the coral holobiont. FEMS Microbiol Ecol 2024; 100:fiae058. [PMID: 38653719 PMCID: PMC11067971 DOI: 10.1093/femsec/fiae058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 03/25/2024] [Accepted: 04/22/2024] [Indexed: 04/25/2024] Open
Abstract
Since their radiation in the Middle Triassic period ∼240 million years ago, stony corals have survived past climate fluctuations and five mass extinctions. Their long-term survival underscores the inherent resilience of corals, particularly when considering the nutrient-poor marine environments in which they have thrived. However, coral bleaching has emerged as a global threat to coral survival, requiring rapid advancements in coral research to understand holobiont stress responses and allow for interventions before extensive bleaching occurs. This review encompasses the potential, as well as the limits, of multiomics data applications when applied to the coral holobiont. Synopses for how different omics tools have been applied to date and their current restrictions are discussed, in addition to ways these restrictions may be overcome, such as recruiting new technology to studies, utilizing novel bioinformatics approaches, and generally integrating omics data. Lastly, this review presents considerations for the design of holobiont multiomics studies to support lab-to-field advancements of coral stress marker monitoring systems. Although much of the bleaching mechanism has eluded investigation to date, multiomic studies have already produced key findings regarding the holobiont's stress response, and have the potential to advance the field further.
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Affiliation(s)
- Amanda Williams
- Microbial Biology Graduate Program, Rutgers University, 76 Lipman Drive, New Brunswick, NJ 08901, United States
- Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Drive, New Brunswick, NJ 08901, United States
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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] [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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Grupstra CGB, Gómez-Corrales M, Fifer JE, Aichelman HE, Meyer-Kaiser KS, Prada C, Davies SW. Integrating cryptic diversity into coral evolution, symbiosis and conservation. Nat Ecol Evol 2024; 8:622-636. [PMID: 38351091 DOI: 10.1038/s41559-023-02319-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 12/12/2023] [Indexed: 04/13/2024]
Abstract
Understanding how diversity evolves and is maintained is critical to predicting the future trajectories of ecosystems under climate change; however, our understanding of these processes is limited in marine systems. Corals, which engineer reef ecosystems, are critically threatened by climate change, and global efforts are underway to conserve and restore populations as attempts to mitigate ocean warming continue. Recently, sequencing efforts have uncovered widespread undescribed coral diversity, including 'cryptic lineages'-genetically distinct but morphologically similar coral taxa. Such cryptic lineages have been identified in at least 24 coral genera spanning the anthozoan phylogeny and across ocean basins. These cryptic lineages co-occur in many reef systems, but their distributions often differ among habitats. Research suggests that cryptic lineages are ecologically specialized and several examples demonstrate differences in thermal tolerance, highlighting the critical implications of this diversity for predicting coral responses to future warming. Here, we draw attention to recent discoveries, discuss how cryptic diversity affects the study of coral adaptation and acclimation to future environments, explore how it shapes symbiotic partnerships, and highlight challenges and opportunities for conservation and restoration efforts.
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Affiliation(s)
| | | | - James E Fifer
- Department of Biology, Boston University, Boston, MA, USA
| | | | | | - Carlos Prada
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, USA
| | - Sarah W Davies
- Department of Biology, Boston University, Boston, MA, USA.
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10
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A L, J K. At the root of plant symbioses: Untangling the genetic mechanisms behind mutualistic associations. CURRENT OPINION IN PLANT BIOLOGY 2024; 77:102448. [PMID: 37758591 DOI: 10.1016/j.pbi.2023.102448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 08/04/2023] [Accepted: 08/14/2023] [Indexed: 09/29/2023]
Abstract
Mutualistic interactions between plants and microorganisms shape the continuous evolution and adaptation of plants such as to the terrestrial environment that was a founding event of subsequent life on land. Such interactions also play a central role in the natural and agricultural ecosystems and are of primary importance for a sustainable future. To boost plant's productivity and resistance to biotic and abiotic stresses, new approaches involving associated symbiotic organisms have recently been explored. New discoveries on mutualistic symbioses evolution and the interaction between partners will be key steps to enhance plant potential.
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Affiliation(s)
- Lebreton A
- INRAE, Aix-Marseille Université, Biodiversité et Biotechnologie Fongiques, 13009 Marseille, France; Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, UMR 7257, 13288 Marseille, France.
| | - Keller J
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany.
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11
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Maire J, Tsang Min Ching SJ, Damjanovic K, Epstein HE, Judd LM, Blackall LL, van Oppen MJH. Tissue-associated and vertically transmitted bacterial symbiont in the coral Pocillopora acuta. THE ISME JOURNAL 2024; 18:wrad027. [PMID: 38365239 PMCID: PMC10833068 DOI: 10.1093/ismejo/wrad027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/07/2023] [Accepted: 12/09/2023] [Indexed: 02/18/2024]
Abstract
Coral microhabitats are colonized by a myriad of microorganisms, including diverse bacteria which are essential for host functioning and survival. However, the location, transmission, and functions of individual bacterial species living inside the coral tissues remain poorly studied. Here, we show that a previously undescribed bacterial symbiont of the coral Pocillopora acuta forms cell-associated microbial aggregates (CAMAs) within the mesenterial filaments. CAMAs were found in both adults and larval offspring, suggesting vertical transmission. In situ laser capture microdissection of CAMAs followed by 16S rRNA gene amplicon sequencing and shotgun metagenomics produced a near complete metagenome-assembled genome. We subsequently cultured the CAMA bacteria from Pocillopora acuta colonies, and sequenced and assembled their genomes. Phylogenetic analyses showed that the CAMA bacteria belong to an undescribed Endozoicomonadaceae genus and species, which we propose to name Candidatus Sororendozoicomonas aggregata gen. nov sp. nov. Metabolic pathway reconstruction from its genome sequence suggests this species can synthesize most amino acids, several B vitamins, and antioxidants, and participate in carbon cycling and prey digestion, which may be beneficial to its coral hosts. This study provides detailed insights into a new member of the widespread Endozoicomonadaceae family, thereby improving our understanding of coral holobiont functioning. Vertically transmitted, tissue-associated bacteria, such as Sororendozoicomonas aggregata may be key candidates for the development of microbiome manipulation approaches with long-term positive effects on the coral host.
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Affiliation(s)
- Justin Maire
- School of BioSciences, The University of Melbourne, Parkville, 3010 VIC, Australia
| | | | - Katarina Damjanovic
- School of BioSciences, The University of Melbourne, Parkville, 3010 VIC, Australia
- Australian Institute of Marine Science, PMB No 3, Townsville, 4810 QLD, Australia
| | - Hannah E Epstein
- Australian Institute of Marine Science, PMB No 3, Townsville, 4810 QLD, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, 4811 QLD, Australia
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, United Kingdom
| | - Louise M Judd
- Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, 3010 VIC, Australia
| | - Linda L Blackall
- School of BioSciences, The University of Melbourne, Parkville, 3010 VIC, Australia
| | - Madeleine J H van Oppen
- School of BioSciences, The University of Melbourne, Parkville, 3010 VIC, Australia
- Australian Institute of Marine Science, PMB No 3, Townsville, 4810 QLD, Australia
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12
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Chuang PS, Yu SP, Liu PY, Hsu MT, Chiou YJ, Lu CY, Tang SL. A gauge of coral physiology: re-examining temporal changes in Endozoicomonas abundance correlated with natural coral bleaching. ISME COMMUNICATIONS 2024; 4:ycae001. [PMID: 38371393 PMCID: PMC10872716 DOI: 10.1093/ismeco/ycae001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/14/2023] [Accepted: 01/04/2024] [Indexed: 02/20/2024]
Abstract
Bacteria contribute to many physiological functions of coral holobionts, including responses to bleaching. The bacterial genus, Endozoicomonas, dominates the microbial flora of many coral species and its abundance appears to be correlated with coral bleaching. However, evidences for decoupling of bleaching and Endozoicomonas abundance changes have also been reported. In 2020, a severe bleaching event was recorded at reefs in Taiwan, providing a unique opportunity to re-examine bleaching-Endozoicomonas association using multiple stony corals in natural environments. In this study, we monitored tissue color and microbiome changes in three coral species (Montipora sp., Porites sp., and Stylophora pistillata) in Kenting National Park, following the bleaching event. All tagged Montipora sp. and Porites sp. recovered from bleaching within 1 year, while high mortality occurred in S. pistillata. Microbiome analysis found no correlation of Endozoicomonas relative abundance and bleaching severity during the sampling period, but found a stronger correlation when the month in which bleaching occurred was excluded. Moreover, Endozoicomonas abundance increased during recovery months in Montipora sp. and Porites sp., whereas in S. pistillata it was nearly depleted. These results suggest that Endozoicomonas abundance may represent a gauge of coral health and reflect recovery of some corals from stress. Interestingly, even though different Endozoicomonas strains predominated in the three corals, these Endozoicomonas strains were also shared among coral taxa. Meanwhile, several Endozoicomonas strains showed secondary emergence during coral recovery, suggesting possible symbiont switching in Endozoicomonas. These findings indicate that it may be possible to introduce Endozoicomonas to non-native coral hosts as a coral probiotic.
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Affiliation(s)
- Po-Shun Chuang
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Sheng-Ping Yu
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Po-Yu Liu
- School of Medicine, College of Medicine, National Sun Yat-sen University, Kaohsiung 804, Taiwan
| | - Ming-Tsung Hsu
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yu-Jing Chiou
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
- Centre for Marine Science and Innovation, School of Biological Earth and Environmental Sciences, University of New South Wales, Sydney 2052, Australia
| | - Chih-Ying Lu
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei 115, Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 402, Taiwan
| | - Sen-Lin Tang
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
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13
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Maire J, Philip GK, Livingston J, Judd LM, Blackall LL, van Oppen MJH. Functional potential and evolutionary response to long-term heat selection of bacterial associates of coral photosymbionts. mSystems 2023; 8:e0086023. [PMID: 37909753 PMCID: PMC10746172 DOI: 10.1128/msystems.00860-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 09/28/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE Symbiotic microorganisms are crucial for the survival of corals and their resistance to coral bleaching in the face of climate change. However, the impact of microbe-microbe interactions on coral functioning is mostly unknown but could be essential factors for coral adaption to future climates. Here, we investigated interactions between cultured dinoflagellates of the Symbiodiniaceae family, essential photosymbionts of corals, and associated bacteria. By assessing the genomic potential of 49 bacteria, we found that they are likely beneficial for Symbiodiniaceae, through the production of B vitamins and antioxidants. Additionally, bacterial genes involved in host-symbiont interactions, such as secretion systems, accumulated mutations following long-term exposure to heat, suggesting symbiotic interactions may change under climate change. This highlights the importance of microbe-microbe interactions in coral functioning.
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Affiliation(s)
- Justin Maire
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Gayle K. Philip
- Melbourne Bioinformatics, The University of Melbourne, Parkville, Victoria, Australia
| | - Jadzia Livingston
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Louise M. Judd
- Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Linda L. Blackall
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Madeleine J. H. van Oppen
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
- Australian Institute of Marine Science, Townsville, Queensland, Australia
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14
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Prioux C, Tignat-Perrier R, Gervais O, Estaque T, Schull Q, Reynaud S, Béraud E, Mérigot B, Beauvieux A, Marcus MI, Richaume J, Bianchimani O, Cheminée A, Allemand D, Ferrier-Pagès C. Unveiling microbiome changes in Mediterranean octocorals during the 2022 marine heatwaves: quantifying key bacterial symbionts and potential pathogens. MICROBIOME 2023; 11:271. [PMID: 38053218 PMCID: PMC10696765 DOI: 10.1186/s40168-023-01711-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 10/27/2023] [Indexed: 12/07/2023]
Abstract
BACKGROUND Climate change has accelerated the occurrence and severity of heatwaves in the Mediterranean Sea and poses a significant threat to the octocoral species that form the foundation of marine animal forests (MAFs). As coral health intricately relies on the symbiotic relationships established between corals and microbial communities, our goal was to gain a deeper understanding of the role of bacteria in the observed tissue loss of key octocoral species following the unprecedented heatwaves in 2022. RESULTS Using amplicon sequencing and taxon-specific qPCR analyses, we unexpectedly found that the absolute abundance of the major bacterial symbionts, Spirochaetaceae (C. rubrum) and Endozoicomonas (P. clavata), remained, in most cases, unchanged between colonies with 0% and 90% tissue loss. These results suggest that the impairment of coral health was not due to the loss of the main bacterial symbionts. However, we observed a significant increase in the total abundance of bacterial opportunists, including putative pathogens such as Vibrio, which was not evident when only their relative abundance was considered. In addition, there was no clear relation between bacterial symbiont loss and the intensity of thermal stress, suggesting that factors other than temperature may have influenced the differential response of octocoral microbiomes at different sampling sites. CONCLUSIONS Our results indicate that tissue loss in octocorals is not directly caused by the decline of the main bacterial symbionts but by the proliferation of opportunistic and pathogenic bacteria. Our findings thus underscore the significance of considering both relative and absolute quantification approaches when evaluating the impact of stressors on coral microbiome as the relative quantification does not accurately depict the actual changes in the microbiome. Consequently, this research enhances our comprehension of the intricate interplay between host organisms, their microbiomes, and environmental stressors, while offering valuable insights into the ecological implications of heatwaves on marine animal forests. Video Abstract.
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Affiliation(s)
- Camille Prioux
- Collège Doctoral, Sorbonne Université, Paris, France
- Unité de Recherche sur la Biologie des Coraux Précieux CSM - CHANEL, Centre Scientifique de Monaco, 8 Quai Antoine 1er, Monaco, MC-98000 Monaco, Principality of Monaco
- Centre Scientifique de Monaco, 8 Quai Antoine 1er, Monaco, MC 98000, Principality of Monaco
| | - Romie Tignat-Perrier
- Unité de Recherche sur la Biologie des Coraux Précieux CSM - CHANEL, Centre Scientifique de Monaco, 8 Quai Antoine 1er, Monaco, MC-98000 Monaco, Principality of Monaco
- Centre Scientifique de Monaco, 8 Quai Antoine 1er, Monaco, MC 98000, Principality of Monaco
| | - Ophélie Gervais
- Unité de Recherche sur la Biologie des Coraux Précieux CSM - CHANEL, Centre Scientifique de Monaco, 8 Quai Antoine 1er, Monaco, MC-98000 Monaco, Principality of Monaco
- Centre Scientifique de Monaco, 8 Quai Antoine 1er, Monaco, MC 98000, Principality of Monaco
| | - Tristan Estaque
- Septentrion Environnement, Campus Nature Provence, Marseille, 13008, France
| | - Quentin Schull
- MARBEC, Univ. Montpellier, CNRS, IFREMER, IRD, Sète, France
| | - Stéphanie Reynaud
- Centre Scientifique de Monaco, 8 Quai Antoine 1er, Monaco, MC 98000, Principality of Monaco
| | - Eric Béraud
- Centre Scientifique de Monaco, 8 Quai Antoine 1er, Monaco, MC 98000, Principality of Monaco
| | | | | | - Maria-Isabelle Marcus
- Centre Scientifique de Monaco, 8 Quai Antoine 1er, Monaco, MC 98000, Principality of Monaco
| | - Justine Richaume
- Septentrion Environnement, Campus Nature Provence, Marseille, 13008, France
| | | | - Adrien Cheminée
- Septentrion Environnement, Campus Nature Provence, Marseille, 13008, France
| | - Denis Allemand
- Centre Scientifique de Monaco, 8 Quai Antoine 1er, Monaco, MC 98000, Principality of Monaco
| | - Christine Ferrier-Pagès
- Centre Scientifique de Monaco, 8 Quai Antoine 1er, Monaco, MC 98000, Principality of Monaco.
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15
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Chiou YJ, Chan YF, Yu SP, Lu CY, Hsiao SSY, Chiang PW, Hsu TC, Liu PY, Wada N, Lee Y, Jane WN, Lee DC, Huang YW, Tang SL. Similar but different: Characterization of dddD gene-mediated DMSP metabolism among coral-associated Endozoicomonas. SCIENCE ADVANCES 2023; 9:eadk1910. [PMID: 37992165 PMCID: PMC10664990 DOI: 10.1126/sciadv.adk1910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 10/20/2023] [Indexed: 11/24/2023]
Abstract
Endozoicomonas are often predominant bacteria and prominently important in coral health. Their role in dimethylsulfoniopropionate (DMSP) degradation has been a subject of discussion for over a decade. A previous study found that Endozoicomonas degraded DMSP through the dddD pathway. This process releases dimethyl sulfide, which is vital for corals coping with thermal stress. However, little is known about the related gene regulation and metabolic abilities of DMSP metabolism in Endozoicomonadaceae. In this study, we isolated a novel Endozoicomonas DMSP degrader and observed a distinct DMSP metabolic trend in two phylogenetically close dddD-harboring Endozoicomonas species, confirmed genetically by comparative transcriptomic profiling and visualization of the change of DMSP stable isotopes in bacterial cells using nanoscale secondary ion spectrometry. Furthermore, we found that DMSP cleavage enzymes are ubiquitous in coral Endozoicomonas with a preference for having DddD lyase. We speculate that harboring DMSP degrading genes enables Endozoicomonas to successfully colonize various coral species across the globe.
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Affiliation(s)
- Yu-Jing Chiou
- Institute of Oceanography, National Taiwan University, Taipei 106, Taiwan
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Ya-Fan Chan
- Department of Microbiology, Soochow University, Taipei 111, Taiwan
| | - Sheng-Ping Yu
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chih-Ying Lu
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei 115, Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 402, Taiwan
| | | | - Pei-Wen Chiang
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Ting-Chang Hsu
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Po-Yu Liu
- School of Medicine, College of Medicine, National Sun Yat-Sen University, Kaohsiung 804, Taiwan
| | - Naohisa Wada
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yu Lee
- Department of Chemistry, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Wann-Neng Jane
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115, Taiwan
| | - Der-Chuen Lee
- Institute of Astronomy and Astrophysics, Academia Sinica, Taipei 115, Taiwan
| | - Yu-Wen Huang
- Department of Chemistry, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Sen-Lin Tang
- Institute of Oceanography, National Taiwan University, Taipei 106, Taiwan
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
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16
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Hu Y, Zhang J, Wang Y, Hu S. Distinct mechanisms shape prokaryotic community assembly across different land-use intensification. WATER RESEARCH 2023; 245:120601. [PMID: 37708774 DOI: 10.1016/j.watres.2023.120601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/24/2023] [Accepted: 09/07/2023] [Indexed: 09/16/2023]
Abstract
Changes in land-use intensity can have a far-reaching impact on river water quality and prokaryotic community composition. While research has been conducted to investigate the assembly mechanism of prokaryotic communities, the contributions of neutral theory and niche theory to prokaryotic community assembly under different land-use intensities remain unknown. In this study, a total of 251 sampling sites were set up in the Yangtze River basin to explore the assembly mechanism under different land-use intensities. Briefly, a "source" landscape can generate pollution, whereas a "sink" landscape can prevent pollution. Firstly, our result showed that higher land-use intensity might disturb the balance between the "source" and "sink" landscape patterns, resulting in water quality deterioration. Then the prokaryotic community assembly was classified into five ecological processes, namely homogeneous selection, homogenizing dispersal, undominated processes, dispersal limitation, and variable selection. The higher land-use intensity was found to strengthen the homogeneous selection, leading to the homogenization of the community at the whole basin scale. Finally, our findings demonstrated that the Yangtze River Basin's prokaryotic community displayed a distance-decay pattern when land-use intensity was low, with a greater contribution from neutral theory to its assembly. On the other hand, with a higher land-use intensity, the degradation of the aquatic environment increased the impacts of environmental filtering on the prokaryotic community, and niche theory played a stronger role in its assembly. Our findings show how land-use intensity influence the formation of prokaryotic communities, which will be an invaluable guide for managing land use and understanding the prokaryotic community assembly mechanisms in the Yangtze River Basin.
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Affiliation(s)
- Yuxin Hu
- Yangtze River Basin Ecological Environment Monitoring and Scientific Research Center, Yangtze River Basin Ecological Environment Supervision and Administration Bureau, Ministry of Ecology and Environment, Wuhan 430010, Hubei, China.
| | - Jing Zhang
- Yangtze River Basin Ecological Environment Monitoring and Scientific Research Center, Yangtze River Basin Ecological Environment Supervision and Administration Bureau, Ministry of Ecology and Environment, Wuhan 430010, Hubei, China
| | - Yingcai Wang
- Yangtze River Basin Ecological Environment Monitoring and Scientific Research Center, Yangtze River Basin Ecological Environment Supervision and Administration Bureau, Ministry of Ecology and Environment, Wuhan 430010, Hubei, China.
| | - Sheng Hu
- Yangtze River Basin Ecological Environment Monitoring and Scientific Research Center, Yangtze River Basin Ecological Environment Supervision and Administration Bureau, Ministry of Ecology and Environment, Wuhan 430010, Hubei, China.
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17
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da Silva DMG, Pedrosa FR, Ângela Taipa M, Costa R, Keller-Costa T. Widespread occurrence of chitinase-encoding genes suggests the Endozoicomonadaceae family as a key player in chitin processing in the marine benthos. ISME COMMUNICATIONS 2023; 3:109. [PMID: 37838809 PMCID: PMC10576748 DOI: 10.1038/s43705-023-00316-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 09/24/2023] [Accepted: 10/05/2023] [Indexed: 10/16/2023]
Abstract
Chitin is the most abundant natural polymer in the oceans, where it is primarily recycled by chitin-degrading microorganisms. Endozoicomonadaceae (Oceanospirillales) bacteria are prominent symbionts of sessile marine animals, particularly corals, and presumably contribute to nutrient cycling in their hosts. To reveal the chitinolytic potential of this iconic, animal-dwelling bacterial family, we examined 42 publicly available genomes of cultured and uncultured Endozoicomonadaceae strains for the presence of chitinase-encoding genes. Thirty-two of 42 Endozoicomonadaceae genomes harbored endo-chitinase- (EC 3.2.1.14), 25 had exo-chitinase- (EC 3.2.1.52) and 23 polysaccharide deacetylase-encoding genes. Chitinases were present in cultured and uncultured Endozoicomonadaceae lineages associated with diverse marine animals, including the three formally described genera Endozoicomonas, Paraendozoicomonas and Kistimonas, the new genus Candidatus Gorgonimonas, and other, yet unclassified, groups of the family. Most endo-chitinases belonged to the glycoside hydrolase family GH18 but five GH19 endo-chitinases were also present. Many endo-chitinases harbored an active site and a signal peptide domain, indicating the enzymes are likely functional and exported to the extracellular environment where endo-chitinases usually act. Phylogenetic analysis revealed clade-specific diversification of endo-chitinases across the family. The presence of multiple, distinct endo-chitinases on the genomes of several Endozoicomonadaceae species hints at functional variation to secure effective chitin processing in diverse micro-niches and changing environmental conditions. We demonstrate that endo-chitinases and other genes involved in chitin degradation are widespread in the Endozoicomonadaceae family and posit that these symbionts play important roles in chitin turnover in filter- and suspension-feeding animals and in benthic, marine ecosystems at large.
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Affiliation(s)
- Daniela M G da Silva
- Department of Bioengineering, Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais, 1049-001, Lisbon, Portugal
- iBB-Institute for Bioengineering and Biosciences and i4HB-Institute for Health and Bioeconomy, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001, Lisbon, Portugal
| | - Filipa R Pedrosa
- Department of Bioengineering, Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais, 1049-001, Lisbon, Portugal
| | - M Ângela Taipa
- Department of Bioengineering, Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais, 1049-001, Lisbon, Portugal
- iBB-Institute for Bioengineering and Biosciences and i4HB-Institute for Health and Bioeconomy, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001, Lisbon, Portugal
| | - Rodrigo Costa
- Department of Bioengineering, Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais, 1049-001, Lisbon, Portugal
- iBB-Institute for Bioengineering and Biosciences and i4HB-Institute for Health and Bioeconomy, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001, Lisbon, Portugal
| | - Tina Keller-Costa
- Department of Bioengineering, Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais, 1049-001, Lisbon, Portugal.
- iBB-Institute for Bioengineering and Biosciences and i4HB-Institute for Health and Bioeconomy, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001, Lisbon, Portugal.
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18
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Wang M, Cernava T. Soterobionts: disease-preventing microorganisms and proposed strategies to facilitate their discovery. Curr Opin Microbiol 2023; 75:102349. [PMID: 37369150 DOI: 10.1016/j.mib.2023.102349] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/25/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023]
Abstract
Crop production and the food security that it provides are currently threatened worldwide by plant pathogens. Conventional control measures, such as breeding for resistant plants, are progressively losing their efficacy due to rapidly evolving pathogens. The plant microbiota contributes to essential functions of host plants, among which is protection against pathogens. Only recently, microorganisms that provide holistic protection against certain plant diseases were identified. They were termed as 'soterobionts' and extend their host's immune system, which results in disease-resistant phenotypes. Further exploration of such microorganisms could not only provide answers to better understand the implications of the plant microbiota in health and disease, but also contribute to new developments in agriculture and beyond. The aim of this work is to point out how the identification of plant-associated soterobionts can be facilitated, and to discuss technologies that will be required to enable this.
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Affiliation(s)
- Mengcen Wang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou 310058, China; Global Education Program for AgriScience Frontiers, Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Tomislav Cernava
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom.
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19
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Tignat-Perrier R, van de Water JAJM, Allemand D, Ferrier-Pagès C. Holobiont responses of mesophotic precious red coral Corallium rubrum to thermal anomalies. ENVIRONMENTAL MICROBIOME 2023; 18:70. [PMID: 37580830 PMCID: PMC10424431 DOI: 10.1186/s40793-023-00525-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 07/31/2023] [Indexed: 08/16/2023]
Abstract
Marine heat waves (MHWs) have increased in frequency and intensity worldwide, causing mass mortality of benthic organisms and loss of biodiversity in shallow waters. The Mediterranean Sea is no exception, with shallow populations of habitat-forming octocorals facing the threat of local extinction. The mesophotic zone, which is less affected by MHWs, may be of ecological importance in conservation strategies for these species. However, our understanding of the response of mesophotic octocoral holobionts to changes in seawater temperature remains limited. To address this knowledge gap, we conducted a study on an iconic Mediterranean octocoral, the red coral Corallium rubrum sampled at 60 m depth and 15 °C. We exposed the colonies to temperatures they occasionally experience (18 °C) and temperatures that could occur at the end of the century if global warming continues (21 °C). We also tested their response to extremely cold and warm temperatures (12 °C and 24 °C). Our results show a high tolerance of C. rubrum to a two-month long exposure to temperatures ranging from 12 to 21 °C as no colony showed signs of tissue loss, reduced feeding ability, stress-induced gene expression, or disruption of host-bacterial symbioses. At 24 °C, however, we measured a sharp decrease in the relative abundance of Spirochaetaceae, which are the predominant bacterial symbionts under healthy conditions, along with a relative increase in Vibrionaceae. Tissue loss and overexpression of the tumor necrosis factor receptor 1 gene were also observed after two weeks of exposure. In light of ongoing global warming, our study helps predict the consequences of MHWs on mesophotic coralligenous reefs and the biodiversity that depends on them.
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Affiliation(s)
- Romie Tignat-Perrier
- Unité de Recherche sur la Biologie des Coraux Précieux CSM-CHANEL, Centre Scientifique de Monaco, 8 Quai Antoine 1er, 98000, Monaco, Principality of Monaco.
- Coral Ecophysiology Laboratory, Centre Scientifique de Monaco, 8 Quai Antoine 1er, 98000, Monaco, Principality of Monaco.
| | - Jeroen A J M van de Water
- Unité de Recherche sur la Biologie des Coraux Précieux CSM-CHANEL, Centre Scientifique de Monaco, 8 Quai Antoine 1er, 98000, Monaco, Principality of Monaco
- Coral Ecophysiology Laboratory, Centre Scientifique de Monaco, 8 Quai Antoine 1er, 98000, Monaco, Principality of Monaco
- Department of Estuarine and Delta Systems, Royal Netherlands Institute for Sea Research, Korringaweg 7, 4401 NT, Yerseke, The Netherlands
| | - Denis Allemand
- Centre Scientifique de Monaco, 8 Quai Antoine 1er, 98000, Monaco, Principality of Monaco
| | - Christine Ferrier-Pagès
- Coral Ecophysiology Laboratory, Centre Scientifique de Monaco, 8 Quai Antoine 1er, 98000, Monaco, Principality of Monaco
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McCauley M, Goulet TL, Jackson CR, Loesgen S. Systematic review of cnidarian microbiomes reveals insights into the structure, specificity, and fidelity of marine associations. Nat Commun 2023; 14:4899. [PMID: 37580316 PMCID: PMC10425419 DOI: 10.1038/s41467-023-39876-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 06/30/2023] [Indexed: 08/16/2023] Open
Abstract
Microorganisms play essential roles in the health and resilience of cnidarians. Understanding the factors influencing cnidarian microbiomes requires cross study comparisons, yet the plethora of protocols used hampers dataset integration. We unify 16S rRNA gene sequences from cnidarian microbiome studies under a single analysis pipeline. We reprocess 12,010 cnidarian microbiome samples from 186 studies, alongside 3,388 poriferan, 370 seawater samples, and 245 cultured Symbiodiniaceae, unifying ~6.5 billion sequence reads. Samples are partitioned by hypervariable region and sequencing platform to reduce sequencing variability. This systematic review uncovers an incredible diversity of 86 archaeal and bacterial phyla associated with Cnidaria, and highlights key bacteria hosted across host sub-phylum, depth, and microhabitat. Shallow (< 30 m) water Alcyonacea and Actinaria are characterized by highly shared and relatively abundant microbial communities, unlike Scleractinia and most deeper cnidarians. Utilizing the V4 region, we find that cnidarian microbial composition, richness, diversity, and structure are primarily influenced by host phylogeny, sampling depth, and ocean body, followed by microhabitat and sampling date. We identify host and geographical generalist and specific Endozoicomonas clades within Cnidaria and Porifera. This systematic review forms a framework for understanding factors governing cnidarian microbiomes and creates a baseline for assessing stress associated dysbiosis.
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Affiliation(s)
- M McCauley
- Department of Chemistry, Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA.
- Department of Biology, University of Mississippi, University, MS, USA.
- U.S. Geological Survey, Wetland and Aquatic Research Centre, Gainesville, FL, USA.
| | - T L Goulet
- Department of Biology, University of Mississippi, University, MS, USA
| | - C R Jackson
- Department of Biology, University of Mississippi, University, MS, USA
| | - S Loesgen
- Department of Chemistry, Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA
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21
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Wuerz M, Lawson CA, Oakley CA, Possell M, Wilkinson SP, Grossman AR, Weis VM, Suggett DJ, Davy SK. Symbiont Identity Impacts the Microbiome and Volatilome of a Model Cnidarian-Dinoflagellate Symbiosis. BIOLOGY 2023; 12:1014. [PMID: 37508443 PMCID: PMC10376011 DOI: 10.3390/biology12071014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 06/28/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023]
Abstract
The symbiosis between cnidarians and dinoflagellates underpins the success of reef-building corals in otherwise nutrient-poor habitats. Alterations to symbiotic state can perturb metabolic homeostasis and thus alter the release of biogenic volatile organic compounds (BVOCs). While BVOCs can play important roles in metabolic regulation and signalling, how the symbiotic state affects BVOC output remains unexplored. We therefore characterised the suite of BVOCs that comprise the volatilome of the sea anemone Exaiptasia diaphana ('Aiptasia') when aposymbiotic and in symbiosis with either its native dinoflagellate symbiont Breviolum minutum or the non-native symbiont Durusdinium trenchii. In parallel, the bacterial community structure in these different symbiotic states was fully characterised to resolve the holobiont microbiome. Based on rRNA analyses, 147 unique amplicon sequence variants (ASVs) were observed across symbiotic states. Furthermore, the microbiomes were distinct across the different symbiotic states: bacteria in the family Vibrionaceae were the most abundant in aposymbiotic anemones; those in the family Crocinitomicaceae were the most abundant in anemones symbiotic with D. trenchii; and anemones symbiotic with B. minutum had the highest proportion of low-abundance ASVs. Across these different holobionts, 142 BVOCs were detected and classified into 17 groups based on their chemical structure, with BVOCs containing multiple functional groups being the most abundant. Isoprene was detected in higher abundance when anemones hosted their native symbiont, and dimethyl sulphide was detected in higher abundance in the volatilome of both Aiptasia-Symbiodiniaceae combinations relative to aposymbiotic anemones. The volatilomes of aposymbiotic anemones and anemones symbiotic with B. minutum were distinct, while the volatilome of anemones symbiotic with D. trenchii overlapped both of the others. Collectively, our results are consistent with previous reports that D. trenchii produces a metabolically sub-optimal symbiosis with Aiptasia, and add to our understanding of how symbiotic cnidarians, including corals, may respond to climate change should they acquire novel dinoflagellate partners.
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Affiliation(s)
- Maggie Wuerz
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Caitlin A Lawson
- Climate Change Cluster, University of Technology Sydney, Sydney Broadway, Sydney, NSW 2007, Australia
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Clinton A Oakley
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Malcolm Possell
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | | | - Arthur R Grossman
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA 94305, USA
| | - Virginia M Weis
- Department of Integrative Biology, Oregon State University, Corvallis, OR 97331, USA
| | - David J Suggett
- Climate Change Cluster, University of Technology Sydney, Sydney Broadway, Sydney, NSW 2007, Australia
- KAUST Reefscape Restoration Initiative (KRRI) and Red Sea Research Center (RSRC), King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Simon K Davy
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
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22
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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: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [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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23
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Maire J, Tandon K, Collingro A, van de Meene A, Damjanovic K, Gotze CR, Stephenson S, Philip GK, Horn M, Cantin NE, Blackall LL, van Oppen MJH. Colocalization and potential interactions of Endozoicomonas and chlamydiae in microbial aggregates of the coral Pocillopora acuta. SCIENCE ADVANCES 2023; 9:eadg0773. [PMID: 37196086 DOI: 10.1126/sciadv.adg0773] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 04/13/2023] [Indexed: 05/19/2023]
Abstract
Corals are associated with a variety of bacteria, which occur in the surface mucus layer, gastrovascular cavity, skeleton, and tissues. Some tissue-associated bacteria form clusters, termed cell-associated microbial aggregates (CAMAs), which are poorly studied. Here, we provide a comprehensive characterization of CAMAs in the coral Pocillopora acuta. Combining imaging techniques, laser capture microdissection, and amplicon and metagenome sequencing, we show that (i) CAMAs are located in the tentacle tips and may be intracellular; (ii) CAMAs contain Endozoicomonas (Gammaproteobacteria) and Simkania (Chlamydiota) bacteria; (iii) Endozoicomonas may provide vitamins to its host and use secretion systems and/or pili for colonization and aggregation; (iv) Endozoicomonas and Simkania occur in distinct, but adjacent, CAMAs; and (v) Simkania may receive acetate and heme from neighboring Endozoicomonas. Our study provides detailed insight into coral endosymbionts, thereby improving our understanding of coral physiology and health and providing important knowledge for coral reef conservation in the climate change era.
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Affiliation(s)
- Justin Maire
- School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Kshitij Tandon
- School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Astrid Collingro
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna 1030, Austria
| | - Allison van de Meene
- School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Katarina Damjanovic
- Australian Institute of Marine Science, PMB No 3, Townsville, QLD 4810, Australia
| | - Cecilie Ravn Gotze
- School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia
- Australian Institute of Marine Science, PMB No 3, Townsville, QLD 4810, Australia
| | - Sophie Stephenson
- Australian Institute of Marine Science, PMB No 3, Townsville, QLD 4810, Australia
| | - Gayle K Philip
- Melbourne Bioinformatics, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Matthias Horn
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna 1030, Austria
| | - Neal E Cantin
- Australian Institute of Marine Science, PMB No 3, Townsville, QLD 4810, Australia
| | - Linda L Blackall
- School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Madeleine J H van Oppen
- School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia
- Australian Institute of Marine Science, PMB No 3, Townsville, QLD 4810, Australia
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24
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Genome Sequence of the Endosymbiont Endozoicomonas sp. Strain GU-1 ( Gammaproteobacteria), Isolated from the Staghorn Coral Acropora pulchra (Cnidaria: Scleractinia). Microbiol Resour Announc 2023; 12:e0135522. [PMID: 36809083 PMCID: PMC10019302 DOI: 10.1128/mra.01355-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023] Open
Abstract
Endozoicomonas sp. strain GU-1 was isolated from two separate staghorn coral (Acropora pulchra) colonies collected in Guam, Micronesia. Both isolates were grown in marine broth prior to DNA extraction and Oxford Nanopore Technologies (ONT) sequencing. Genomes were approximately 6.1 Mbp in size, containing highly similar gene content and matching sets of rRNA sequences.
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25
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Mohamed AR, Ochsenkühn MA, Kazlak AM, Moustafa A, Amin SA. The coral microbiome: towards an understanding of the molecular mechanisms of coral-microbiota interactions. FEMS Microbiol Rev 2023; 47:fuad005. [PMID: 36882224 PMCID: PMC10045912 DOI: 10.1093/femsre/fuad005] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 02/10/2023] [Accepted: 02/15/2023] [Indexed: 03/09/2023] Open
Abstract
Corals live in a complex, multipartite symbiosis with diverse microbes across kingdoms, some of which are implicated in vital functions, such as those related to resilience against climate change. However, knowledge gaps and technical challenges limit our understanding of the nature and functional significance of complex symbiotic relationships within corals. Here, we provide an overview of the complexity of the coral microbiome focusing on taxonomic diversity and functions of well-studied and cryptic microbes. Mining the coral literature indicate that while corals collectively harbour a third of all marine bacterial phyla, known bacterial symbionts and antagonists of corals represent a minute fraction of this diversity and that these taxa cluster into select genera, suggesting selective evolutionary mechanisms enabled these bacteria to gain a niche within the holobiont. Recent advances in coral microbiome research aimed at leveraging microbiome manipulation to increase coral's fitness to help mitigate heat stress-related mortality are discussed. Then, insights into the potential mechanisms through which microbiota can communicate with and modify host responses are examined by describing known recognition patterns, potential microbially derived coral epigenome effector proteins and coral gene regulation. Finally, the power of omics tools used to study corals are highlighted with emphasis on an integrated host-microbiota multiomics framework to understand the underlying mechanisms during symbiosis and climate change-driven dysbiosis.
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Affiliation(s)
- Amin R Mohamed
- Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
| | - Michael A Ochsenkühn
- Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
| | - Ahmed M Kazlak
- Systems Genomics Laboratory, American University in Cairo, New Cairo 11835, Egypt
- Biotechnology Graduate Program, American University in Cairo, New Cairo 11835, Egypt
| | - Ahmed Moustafa
- Systems Genomics Laboratory, American University in Cairo, New Cairo 11835, Egypt
- Biotechnology Graduate Program, American University in Cairo, New Cairo 11835, Egypt
- Department of Biology, American University in Cairo, New Cairo 11835, Egypt
| | - Shady A Amin
- Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
- Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
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26
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Tandon K, Ricci F, Costa J, Medina M, Kühl M, Blackall LL, Verbruggen H. Genomic view of the diversity and functional role of archaea and bacteria in the skeleton of the reef-building corals Porites lutea and Isopora palifera. Gigascience 2022; 12:giac127. [PMID: 36683362 PMCID: PMC9868349 DOI: 10.1093/gigascience/giac127] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/17/2022] [Accepted: 12/22/2022] [Indexed: 01/24/2023] Open
Abstract
At present, our knowledge on the compartmentalization of coral holobiont microbiomes is highly skewed toward the millimeter-thin coral tissue, leaving the diverse coral skeleton microbiome underexplored. Here, we present a genome-centric view of the skeleton of the reef-building corals Porites lutea and Isopora palifera, through a compendium of ∼400 high-quality bacterial and archaeal metagenome-assembled genomes (MAGs), spanning 34 phyla and 57 classes. Skeletal microbiomes harbored a diverse array of stress response genes, including dimethylsulfoniopropionate synthesis (dsyB) and metabolism (DMSP lyase). Furthermore, skeletal MAGs encoded an average of 22 ± 15 genes in P. lutea and 28 ± 23 in I. palifera with eukaryotic-like motifs thought to be involved in maintaining host association. We provide comprehensive insights into the putative functional role of the skeletal microbiome on key metabolic processes such as nitrogen fixation, dissimilatory and assimilatory nitrate, and sulfate reduction. Our study provides critical genomic resources for a better understanding of the coral skeletal microbiome and its role in holobiont functioning.
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Affiliation(s)
- Kshitij Tandon
- School of BioSciences, University of Melbourne, Parkville 3010, Australia
| | - Francesco Ricci
- School of BioSciences, University of Melbourne, Parkville 3010, Australia
- Biological, Earth and Environmental Sciences, The University of New South Wales, Kensington, NSW 2052, Australia
| | - Joana Costa
- School of BioSciences, University of Melbourne, Parkville 3010, Australia
| | - Mónica Medina
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Michael Kühl
- Marine Biological Section, Department of Biology, University of Copenhagen, DK-3000 Helsingør, Denmark
| | - Linda L Blackall
- School of BioSciences, University of Melbourne, Parkville 3010, Australia
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Parkville 3010, Australia
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27
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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: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [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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28
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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 COMMUNICATIONS 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] [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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Ide K, Nakano Y, Ito M, Nishikawa Y, Fujimura H, Takeyama H. The Effect of Co-Culture of Two Coral Species on Their Bacterial Composition Under Captive Environments. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:871-881. [PMID: 35997836 DOI: 10.1007/s10126-022-10149-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Coral symbionts are important members of the coral holobiont, and coral bacterial flora are essential in host health maintenance and coral conservation. Coral symbionts are affected by various environmental factors, such as seawater temperature, pH, and salinity. Although physicochemical and chemical factors have been highlighted as possible causes of these effects, the effects of water flow and the co-culture of different species corals have not been elucidated. In this study, we designed an artificial rearing environment to examine the impact of environmental and biological factors on Acropora tenuis, one of the major coral species in Okinawa, and Montipora digitata, during their co-culture. We intervened with the water flow to reveal that the movement of the rearing environment alters the bacterial flora of A. tenuis. During the rearing under captive environment, the alpha diversity of the coral microbiota increased, suggesting the establishment of rare bacteria from the ocean. No differences in the bacterial composition between the control and water flow groups were observed under the rearing conditions. However, the structure of the bacterial flora was significantly different in the co-culture group. Comparison of bacterial community succession strongly suggested that the differences observed were due to the suppressed transmission of bacteria from the ocean in the co-culture group. These results enhance our understanding of interactions between corals and shed light on the importance of regional differences and bacterial composition of coral flora.
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Affiliation(s)
- Keigo Ide
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Yoshikatsu Nakano
- Tropical Biosphere Research Center, University of the Ryukyus, Tokyo, Japan
- Marine Science Section, Research Support Division, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Michihiro Ito
- Tropical Biosphere Research Center, University of the Ryukyus, Tokyo, Japan
| | - Yohei Nishikawa
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
- Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan
| | - Hiroyuki Fujimura
- Department of Chemistry, Biology and Marine Science, University of the Ryukyus, Okinawa, Japan
| | - Haruko Takeyama
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan.
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, Tokyo, Japan.
- Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan.
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Tokyo, Japan.
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30
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Keller-Costa T, Kozma L, Silva SG, Toscan R, Gonçalves J, Lago-Lestón A, Kyrpides NC, Nunes da Rocha U, Costa R. Metagenomics-resolved genomics provides novel insights into chitin turnover, metabolic specialization, and niche partitioning in the octocoral microbiome. MICROBIOME 2022; 10:151. [PMID: 36138466 PMCID: PMC9502895 DOI: 10.1186/s40168-022-01343-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 08/03/2022] [Indexed: 05/31/2023]
Abstract
BACKGROUND The role of bacterial symbionts that populate octocorals (Cnidaria, Octocorallia) is still poorly understood. To shed light on their metabolic capacities, we examined 66 high-quality metagenome-assembled genomes (MAGs) spanning 30 prokaryotic species, retrieved from microbial metagenomes of three octocoral species and seawater. RESULTS Symbionts of healthy octocorals were affiliated with the taxa Endozoicomonadaceae, Candidatus Thioglobaceae, Metamycoplasmataceae, unclassified Pseudomonadales, Rhodobacteraceae, unclassified Alphaproteobacteria and Ca. Rhabdochlamydiaceae. Phylogenomics inference revealed that the Endozoicomonadaceae symbionts uncovered here represent two species of a novel genus unique to temperate octocorals, here denoted Ca. Gorgonimonas eunicellae and Ca. Gorgonimonas leptogorgiae. Their genomes revealed metabolic capacities to thrive under suboxic conditions and high gene copy numbers of serine-threonine protein kinases, type 3-secretion system, type-4 pili, and ankyrin-repeat proteins, suggesting excellent capabilities to colonize, aggregate, and persist inside their host. Contrarily, MAGs obtained from seawater frequently lacked symbiosis-related genes. All Endozoicomonadaceae symbionts harbored endo-chitinase and chitin-binging protein-encoding genes, indicating that they can hydrolyze the most abundant polysaccharide in the oceans. Other symbionts, including Metamycoplasmataceae and Ca. Thioglobaceae, may assimilate the smaller chitin oligosaccharides resulting from chitin breakdown and engage in chitin deacetylation, respectively, suggesting possibilities for substrate cross-feeding and a role for the coral microbiome in overall chitin turnover. We also observed sharp differences in secondary metabolite production potential between symbiotic lineages. Specific Proteobacteria taxa may specialize in chemical defense and guard other symbionts, including Endozoicomonadaceae, which lack such capacity. CONCLUSION This is the first study to recover MAGs from dominant symbionts of octocorals, including those of so-far unculturable Endozoicomonadaceae, Ca. Thioglobaceae and Metamycoplasmataceae symbionts. We identify a thus-far unanticipated, global role for Endozoicomonadaceae symbionts of corals in the processing of chitin, the most abundant natural polysaccharide in the oceans and major component of the natural zoo- and phytoplankton feed of octocorals. We conclude that niche partitioning, metabolic specialization, and adaptation to low oxygen conditions among prokaryotic symbionts likely contribute to the plasticity and adaptability of the octocoral holobiont in changing marine environments. These findings bear implications not only for our understanding of symbiotic relationships in the marine realm but also for the functioning of benthic ecosystems at large. Video Abstract.
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Affiliation(s)
- Tina Keller-Costa
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
| | - Lydia Kozma
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
- École Polytechnique Fédérale de Lausanne, Écublens, Switzerland
| | - Sandra G. Silva
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
| | - Rodolfo Toscan
- Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Jorge Gonçalves
- Centro de Ciências Do Mar, Universidade Do Algarve, Faro, Portugal
| | - Asunción Lago-Lestón
- Centro de Investigación Científica Y de Educación Superior de Ensenada, Ensenada, Mexico
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | | | - Rodrigo Costa
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
- Centro de Ciências Do Mar, Universidade Do Algarve, Faro, Portugal
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Abstract
The vast majority of environmental microbes have not yet been cultured, and most of the knowledge on coral-associated microbes (CAMs) has been generated from amplicon sequencing and metagenomes. However, exploring cultured CAMs is key for a detailed and comprehensive characterization of the roles of these microbes in shaping coral health and, ultimately, for their biotechnological use as, for example, coral probiotics and other natural products. Here, the strategies and technologies that have been used to access cultured CAMs are presented, while advantages and disadvantages associated with each of these strategies are discussed. We highlight the existing gaps and potential improvements in culture-dependent methodologies, indicating several possible alternatives (including culturomics and in situ diffusion devices) that could be applied to retrieve the CAM "dark matter" (i.e., the currently undescribed CAMs). This study provides the most comprehensive synthesis of the methodologies used to recover the cultured coral microbiome to date and draws suggestions for the development of the next generation of CAM culturomics.
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