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Chen J, Yu X, Yu K, Chen B, Qin Z, Liao Z, Ma Y, Xu L, Wang Y. Potential adaptation of scleractinian coral Pocillopora damicornis during hypo-salinity stress caused by extreme pre-flood rainfall over south China. ENVIRONMENTAL RESEARCH 2024; 262:119848. [PMID: 39216737 DOI: 10.1016/j.envres.2024.119848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 08/23/2024] [Accepted: 08/25/2024] [Indexed: 09/04/2024]
Abstract
Global warming intensifies the water cycle, resulting in significant increases in precipitation and river runoff, which brings severe hypo-salinity stress to nearshore coral reefs. Ecological investigations have found that some corals exhibit remarkable adaptability to hypo-salinity stress during mass-bleaching events. However, the exact cause of this phenomenon remains unclear. To elucidate the potential molecular mechanism leading to high tolerance to hypo-salinity stress, Pocillopora damicornis was used as a research object in this study. We compared the differences in transcriptional responses and symbiotic microbiomes between bleaching and unbleaching P. damicornis during hypo-salinity stress caused by extreme pre-flood rainfall over South China in 2022. The results showed that: (1) Under hypo-salinity stress, the coral genes related to immune defense and cellular stress were significantly upregulated in bleaching corals, indicating more severe immune damage and stress, and the Symbiodiniaceae had no significant gene enrichment. Conversely, metabolic genes related to glycolysis/gluconeogenesis were significantly downregulated in unbleaching corals, whereas Symbiodiniaceae genes related to oxidative phosphorylation were significantly upregulated to meet the energy requirements of coral holobiont; (2) C1d was the dominant Symbiodiniaceae subclade in all samples, with no significant difference between the two groups; (3) The symbiotic bacterial community structure was reorganized under hypo-salinity stress. The abundance of opportunistic bacteria increased significantly in bleaching coral, whereas the relative abundance of probiotics was higher in unbleaching coral. This may be due to severe immune damage, making the coral more susceptible to opportunistic infection and bleaching. These results suggest that long-term hypo-salinity acclimation in the Pearl River Estuary enhances the tolerance of some corals to hypo-salinity stress. Corals with higher tolerance may reduce energy consumption by slowing down their metabolism, improve the energy metabolism of Symbiodiniaceae to meet the energy requirements of the coral holobiont, and alter the structure of symbiotic bacterial communities to avoid bleaching.
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Affiliation(s)
- Junling Chen
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Xiaopeng Yu
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Kefu Yu
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China.
| | - Biao Chen
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Zhenjun Qin
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Zhiheng Liao
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China; Nanning Normal University, Nanning, China
| | - Yuling Ma
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Lijia Xu
- South China Institute of Environmental Sciences, Ministry of Ecology and Environment, Guangzhou, China.
| | - Yongzhi Wang
- South China Institute of Environmental Sciences, Ministry of Ecology and Environment, Guangzhou, China
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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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3
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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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Stephens D, Faghihi Z, Moniruzzaman M. Widespread occurrence and diverse origins of polintoviruses influence lineage-specific genome dynamics in stony corals. Virus Evol 2024; 10:veae039. [PMID: 38808038 PMCID: PMC11131425 DOI: 10.1093/ve/veae039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 04/29/2024] [Accepted: 05/12/2024] [Indexed: 05/30/2024] Open
Abstract
Stony corals (Order: Scleractinia) are central to vital marine habitats known as coral reefs. Numerous stressors in the Anthropocene are contributing to the ongoing decline in coral reef health and coverage. While viruses are established modulators of marine microbial dynamics, their interactions within the coral holobiont and impact on coral health and physiology remain unclear. To address this key knowledge gap, we investigated diverse stony coral genomes for 'endogenous' viruses. Our study uncovered a remarkable number of integrated viral elements recognized as 'Polintoviruses' (Class Polintoviricetes) in thirty Scleractinia genomes; with several species harboring hundreds to thousands of polintoviruses. We reveal massive paralogous expansion of polintoviruses in stony coral genomes, alongside the presence of integrated elements closely related to Polinton-like viruses (PLVs), a group of viruses that exist as free virions. These results suggest multiple integrations of polintoviruses and PLV-relatives, along with paralogous expansions, shaped stony coral genomes. Re-analysis of existing gene expression data reveals all polintovirus structural and non-structural hallmark genes are expressed, providing support for free virion production from polintoviruses. Our results, revealing a significant diversity of polintovirus across the Scleractinia order, open a new research avenue into polintovirus and their possible roles in disease, genomic plasticity, and environmental adaptation in this key group of organisms.
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Affiliation(s)
- Danae Stephens
- Department of Marine Biology and Ecology, The Rosenstiel School of Marine, Atmospheric and Earth Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149-1031, USA
| | - Zahra Faghihi
- Department of Marine Biology and Ecology, The Rosenstiel School of Marine, Atmospheric and Earth Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149-1031, USA
| | - Mohammad Moniruzzaman
- Department of Marine Biology and Ecology, The Rosenstiel School of Marine, Atmospheric and Earth Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149-1031, USA
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Tran C, Rosenfield GR, Cleves PA, Krediet CJ, Paul MR, Clowez S, Grossman AR, Pringle JR. Photosynthesis and other factors affecting the establishment and maintenance of cnidarian-dinoflagellate symbiosis. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230079. [PMID: 38497261 PMCID: PMC10945401 DOI: 10.1098/rstb.2023.0079] [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: 09/18/2023] [Accepted: 02/07/2024] [Indexed: 03/19/2024] Open
Abstract
Coral growth depends on the partnership between the animal hosts and their intracellular, photosynthetic dinoflagellate symbionts. In this study, we used the sea anemone Aiptasia, a laboratory model for coral biology, to investigate the poorly understood mechanisms that mediate symbiosis establishment and maintenance. We found that initial colonization of both adult polyps and larvae by a compatible algal strain was more effective when the algae were able to photosynthesize and that the long-term maintenance of the symbiosis also depended on photosynthesis. In the dark, algal cells were taken up into host gastrodermal cells and not rapidly expelled, but they seemed unable to reproduce and thus were gradually lost. When we used confocal microscopy to examine the interaction of larvae with two algal strains that cannot establish stable symbioses with Aiptasia, it appeared that both pre- and post-phagocytosis mechanisms were involved. With one strain, algae entered the gastric cavity but appeared to be completely excluded from the gastrodermal cells. With the other strain, small numbers of algae entered the gastrodermal cells but appeared unable to proliferate there and were slowly lost upon further incubation. We also asked if the exclusion of either incompatible strain could result simply from their cells' being too large for the host cells to accommodate. However, the size distributions of the compatible and incompatible strains overlapped extensively. Moreover, examination of macerates confirmed earlier reports that individual gastrodermal cells could expand to accommodate multiple algal cells. This article is part of the theme issue 'Sculpting the microbiome: how host factors determine and respond to microbial colonization'.
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Affiliation(s)
- Cawa Tran
- Department of Genetics, Stanford University School of Medicine, Stanford CA 94305, USA
- Department of Biology, University of San Diego, San Diego, CA 92110, USA
| | - Gabriel R. Rosenfield
- Department of Genetics, Stanford University School of Medicine, Stanford CA 94305, USA
| | - Phillip A. Cleves
- Department of Genetics, Stanford University School of Medicine, Stanford CA 94305, USA
| | - Cory J. Krediet
- Department of Genetics, Stanford University School of Medicine, Stanford CA 94305, USA
| | - Maitri R. Paul
- Department of Genetics, Stanford University School of Medicine, Stanford CA 94305, USA
| | - Sophie Clowez
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Arthur R. Grossman
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - John R. Pringle
- Department of Genetics, Stanford University School of Medicine, Stanford CA 94305, USA
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6
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Kim KH, Kim JM, Baek JH, Jeong SE, Kim H, Yoon HS, Jeon CO. Metabolic relationships between marine red algae and algae-associated bacteria. MARINE LIFE SCIENCE & TECHNOLOGY 2024; 6:298-314. [PMID: 38827136 PMCID: PMC11136935 DOI: 10.1007/s42995-024-00227-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 12/28/2023] [Indexed: 06/04/2024]
Abstract
Mutualistic interactions between marine phototrophs and associated bacteria are an important strategy for their successful survival in the ocean, but little is known about their metabolic relationships. Here, bacterial communities in the algal sphere (AS) and bulk solution (BS) of nine marine red algal cultures were analyzed, and Roseibium and Phycisphaera were identified significantly more abundantly in AS than in BS. The metabolic features of Roseibium RMAR6-6 (isolated and genome-sequenced), Phycisphaera MAG 12 (obtained by metagenomic sequencing), and a marine red alga, Porphyridium purpureum CCMP1328 (from GenBank), were analyzed bioinformatically. RMAR6-6 has the genetic capability to fix nitrogen and produce B vitamins (B1, B2, B5, B6, B9, and B12), bacterioferritin, dimethylsulfoniopropionate (DMSP), and phenylacetate that may enhance algal growth, whereas MAG 12 may have a limited metabolic capability, not producing vitamins B9 and B12, DMSP, phenylacetate, and siderophores, but with the ability to produce bacitracin, possibly modulating algal microbiome. P. purpureum CCMP1328 lacks the genetic capability to fix nitrogen and produce vitamin B12, DMSP, phenylacetate, and siderophore. It was shown that the nitrogen-fixing ability of RMAR6-6 promoted the growth of P. purpureum, and DMSP reduced the oxidative stress of P. purpureum. The metabolic interactions between strain RMAR6-6 and P. purpureum CCMP1328 were also investigated by the transcriptomic analyses of their monoculture and co-culture. Taken together, potential metabolic relationships between Roseibium and P. purpureum were proposed. This study provides a better understanding of the metabolic relationships between marine algae and algae-associated bacteria for successful growth. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-024-00227-z.
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Affiliation(s)
- Kyung Hyun Kim
- Department of Biological Sciences and Biotechnology, Hannam University, Daejon, 34054 Republic of Korea
| | - Jeong Min Kim
- Department of Life Science, Chung-Ang University, Seoul, 06974 Republic of Korea
| | - Ju Hye Baek
- Department of Life Science, Chung-Ang University, Seoul, 06974 Republic of Korea
| | - Sang Eun Jeong
- Department of Life Science, Chung-Ang University, Seoul, 06974 Republic of Korea
| | - Hocheol Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419 Republic of Korea
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419 Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul, 06974 Republic of Korea
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7
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Hill LJ, Messias CSMDA, Vilela CLS, Garritano AN, Villela HDM, do Carmo FL, Thomas T, Peixoto RS. Bacteria associated with the in hospite Symbiodiniaceae's phycosphere. iScience 2024; 27:109531. [PMID: 38585661 PMCID: PMC10995889 DOI: 10.1016/j.isci.2024.109531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 12/23/2023] [Accepted: 03/16/2024] [Indexed: 04/09/2024] Open
Abstract
Symbiotic interactions between Symbiodiniaceae and bacteria are still poorly explored, especially those in hospite. Here, we adapted a technique that allows for the enrichment of intact and metabolically active in hospite Symbiodiniaceae cells (ihSC) and their associated bacteria from the tissue of the model coral Pocillopora damicornis, using a discontinuous gradient of solution of isotonic Percoll (SIP). The ihSC were concentrated in the 50% SIP fraction, as determined by microscopy. The presence of bacteria associated with ihSC was confirmed by fluorescence in situ hybridization, while microbiome analysis indicated that bacteria of the families Halieaceae, Flavobacteriaceae, and Alcanivoraceae are significantly associated with ihSC. Extracellular vesicles that could be exuding molecules were detected on the symbiosome membranes. Our technique and data contribute to elucidate ihSC-bacteria interactions.
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Affiliation(s)
- Lilian Jorge Hill
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | | | - Caren Leite Spindola Vilela
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | - Alessandro N Garritano
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Helena Dias Muller Villela
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955, Kingdom of Saudi Arabia
| | - Flavia Lima do Carmo
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | - Torsten Thomas
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Raquel S. Peixoto
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955, Kingdom of Saudi Arabia
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8
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Xu M, Cai Z, Cheng K, Chen G, Zhou J. Mitigation of Vibrio coralliilyticus-induced coral bleaching through bacterial dysbiosis prevention by Ruegeria profundi. Appl Environ Microbiol 2024; 90:e0227423. [PMID: 38470181 PMCID: PMC11022554 DOI: 10.1128/aem.02274-23] [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: 12/18/2023] [Accepted: 02/08/2024] [Indexed: 03/13/2024] Open
Abstract
Vibrio species are prevalent in ocean ecosystems, particularly Vibrio coralliilyticus, and pose a threat to corals and other marine organisms under global warming conditions. While microbiota manipulation is considered for coral disease management, understanding the role of commensal bacteria in stress resilience remains limited. Here, a single bacterial species (Ruegeria profundi) rather than a consortium of native was used to combat pathogenic V. coralliilyticus and protect corals from bleaching. R. profundi showed therapeutic activity in vivo, preventing a significant reduction in bacterial diversity in bleached corals. Notably, the structure of the bacterial community differed significantly among all the groups. In addition, compared with the bleached corals caused by V. coralliilyticus, the network analysis revealed that complex interactions and positive correlations in the bacterial community of the R. profundi protected non-bleached corals, indicating R. profundi's role in fostering synergistic associations. Many genera of bacteria significantly increased in abundance during V. coralliilyticus infection, including Vibrio, Alteromonas, Amphritea, and Nautella, contributing to the pathogenicity of the bacterial community. However, R. profundi effectively countered the proliferation of these genera, promoting potential probiotic Endozoicomonas and other taxa, while reducing the abundance of betaine lipids and the type VI section system of the bacterial community. These changes ultimately influenced the interactive relationships among symbionts and demonstrated that probiotic R. profundi intervention can modulate coral-associated bacterial community, alleviate pathogenic-induced dysbiosis, and preserve coral health. These findings elucidated the relationship between the behavior of the coral-associated bacterial community and the occurrence of pathological coral bleaching.IMPORTANCEChanges in the global climate and marine environment can influence coral host and pathogen repartition which refers to an increased likelihood of pathogen infection in hosts. The risk of Vibrio coralliilyticus-induced coral disease is significantly heightened, primarily due to its thermos-dependent expression of virulent and populations. This study investigates how coral-associated bacterial communities respond to bleaching induced by V. coralliilyticus. Our findings demonstrate that Ruegeria profundi exhibits clear evidence of defense against pathogenic bacterial infection, contributing to the maintenance of host health and symbiont homeostasis. This observation suggests that bacterial pathogens could cause dysbiosis in coral holobionts. Probiotic bacteria display an essential capability in restructuring and manipulating coral-associated bacterial communities. This restructuring effectively reduces bacterial community virulence and enhances the pathogenic resistance of holobionts. The study provides valuable insights into the correlation between the health status of corals and how coral-associated bacterial communities may respond to both pathogens and probiotics.
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Affiliation(s)
- Meiting Xu
- School of Environment, Harbin Institute of Technology, Harbin, China
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai, China
| | - Zhonghua Cai
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Keke Cheng
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Guofu Chen
- School of Environment, Harbin Institute of Technology, Harbin, China
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai, China
| | - Jin Zhou
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
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9
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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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10
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Shoguchi E, Kawachi M, Shinzato C, Beedessee G. Functional analyses of bacterial genomes found in Symbiodiniaceae genome assemblies. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13238. [PMID: 38444256 PMCID: PMC10915500 DOI: 10.1111/1758-2229.13238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 01/25/2024] [Indexed: 03/07/2024]
Abstract
Bacterial-algal interactions strongly influence marine ecosystems. Bacterial communities in cultured dinoflagellates of the family Symbiodiniaceae have been characterized by metagenomics. However, little is known about whole-genome analysis of marine bacteria associated with these dinoflagellates. We performed in silico analysis of four bacterial genomes from cultures of four dinoflagellates of the genera Symbiodinium, Breviolum, Cladocopium and Durusdinium. Comparative analysis showed that the former three contain the alphaproteobacterial family Parvibaculaceae and that the Durusdinium culture includes the family Sphingomonadaceae. There were no large genomic reductions in the alphaproteobacteria with genome sizes of 2.9-3.9 Mb, implying they are not obligate intracellular bacteria. Genomic annotations of three Parvibaculaceae detected the gene for diacetylchitobiose deacetylase (Dac), which may be involved in the degradation of dinoflagellate cell surfaces. They also had metabolic genes for dissimilatory nitrate reduction to ammonium (DNRA) in the nitrogen (N) cycle and cobalamin (vitamin B12 ) biosynthetic genes in the salvage pathway. Those three characters were not found in the Sphingomonadaceae genome. Predicted biosynthetic gene clusters for secondary metabolites indicated that the Parvibaculaceae likely produce the same secondary metabolites. Our study suggests that the Parvibaculaceae is a major resident of Symbiodiniaceae cultures with antibiotics.
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Affiliation(s)
- Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate UniversityOnnaJapan
| | - Masanobu Kawachi
- Center for Environmental Biology and Ecosystem StudiesNational Institute for Environmental StudiesTsukubaJapan
| | - Chuya Shinzato
- Atmosphere and Ocean Research Institute, The University of TokyoKashiwaJapan
| | - Girish Beedessee
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate UniversityOnnaJapan
- Department of BiochemistryUniversity of CambridgeCambridgeUK
- Present address:
Faculty of Health & Life SciencesNorthumbria UniversityNewcastle upon TyneUK
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11
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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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12
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Dungan AM, Geissler L, Williams AS, Gotze CR, Flynn EC, Blackall LL, van Oppen MJH. DNA from non-viable bacteria biases diversity estimates in the corals Acropora loripes and Pocillopora acuta. ENVIRONMENTAL MICROBIOME 2023; 18:86. [PMID: 38062479 PMCID: PMC10704692 DOI: 10.1186/s40793-023-00541-6] [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: 07/24/2023] [Accepted: 11/23/2023] [Indexed: 06/30/2024]
Abstract
BACKGROUND Nucleic acid-based analytical methods have greatly expanded our understanding of global prokaryotic diversity, yet standard metabarcoding methods provide no information on the most fundamental physiological state of bacteria, viability. Scleractinian corals harbour a complex microbiome in which bacterial symbionts play critical roles in maintaining health and functioning of the holobiont. However, the coral holobiont contains both dead and living bacteria. The former can be the result of corals feeding on bacteria, rapid swings from hyper- to hypoxic conditions in the coral tissue, the presence of antimicrobial compounds in coral mucus, and an abundance of lytic bacteriophages. RESULTS By combining propidium monoazide (PMA) treatment with high-throughput sequencing on six coral species (Acropora loripes, A. millepora, A. kenti, Platygyra daedalea, Pocillopora acuta, and Porites lutea) we were able to obtain information on bacterial communities with little noise from non-viable microbial DNA. Metabarcoding of the 16S rRNA gene showed significantly higher community evenness (85%) and species diversity (31%) in untreated compared with PMA-treated tissue for A. loripes only. While PMA-treated coral did not differ significantly from untreated samples in terms of observed number of ASVs, > 30% of ASVs were identified in untreated samples only, suggesting that they originated from cell-free/non-viable DNA. Further, the bacterial community structure was significantly different between PMA-treated and untreated samples for A. loripes and P. acuta indicating that DNA from non-viable microbes can bias community composition data in coral species with low bacterial diversity. CONCLUSIONS Our study is highly relevant to microbiome studies on coral and other host organisms as it delivers a solution to excluding non-viable DNA in a complex community. These results provide novel insights into the dynamic nature of host-associated microbiomes and underline the importance of applying versatile tools in the analysis of metabarcoding or next-generation sequencing data sets.
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Affiliation(s)
- Ashley M Dungan
- School of BioSciences, University of Melbourne, Melbourne, VIC, Australia.
| | - Laura Geissler
- School of BioSciences, University of Melbourne, Melbourne, VIC, Australia
| | - Amanda S Williams
- School of BioSciences, University of Melbourne, Melbourne, VIC, Australia
| | - Cecilie Ravn Gotze
- School of BioSciences, University of Melbourne, Melbourne, VIC, Australia
- Australian Institute of Marine Science, Townsville, QLD, Australia
| | - Emily C Flynn
- School of BioSciences, University of Melbourne, Melbourne, VIC, Australia
| | - Linda L Blackall
- School of BioSciences, University of Melbourne, Melbourne, VIC, Australia
| | - Madeleine J H van Oppen
- School of BioSciences, University of Melbourne, Melbourne, VIC, Australia
- Australian Institute of Marine Science, Townsville, QLD, Australia
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13
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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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14
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Maire J, Deore P, Jameson VJ, Sakkas M, Perez-Gonzalez A, Blackall LL, van Oppen MJH. Assessing the contribution of bacteria to the heat tolerance of experimentally evolved coral photosymbionts. Environ Microbiol 2023; 25:3298-3318. [PMID: 37849020 DOI: 10.1111/1462-2920.16521] [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: 03/07/2023] [Accepted: 09/28/2023] [Indexed: 10/19/2023]
Abstract
Coral reefs are extremely vulnerable to ocean warming, which triggers coral bleaching-the loss of endosymbiotic microalgae (Symbiodiniaceae) from coral tissues, often leading to death. To enhance coral climate resilience, the symbiont, Cladocopium proliferum was experimentally evolved for >10 years under elevated temperatures resulting in increased heat tolerance. Bacterial 16S rRNA gene metabarcoding showed the composition of intra- and extracellular bacterial communities of heat-evolved strains was significantly different from that of wild-type strains, suggesting bacteria responded to elevated temperatures, and may even play a role in C. proliferum thermal tolerance. To assess whether microbiome transplantation could enhance heat tolerance of the sensitive wild-type C. proliferum, we transplanted bacterial communities from heat-evolved to the wild-type strain and subjected it to acute heat stress. Microbiome transplantation resulted in the incorporation of only 30 low-abundance strains into the microbiome of wild-type cultures, while the relative abundance of 14 pre-existing strains doubled in inoculated versus uninoculated samples. Inoculation with either wild-type or heat-evolved bacterial communities boosted C. proliferum growth, although no difference in heat tolerance was observed between the two inoculation treatments. This study provides evidence that Symbiodiniaceae-associated bacterial communities respond to heat selection and may contribute to coral adaptation to climate change.
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Affiliation(s)
- Justin Maire
- School of Biosciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Pranali Deore
- School of Biosciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Vanta J Jameson
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute of Infection and Immunity, Parkville, Victoria, Australia
- Melbourne Cytometry Platform, The University of Melbourne, Parkville, Victoria, Australia
| | - Magdaline Sakkas
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute of Infection and Immunity, Parkville, Victoria, Australia
- Melbourne Cytometry Platform, The University of Melbourne, Parkville, Victoria, Australia
| | - Alexis Perez-Gonzalez
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute of Infection and Immunity, Parkville, Victoria, Australia
- Melbourne Cytometry Platform, The University of Melbourne, 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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15
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Matthews JL, Hoch L, Raina JB, Pablo M, Hughes DJ, Camp EF, Seymour JR, Ralph PJ, Suggett DJ, Herdean A. Symbiodiniaceae photophysiology and stress resilience is enhanced by microbial associations. Sci Rep 2023; 13:20724. [PMID: 38007500 PMCID: PMC10676399 DOI: 10.1038/s41598-023-48020-9] [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: 06/01/2023] [Accepted: 11/21/2023] [Indexed: 11/27/2023] Open
Abstract
Symbiodiniaceae form associations with extra- and intracellular bacterial symbionts, both in culture and in symbiosis with corals. Bacterial associates can regulate Symbiodiniaceae fitness in terms of growth, calcification and photophysiology. However, the influence of these bacteria on interactive stressors, such as temperature and light, which are known to influence Symbiodiniaceae physiology, remains unclear. Here, we examined the photophysiological response of two Symbiodiniaceae species (Symbiodinium microadriaticum and Breviolum minutum) cultured under acute temperature and light stress with specific bacterial partners from their microbiome (Labrenzia (Roseibium) alexandrii, Marinobacter adhaerens or Muricauda aquimarina). Overall, bacterial presence positively impacted Symbiodiniaceae core photosynthetic health (photosystem II [PSII] quantum yield) and photoprotective capacity (non-photochemical quenching; NPQ) compared to cultures with all extracellular bacteria removed, although specific benefits were variable across Symbiodiniaceae genera and growth phase. Symbiodiniaceae co-cultured with M. aquimarina displayed an inverse NPQ response under high temperatures and light, and those with L. alexandrii demonstrated a lowered threshold for induction of NPQ, potentially through the provision of antioxidant compounds such as zeaxanthin (produced by Muricauda spp.) and dimethylsulfoniopropionate (DMSP; produced by this strain of L. alexandrii). Our co-culture approach empirically demonstrates the benefits bacteria can deliver to Symbiodiniaceae photochemical performance, providing evidence that bacterial associates can play important functional roles for Symbiodiniaceae.
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Affiliation(s)
- Jennifer L Matthews
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia.
| | - Lilian Hoch
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Jean-Baptiste Raina
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Marine Pablo
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
- Sorbonne University, Paris, France
| | - David J Hughes
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
- Australian Institute of Marine Sciences, Townsville, QLD, Australia
| | - Emma F Camp
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Justin R Seymour
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Peter J Ralph
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - David J Suggett
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
- KAUST Reefscape Restoration Initiative (KRRI) and Red Sea Reseach Centre (RSRC), King Abdullah University of Science & Technology, 23955, Thuwal, Saudi Arabia
| | - Andrei Herdean
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
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16
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Pfister CA, Cardini U, Mirasole A, Montilla LM, Veseli I, Gattuso JP, Teixido N. Microbial associates of an endemic Mediterranean seagrass enhance the access of the host and the surrounding seawater to inorganic nitrogen under ocean acidification. Sci Rep 2023; 13:19996. [PMID: 37968499 PMCID: PMC10651887 DOI: 10.1038/s41598-023-47126-4] [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: 04/29/2023] [Accepted: 11/09/2023] [Indexed: 11/17/2023] Open
Abstract
Seagrasses are important primary producers in oceans worldwide. They live in shallow coastal waters that are experiencing carbon dioxide enrichment and ocean acidification. Posidonia oceanica, an endemic seagrass species that dominates the Mediterranean Sea, achieves high abundances in seawater with relatively low concentrations of dissolved inorganic nitrogen. Here we tested whether microbial metabolisms associated with P. oceanica and surrounding seawater enhance seagrass access to nitrogen. Using stable isotope enrichments of intact seagrass with amino acids, we showed that ammonification by free-living and seagrass-associated microbes produce ammonium that is likely used by seagrass and surrounding particulate organic matter. Metagenomic analysis of the epiphytic biofilm on the blades and rhizomes support the ubiquity of microbial ammonification genes in this system. Further, we leveraged the presence of natural carbon dioxide vents and show that the presence of P. oceanica enhanced the uptake of nitrogen by water column particulate organic matter, increasing carbon fixation by a factor of 8.6-17.4 with the greatest effect at CO2 vent sites. However, microbial ammonification was reduced at lower pH, suggesting that future ocean climate change will compromise this microbial process. Thus, the seagrass holobiont enhances water column productivity, even in the context of ocean acidification.
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Affiliation(s)
- Catherine A Pfister
- The Department of Ecology and Evolution, The University of Chicago, Chicago, IL, USA.
| | - Ulisse Cardini
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn - National Institute of Marine Biology, Ecology and Biotechnology, Naples, Italy
| | - Alice Mirasole
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn - National Institute of Marine Biology, Ecology and Biotechnology, Naples, Italy
| | - Luis M Montilla
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn - National Institute of Marine Biology, Ecology and Biotechnology, Naples, Italy
| | - Iva Veseli
- Biophysical Sciences Program, The University of Chicago, Chicago, IL, USA
| | - Jean-Pierre Gattuso
- CNRS, Laboratoire d'Océanographie de Villefranche, Sorbonne Université, 181 Chemin du Lazaret, 06230, Villefranche-sur-Mer, France
- Institute for Sustainable Development and International Relations, Sciences Po, 27 Rue Saint Guillaume, 75007, Paris, France
| | - Nuria Teixido
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn - National Institute of Marine Biology, Ecology and Biotechnology, Naples, Italy
- CNRS, Laboratoire d'Océanographie de Villefranche, Sorbonne Université, 181 Chemin du Lazaret, 06230, Villefranche-sur-Mer, France
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17
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Matthews JL, Khalil A, Siboni N, Bougoure J, Guagliardo P, Kuzhiumparambil U, DeMaere M, Le Reun NM, Seymour JR, Suggett DJ, Raina JB. Coral endosymbiont growth is enhanced by metabolic interactions with bacteria. Nat Commun 2023; 14:6864. [PMID: 37891154 PMCID: PMC10611727 DOI: 10.1038/s41467-023-42663-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 10/18/2023] [Indexed: 10/29/2023] Open
Abstract
Bacteria are key contributors to microalgae resource acquisition, competitive performance, and functional diversity, but their potential metabolic interactions with coral microalgal endosymbionts (Symbiodiniaceae) have been largely overlooked. Here, we show that altering the bacterial composition of two widespread Symbiodiniaceae species, during their free-living stage, results in a significant shift in their cellular metabolism. Indeed, the abundance of monosaccharides and the key phytohormone indole-3-acetic acid (IAA) were correlated with the presence of specific bacteria, including members of the Labrenzia (Roseibium) and Marinobacter genera. Single-cell stable isotope tracking revealed that these two bacterial genera are involved in reciprocal exchanges of carbon and nitrogen with Symbiodiniaceae. We identified the provision of IAA by Labrenzia and Marinobacter, and this metabolite caused a significant growth enhancement of Symbiodiniaceae. By unravelling these interkingdom interactions, our work demonstrates how specific bacterial associates fundamentally govern Symbiodiniaceae fitness.
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Affiliation(s)
- Jennifer L Matthews
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, 2007, Australia.
| | - Abeeha Khalil
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Nachshon Siboni
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Jeremy Bougoure
- Centre for Microscopy, Characterisation and Analysis, University of Western Australia, Perth, WA, 6009, Australia
| | - Paul Guagliardo
- Centre for Microscopy, Characterisation and Analysis, University of Western Australia, Perth, WA, 6009, Australia
| | | | - Matthew DeMaere
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Nine M Le Reun
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Justin R Seymour
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - David J Suggett
- Climate Change Cluster, University of Technology Sydney, Ultimo, 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
| | - Jean-Baptiste Raina
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, 2007, Australia
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18
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Mannochio-Russo H, Swift SOI, Nakayama KK, Wall CB, Gentry EC, Panitchpakdi M, Caraballo-Rodriguez AM, Aron AT, Petras D, Dorrestein K, Dorrestein TK, Williams TM, Nalley EM, Altman-Kurosaki NT, Martinelli M, Kuwabara JY, Darcy JL, Bolzani VS, Wegley Kelly L, Mora C, Yew JY, Amend AS, McFall-Ngai M, Hynson NA, Dorrestein PC, Nelson CE. Microbiomes and metabolomes of dominant coral reef primary producers illustrate a potential role for immunolipids in marine symbioses. Commun Biol 2023; 6:896. [PMID: 37653089 PMCID: PMC10471604 DOI: 10.1038/s42003-023-05230-1] [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: 12/01/2022] [Accepted: 08/08/2023] [Indexed: 09/02/2023] Open
Abstract
The dominant benthic primary producers in coral reef ecosystems are complex holobionts with diverse microbiomes and metabolomes. In this study, we characterize the tissue metabolomes and microbiomes of corals, macroalgae, and crustose coralline algae via an intensive, replicated synoptic survey of a single coral reef system (Waimea Bay, O'ahu, Hawaii) and use these results to define associations between microbial taxa and metabolites specific to different hosts. Our results quantify and constrain the degree of host specificity of tissue metabolomes and microbiomes at both phylum and genus level. Both microbiome and metabolomes were distinct between calcifiers (corals and CCA) and erect macroalgae. Moreover, our multi-omics investigations highlight common lipid-based immune response pathways across host organisms. In addition, we observed strong covariation among several specific microbial taxa and metabolite classes, suggesting new metabolic roles of symbiosis to further explore.
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Affiliation(s)
- Helena Mannochio-Russo
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA.
- Department of Biochemistry and Organic Chemistry, Institute of Chemistry, São Paulo State University, Araraquara, SP, 14800-060, Brazil.
| | - Sean O I Swift
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, Department of Oceanography and Sea Grant College Program, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA.
| | - Kirsten K Nakayama
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Christopher B Wall
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
- Ecology Behavior and Evolution Section, Department of Biological Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Emily C Gentry
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Morgan Panitchpakdi
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Andrés M Caraballo-Rodriguez
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Allegra T Aron
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO, 80210, USA
| | - Daniel Petras
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
- Cluster of Excellence "Controlling Microbes to Fight Infections" (CMFI), University of Tuebingen, Tuebingen, Germany
| | - Kathleen Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | | | - Taylor M Williams
- Marine Option Program, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Eileen M Nalley
- Hawai'i Sea Grant College Program, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Noam T Altman-Kurosaki
- School of Biological Sciences, Georgia Institute of Technology, 311 Ferst Drive, Atlanta, GA, 30332, USA
| | | | - Jeff Y Kuwabara
- Marine Option Program, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - John L Darcy
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Vanderlan S Bolzani
- Department of Biochemistry and Organic Chemistry, Institute of Chemistry, São Paulo State University, Araraquara, SP, 14800-060, Brazil
| | - Linda Wegley Kelly
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, CA, USA
| | - Camilo Mora
- Geography, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Joanne Y Yew
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Anthony S Amend
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Margaret McFall-Ngai
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Nicole A Hynson
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Craig E Nelson
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, Department of Oceanography and Sea Grant College Program, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
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19
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Doering T, Tandon K, Topa SH, Pidot SJ, Blackall LL, van Oppen MJH. Genomic exploration of coral-associated bacteria: identifying probiotic candidates to increase coral bleaching resilience in Galaxea fascicularis. MICROBIOME 2023; 11:185. [PMID: 37596630 PMCID: PMC10439622 DOI: 10.1186/s40168-023-01622-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 07/14/2023] [Indexed: 08/20/2023]
Abstract
BACKGROUND Reef-building corals are acutely threatened by ocean warming, calling for active interventions to reduce coral bleaching and mortality. Corals associate with a wide diversity of bacteria which can influence coral health, but knowledge of specific functions that may be beneficial for corals under thermal stress is scant. Under the oxidative stress theory of coral bleaching, bacteria that scavenge reactive oxygen (ROS) or nitrogen species (RNS) are expected to enhance coral thermal resilience. Further, bacterial carbon export might substitute the carbon supply from algal photosymbionts, enhance thermal resilience and facilitate bleaching recovery. To identify probiotic bacterial candidates, we sequenced the genomes of 82 pure-cultured bacteria that were isolated from the emerging coral model Galaxea fascicularis. RESULTS Genomic analyses showed bacterial isolates were affiliated with 37 genera. Isolates such as Ruegeria, Muricauda and Roseovarius were found to encode genes for the synthesis of the antioxidants mannitol, glutathione, dimethylsulfide, dimethylsulfoniopropionate, zeaxanthin and/or β-carotene. Genes involved in RNS-scavenging were found in many G. fascicularis-associated bacteria, which represents a novel finding for several genera (including Pseudophaeobacter). Transporters that are suggested to export carbon (semiSWEET) were detected in seven isolates, including Pseudovibrio and Roseibium. Further, a range of bacterial strains, including strains of Roseibium and Roseovarius, revealed genomic features that may enhance colonisation and association of bacteria with the coral host, such as secretion systems and eukaryote-like repeat proteins. CONCLUSIONS Our work provides an in-depth genomic analysis of the functional potential of G. fascicularis-associated bacteria and identifies novel combinations of traits that may enhance the coral's ability to withstand coral bleaching. Identifying and characterising bacteria that are beneficial for corals is critical for the development of effective probiotics that boost coral climate resilience. Video Abstract.
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Affiliation(s)
- Talisa Doering
- School of BioSciences, The University of Melbourne, Parkville, VIC Australia
| | - Kshitij Tandon
- School of BioSciences, The University of Melbourne, Parkville, VIC Australia
| | - Sanjida H. Topa
- School of BioSciences, The University of Melbourne, Parkville, VIC Australia
| | - Sacha J. Pidot
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, VIC Australia
| | - Linda L. Blackall
- School of BioSciences, The University of Melbourne, Parkville, VIC Australia
| | - Madeleine J. H. van Oppen
- School of BioSciences, The University of Melbourne, Parkville, VIC Australia
- Australian Institute of Marine Science, Townsville, QLD Australia
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20
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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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Veglia AJ, Bistolas KSI, Voolstra CR, Hume BCC, Ruscheweyh HJ, Planes S, Allemand D, Boissin E, Wincker P, Poulain J, Moulin C, Bourdin G, Iwankow G, Romac S, Agostini S, Banaigs B, Boss E, Bowler C, de Vargas C, Douville E, Flores M, Forcioli D, Furla P, Galand PE, Gilson E, Lombard F, Pesant S, Reynaud S, Sunagawa S, Thomas OP, Troublé R, Zoccola D, Correa AMS, Vega Thurber RL. Endogenous viral elements reveal associations between a non-retroviral RNA virus and symbiotic dinoflagellate genomes. Commun Biol 2023; 6:566. [PMID: 37264063 DOI: 10.1038/s42003-023-04917-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 04/24/2023] [Indexed: 06/03/2023] Open
Abstract
Endogenous viral elements (EVEs) offer insight into the evolutionary histories and hosts of contemporary viruses. This study leveraged DNA metagenomics and genomics to detect and infer the host of a non-retroviral dinoflagellate-infecting +ssRNA virus (dinoRNAV) common in coral reefs. As part of the Tara Pacific Expedition, this study surveyed 269 newly sequenced cnidarians and their resident symbiotic dinoflagellates (Symbiodiniaceae), associated metabarcodes, and publicly available metagenomes, revealing 178 dinoRNAV EVEs, predominantly among hydrocoral-dinoflagellate metagenomes. Putative associations between Symbiodiniaceae and dinoRNAV EVEs were corroborated by the characterization of dinoRNAV-like sequences in 17 of 18 scaffold-scale and one chromosome-scale dinoflagellate genome assembly, flanked by characteristically cellular sequences and in proximity to retroelements, suggesting potential mechanisms of integration. EVEs were not detected in dinoflagellate-free (aposymbiotic) cnidarian genome assemblies, including stony corals, hydrocorals, jellyfish, or seawater. The pervasive nature of dinoRNAV EVEs within dinoflagellate genomes (especially Symbiodinium), as well as their inconsistent within-genome distribution and fragmented nature, suggest ancestral or recurrent integration of this virus with variable conservation. Broadly, these findings illustrate how +ssRNA viruses may obscure their genomes as members of nested symbioses, with implications for host evolution, exaptation, and immunity in the context of reef health and disease.
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Affiliation(s)
- Alex J Veglia
- BioSciences Department, Rice University, Houston, TX, USA
| | | | | | | | - Hans-Joachim Ruscheweyh
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, Vladimir-Prelog-Weg 4, ETH Zürich, CH-8093, Zürich, Switzerland
| | - Serge Planes
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Denis Allemand
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, Monaco, MC-98000, Principality of Monaco
| | - Emilie Boissin
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Clémentine Moulin
- Fondation Tara Océan, Base Tara, 8 rue de Prague, 75012, Paris, France
| | | | - Guillaume Iwankow
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Sarah Romac
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, Roscoff, France
| | - Sylvain Agostini
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1, Shimoda, Shizuoka, Japan
| | - Bernard Banaigs
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, ME, USA
| | - Chris Bowler
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Colomban de Vargas
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, Roscoff, France
| | - Eric Douville
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, F-91191, Gif-sur-Yvette, France
| | - Michel Flores
- Weizmann Institute of Science, Department of Earth and Planetary Sciences, 76100, Rehovot, Israel
| | - Didier Forcioli
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Medical School, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco, LIA ROPSE, Monaco, France
| | - Paola Furla
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Medical School, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco, LIA ROPSE, Monaco, France
| | - Pierre E Galand
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, 66650, Banyuls sur mer, France
| | - Eric Gilson
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Medical School, Nice, France
- Department of Medical Genetics, CHU of Nice, Nice, France
| | - Fabien Lombard
- Sorbonne Université, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, F-06230, Villefranche-sur-Mer, France
| | - Stéphane Pesant
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Stéphanie Reynaud
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, Monaco, MC-98000, Principality of Monaco
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, Vladimir-Prelog-Weg 4, ETH Zürich, CH-8093, Zürich, Switzerland
| | - Olivier P Thomas
- School of Biological and Chemical Sciences, Ryan Institute, University of Galway, University Road H91 TK33, Galway, Ireland
| | - Romain Troublé
- Fondation Tara Océan, Base Tara, 8 rue de Prague, 75012, Paris, France
| | - Didier Zoccola
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, Monaco, MC-98000, Principality of Monaco
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22
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Zhu W, Liu X, Zhang J, Zhao H, Li Z, Wang H, Chen R, Wang A, Li X. Response of coral bacterial composition and function to water quality variations under anthropogenic influence. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 884:163837. [PMID: 37137368 DOI: 10.1016/j.scitotenv.2023.163837] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 04/06/2023] [Accepted: 04/26/2023] [Indexed: 05/05/2023]
Abstract
Microbial communities play key roles in the adaptation of corals living in adverse environments, as the microbiome flexibility can enhance environmental plasticity of coral holobiont. However, the ecological association of coral microbiome and related function to locally deteriorating water quality remains underexplored. In this work, we used 16S rRNA gene sequencing and quantitative microbial element cycling (QMEC) to investigate the seasonal changes of bacterial communities, particularly their functional genes related to carbon (C), nitrogen (N), phosphorus (P) and sulfur (S) cycle, of the scleractinian coral Galaxea fascicularis from nearshore reefs exposed anthropogenic influence. We used nutrient concentrations as the indicator of anthropogenic activities in coastal reefs, and found a higher nutrient pressure in spring than summer. The bacterial diversity, community structure and dominant bacteria of coral shifted significantly due to seasonal variations dominated by nutrient concentrations. Additionally, the network structure and nutrient cycling gene profiles in summer under low nutrient stress was distinct from that under poor environmental conditions in spring, with lower network complexity and abundance of CNPS cycling genes in summer compared with spring. We further identified significant correlations between microbial community (taxonomic composition and co-occurrence network) and geochemical functions (abundance of multiple functional genes and functional community). Nutrient enrichment was proved to be the most important environmental fluctuation in controlling the diversity, community structure, interactional network and functional genes of the coral microbiome. These results highlight that seasonal shifts in coral-associated bacteria due to anthropogenic activities alter the functional potentials, and provide novel insight about the mechanisms of coral adaptation to locally deteriorating environments.
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Affiliation(s)
- Wentao Zhu
- College of Ecology and Environment, Hainan University, Haikou, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Xiangbo Liu
- College of Marine Science, Hainan University, Haikou, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Junling Zhang
- College of Marine Science, Hainan University, Haikou, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - He Zhao
- College of Marine Science, Hainan University, Haikou, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Zhuoran Li
- College of Marine Science, Hainan University, Haikou, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Hao Wang
- College of Marine Science, Hainan University, Haikou, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Rouwen Chen
- College of Marine Science, Hainan University, Haikou, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Aimin Wang
- College of Marine Science, Hainan University, Haikou, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Xiubao Li
- College of Marine Science, Hainan University, Haikou, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China.
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23
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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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24
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Exploring the Potential Molecular Mechanisms of Interactions between a Probiotic Consortium and Its Coral Host. mSystems 2023; 8:e0092122. [PMID: 36688656 PMCID: PMC9948713 DOI: 10.1128/msystems.00921-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Beneficial microorganisms for corals (BMCs) have been demonstrated to be effective probiotics to alleviate bleaching and mitigate coral mortality in vivo. The selection of putative BMCs is traditionally performed manually, using an array of biochemical and molecular tests for putative BMC traits. We present a comprehensive genetic survey of BMC traits using a genome-based framework for the identification of alternative mechanisms that can be used for future in silico selection of BMC strains. We identify exclusive BMC traits associated with specific strains and propose new BMC mechanisms, such as the synthesis of glycine betaine and ectoines. Our roadmap facilitates the selection of BMC strains while increasing the array of genetic targets that can be included in the selection of putative BMC strains to be tested as coral probiotics. IMPORTANCE Probiotics are currently the main hope as a potential medicine for corals, organisms that are considered the marine "canaries of the coal mine" and that are threatened with extinction. Our experiments have proved the concept that probiotics mitigate coral bleaching and can also prevent coral mortality. Here, we present a comprehensive genetic survey of probiotic traits using a genome-based framework. The main outcomes are a roadmap that facilitates the selection of coral probiotic strains while increasing the array of mechanisms that can be included in the selection of coral probiotics.
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25
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Haydon TD, Matthews JL, Seymour JR, Raina JB, Seymour JE, Chartrand K, Camp EF, Suggett DJ. Metabolomic signatures of corals thriving across extreme reef habitats reveal strategies of heat stress tolerance. Proc Biol Sci 2023; 290:20221877. [PMID: 36750192 PMCID: PMC9904954 DOI: 10.1098/rspb.2022.1877] [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: 09/19/2022] [Accepted: 01/11/2023] [Indexed: 02/09/2023] Open
Abstract
Anthropogenic stressors continue to escalate worldwide, driving unprecedented declines in reef environmental conditions and coral health. One approach to better understand how corals can function in the future is to examine coral populations that thrive within present day naturally extreme habitats. We applied untargeted metabolomics (gas chromatography-mass spectrometry (GC-MS)) to contrast metabolite profiles of Pocillopora acuta colonies from hot, acidic and deoxygenated mangrove environments versus those from adjacent reefs. Under ambient temperatures, P. acuta predominantly associated with endosymbionts of the genera Cladocopium (reef) or Durusdinium (mangrove), exhibiting elevated metabolism in mangrove through energy-generating and biosynthesis pathways compared to reef populations. Under transient heat stress, P. acuta endosymbiont associations were unchanged. Reef corals bleached and exhibited extensive shifts in symbiont metabolic profiles (whereas host metabolite profiles were unchanged). By contrast, mangrove populations did not bleach and solely the host metabolite profiles were altered, including cellular responses in inter-partner signalling, antioxidant capacity and energy storage. Thus mangrove P. acuta populations resist periodically high-temperature exposure via association with thermally tolerant endosymbionts coupled with host metabolic plasticity. Our findings highlight specific metabolites that may be biomarkers of heat tolerance, providing novel insight into adaptive coral resilience to elevated temperatures.
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Affiliation(s)
- Trent D. Haydon
- Center for Genomics and Systems Biology, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, UAE
- Faculty of Science, Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales 2007, Australia
| | - Jennifer L. Matthews
- Faculty of Science, Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales 2007, Australia
| | - Justin R. Seymour
- Faculty of Science, Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales 2007, Australia
| | - Jean-Baptiste Raina
- Faculty of Science, Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales 2007, Australia
| | - Jamie E. Seymour
- Division of Tropical Health and Medicine, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD 4811, Australia
| | - Kathryn Chartrand
- Centre for tropical Water and Aquatic Ecosystem Research, James Cook University, Cairns, QLD 4811, Australia
| | - Emma F. Camp
- Faculty of Science, Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales 2007, Australia
| | - David J. Suggett
- Faculty of Science, Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales 2007, Australia
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26
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Gold DA, Vermeij GJ. Deep resilience: An evolutionary perspective on calcification in an age of ocean acidification. Front Physiol 2023; 14:1092321. [PMID: 36818444 PMCID: PMC9935589 DOI: 10.3389/fphys.2023.1092321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 01/23/2023] [Indexed: 02/05/2023] Open
Abstract
The success of today's calcifying organisms in tomorrow's oceans depends, in part, on the resilience of their skeletons to ocean acidification. To the extent this statement is true there is reason to have hope. Many marine calcifiers demonstrate resilience when exposed to environments that mimic near-term ocean acidification. The fossil record similarly suggests that resilience in skeletons has increased dramatically over geologic time. This "deep resilience" is seen in the long-term stability of skeletal chemistry, as well as a decreasing correlation between skeletal mineralogy and extinction risk over time. Such resilience over geologic timescales is often attributed to genetic canalization-the hardening of genetic pathways due to the evolution of increasingly complex regulatory systems. But paradoxically, our current knowledge on biomineralization genetics suggests an opposing trend, where genes are co-opted and shuffled at an evolutionarily rapid pace. In this paper we consider two possible mechanisms driving deep resilience in skeletons that fall outside of genetic canalization: microbial co-regulation and macroevolutionary trends in skeleton structure. The mechanisms driving deep resilience should be considered when creating risk assessments for marine organisms facing ocean acidification and provide a wealth of research avenues to explore.
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Dong X, Lan H, Huang L, Zhang H, Lin X, Weng S, Peng Y, Lin J, Wang JH, Peng J, Yang Y. Metagenomic Views of Microbial Communities in Sand Sediments Associated with Coral Reefs. MICROBIAL ECOLOGY 2023; 85:465-477. [PMID: 35113183 DOI: 10.1007/s00248-021-01957-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 12/29/2021] [Indexed: 06/14/2023]
Abstract
Reef sediments, the home for microbes with high abundances, provide an important source of carbonates and nutrients for the growth and maintenance of coral reefs. However, there is a lack of systematic research on the composition of microbial community in sediments of different geographic sites and their potential effect on nutrient recycling and health of the coral reef ecosystem. In combination of biogeochemical measurements with gene- and genome-centric metagenomics, we assessed microbial community compositions and functional diversity, as well as profiles of antibiotic resistance genes in surface sediments of 16 coral reef sites at different depths from the Xisha islands in the South China Sea. Reef sediment microbiomes are diverse and novel at lower taxonomic ranks, dominated by Proteobacteria and Planctomycetota. Most reef sediment bacteria potentially participate in biogeochemical cycling via oxidizing various organic and inorganic compounds as energy sources. High abundances of Proteobacteria (mostly Rhizobiales and Woeseiales) are metabolically flexible and contain rhodopsin genes. Various classes of antibiotic resistance genes, hosted by diverse bacterial lineages, were identified to confer resistance to multidrug, aminoglycoside, and other antibiotics. Overall, our findings expanded the understanding of reef sediment microbial ecology and provided insights for their link to the coral reef ecosystem health.
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Affiliation(s)
- Xiyang Dong
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China.
| | - Haoyu Lan
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Liangtian Huang
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Haikun Zhang
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
| | - Xianbiao Lin
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Shengze Weng
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Yongyi Peng
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Jia Lin
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Jiang-Hai Wang
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Juan Peng
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Ying Yang
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China.
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Dong R, Li W, Wang P, Dong D, Song X, Li X. Effects of light intensity and photoperiod on the cultivation of the soft coral Sarcophyton trocheliophorum. MARINE ENVIRONMENTAL RESEARCH 2023; 184:105856. [PMID: 36592545 DOI: 10.1016/j.marenvres.2022.105856] [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: 09/19/2022] [Revised: 12/03/2022] [Accepted: 12/18/2022] [Indexed: 06/17/2023]
Abstract
Coral reefs are one of the most diverse, productive ecosystems in the world, and light plays crucial role in its survival. Notably, the effects of light conditions on soft coral and its adaptive mechanism were unclear. Thus, the present study aimed to investigate and evaluate the effects of different light intensities (30, 80 and 130 μmol m-2 s-1) and photoperiods (18D:6L, 12D:12L and 6D:18L) on cultivation of soft coral Sarcophyton trocheliophorum. During two 50-day of the experiments, we monitored the zooxanthellae density, Chl a content, enzyme activities (SOD, CAT and GST) and microbial diversity of S. trocheliophorum. Our study's outcomes found that, at the end of the experiment, the 80 μmol m-2 s-1 light intensity group and 12D:12L photoperiod group both possessed the highest zooxanthellae density (2.54 × 108 ± 0.14 × 108 cells g-1 DW and 2.40 × 108 ± 0.07 × 108 cells g-1 DW, respectively), Chl a content (295.01 ± 14.13 μg g-1 DW and 287.78 ± 16.13 μg g-1 DW, respectively) and microbial diversity and relatively stable enzyme activities level. Besides, we speculated that the reason for the decline of zooxanthellae density, Chl a content and microbial diversity under other light conditions might be that it induced light stress and caused oxidative damage. The main bacterial composition of S. trocheliophorum in different light conditions was similar at the phylum level, showing the stability of microbial community structure. Proteobacteria, Actinobacteria and Firmicutes were dominant under all light conditions, so we hypothesized that these bacteria phylum play a crucial role in coral growth and survival. In conclusion, compared with the other treatments, 80 μmol m-2 s-1 light intensity and 12D:12L photoperiod were more beneficial to the growth performance of S. trocheliophorum and could be recommended for its cultivation condition. Our study could provide helpful information for sustainable management plans for the cultivation and conservation of soft corals, which was especially important to the protection and restoration of degraded coral reefs.
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Affiliation(s)
- Ruiguang Dong
- Key Laboratory of Mariculture (Ministry of Education), College of Fisheries, Ocean University of China, Qingdao, 266003, China
| | - Weidong Li
- College of Ecology and Environment, Hainan University, Haikou, 570000, China
| | - Peizheng Wang
- Key Laboratory of Utilization and Protection of Tropical Marine Living Resources, Ministry of Education, Hainan Tropical Ocean University, Sanya, 572000, China
| | - Dengpan Dong
- Key Laboratory of Mariculture (Ministry of Education), College of Fisheries, Ocean University of China, Qingdao, 266003, China
| | - Xiefa Song
- Key Laboratory of Mariculture (Ministry of Education), College of Fisheries, Ocean University of China, Qingdao, 266003, China.
| | - Xian Li
- Key Laboratory of Mariculture (Ministry of Education), College of Fisheries, Ocean University of China, Qingdao, 266003, China.
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Davies SW, Gamache MH, Howe-Kerr LI, Kriefall NG, Baker AC, Banaszak AT, Bay LK, Bellantuono AJ, Bhattacharya D, Chan CX, Claar DC, Coffroth MA, Cunning R, Davy SK, del Campo J, Díaz-Almeyda EM, Frommlet JC, Fuess LE, González-Pech RA, Goulet TL, Hoadley KD, Howells EJ, Hume BCC, Kemp DW, Kenkel CD, Kitchen SA, LaJeunesse TC, Lin S, McIlroy SE, McMinds R, Nitschke MR, Oakley CA, Peixoto RS, Prada C, Putnam HM, Quigley K, Reich HG, Reimer JD, Rodriguez-Lanetty M, Rosales SM, Saad OS, Sampayo EM, Santos SR, Shoguchi E, Smith EG, Stat M, Stephens TG, Strader ME, Suggett DJ, Swain TD, Tran C, Traylor-Knowles N, Voolstra CR, Warner ME, Weis VM, Wright RM, Xiang T, Yamashita H, Ziegler M, Correa AMS, Parkinson JE. Building consensus around the assessment and interpretation of Symbiodiniaceae diversity. PeerJ 2023; 11:e15023. [PMID: 37151292 PMCID: PMC10162043 DOI: 10.7717/peerj.15023] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 02/17/2023] [Indexed: 05/09/2023] Open
Abstract
Within microeukaryotes, genetic variation and functional variation sometimes accumulate more quickly than morphological differences. To understand the evolutionary history and ecology of such lineages, it is key to examine diversity at multiple levels of organization. In the dinoflagellate family Symbiodiniaceae, which can form endosymbioses with cnidarians (e.g., corals, octocorals, sea anemones, jellyfish), other marine invertebrates (e.g., sponges, molluscs, flatworms), and protists (e.g., foraminifera), molecular data have been used extensively over the past three decades to describe phenotypes and to make evolutionary and ecological inferences. Despite advances in Symbiodiniaceae genomics, a lack of consensus among researchers with respect to interpreting genetic data has slowed progress in the field and acted as a barrier to reconciling observations. Here, we identify key challenges regarding the assessment and interpretation of Symbiodiniaceae genetic diversity across three levels: species, populations, and communities. We summarize areas of agreement and highlight techniques and approaches that are broadly accepted. In areas where debate remains, we identify unresolved issues and discuss technologies and approaches that can help to fill knowledge gaps related to genetic and phenotypic diversity. We also discuss ways to stimulate progress, in particular by fostering a more inclusive and collaborative research community. We hope that this perspective will inspire and accelerate coral reef science by serving as a resource to those designing experiments, publishing research, and applying for funding related to Symbiodiniaceae and their symbiotic partnerships.
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Affiliation(s)
- Sarah W. Davies
- Department of Biology, Boston University, Boston, MA, United States
| | - Matthew H. Gamache
- Department of Integrative Biology, University of South Florida, Tampa, FL, United States
| | | | | | - Andrew C. Baker
- Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL, United States
| | - Anastazia T. Banaszak
- Unidad Académica de Sistemas Arrecifales, Universidad Nacional Autónoma de México, Puerto Morelos, Mexico
| | - Line Kolind Bay
- Australian Institute of Marine Science, Townsville, Australia
| | - Anthony J. Bellantuono
- Department of Biological Sciences, Florida International University, Miami, FL, United States
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, United States
| | - Cheong Xin Chan
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Danielle C. Claar
- Nearshore Habitat Program, Washington State Department of Natural Resources, Olympia, WA, USA
| | | | - Ross Cunning
- Daniel P. Haerther Center for Conservation and Research, John G. Shedd Aquarium, Chicago, IL, United States
| | - Simon K. Davy
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Javier del Campo
- Institut de Biologia Evolutiva (CSIC - Universitat Pompeu Fabra), Barcelona, Catalonia, Spain
| | | | - Jörg C. Frommlet
- Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
| | - Lauren E. Fuess
- Department of Biology, Texas State University, San Marcos, TX, United States
| | - Raúl A. González-Pech
- Department of Integrative Biology, University of South Florida, Tampa, FL, United States
- Department of Biology, Pennsylvania State University, State College, PA, United States
| | - Tamar L. Goulet
- Department of Biology, University of Mississippi, University, MS, United States
| | - Kenneth D. Hoadley
- Department of Biological Sciences, University of Alabama—Tuscaloosa, Tuscaloosa, AL, United States
| | - Emily J. Howells
- National Marine Science Centre, Faculty of Science and Engineering, Southern Cross University, Coffs Harbour, NSW, Australia
| | | | - Dustin W. Kemp
- Department of Biology, University of Alabama—Birmingham, Birmingham, Al, United States
| | - Carly D. Kenkel
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Sheila A. Kitchen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
| | - Todd C. LaJeunesse
- Department of Biology, Pennsylvania State University, University Park, PA, United States
| | - Senjie Lin
- Department of Marine Sciences, University of Connecticut, Mansfield, CT, United States
| | - Shelby E. McIlroy
- Swire Institute of Marine Science, School of Biological Sciences, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Ryan McMinds
- Center for Global Health and Infectious Disease Research, University of South Florida, Tampa, FL, United States
| | | | - Clinton A. Oakley
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Raquel S. Peixoto
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Carlos Prada
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, United States
| | - Hollie M. Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, United States
| | | | - Hannah G. Reich
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, United States
| | - James Davis Reimer
- Department of Biology, Chemistry and Marine Sciences, Faculty of Science, University of the Ryukyus, Nishihara, Okinawa, Japan
| | | | - Stephanie M. Rosales
- The Cooperative Institute For Marine and Atmospheric Studies, Miami, FL, United States
| | - Osama S. Saad
- Department of Biological Oceanography, Red Sea University, Port-Sudan, Sudan
| | - Eugenia M. Sampayo
- School of Biological Sciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Scott R. Santos
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, United States
| | - Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Edward G. Smith
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Michael Stat
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, Australia
| | - Timothy G. Stephens
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, United States
| | - Marie E. Strader
- Department of Biology, Texas A&M University, College Station, TX, United States
| | - David J. Suggett
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Timothy D. Swain
- Department of Marine and Environmental Science, Nova Southeastern University, Dania Beach, FL, United States
| | - Cawa Tran
- Department of Biology, University of San Diego, San Diego, CA, United States
| | - Nikki Traylor-Knowles
- Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL, United States
| | | | - Mark E. Warner
- School of Marine Science and Policy, University of Delaware, Lewes, DE, United States
| | - Virginia M. Weis
- Department of Integrative Biology, Oregon State University, Corvallis, OR, United States
| | - Rachel M. Wright
- Department of Biological Sciences, Southern Methodist University, Dallas, TX, United States
| | - Tingting Xiang
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Hiroshi Yamashita
- Fisheries Technology Institute, Japan Fisheries Research and Education Agency, Ishigaki, Okinawa, Japan
| | - Maren Ziegler
- Department of Animal Ecology & Systematics, Justus Liebig University Giessen (Germany), Giessen, Germany
| | | | - John Everett Parkinson
- Department of Integrative Biology, University of South Florida, Tampa, FL, United States
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30
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Bove CB, Ingersoll MV, Davies SW. Help Me, Symbionts, You're My Only Hope: Approaches to Accelerate our Understanding of Coral Holobiont Interactions. Integr Comp Biol 2022; 62:1756-1769. [PMID: 36099871 DOI: 10.1093/icb/icac141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/24/2022] [Accepted: 09/05/2022] [Indexed: 01/05/2023] Open
Abstract
Tropical corals construct the three-dimensional framework for one of the most diverse ecosystems on the planet, providing habitat to a plethora of species across taxa. However, these ecosystem engineers are facing unprecedented challenges, such as increasing disease prevalence and marine heatwaves associated with anthropogenic global change. As a result, major declines in coral cover and health are being observed across the world's oceans, often due to the breakdown of coral-associated symbioses. Here, we review the interactions between the major symbiotic partners of the coral holobiont-the cnidarian host, algae in the family Symbiodiniaceae, and the microbiome-that influence trait variation, including the molecular mechanisms that underlie symbiosis and the resulting physiological benefits of different microbial partnerships. In doing so, we highlight the current framework for the formation and maintenance of cnidarian-Symbiodiniaceae symbiosis, and the role that immunity pathways play in this relationship. We emphasize that understanding these complex interactions is challenging when you consider the vast genetic variation of the cnidarian host and algal symbiont, as well as their highly diverse microbiome, which is also an important player in coral holobiont health. Given the complex interactions between and among symbiotic partners, we propose several research directions and approaches focused on symbiosis model systems and emerging technologies that will broaden our understanding of how these partner interactions may facilitate the prediction of coral holobiont phenotype, especially under rapid environmental change.
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Affiliation(s)
- Colleen B Bove
- Department of Biology, Boston University, Boston, MA 02215, USA
| | | | - Sarah W Davies
- Department of Biology, Boston University, Boston, MA 02215, USA
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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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Cárdenas A, Raina JB, Pogoreutz C, Rädecker N, Bougoure J, Guagliardo P, Pernice M, Voolstra CR. Greater functional diversity and redundancy of coral endolithic microbiomes align with lower coral bleaching susceptibility. THE ISME JOURNAL 2022; 16:2406-2420. [PMID: 35840731 PMCID: PMC9478130 DOI: 10.1038/s41396-022-01283-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 06/14/2022] [Accepted: 06/28/2022] [Indexed: 04/14/2023]
Abstract
The skeleton of reef-building coral harbors diverse microbial communities that could compensate for metabolic deficiencies caused by the loss of algal endosymbionts, i.e., coral bleaching. However, it is unknown to what extent endolith taxonomic diversity and functional potential might contribute to thermal resilience. Here we exposed Goniastrea edwardsi and Porites lutea, two common reef-building corals from the central Red Sea to a 17-day long heat stress. Using hyperspectral imaging, marker gene/metagenomic sequencing, and NanoSIMS, we characterized their endolithic microbiomes together with 15N and 13C assimilation of two skeletal compartments: the endolithic band directly below the coral tissue and the deep skeleton. The bleaching-resistant G. edwardsi was associated with endolithic microbiomes of greater functional diversity and redundancy that exhibited lower N and C assimilation than endoliths in the bleaching-sensitive P. lutea. We propose that the lower endolithic primary productivity in G. edwardsi can be attributed to the dominance of chemolithotrophs. Lower primary production within the skeleton may prevent unbalanced nutrient fluxes to coral tissues under heat stress, thereby preserving nutrient-limiting conditions characteristic of a stable coral-algal symbiosis. Our findings link coral endolithic microbiome structure and function to bleaching susceptibility, providing new avenues for understanding and eventually mitigating reef loss.
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Affiliation(s)
- Anny Cárdenas
- Department of Biology, University of Konstanz, Konstanz, 78457, Germany.
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.
| | - Jean-Baptiste Raina
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, 2007, Australia.
| | - Claudia Pogoreutz
- Department of Biology, University of Konstanz, Konstanz, 78457, Germany
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, 1015, Switzerland
| | - Nils Rädecker
- Department of Biology, University of Konstanz, Konstanz, 78457, Germany
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, 1015, Switzerland
| | - Jeremy Bougoure
- Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, Perth, WA, 6009, Australia
| | - Paul Guagliardo
- Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, Perth, WA, 6009, Australia
| | - Mathieu Pernice
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Christian R Voolstra
- Department of Biology, University of Konstanz, Konstanz, 78457, Germany.
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.
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Nitschke MR, Rosset SL, Oakley CA, Gardner SG, Camp EF, Suggett DJ, Davy SK. The diversity and ecology of Symbiodiniaceae: A traits-based review. ADVANCES IN MARINE BIOLOGY 2022; 92:55-127. [PMID: 36208879 DOI: 10.1016/bs.amb.2022.07.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Among the most successful microeukaryotes to form mutualisms with animals are dinoflagellates in the family Symbiodiniaceae. These photosynthetic symbioses drive significant primary production and are responsible for the formation of coral reef ecosystems but are particularly sensitive when environmental conditions become extreme. Annual episodes of widespread coral bleaching (disassociation of the mutualistic partnership) and mortality are forecasted from the year 2060 under current trends of ocean warming. However, host cnidarians and dinoflagellate symbionts display exceptional genetic and functional diversity, and meaningful predictions of the future that embrace this biological complexity are difficult to make. A recent move to trait-based biology (and an understanding of how traits are shaped by the environment) has been adopted to move past this problem. The aim of this review is to: (1) provide an overview of the major cnidarian lineages that are symbiotic with Symbiodiniaceae; (2) summarise the symbiodiniacean genera associated with cnidarians with reference to recent changes in taxonomy and systematics; (3) examine the knowledge gaps in Symbiodiniaceae life history from a trait-based perspective; (4) review Symbiodiniaceae trait variation along three abiotic gradients (light, nutrients, and temperature); and (5) provide recommendations for future research of Symbiodiniaceae traits. We anticipate that a detailed understanding of traits will further reveal basic knowledge of the evolution and functional diversity of these mutualisms, as well as enhance future efforts to model stability and change in ecosystems dependent on cnidarian-dinoflagellate organisms.
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Affiliation(s)
- Matthew R Nitschke
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand; Climate Change Cluster, University of Technology Sydney, Broadway, NSW, Australia.
| | - Sabrina L Rosset
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Clinton A Oakley
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Stephanie G Gardner
- Center for Marine Science and Innovation, University of New South Wales Sydney, Kensington, NSW, Australia
| | - Emma F Camp
- Climate Change Cluster, University of Technology Sydney, Broadway, NSW, Australia
| | - David J Suggett
- Climate Change Cluster, University of Technology Sydney, Broadway, NSW, Australia
| | - Simon K Davy
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
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Díaz-Almeyda EM, Ryba T, Ohdera AH, Collins SM, Shafer N, Link C, Prado-Zapata M, Ruhnke C, Moore M, González Angel AM, Pollock FJ, Medina M. Thermal Stress Has Minimal Effects on Bacterial Communities of Thermotolerant Symbiodinium Cultures. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.764086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Algae in the dinoflagellate family Symbiodiniaceae are endocellular photosymbionts of corals and other cnidarians. This close relationship is disrupted when seawater temperature increases, causing coral bleaching eventually affecting entire coral reefs. Although the relationship between animal host and photosymbiont has been well-studied, little is known about the bacterial community associated with Symbiodiniaceae in culture. We compared the microbial communities of three isolates from different species of the genus Symbiodinium (formerly known as Symbiodinium clade A) with different ecophysiology, levels of interaction with the animal host, and thermal adaptations. Two species, Symbiodinium microadriaticum and Symbiodinium necroappettens, exhibit intermediate thermotolerance, with a decrease of both growth rate and photochemical efficiency with increased temperature. The third species, Symbiodinium pilosum, has high thermotolerance with no difference in growth rate or photochemical efficiency at 32°C. Microbial communities were characterized after 27 days of growth under control (26°C) and high temperature (32°C). Data shows stronger grouping of bacterial assemblages based on Symbiodinium species than temperature. Microbial communities did not group phylogenetically. We found a shared set of fifteen ASVs belonging to four genera and three families that remained in all three Symbiodiniaceae species. These included Labrenzia, Phycisphaeraceae (SM1A02), Roseovarius, and Muricauda, which are all commonly associated with corals and Symbiodiniaceae cultures. Few ASVs differed significantly by temperature within species. S. pilosum displayed significantly lower levels of microbial diversity and greater individual variability in community composition at 32°C compared to 26°C. These results suggest that bacteria associated or co-cultured with thermotolerant Symbiodinium might play an important role in thermotolerance. Further research on the functional metabolic pathways of these bacteria might hold the key to understanding Symbiodinium’s ability to tolerate thermal stress.
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Long-Term Heat Selection of the Coral Endosymbiont Cladocopium C1 acro (Symbiodiniaceae) Stabilizes Associated Bacterial Communities. Int J Mol Sci 2022; 23:ijms23094913. [PMID: 35563303 PMCID: PMC9101544 DOI: 10.3390/ijms23094913] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/26/2022] [Accepted: 04/27/2022] [Indexed: 02/04/2023] Open
Abstract
Heat-tolerant strains of the coral endosymbiont, Cladocopium C1acro (Symbiodiniaceae), have previously been developed via experimental evolution. Here, we examine physiological responses and bacterial community composition (using 16S rRNA gene metabarcoding) in cultures of 10 heat-evolved (SS) and 9 wild-type (WT) strains, which had been exposed for 6 years to 31 °C and 27 °C, respectively. We also examine whether the associated bacterial communities were affected by a three-week reciprocal transplantation to both temperatures. The SS strains had bacterial communities with lower diversities that showed more stability and lower variability when exposed to elevated temperatures compared with the WT strains. Amplicon sequence variants (ASVs) of the bacterial genera Labrenzia, Algiphilus, Hyphobacterium and Roseitalea were significantly more associated with the SS strains compared with the WT strains. WT strains showed higher abundance of ASVs assigned to the genera Fabibacter and Tropicimonas. We hypothesize that these compositional differences in associated bacterial communities between SS and WT strains also contribute to the thermal tolerance of the microalgae. Future research should explore functional potential between bacterial communities using metagenomics to unravel specific genomic adaptations.
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Deutsch JM, Mandelare-Ruiz P, Yang Y, Foster G, Routhu A, Houk J, De La Flor YT, Ushijima B, Meyer JL, Paul VJ, Garg N. Metabolomics Approaches to Dereplicate Natural Products from Coral-Derived Bioactive Bacteria. JOURNAL OF NATURAL PRODUCTS 2022; 85:462-478. [PMID: 35112871 DOI: 10.1021/acs.jnatprod.1c01110] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Stony corals (Scleractinia) are invertebrates that form symbiotic relationships with eukaryotic algal endosymbionts and the prokaryotic microbiome. The microbiome has the potential to produce bioactive natural products providing defense and resilience to the coral host against pathogenic microorganisms, but this potential has not been extensively explored. Bacterial pathogens can pose a significant threat to corals, with some species implicated in primary and opportunistic infections of various corals. In response, probiotics have been proposed as a potential strategy to protect corals in the face of increased incidence of disease outbreaks. In this study, we screened bacterial isolates from healthy and diseased corals for antibacterial activity. The bioactive extracts were analyzed using untargeted metabolomics. Herein, an UpSet plot and hierarchical clustering analyses were performed to identify isolates with the largest number of unique metabolites. These isolates also displayed different antibacterial activities. Through application of in silico and experimental approaches coupled with genome analysis, we dereplicated natural products from these coral-derived bacteria from Florida's coral reef environments. The metabolomics approach highlighted in this study serves as a useful resource to select probiotic candidates and enables insights into natural product-mediated chemical ecology in holobiont symbiosis.
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Affiliation(s)
- Jessica M Deutsch
- School of Chemistry and Biochemistry, Engineered Biosystems Building, Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Paige Mandelare-Ruiz
- Smithsonian Marine Station, Smithsonian Institution, Fort Pierce, Florida 34949, United States
| | - Yingzhe Yang
- School of Chemistry and Biochemistry, Engineered Biosystems Building, Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Gabriel Foster
- School of Chemistry and Biochemistry, Engineered Biosystems Building, Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Apurva Routhu
- School of Chemistry and Biochemistry, Engineered Biosystems Building, Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Jay Houk
- Smithsonian Marine Station, Smithsonian Institution, Fort Pierce, Florida 34949, United States
| | - Yesmarie T De La Flor
- Smithsonian Marine Station, Smithsonian Institution, Fort Pierce, Florida 34949, United States
| | - Blake Ushijima
- Smithsonian Marine Station, Smithsonian Institution, Fort Pierce, Florida 34949, United States
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, North Carolina 28403, United States
| | - Julie L Meyer
- Department of Soil and Water Sciences, University of Florida, Gainesville, Florida 32603, United States
| | - Valerie J Paul
- Smithsonian Marine Station, Smithsonian Institution, Fort Pierce, Florida 34949, United States
| | - Neha Garg
- School of Chemistry and Biochemistry, Engineered Biosystems Building, Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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Maire J, Buerger P, Chan WY, Deore P, Dungan AM, Nitschke MR, van Oppen MJH. Effects of Ocean Warming on the Underexplored Members of the Coral Microbiome. Integr Comp Biol 2022; 62:1700-1709. [PMID: 35259253 PMCID: PMC9801979 DOI: 10.1093/icb/icac005] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 03/01/2022] [Accepted: 03/05/2022] [Indexed: 01/05/2023] Open
Abstract
The climate crisis is one of the most significant threats to marine ecosystems. It is leading to severe increases in sea surface temperatures and in the frequency and magnitude of marine heatwaves. These changing conditions are directly impacting coral reef ecosystems, which are among the most biodiverse ecosystems on Earth. Coral-associated symbionts are particularly affected because summer heatwaves cause coral bleaching-the loss of endosymbiotic microalgae (Symbiodiniaceae) from coral tissues, leading to coral starvation and death. Coral-associated Symbiodiniaceae and bacteria have been extensively studied in the context of climate change, especially in terms of community diversity and dynamics. However, data on other microorganisms and their response to climate change are scarce. Here, we review current knowledge on how increasing temperatures affect understudied coral-associated microorganisms such as archaea, fungi, viruses, and protists other than Symbiodiniaceae, as well as microbe-microbe interactions. We show that the coral-microbe symbiosis equilibrium is at risk under current and predicted future climate change and argue that coral reef conservation initiatives should include microbe-focused approaches.
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Affiliation(s)
| | - Patrick Buerger
- School of BioSciences, University of Melbourne, Parkville, VIC 3010, Australia,Applied BioSciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Wing Yan Chan
- School of BioSciences, University of Melbourne, Parkville, VIC 3010, Australia
| | - Pranali Deore
- School of BioSciences, University of Melbourne, Parkville, VIC 3010, Australia
| | - Ashley M Dungan
- School of BioSciences, University of Melbourne, Parkville, VIC 3010, Australia
| | | | - Madeleine J H van Oppen
- School of BioSciences, University of Melbourne, Parkville, VIC 3010, Australia,Australian Institute of Marine Science, Townsville, QLD 4810, Australia
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Coral-microbe interactions: their importance to reef function and survival. Emerg Top Life Sci 2022; 6:33-44. [PMID: 35119475 DOI: 10.1042/etls20210229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 01/04/2022] [Accepted: 01/12/2022] [Indexed: 11/17/2022]
Abstract
Many different microorganisms associate with the coral host in a single entity known as the holobiont, and their interactions with the host contribute to coral health, thereby making them a fundamental part of reef function, survival, and conservation. As corals continue to be susceptible to bleaching due to environmental stress, coral-associated bacteria may have a potential role in alleviating bleaching. This review provides a synthesis of the various roles bacteria have in coral physiology and development, and explores the possibility that changes in the microbiome with environmental stress could have major implications in how corals acclimatize and survive. Recent studies on the interactions between the coral's algal and bacterial symbionts elucidate how bacteria may stabilize algal health and, therefore, mitigate bleaching. A summary of the innovative tools and experiments to examine host-microbe interactions in other cnidarians (a temperate coral, a jellyfish, two anemones, and a freshwater hydroid) is offered in this review to delineate our current knowledge of mechanisms underlying microbial establishment and maintenance in the animal host. A better understanding of these mechanisms may enhance the success of maintaining probiotics long-term in corals as a conservation strategy.
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Shoguchi E. Gene clusters for biosynthesis of mycosporine-like amino acids in dinoflagellate nuclear genomes: Possible recent horizontal gene transfer between species of Symbiodiniaceae (Dinophyceae). JOURNAL OF PHYCOLOGY 2022; 58:1-11. [PMID: 34699617 PMCID: PMC9298759 DOI: 10.1111/jpy.13219] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 10/01/2021] [Accepted: 10/12/2021] [Indexed: 05/12/2023]
Abstract
Global warming increases the temperature of the ocean surface, which can disrupt dinoflagellate-coral symbioses and result in coral bleaching. Photosynthetic dinoflagellates of the family Symbiodiniaceae include bleaching-tolerant and bleaching-sensitive coral symbionts. Therefore, understanding the molecular mechanisms for changing symbiont diversity is potentially useful to assist recovery of coral holobionts (corals and their associated microbes, including multiple species of Symbiodiniaceae), although sexual reproduction has not been observed in the Symbiodiniaceae. Recent molecular phylogenetic analyses estimate that the Symbiodiniaceae appeared 160 million years ago and diversified into 15 groups, five genera of which now have available draft genomes (i.e., Symbiodinium, Durusdinium, Breviolum, Fugacium, and Cladocopium). Comparative genomic analyses have suggested that crown groups have fewer gene families than early-diverging groups, although many genes that were probably acquired via gene duplications and horizontal gene transfers (HGTs) have been found in each decoded genome. Because UV stress is likely a contributor to coral bleaching, and because the highly conserved gene cluster for mycosporine-like amino acid (MAA) biosynthesis has been found in thermal-tolerant symbiont genomes, I reviewed genomic features of the Symbiodiniaceae, focusing on possible acquisition of a biosynthetic gene cluster for MAAs, which absorb UV radiation. On the basis of highly conserved noncoding sequences, I hypothesized that HGTs have occurred among members of the Symbiodiniaceae and have contributed to the diversification of Symbiodiniaceae-host relationships. Finally, I proposed that bleaching tolerance may be strengthened by multiple MAAs from both symbiotic dinoflagellates and corals.
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Affiliation(s)
- Eiichi Shoguchi
- Marine Genomics UnitOkinawa Institute of Science and Technology Graduate UniversityOnnaOkinawa904‐0495Japan
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40
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Medina M, Baker DM, Baltrus DA, Bennett GM, Cardini U, Correa AMS, Degnan SM, Christa G, Kim E, Li J, Nash DR, Marzinelli E, Nishiguchi M, Prada C, Roth MS, Saha M, Smith CI, Theis KR, Zaneveld J. Grand Challenges in Coevolution. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2021.618251] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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Liang J, Luo W, Yu K, Xu Y, Chen J, Deng C, Ge R, Su H, Huang W, Wang G. Multi-Omics Revealing the Response Patterns of Symbiotic Microorganisms and Host Metabolism in Scleractinian Coral Pavona minuta to Temperature Stresses. Metabolites 2021; 12:metabo12010018. [PMID: 35050140 PMCID: PMC8780272 DOI: 10.3390/metabo12010018] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 12/21/2021] [Accepted: 12/21/2021] [Indexed: 12/30/2022] Open
Abstract
Global climate change has resulted in large-scale coral reef decline worldwide, for which the ocean warming has paid more attention. Coral is a typical mutually beneficial symbiotic organism with diverse symbiotic microorganisms, which maintain the stability of physiological functions. This study compared the responses of symbiotic microorganisms and host metabolism in a common coral species, Pavona minuta, under indoor simulated thermal and cold temperatures. The results showed that abnormal temperature stresses had unfavorable impact on the phenotypes of corals, resulting in bleaching and color change. The compositions of symbiotic bacteria and dinoflagellate communities only presented tiny changes under temperature stresses. However, some rare symbiotic members have been showed to be significantly influenced by water temperatures. Finally, by using ultra-performance liquid chromatography tandem mass spectrometry (UPLC–MS) method, we found that different temperature stresses had very different impacts on the metabolism of coral holobiont. The thermal and cold stresses induced the decrease of anti-oxidation metabolites, several monogalactosyldiacylglycerols (MGDGs), and the increase of lipotoxic metabolite, 10-oxo-nonadecanoic acid, in the coral holobiont, respectively. Our study indicated the response patterns of symbiotic microorganisms and host metabolism in coral to the thermal and cold stresses, providing theoretical data for the adaptation and evolution of coral to a different climate in the future.
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Affiliation(s)
- Jiayuan Liang
- Coral Reef Research Center of China, Guangxi University, Nanning 530004, China; (J.L.); (H.S.); (W.H.); (G.W.)
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Nanning 530004, China
- School of Marine Sciences, Guangxi University, Nanning 530004, China; (W.L.); (Y.X.); (J.C.); (C.D.); (R.G.)
| | - Wenwen Luo
- School of Marine Sciences, Guangxi University, Nanning 530004, China; (W.L.); (Y.X.); (J.C.); (C.D.); (R.G.)
| | - Kefu Yu
- Coral Reef Research Center of China, Guangxi University, Nanning 530004, China; (J.L.); (H.S.); (W.H.); (G.W.)
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Nanning 530004, China
- School of Marine Sciences, Guangxi University, Nanning 530004, China; (W.L.); (Y.X.); (J.C.); (C.D.); (R.G.)
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai 519080, China
- Correspondence: ; Tel./Fax: +86-771-3231358
| | - Yongqian Xu
- School of Marine Sciences, Guangxi University, Nanning 530004, China; (W.L.); (Y.X.); (J.C.); (C.D.); (R.G.)
| | - Jinni Chen
- School of Marine Sciences, Guangxi University, Nanning 530004, China; (W.L.); (Y.X.); (J.C.); (C.D.); (R.G.)
| | - Chuanqi Deng
- School of Marine Sciences, Guangxi University, Nanning 530004, China; (W.L.); (Y.X.); (J.C.); (C.D.); (R.G.)
| | - Ruiqi Ge
- School of Marine Sciences, Guangxi University, Nanning 530004, China; (W.L.); (Y.X.); (J.C.); (C.D.); (R.G.)
| | - Hongfei Su
- Coral Reef Research Center of China, Guangxi University, Nanning 530004, China; (J.L.); (H.S.); (W.H.); (G.W.)
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Nanning 530004, China
- School of Marine Sciences, Guangxi University, Nanning 530004, China; (W.L.); (Y.X.); (J.C.); (C.D.); (R.G.)
| | - Wen Huang
- Coral Reef Research Center of China, Guangxi University, Nanning 530004, China; (J.L.); (H.S.); (W.H.); (G.W.)
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Nanning 530004, China
- School of Marine Sciences, Guangxi University, Nanning 530004, China; (W.L.); (Y.X.); (J.C.); (C.D.); (R.G.)
| | - Guanghua Wang
- Coral Reef Research Center of China, Guangxi University, Nanning 530004, China; (J.L.); (H.S.); (W.H.); (G.W.)
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Nanning 530004, China
- School of Marine Sciences, Guangxi University, Nanning 530004, China; (W.L.); (Y.X.); (J.C.); (C.D.); (R.G.)
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Contrasting microbiome dynamics of putative denitrifying bacteria in two octocoral species exposed to dissolved organic carbon (DOC) and warming. Appl Environ Microbiol 2021; 88:e0188621. [PMID: 34788073 PMCID: PMC8788706 DOI: 10.1128/aem.01886-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Mutualistic nutrient cycling in the coral-algae symbiosis depends on limited nitrogen (N) availability for algal symbionts. Denitrifying prokaryotes capable of reducing nitrate or nitrite to dinitrogen could thus support coral holobiont functioning by limiting N availability. Octocorals show some of the highest denitrification rates among reef organisms; however, little is known about the community structures of associated denitrifiers and their response to environmental fluctuations. Combining 16S rRNA gene amplicon sequencing with nirS in-silico PCR and quantitative PCR, we found differences in bacterial community dynamics between two octocorals exposed to excess dissolved organic carbon (DOC) and concomitant warming. Although bacterial communities of the gorgonian Pinnigorgia flava remained largely unaffected by DOC and warming, the soft coral Xenia umbellata exhibited a pronounced shift toward Alphaproteobacteria dominance under excess DOC. Likewise, the relative abundance of denitrifiers was not altered in P. flava but decreased by 1 order of magnitude in X. umbellata under excess DOC, likely due to decreased proportions of Ruegeria spp. Given that holobiont C:N ratios remained stable in P. flava but showed a pronounced increase with excess DOC in X. umbellata, our results suggest that microbial community dynamics may reflect the nutritional status of the holobiont. Hence, denitrifier abundance may be directly linked to N availability. This suggests a passive regulation of N cycling microbes based on N availability, which could help stabilize nutrient limitation in the coral-algal symbiosis and thereby support holobiont functioning in a changing environment. IMPORTANCE Octocorals are important members of reef-associated benthic communities that can rapidly replace scleractinian corals as the dominant ecosystem engineers on degraded reefs. Considering the substantial change in the (a)biotic environment that is commonly driving reef degradation, maintaining a dynamic and metabolically diverse microbial community might contribute to octocoral acclimatization. Nitrogen (N) cycling microbes, in particular denitrifying prokaryotes, may support holobiont functioning by limiting internal N availability, but little is known about the identity and (a)biotic drivers of octocoral-associated denitrifiers. Here, we show contrasting dynamics of bacterial communities associated with two common octocoral species, the soft coral Xenia umbellata and the gorgonian Pinnigorgia flava after a 6-week exposure to excess dissolved organic carbon under concomitant warming conditions. The specific responses of denitrifier communities of the two octocoral species aligned with the nutritional status of holobiont members. This suggests a passive regulation based on N availability in the coral holobiont.
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Maire J, Blackall LL, van Oppen MJH. Intracellular Bacterial Symbionts in Corals: Challenges and Future Directions. Microorganisms 2021; 9:2209. [PMID: 34835335 PMCID: PMC8619543 DOI: 10.3390/microorganisms9112209] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/21/2021] [Accepted: 10/21/2021] [Indexed: 02/07/2023] Open
Abstract
Corals are the main primary producers of coral reefs and build the three-dimensional reef structure that provides habitat to more than 25% of all marine eukaryotes. They harbor a complex consortium of microorganisms, including bacteria, archaea, fungi, viruses, and protists, which they rely on for their survival. The symbiosis between corals and bacteria is poorly studied, and their symbiotic relationships with intracellular bacteria are only just beginning to be acknowledged. In this review, we emphasize the importance of characterizing intracellular bacteria associated with corals and explore how successful approaches used to study such microorganisms in other systems could be adapted for research on corals. We propose a framework for the description, identification, and functional characterization of coral-associated intracellular bacterial symbionts. Finally, we highlight the possible value of intracellular bacteria in microbiome manipulation and mitigating coral bleaching.
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Affiliation(s)
- Justin Maire
- School of Biosciences, The University of Melbourne, Melbourne, VIC 3010, Australia; (L.L.B.); (M.J.H.v.O.)
| | - Linda L. Blackall
- School of Biosciences, The University of Melbourne, Melbourne, VIC 3010, Australia; (L.L.B.); (M.J.H.v.O.)
| | - Madeleine J. H. van Oppen
- School of Biosciences, The University of Melbourne, Melbourne, VIC 3010, Australia; (L.L.B.); (M.J.H.v.O.)
- Australian Institute of Marine Science, Townsville, QLD 4810, Australia
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Characterization of the Microbiome of Corals with Stony Coral Tissue Loss Disease along Florida's Coral Reef. Microorganisms 2021; 9:microorganisms9112181. [PMID: 34835306 PMCID: PMC8623284 DOI: 10.3390/microorganisms9112181] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/05/2021] [Accepted: 10/12/2021] [Indexed: 01/04/2023] Open
Abstract
Stony coral tissue loss disease (SCTLD) is an emergent and often lethal coral disease that was first reported near Miami, FL (USA) in 2014. Our objective was to determine if coral colonies showing signs of SCTLD possess a specific microbial signature across five susceptible species sampled in Florida’s Coral Reef. Three sample types were collected: lesion tissue and apparently unaffected tissue of diseased colonies, and tissue of apparently healthy colonies. Using 16S rRNA high-throughput gene sequencing, our results show that, for every species, the microbial community composition of lesion tissue was significantly different from healthy colony tissue and from the unaffected tissue of diseased colonies. The lesion tissue of all but one species (Siderastrea siderea) had higher relative abundances of the order Rhodobacterales compared with other types of tissue samples, which may partly explain why S. siderea lesions often differed in appearance compared to other species. The order Clostridiales was also present at relatively high abundances in the lesion tissue of three species compared to healthy and unaffected tissues. Stress often leads to the dysbiosis of coral microbiomes and increases the abundance of opportunistic pathogens. The present study suggests that Rhodobacterales and Clostridiales likely play an important role in SCTLD.
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45
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Dungan AM, Bulach D, Lin H, van Oppen MJH, Blackall LL. Development of a free radical scavenging bacterial consortium to mitigate oxidative stress in cnidarians. Microb Biotechnol 2021; 14:2025-2040. [PMID: 34259383 PMCID: PMC8449677 DOI: 10.1111/1751-7915.13877] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 06/13/2021] [Indexed: 12/19/2022] Open
Abstract
Corals are colonized by symbiotic microorganisms that profoundly influence the animal’s health. One noted symbiont is a single‐celled alga (in the dinoflagellate family Symbiodiniaceae), which provides the coral with most of its fixed carbon. Thermal stress increases the production of reactive oxygen species (ROS) by Symbiodiniaceae during photosynthesis. ROS can both damage the algal symbiont’s photosynthetic machinery and inhibit its repair, causing a positive feedback loop for the toxic accumulation of ROS. If not scavenged by the antioxidant network, excess ROS may trigger a signaling cascade ending with the coral host and algal symbiont disassociating in a process known as bleaching. We use Exaiptasia diaphana as a model for corals and constructed a consortium comprised of E. diaphana–associated bacteria capable of neutralizing ROS. We identified six strains with high free radical scavenging (FRS) ability belonging to the families Alteromonadaceae, Rhodobacteraceae, Flavobacteriaceae and Micrococcaceae. In parallel, we established a consortium of low FRS isolates consisting of genetically related strains. Bacterial whole genome sequences were used to identify key pathways that are known to influence ROS.
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Affiliation(s)
- Ashley M Dungan
- School of Biosciences, The University of Melbourne, Melbourne, Vic., Australia
| | - Dieter Bulach
- Melbourne Bioinformatics, The University of Melbourne, Melbourne, Vic., Australia
| | - Heyu Lin
- School of Earth Sciences, The University of Melbourne, Melbourne, Vic., Australia
| | - Madeleine J H van Oppen
- School of Biosciences, The University of Melbourne, Melbourne, Vic., Australia.,Australian Institute of Marine Science, Townsville, Qld, Australia
| | - Linda L Blackall
- School of Biosciences, The University of Melbourne, Melbourne, Vic., Australia
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Kumar P, Lee JH, Lee J. Diverse roles of microbial indole compounds in eukaryotic systems. Biol Rev Camb Philos Soc 2021; 96:2522-2545. [PMID: 34137156 PMCID: PMC9290978 DOI: 10.1111/brv.12765] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 06/07/2021] [Accepted: 06/08/2021] [Indexed: 02/06/2023]
Abstract
Indole and its derivatives are widespread across different life forms, functioning as signalling molecules in prokaryotes and with more diverse roles in eukaryotes. A majority of indoles found in the environment are attributed to bacterial enzymes converting tryptophan into indole and its derivatives. The involvement of indoles among lower organisms as an interspecies and intraspecies signal is well known, with many reports showing that inter‐kingdom interactions involving microbial indole compounds are equally important as they influence defence systems and even the behaviour of higher organisms. This review summarizes recent advances in our understanding of the functional properties of indole and indole derivatives in diverse eukaryotes. Furthermore, we discuss current perspectives on the role of microbial indoles in human diseases such as diabetes, obesity, atherosclerosis, and cancers. Deciphering the function of indoles as biomarkers of metabolic state will facilitate the formulation of diet‐based treatments and open unique therapeutic opportunities.
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Affiliation(s)
- Prasun Kumar
- School of Chemical Engineering, Yeungnam University, 280 Daehak-Ro, Gyeongsan, 38541, Republic of Korea
| | - Jin-Hyung Lee
- School of Chemical Engineering, Yeungnam University, 280 Daehak-Ro, Gyeongsan, 38541, Republic of Korea
| | - Jintae Lee
- School of Chemical Engineering, Yeungnam University, 280 Daehak-Ro, Gyeongsan, 38541, Republic of Korea
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Röthig T, Puntin G, Wong JCY, Burian A, McLeod W, Baker DM. Holobiont nitrogen control and its potential for eutrophication resistance in an obligate photosymbiotic jellyfish. MICROBIOME 2021; 9:127. [PMID: 34078452 PMCID: PMC8173792 DOI: 10.1186/s40168-021-01075-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 04/07/2021] [Indexed: 05/08/2023]
Abstract
BACKGROUND Marine holobionts depend on microbial members for health and nutrient cycling. This is particularly evident in cnidarian-algae symbioses that facilitate energy and nutrient acquisition. However, this partnership is highly sensitive to environmental change-including eutrophication-that causes dysbiosis and contributes to global coral reef decline. Yet, some holobionts exhibit resistance to dysbiosis in eutrophic environments, including the obligate photosymbiotic scyphomedusa Cassiopea xamachana. METHODS Our aim was to assess the mechanisms in C. xamachana that stabilize symbiotic relationships. We combined labelled bicarbonate (13C) and nitrate (15N) with metabarcoding approaches to evaluate nutrient cycling and microbial community composition in symbiotic and aposymbiotic medusae. RESULTS C-fixation and cycling by algal Symbiodiniaceae was essential for C. xamachana as even at high heterotrophic feeding rates aposymbiotic medusae continuously lost weight. Heterotrophically acquired C and N were readily shared among host and algae. This was in sharp contrast to nitrate assimilation by Symbiodiniaceae, which appeared to be strongly restricted. Instead, the bacterial microbiome seemed to play a major role in the holobiont's DIN assimilation as uptake rates showed a significant positive relationship with phylogenetic diversity of medusa-associated bacteria. This is corroborated by inferred functional capacity that links the dominant bacterial taxa (~90 %) to nitrogen cycling. Observed bacterial community structure differed between apo- and symbiotic C. xamachana putatively highlighting enrichment of ammonium oxidizers and nitrite reducers and depletion of nitrogen-fixers in symbiotic medusae. CONCLUSION Host, algal symbionts, and bacterial associates contribute to regulated nutrient assimilation and cycling in C. xamachana. We found that the bacterial microbiome of symbiotic medusae was seemingly structured to increase DIN removal and enforce algal N-limitation-a mechanism that would help to stabilize the host-algae relationship even under eutrophic conditions. Video abstract.
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Affiliation(s)
- Till Röthig
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong, SAR of China
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Giulia Puntin
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong, SAR of China
- Department of Animal Ecology & Systematics, Justus Liebig University, Giessen, Germany
| | - Jane C. Y. Wong
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong, SAR of China
| | - Alfred Burian
- Marine Ecology Department, Lurio University, Nampula, Mozambique
- Department of Computational Landscape Ecology, UFZ– Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Wendy McLeod
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong, SAR of China
| | - David M. Baker
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong, SAR of China
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Costa RM, Cárdenas A, Loussert-Fonta C, Toullec G, Meibom A, Voolstra CR. Surface Topography, Bacterial Carrying Capacity, and the Prospect of Microbiome Manipulation in the Sea Anemone Coral Model Aiptasia. Front Microbiol 2021; 12:637834. [PMID: 33897642 PMCID: PMC8060496 DOI: 10.3389/fmicb.2021.637834] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 02/19/2021] [Indexed: 11/13/2022] Open
Abstract
Aiptasia is an emerging model organism to study cnidarian symbioses due to its taxonomic relatedness to other anthozoans such as stony corals and similarities of its microalgal and bacterial partners, complementing the existing Hydra (Hydrozoa) and Nematostella (Anthozoa) model systems. Despite the availability of studies characterizing the microbiomes of several natural Aiptasia populations and laboratory strains, knowledge on basic information, such as surface topography, bacterial carrying capacity, or the prospect of microbiome manipulation is lacking. Here we address these knowledge gaps. Our results show that the surface topographies of the model hydrozoan Hydra and anthozoans differ substantially, whereas the ultrastructural surface architecture of Aiptasia and stony corals is highly similar. Further, we determined a bacterial carrying capacity of ∼104 and ∼105 bacteria (i.e., colony forming units, CFUs) per polyp for aposymbiotic and symbiotic Aiptasia anemones, respectively, suggesting that the symbiotic status changes bacterial association/density. Microbiome transplants from Acropora humilis and Porites sp. to gnotobiotic Aiptasia showed that only a few foreign bacterial taxa were effective colonizers. Our results shed light on the putative difficulties of transplanting microbiomes between cnidarians in a manner that consistently changes microbial host association at large. At the same time, our study provides an avenue to identify bacterial taxa that exhibit broad ability to colonize different hosts as a starting point for cross-species microbiome manipulation. Our work is relevant in the context of microbial therapy (probiotics) and microbiome manipulation in corals and answers to the need of having cnidarian model systems to test the function of bacteria and their effect on holobiont biology. Taken together, we provide important foundation data to extend Aiptasia as a coral model for bacterial functional studies.
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Affiliation(s)
- Rúben M Costa
- Division of Biological and Environmental Science and Engineering, Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Anny Cárdenas
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Céline Loussert-Fonta
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Gaëlle Toullec
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Anders Meibom
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Center for Advanced Surface Analysis, Institute of Earth Sciences, University of Lausanne, Lausanne, Switzerland
| | - Christian R Voolstra
- Division of Biological and Environmental Science and Engineering, Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,Department of Biology, University of Konstanz, Konstanz, Germany
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Intracellular bacteria are common and taxonomically diverse in cultured and in hospite algal endosymbionts of coral reefs. ISME JOURNAL 2021; 15:2028-2042. [PMID: 33558689 PMCID: PMC8245515 DOI: 10.1038/s41396-021-00902-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 01/13/2021] [Accepted: 01/19/2021] [Indexed: 02/06/2023]
Abstract
Corals house a variety of microorganisms which they depend on for their survival, including endosymbiotic dinoflagellates (Symbiodiniaceae) and bacteria. While cnidarian–microorganism interactions are widely studied, Symbiodiniaceae–bacteria interactions are only just beginning to receive attention. Here, we describe the localization and composition of the bacterial communities associated with cultures of 11 Symbiodiniaceae strains from nine species and six genera. Three-dimensional confocal laser scanning and electron microscopy revealed bacteria are present inside the Symbiodiniaceae cells as well as closely associated with their external cell surface. Bacterial pure cultures and 16S rRNA gene metabarcoding from Symbiodiniaceae cultures highlighted distinct and highly diverse bacterial communities occur intracellularly, closely associated with the Symbiodiniaceae outer cell surface and loosely associated (i.e., in the surrounding culture media). The intracellular bacteria are highly conserved across Symbiodiniaceae species, suggesting they may be involved in Symbiodiniaceae physiology. Our findings provide unique new insights into the biology of Symbiodiniaceae.
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Iha C, Dougan KE, Varela JA, Avila V, Jackson CJ, Bogaert KA, Chen Y, Judd LM, Wick R, Holt KE, Pasella MM, Ricci F, Repetti SI, Medina M, Marcelino VR, Chan CX, Verbruggen H. Genomic adaptations to an endolithic lifestyle in the coral-associated alga Ostreobium. Curr Biol 2021; 31:1393-1402.e5. [PMID: 33548192 DOI: 10.1016/j.cub.2021.01.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 11/21/2020] [Accepted: 01/07/2021] [Indexed: 02/06/2023]
Abstract
The green alga Ostreobium is an important coral holobiont member, playing key roles in skeletal decalcification and providing photosynthate to bleached corals that have lost their dinoflagellate endosymbionts. Ostreobium lives in the coral's skeleton, a low-light environment with variable pH and O2 availability. We present the Ostreobium nuclear genome and a metatranscriptomic analysis of healthy and bleached corals to improve our understanding of Ostreobium's adaptations to its extreme environment and its roles as a coral holobiont member. The Ostreobium genome has 10,663 predicted protein-coding genes and shows adaptations for life in low and variable light conditions and other stressors in the endolithic environment. This alga presents a rich repertoire of light-harvesting complex proteins but lacks many genes for photoprotection and photoreceptors. It also has a large arsenal of genes for oxidative stress response. An expansion of extracellular peptidases suggests that Ostreobium may supplement its energy needs by feeding on the organic skeletal matrix, and a diverse set of fermentation pathways allows it to live in the anoxic skeleton at night. Ostreobium depends on other holobiont members for vitamin B12, and our metatranscriptomes identify potential bacterial sources. Metatranscriptomes showed Ostreobium becoming a dominant agent of photosynthesis in bleached corals and provided evidence for variable responses among coral samples and different Ostreobium genotypes. Our work provides a comprehensive understanding of the adaptations of Ostreobium to its extreme environment and an important genomic resource to improve our comprehension of coral holobiont resilience, bleaching, and recovery.
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Affiliation(s)
- Cintia Iha
- School of BioSciences, University of Melbourne, Melbourne, VIC 3010, Australia.
| | - Katherine E Dougan
- School of Chemistry and Molecular Biosciences and Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Javier A Varela
- School of Microbiology, Centre for Synthetic Biology and Biotechnology, Environmental Research Institute, and APC Microbiome Institute, University College Cork, Cork T12 YN60, Ireland
| | - Viridiana Avila
- Pennsylvania State University, University Park, PA 16802, USA
| | | | - Kenny A Bogaert
- Phycology Research Group, Ghent University, Krijgslaan 281 S8, 9000 Gent, Belgium
| | - Yibi Chen
- School of Chemistry and Molecular Biosciences and Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Louise M Judd
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia
| | - Ryan Wick
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia
| | - Kathryn E Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia; London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK
| | - Marisa M Pasella
- School of BioSciences, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Francesco Ricci
- School of BioSciences, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Sonja I Repetti
- School of BioSciences, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Mónica Medina
- Pennsylvania State University, University Park, PA 16802, USA
| | - Vanessa R Marcelino
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia
| | - Cheong Xin Chan
- School of Chemistry and Molecular Biosciences and Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Melbourne, VIC 3010, Australia.
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