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Vohsen SA, Herrera S. Coral microbiomes are structured by environmental gradients in deep waters. ENVIRONMENTAL MICROBIOME 2024; 19:38. [PMID: 38858739 PMCID: PMC11165896 DOI: 10.1186/s40793-024-00579-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 06/02/2024] [Indexed: 06/12/2024]
Abstract
BACKGROUND Coral-associated microbiomes vary greatly between colonies and localities with functional consequences on the host. However, the full extent of variability across the ranges of most coral species remains unknown, especially for corals living in deep waters which span greater ranges. Here, we characterized the microbiomes of four octocoral species from mesophotic and bathyal deep-sea habitats in the northern Gulf of Mexico, Muricea pendula, Swiftia exserta, Callogorgia delta, and Paramuricea biscaya, using 16S rRNA gene metabarcoding. We sampled extensively across their ranges to test for microbiome differentiation between and within species, examining the influence of environmental factors that vary with depth (53-2224 m) and geographic location (over 680 m) as well as the host coral's genotype using RAD-sequencing. RESULTS Coral microbiomes were often dominated by amplicon sequence variants whose abundances varied across their hosts' ranges, including symbiotic taxa: corallicolids, Endozoicomonas, members of the Mollicutes, and the BD1-7 clade. Coral species, depth, and geographic location significantly affected diversity, microbial community composition, and the relative abundance of individual microbes. Depth was the strongest environmental factor determining microbiome structure within species, which influenced the abundance of most dominant symbiotic taxa. Differences in host genotype, bottom temperature, and surface primary productivity could explain a significant part of the microbiome variation associated with depth and geographic location. CONCLUSIONS Altogether, this work demonstrates that the microbiomes of corals in deep waters vary substantially across their ranges in accordance with depth and other environmental conditions. It reveals that the influence of depth on the ecology of mesophotic and deep-sea corals extends to its effects on their microbiomes which may have functional consequences. This work also identifies the distributions of microbes including potential parasites which can be used to inform restoration plans in response to the Deepwater Horizon oil spill.
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Affiliation(s)
- Samuel A Vohsen
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA.
- Lehigh Oceans Research Center, Lehigh University, Bethlehem, PA, USA.
| | - Santiago Herrera
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA.
- Lehigh Oceans Research Center, Lehigh University, Bethlehem, PA, USA.
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2
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Stante M, Weiland-Bräuer N, von Hoyningen-Huene AJE, Schmitz RA. Marine bacteriophages disturb the associated microbiota of Aurelia aurita with a recoverable effect on host morphology. Front Microbiol 2024; 15:1356337. [PMID: 38533338 PMCID: PMC10964490 DOI: 10.3389/fmicb.2024.1356337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 02/21/2024] [Indexed: 03/28/2024] Open
Abstract
The concept of the metaorganism describes a multicellular host and its diverse microbial community, which form one biological unit with a combined genetic repertoire that significantly influences health and survival of the host. The present study delved into the emerging field of bacteriophage research within metaorganisms, focusing on the moon jellyfish Aurelia aurita as a model organism. The previously isolated Pseudomonas phage BSwM KMM1 and Citrobacter phages BSwM KMM2 - KMM4 demonstrated potent infectivity on bacteria present in the A. aurita-associated microbiota. In a host-fitness experiment, Baltic Sea subpopulation polyps were exposed to individual phages and a phage cocktail, monitoring polyp survival and morphology, as well as microbiome changes. The following effects were obtained. First, phage exposure in general led to recoverable malformations in polyps without affecting their survival. Second, analyses of the community structure, using 16S rRNA amplicon sequencing, revealed alterations in the associated microbial community in response to phage exposure. Third, the native microbiota is dominated by an uncultured likely novel Mycoplasma species, potentially specific to A. aurita. Notably, this main colonizer showed resilience through the recovery after initial declines, which aligned with abundance changes in Bacteroidota and Proteobacteria, suggesting a dynamic and adaptable microbial community. Overall, this study demonstrates the resilience of the A. aurita metaorganism facing phage-induced perturbations, emphasizing the importance of understanding host-phage interactions in metaorganism biology. These findings have implications for ecological adaptation and conservation in the rapidly changing marine environment, particularly regarding the regulation of blooming species and the health of marine ecosystems during ongoing environmental changes.
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Affiliation(s)
| | | | | | - Ruth Anne Schmitz
- Institute of General Microbiology, Christian-Albrechts University Kiel, Kiel, Germany
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3
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Hochart C, Paoli L, Ruscheweyh HJ, Salazar G, Boissin E, Romac S, Poulain J, Bourdin G, Iwankow G, Moulin C, Ziegler M, Porro B, Armstrong EJ, Hume BCC, Aury JM, Pogoreutz C, Paz-García DA, Nugues MM, Agostini S, Banaigs B, Boss E, Bowler C, de Vargas C, Douville E, Flores M, Forcioli D, Furla P, Gilson E, Lombard F, Pesant S, Reynaud S, Thomas OP, Troublé R, Wincker P, Zoccola D, Allemand D, Planes S, Thurber RV, Voolstra CR, Sunagawa S, Galand PE. Ecology of Endozoicomonadaceae in three coral genera across the Pacific Ocean. Nat Commun 2023; 14:3037. [PMID: 37264015 DOI: 10.1038/s41467-023-38502-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 04/26/2023] [Indexed: 06/03/2023] Open
Abstract
Health and resilience of the coral holobiont depend on diverse bacterial communities often dominated by key marine symbionts of the Endozoicomonadaceae family. The factors controlling their distribution and their functional diversity remain, however, poorly known. Here, we study the ecology of Endozoicomonadaceae at an ocean basin-scale by sampling specimens from three coral genera (Pocillopora, Porites, Millepora) on 99 reefs from 32 islands across the Pacific Ocean. The analysis of 2447 metabarcoding and 270 metagenomic samples reveals that each coral genus harbored a distinct new species of Endozoicomonadaceae. These species are composed of nine lineages that have distinct biogeographic patterns. The most common one, found in Pocillopora, appears to be a globally distributed symbiont with distinct metabolic capabilities, including the synthesis of amino acids and vitamins not produced by the host. The other lineages are structured partly by the host genetic lineage in Pocillopora and mainly by the geographic location in Porites. Millepora is more rarely associated to Endozoicomonadaceae. Our results show that different coral genera exhibit distinct strategies of host-Endozoicomonadaceae associations that are defined at the bacteria lineage level.
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Affiliation(s)
- Corentin Hochart
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, 66650, Banyuls sur Mer, France
| | - Lucas Paoli
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, 8093, Zürich, Switzerland
| | - Hans-Joachim Ruscheweyh
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, 8093, Zürich, Switzerland
| | - Guillem Salazar
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, 8093, Zürich, Switzerland
| | - Emilie Boissin
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Sarah Romac
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, Roscoff, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France
| | | | - Guillaume Iwankow
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | | | - Maren Ziegler
- Department of Animal Ecology & Systematics, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32 (IFZ), 35392, Giessen, Germany
| | - Barbara Porro
- CNRS, INSERM, Institute for Research on Cancer and Aging (IRCAN), Université Côte d'Azur, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Principality of Monaco
| | - Eric J Armstrong
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Benjamin C C Hume
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France
| | - Claudia Pogoreutz
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - David A Paz-García
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), La Paz, Baja California Sur, 23096, México
| | - Maggy M Nugues
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Sylvain Agostini
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1, Shimoda, Shizuoka, Japan
| | - Bernard Banaigs
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, ME, 04469, USA
| | - Chris Bowler
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Colomban de Vargas
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, Roscoff, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France
| | - Eric Douville
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, 91191, Gif-sur-Yvette, France
| | - Michel Flores
- Weizmann Institute of Science, Department of Earth and Planetary Sciences, 76100, Rehovot, Israel
| | - Didier Forcioli
- CNRS, INSERM, Institute for Research on Cancer and Aging (IRCAN), Université Côte d'Azur, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Principality of Monaco
| | - Paola Furla
- CNRS, INSERM, Institute for Research on Cancer and Aging (IRCAN), Université Côte d'Azur, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Principality of Monaco
| | - Eric Gilson
- CNRS, INSERM, Institute for Research on Cancer and Aging (IRCAN), Université Côte d'Azur, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Principality of Monaco
- Department of Medical Genetics, CHU Nice, Nice, France
| | - Fabien Lombard
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France
- Sorbonne Université, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, 06230, Villefranche-sur-Mer, France
- Institut Universitaire de France, 75231, Paris, France
| | - Stéphane Pesant
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Stéphanie Reynaud
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Principality of Monaco
- Centre Scientifique de Monaco, Monaco, Principality of Monaco
| | - Olivier P Thomas
- School of Biological and Chemical Sciences, Ryan Institute, University of Galway, Galway, Ireland
| | - Romain Troublé
- Fondation Tara Océan, 8 rue de Prague, 75012, Paris, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France
| | - Didier Zoccola
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Principality of Monaco
- Centre Scientifique de Monaco, Monaco, Principality of Monaco
| | - Denis Allemand
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Principality of Monaco
- Centre Scientifique de Monaco, Monaco, Principality of Monaco
| | - Serge Planes
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France
| | | | | | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, 8093, Zürich, Switzerland
| | - Pierre E Galand
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, 66650, Banyuls sur Mer, France.
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France.
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4
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Offret C, Gauthier O, Despréaux G, Bidault A, Corporeau C, Miner P, Petton B, Pernet F, Fabioux C, Paillard C, Le Blay G. Microbiota of the Digestive Glands and Extrapallial Fluids of Clams Evolve Differently Over Time Depending on the Intertidal Position. MICROBIAL ECOLOGY 2023; 85:288-297. [PMID: 35066615 DOI: 10.1007/s00248-022-01959-0] [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: 10/15/2021] [Accepted: 01/04/2022] [Indexed: 02/08/2023]
Abstract
The Manila clam (Ruditapes philippinarum) is the second most exploited bivalve in the world but remains threatened by diseases and global changes. Their associated microbiota play a key role in their fitness and acclimation capacities. This study aimed at better understanding the behavior of clam digestive glands and extrapallial fluids microbiota at small, but contrasting spatial and temporal scales. Results showed that environmental variations impacted clam microbiota differently according to the considered tissue. Each clam tissue presented its own microbiota and showed different dynamics according to the intertidal position and sampling period. Extrapallial fluids microbiota was modified more rapidly than digestive glands microbiota, for clams placed on the upper and lower intertidal position, respectively. Clam tissues could be considered as different microhabitats for bacteria as they presented different responses to small-scale temporal and spatial variabilities in natural conditions. These differences underlined a more stringent environmental filter capacity of the digestive glands.
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Affiliation(s)
- Clément Offret
- Univ Brest, CNRS, IRD, Ifremer, LEMAR, F-29280, Plouzané, France
| | - Olivier Gauthier
- Univ Brest, CNRS, IRD, Ifremer, LEMAR, F-29280, Plouzané, France
| | | | - Adeline Bidault
- Univ Brest, CNRS, IRD, Ifremer, LEMAR, F-29280, Plouzané, France
| | | | - Philippe Miner
- Ifremer, Univ Brest, CNRS, IRD, LEMAR, Plouzané, 29280, Brest, France
| | - Bruno Petton
- Ifremer, Univ Brest, CNRS, IRD, LEMAR, Plouzané, 29280, Brest, France
| | - Fabrice Pernet
- Ifremer, Univ Brest, CNRS, IRD, LEMAR, Plouzané, 29280, Brest, France
| | - Caroline Fabioux
- Univ Brest, CNRS, IRD, Ifremer, LEMAR, F-29280, Plouzané, France
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5
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Woo S, Yum S. Transcriptional response of the azooxanthellate octocoral Scleronephthya gracillimum to seawater acidification and thermal stress. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2022; 42:100978. [PMID: 35259638 DOI: 10.1016/j.cbd.2022.100978] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 01/28/2022] [Accepted: 02/16/2022] [Indexed: 06/14/2023]
Abstract
The stress responses to increased seawater temperature and marine acidification were investigated using a microarray to reveal transcriptional changes in S. gracillimum. For the study, corals were exposed to different stress experiments; high temperature only (26 °C, 28 °C and 30 °C), low-pH only (pH 7.5, pH 7.0 and pH 6.5) and dual stress experiments (28 °C + pH 7.8, 28 °C + pH 7.5 and 28 °C + pH 7.0), mortality and morphological changes in 24 h exposure experiments were investigated. The survival rates of each experimental group were observed. The gene expression changes in single and dual stress exposed coals were measured and the differentially expressed genes were classified with gene ontology analysis. The top three enriched gene ontology terms of DEGs in response to dual stress were metal ion binding (23.4%), extracellular region (17.2%), and calcium ion binding (12.8%). The gene showing the greatest increase in expression as a response to the dual stress was hemagglutinin/amebocyte aggregation factor, followed by interferon-inducible GTPase 5 and the gene showing the greatest decrease as a response to the dual stress was Fas-associating death domain-containing protein, followed by oxidase 2. These results represented the transcriptomic study focused on the stress responses of the temperate asymbiotic soft coral exposed to single and dual stresses. The combined effect of thermal and acidification stress on corals triggered the negative regulation of ion binding and extracellular matrix coding genes and these genes might serve as a basis for research into coral-specific adaptations to stress responses and global climate change.
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Affiliation(s)
- Seonock Woo
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Busan 49111, South Korea
| | - Seungshic Yum
- Ecological Risk Research Division, Korea Institute of Ocean Sciences and Technology, Geoje 53201, South Korea; KIOST School, University of Science and Technology, Geoje 53201, South Korea.
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6
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Haydon TD, Suggett DJ, Siboni N, Kahlke T, Camp EF, Seymour JR. Temporal Variation in the Microbiome of Tropical and Temperate Octocorals. MICROBIAL ECOLOGY 2022; 83:1073-1087. [PMID: 34331071 DOI: 10.1007/s00248-021-01823-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 07/15/2021] [Indexed: 06/13/2023]
Abstract
Bacterial members of the coral holobiont play an important role in determining coral fitness. However, most knowledge of the coral microbiome has come from reef-building scleractinian corals, with far less known about the nature and importance of the microbiome of octocorals (subclass Octocorallia), which contribute significantly to reef biodiversity and functional complexity. We examined the diversity and structure of the bacterial component of octocoral microbiomes over summer and winter, with a focus on two temperate (Erythropodium hicksoni, Capnella gaboensis; Sydney Harbour) and two tropical (Sinularia sp., Sarcophyton sp.; Heron Island) species common to reefs in eastern Australia. Bacterial communities associated with these octocorals were also compared to common temperate (Plesiastrea versipora) and tropical (Acropora aspera) hard corals from the same reefs. Using 16S rRNA amplicon sequencing, bacterial diversity was found to be heterogeneous among octocorals, but we observed changes in composition between summer and winter for some species (C. gaboensis and Sinularia sp.), but not for others (E. hicksoni and Sarcophyton sp.). Bacterial community structure differed significantly between all octocoral species within both the temperate and tropical environments. However, on a seasonal basis, those differences were less pronounced. The microbiomes of C. gaboensis and Sinularia sp. were dominated by bacteria belonging to the genus Endozoicomonas, which were a key conserved feature of their core microbiomes. In contrast to previous studies, our analysis revealed that Endozoicomonas phylotypes are shared across different octocoral species, inhabiting different environments. Together, our data demonstrates that octocorals harbour a broad diversity of bacterial partners, some of which comprise 'core microbiomes' that potentially impart important functional roles to their hosts.
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Affiliation(s)
- Trent D Haydon
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Ultimo, NSW, 2007, Australia.
| | - David J Suggett
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Nachshon Siboni
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Tim Kahlke
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Emma F Camp
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Justin R Seymour
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Ultimo, NSW, 2007, Australia
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7
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Qi Z, Diao X, Yang T, Zeng R, Wang H, Zhou H. Spatial and interspecific differences in coral-associated bacterial diversity in Hainan, China. MARINE POLLUTION BULLETIN 2022; 175:113321. [PMID: 35149312 DOI: 10.1016/j.marpolbul.2022.113321] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 12/13/2021] [Accepted: 01/03/2022] [Indexed: 06/14/2023]
Abstract
Coral reefs are suffering from environmental change and anthropogenic disturbances. It is well known that microbes play an indispensable role in the stable state of coral reef health. Furthermore, the coral reef microbial database helps to understand the connections among microbiomes shifts and ecosystem stress. Hainan Province is the main coral reef distribution area in China. Therefore, targeted microbial reference information from Hainan, including several coral microbiomes, was generated by 16S rRNA gene sequencing in this study. This study focused on a small range of coral-associated bacterial information and found a relationship between microbes and the surrounding environment based on coral interspecific and environmental factors. Interestingly, compared with species, the differences of bacterial community structures are best explained by site. It seems that various environmental factors contribute more to the microbial structure of corals than interspecific influences.
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Affiliation(s)
- Zhao Qi
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China; College of Ecology and Environment, Hainan University, Haikou 570228, China
| | - Xiaoping Diao
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China; College of Life Science, Hainan Normal University, Haikou 571158, China.
| | - Tinghan Yang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China; College of Ecology and Environment, Hainan University, Haikou 570228, China
| | - Ruohan Zeng
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China; College of Ecology and Environment, Hainan University, Haikou 570228, China
| | - Haihua Wang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China; College of Ecology and Environment, Hainan University, Haikou 570228, China
| | - Hailong Zhou
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China; College of Life Sciences and Pharmacy, Hainan University, Haikou 570228, China
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8
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Yu X, Yu K, Liao Z, Chen B, Deng C, Yu J, Yao Q, Qin Z, Liang J. Seasonal fluctuations in symbiotic bacteria and their role in environmental adaptation of the scleractinian coral Acropora pruinosa in high-latitude coral reef area of the South China Sea. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 792:148438. [PMID: 34153755 DOI: 10.1016/j.scitotenv.2021.148438] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 06/09/2021] [Accepted: 06/09/2021] [Indexed: 06/13/2023]
Abstract
Coral-associated bacterial communities are paramount for coral ecosystems and holobiont health. However, the role of symbiotic bacteria in the adaptation of high-latitude corals to seasonal fluctuations remains underexplored. Therefore, we used 16S rRNA-based high-throughput sequencing to analyze the symbiotic bacterial diversity, composition, and core bacterial community in high-latitude coral and explored the seasonal fluctuation characteristics of symbiotic bacterial communities. We found that bacterial richness and α-diversity changed significantly across different seasons. Additionally, the community structure recombined seasonally, with different dominant bacterial phyla and genera in different seasons. However, the symbiotic bacterial community structures of Acropora pruinosa in winter and spring were similar. Proteobacteria were the dominant bacteria in spring, autumn, and winter. In summer, the dominant bacterial taxa were Bacteroidota and Proteobacteria. Ralstonia was the dominant bacterial genus in spring and winter, whereas in autumn, BD1-7_clade was dominant. Linear discriminant analysis effect size identified 20 abundant genera between the different groups. Core microbiome analysis revealed that 12 core bacterial operational taxonomic units were associated with A. pruinosa in all seasons, seven of which varied with the seasons, changing between dominant and rare. Distance-based redundancy and variation partitioning analyses revealed that sea surface temperature was the major contributor of variation in the microbial community structure. We hypothesized that the high diversity and abundance of symbiotic bacteria and the increase in Prosthecochloris abundance in coral in summer can help A. pruinosa maintain its physiological functions, ameliorating the negative physiological effects of the decrease in Symbiodiniaceae density under high-temperature stress. Thus, the rapid reorganization of the symbiotic bacterial community structure and core microflora in different seasons may allow the corals to adapt to large seasonal environmental fluctuations. In conclusion, seasonal variation of bacteria plays an important role in coral adaptation to large environmental fluctuations.
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Affiliation(s)
- 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 (Zhuhai), 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
| | - 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
| | - Chuanqi Deng
- 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
| | - Jiaoyang 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
| | - Qiucui Yao
- 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
| | - Jiayuan Liang
- 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
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9
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Influence of temperature changes on symbiotic Symbiodiniaceae and bacterial communities’ structure: an experimental study on soft coral Sarcophyton trocheliophorum (Anthozoa: Alcyoniidae). JOURNAL OF TROPICAL ECOLOGY 2021. [DOI: 10.1017/s0266467421000109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
AbstractIt is well concluded that microbial composition and diversity of coral species can be affected under temperature alterations. However, the interaction of environmental accumulation of corals and temperature stress on symbiotic Symbiodiniaceae and bacterial communities are rarely studied. In this study, two groups of soft coral Sarcophyton trocheliophorum were cultured under constant (26 °C) and inconstant (22 °C to 26 °C) temperature conditions for 30 days as control treatments. After that, water was cooled rapidly to decrease to 20 °C in 24 h. The results of diversity analysis showed that symbiotic Symbiodiniaceae and bacterial communities had a significant difference between the two accumulated groups. The principal coordinate analyses confirmed that symbiotic Symbiodiniaceae and bacterial communities of both control treatments were clustered into two groups. Our results evidenced that rapid cooling stress could not change symbiotic Symbiodiniaceae and bacterial communities’ composition. On the other hand, cooling stress could alter only bacterial communities in constant group. In conclusion, our study represents a clear relationship between environmental accumulation and the impact of short-term cooling stress in which microbial composition structure can be affected by early adaptation conditions.
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10
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Ketchum RN, Smith EG, Vaughan GO, McParland D, Al-Mansoori N, Burt JA, Reitzel AM. Unraveling the predictive role of temperature in the gut microbiota of the sea urchin Echinometra sp. EZ across spatial and temporal gradients. Mol Ecol 2021; 30:3869-3881. [PMID: 34008895 DOI: 10.1111/mec.15990] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 05/06/2021] [Accepted: 05/11/2021] [Indexed: 01/03/2023]
Abstract
Shifts in microbial communities represent a rapid response mechanism for host organisms to respond to changes in environmental conditions. Therefore, they are likely to be important in assisting the acclimatization of hosts to seasonal temperature changes as well as to variation in temperatures across a species' range. The Persian/Arabian Gulf is the world's warmest sea, with large seasonal fluctuations in temperature (20℃ - 37℃) and is connected to the Gulf of Oman which experiences more typical oceanic conditions (<32℃ in the summer). This system is an informative model for understanding how symbiotic microbial assemblages respond to thermal variation across temporal and spatial scales. Here, we elucidate the role of temperature on the microbial gut community of the sea urchin Echinometra sp. EZ and identify microbial taxa that are tightly correlated with the thermal environment. We generated two independent datasets with a high degree of geographic and temporal resolution. The results show that microbial communities vary across thermally variable habitats, display temporal shifts that correlate with temperature, and can become more disperse as temperatures rise. The relative abundances of several ASVs significantly correlate with temperature in both independent datasets despite the >300 km distance between the furthest sites and the extreme seasonal variations. Notably, over 50% of the temperature predictive ASVs identified from the two datasets belonged to the family Vibrionaceae. Together, our results identify temperature as a robust predictor of community-level variation and highlight specific microbial taxa putatively involved in the response to thermal environment.
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Affiliation(s)
- Remi N Ketchum
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Edward G Smith
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA.,Water Research Center & Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Grace O Vaughan
- Water Research Center & Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Dain McParland
- Water Research Center & Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Noura Al-Mansoori
- Water Research Center & Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - John A Burt
- Water Research Center & Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Adam M Reitzel
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA
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11
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King WL, Siboni N, Kahlke T, Dove M, O'Connor W, Mahbub KR, Jenkins C, Seymour JR, Labbate M. Regional and oyster microenvironmental scale heterogeneity in the Pacific oyster bacterial community. FEMS Microbiol Ecol 2020; 96:5813259. [PMID: 32221598 DOI: 10.1093/femsec/fiaa054] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 03/22/2020] [Indexed: 01/04/2023] Open
Abstract
Different organs of a host represent distinct microenvironments resulting in the establishment of multiple discrete bacterial communities within a host. These discrete bacterial communities can also vary according to geographical location. For the Pacific oyster, Crassostrea gigas, the factors governing bacterial diversity and abundance of different oyster microenvironments are poorly understood. In this study, the factors shaping bacterial abundance, diversity and composition associated with the C. gigas mantle, gill, adductor muscle and digestive gland were characterised using 16S (V3-V4) rRNA amplicon sequencing across six discrete estuaries. Both location and tissue-type, with tissue-type being the stronger determinant, were factors driving bacterial community composition. Bacterial communities from wave-dominated estuaries had similar compositions and higher bacterial abundance despite being geographically distant from one another, possibly indicating that functional estuarine morphology characteristics are a factor shaping the oyster bacterial community. Despite the bacterial community heterogeneity, examinations of the core bacterial community identified Spirochaetaceae bacteria as conserved across all sites and samples. Whereas members of the Vulcaniibacterium, Spirochaetaceae and Margulisbacteria, and Polynucleobacter were regionally conserved members of the digestive gland, gill and mantle bacterial communities, respectively. This indicates that baseline bacterial community profiles for specific locations are necessary when investigating bacterial communities in oyster health.
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Affiliation(s)
- William L King
- University of Technology Sydney, The School of Life Sciences, Ultimo, New South Wales, 2007, Australia.,University of Technology Sydney, Climate Change Cluster, Ultimo, New South Wales, 2007, Australia
| | - Nachshon Siboni
- University of Technology Sydney, Climate Change Cluster, Ultimo, New South Wales, 2007, Australia
| | - Tim Kahlke
- University of Technology Sydney, Climate Change Cluster, Ultimo, New South Wales, 2007, Australia
| | - Michael Dove
- NSW Department of Primary Industries, Port Stephens Fisheries Institute, Port Stephens, New South Wales, 2316, Australia
| | - Wayne O'Connor
- NSW Department of Primary Industries, Port Stephens Fisheries Institute, Port Stephens, New South Wales, 2316, Australia
| | - Khandaker Rayhan Mahbub
- University of Technology Sydney, The School of Life Sciences, Ultimo, New South Wales, 2007, Australia
| | - Cheryl Jenkins
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, New South Wales, 2568, Australia
| | - Justin R Seymour
- University of Technology Sydney, Climate Change Cluster, Ultimo, New South Wales, 2007, Australia
| | - Maurizio Labbate
- University of Technology Sydney, The School of Life Sciences, Ultimo, New South Wales, 2007, Australia
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12
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Yang SH, Tseng CH, Lo HP, Chiang PW, Chen HJ, Shiu JH, Lai HC, Tandon K, Isomura N, Mezaki T, Yamamoto H, Tang SL. Locality Effect of Coral-Associated Bacterial Community in the Kuroshio Current From Taiwan to Japan. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.569107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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13
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Mhuantong W, Nuryadi H, Trianto A, Sabdono A, Tangphatsornruang S, Eurwilaichitr L, Kanokratana P, Champreda V. Comparative analysis of bacterial communities associated with healthy and diseased corals in the Indonesian sea. PeerJ 2019; 7:e8137. [PMID: 31875145 PMCID: PMC6925950 DOI: 10.7717/peerj.8137] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 11/01/2019] [Indexed: 01/22/2023] Open
Abstract
Coral reef ecosystems are impacted by climate change and human activities, such as increasing coastal development, overfishing, sewage and other pollutant discharge, and consequent eutrophication, which triggers increasing incidents of diseases and deterioration of corals worldwide. In this study, bacterial communities associated with four species of corals: Acropora aspera, Acropora formosa, Cyphastrea sp., and Isopora sp. in the healthy and disease stages with different diseases were compared using tagged 16S rRNA sequencing. In total, 59 bacterial phyla, 190 orders, and 307 genera were assigned in coral metagenomes where Proteobacteria and Firmicutes were pre-dominated followed by Bacteroidetes together with Actinobacteria, Fusobacteria, and Lentisphaerae as minor taxa. Principal Coordinates Analysis (PCoA) showed separated clustering of bacterial diversity in healthy and infected groups for individual coral species. Fusibacter was found as the major bacterial genus across all corals. The lower number of Fusibacter was found in A. aspera infected with white band disease and Isopora sp. with white plaque disease, but marked increases of Vibrio and Acrobacter, respectively, were observed. This was in contrast to A. formosa infected by a black band and Cyphastrea sp. infected by yellow blotch diseases which showed an increasing abundance of Fusibacter but a decrease in WH1-8 bacteria. Overall, infection was shown to result in disturbance in the complexity and structure of the associated bacterial microbiomes which can be relevant to the pathogenicity of the microbes associated with infected corals.
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Affiliation(s)
- Wuttichai Mhuantong
- Biorefinery and Bioproduct Technology Research Group, National Center for Genetic Engineering and Biotechnology, Pathum Thani, Thailand
| | - Handung Nuryadi
- Faculty of Fisheries and Marine Science, Diponegoro University, Semarang, Indonesia
| | - Agus Trianto
- Faculty of Fisheries and Marine Science, Diponegoro University, Semarang, Indonesia
| | - Agus Sabdono
- Faculty of Fisheries and Marine Science, Diponegoro University, Semarang, Indonesia
| | | | - Lily Eurwilaichitr
- Biorefinery and Bioproduct Technology Research Group, National Center for Genetic Engineering and Biotechnology, Pathum Thani, Thailand
| | - Pattanop Kanokratana
- Biorefinery and Bioproduct Technology Research Group, National Center for Genetic Engineering and Biotechnology, Pathum Thani, Thailand
| | - Verawat Champreda
- Biorefinery and Bioproduct Technology Research Group, National Center for Genetic Engineering and Biotechnology, Pathum Thani, Thailand
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