101
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Pootakham W, Mhuantong W, Yoocha T, Putchim L, Jomchai N, Sonthirod C, Naktang C, Kongkachana W, Tangphatsornruang S. Heat-induced shift in coral microbiome reveals several members of the Rhodobacteraceae family as indicator species for thermal stress in Porites lutea. Microbiologyopen 2019; 8:e935. [PMID: 31544365 PMCID: PMC6925168 DOI: 10.1002/mbo3.935] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 08/25/2019] [Accepted: 08/28/2019] [Indexed: 02/01/2023] Open
Abstract
The coral holobiont is a complex ecosystem consisting of coral animals and a highly diverse consortium of associated microorganisms including algae, fungi, and bacteria. Several studies have highlighted the importance of coral‐associated bacteria and their potential roles in promoting the host fitness and survival. Recently, dynamics of coral‐associated microbiomes have been demonstrated to be linked to patterns of coral heat tolerance. Here, we examined the effect of elevated seawater temperature on the structure and diversity of bacterial populations associated with Porites lutea, using full‐length 16S rRNA sequences obtained from Pacific Biosciences circular consensus sequencing. We observed a significant increase in alpha diversity indices and a distinct shift in microbiome composition during thermal stress. There was a marked decline in the apparent relative abundance of Gammaproteobacteria family Endozoicomonadaceae after P. lutea had been exposed to elevated seawater temperature. Concomitantly, the bacterial community structure shifted toward the predominance of Alphaproteobacteria family Rhodobacteraceae. Interestingly, we did not observe an increase in relative abundance of Vibrio‐related sequences in our heat‐stressed samples even though the appearance of Vibrio spp. has often been detected in parallel with the increase in the relative abundance of Rhodobacteraceae during thermal bleaching in other coral species. The ability of full‐length 16S rRNA sequences in resolving taxonomic uncertainty of associated bacteria at a species level enabled us to identify 24 robust indicator bacterial species for thermally stressed corals. It is worth noting that the majority of those indicator species were members of the family Rhodobacteraceae. The comparison of bacterial community structure and diversity between corals in ambient water temperature and thermally stressed corals may provide a better understanding on how bacteria symbionts contribute to the resilience of their coral hosts to ocean warming.
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Affiliation(s)
- Wirulda Pootakham
- National Omics Center, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Wuttichai Mhuantong
- Enzyme Technology Research Team, Biorefinery and Bioproduct Technology Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Thippawan Yoocha
- National Omics Center, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | | | - Nukoon Jomchai
- National Omics Center, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Chutima Sonthirod
- National Omics Center, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Chaiwat Naktang
- National Omics Center, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Wasitthee Kongkachana
- National Omics Center, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Sithichoke Tangphatsornruang
- National Omics Center, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
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102
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Pogoreutz C, Gore MA, Perna G, Millar C, Nestler R, Ormond RF, Clarke CR, Voolstra CR. Similar bacterial communities on healthy and injured skin of black tip reef sharks. Anim Microbiome 2019; 1:9. [PMID: 33499949 PMCID: PMC7807711 DOI: 10.1186/s42523-019-0011-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 07/22/2019] [Indexed: 02/07/2023] Open
Abstract
Background Sharks are in severe global decline due to human exploitation. The additional concern of emerging diseases for this ancient group of fish, however, remains poorly understood. While wild-caught and captive sharks may be susceptible to bacterial and transmissible diseases, recent reports suggest that shark skin may harbor properties that prevent infection, such as a specialized ultrastructure or innate immune properties, possibly related to associated microbial assemblages. To assess whether bacterial community composition differs between visibly healthy and insulted (injured) shark skin, we compared bacterial assemblages of skin covering the gills and the back from 44 wild-caught black-tip reef sharks (Carcharhinus melanopterus) from the Amirante Islands (Seychelles) via 16S rRNA gene amplicon sequencing. Results Shark skin-associated bacterial communities were diverse (5971 bacterial taxa from 375 families) and dominated by three families of the phylum Proteobacteria typical of marine organisms and environments (Rhodobacteraceae, Alteromonadaceae, Halomonadaceae). Significant differences in bacterial community composition of skin were observed for sharks collected from different sites, but not between healthy or injured skin samples or skin type (gills vs. back). The core microbiome (defined as bacterial taxa present in ≥50% of all samples) consisted of 12 bacterial taxa, which are commonly observed in marine organisms, some of which may be associated with animal host health. Conclusion The conserved bacterial community composition of healthy and injured shark skin samples suggests absence of severe bacterial infections or substantial pathogen propagation upon skin insult. While a mild bacterial infection may have gone undetected, the overall conserved bacterial community implies that bacterial function(s) may be maintained in injured skin. At present, the contribution of bacteria, besides intrinsic animal host factors, to counter skin infection and support rapid wound healing in sharks are unknown. This represents clear knowledge gaps that should be addressed in future work, e.g. by screening for antimicrobial properties of skin-associated bacterial isolates. Electronic supplementary material The online version of this article (10.1186/s42523-019-0011-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Claudia Pogoreutz
- Red Sea Research Center, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955, Saudi Arabia
| | - Mauvis A Gore
- Marine Conservation International, South Queensferry, Edinburgh, Scotland, UK.,Centre for Marine Biodiversity & Biotechnology, Heriot-Watt University, Riccarton, Edinburgh, Scotland, UK
| | - Gabriela Perna
- Red Sea Research Center, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955, Saudi Arabia
| | - Catriona Millar
- Marine Conservation International, South Queensferry, Edinburgh, Scotland, UK.,Centre for Marine Biodiversity & Biotechnology, Heriot-Watt University, Riccarton, Edinburgh, Scotland, UK
| | - Robert Nestler
- Veterinär-Physiologisch-Chemisches Institut, University of Leipzig, 04107 Leipzig, Germany
| | - Rupert F Ormond
- Marine Conservation International, South Queensferry, Edinburgh, Scotland, UK. .,Centre for Marine Biodiversity & Biotechnology, Heriot-Watt University, Riccarton, Edinburgh, Scotland, UK. .,Faculty of Marine Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia.
| | | | - Christian R Voolstra
- Red Sea Research Center, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955, Saudi Arabia. .,Department of Biology, University of Konstanz, 78457, Konstanz, Germany.
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103
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Epstein HE, Smith HA, Cantin NE, Mocellin VJL, Torda G, van Oppen MJH. Temporal Variation in the Microbiome of Acropora Coral Species Does Not Reflect Seasonality. Front Microbiol 2019; 10:1775. [PMID: 31474944 PMCID: PMC6706759 DOI: 10.3389/fmicb.2019.01775] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 07/18/2019] [Indexed: 12/22/2022] Open
Abstract
The coral microbiome is known to fluctuate in response to environmental variation and has been suggested to vary seasonally. However, most studies to date, particularly studies on bacterial communities, have examined temporal variation over a time frame of less than 1 year, which is insufficient to establish if microbiome variations are indeed seasonal in nature. The present study focused on expanding our understanding of long-term variability in microbial community composition using two common coral species, Acropora hyacinthus, and Acropora spathulata, at two mid-shelf reefs on the Great Barrier Reef. By sampling over a 2-year time period, this study aimed to determine whether temporal variations reflect seasonal cycles. Community composition of both bacteria and Symbiodiniaceae was characterized through 16S rRNA gene and ITS2 rDNA metabarcoding. We observed significant variations in community composition of both bacteria and Symbiodiniaceae among time points for A. hyacinthus and A. spathulata. However, there was no evidence to suggest that temporal variations were cyclical in nature and represented seasonal variation. Clear evidence for differences in the microbial communities found between reefs suggests that reef location and coral species play a larger role than season in driving microbial community composition in corals. In order to identify the basis of temporal patterns in coral microbial community composition, future studies should employ longer time series of sampling at sufficient temporal resolution to identify the environmental correlates of microbiome variation.
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Affiliation(s)
- Hannah E. Epstein
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, Australia
- AIMS@JCU, James Cook University, Townsville, QLD, Australia
- Australian Institute of Marine Science, Townsville, QLD, Australia
| | - Hillary A. Smith
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia
| | - Neal E. Cantin
- Australian Institute of Marine Science, Townsville, QLD, Australia
| | | | - Gergely Torda
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, Australia
- Australian Institute of Marine Science, Townsville, QLD, Australia
| | - Madeleine J. H. van Oppen
- Australian Institute of Marine Science, Townsville, QLD, Australia
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia
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104
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Chan WY, Peplow LM, Menéndez P, Hoffmann AA, Oppen MJH. The roles of age, parentage and environment on bacterial and algal endosymbiont communities in
Acropora
corals. Mol Ecol 2019; 28:3830-3843. [DOI: 10.1111/mec.15187] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 06/28/2019] [Accepted: 07/15/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Wing Yan Chan
- Australian Institute of Marine Science Townsville Qld Australia
- School of BioSciences University of Melbourne Parkville Vic. Australia
| | - Lesa M. Peplow
- Australian Institute of Marine Science Townsville Qld Australia
| | - Patricia Menéndez
- Australian Institute of Marine Science Townsville Qld Australia
- Department of Econometrics and Business Statistics, School of Mathematics and Physics Monash University Clayton Vic. Australia
| | - Ary A. Hoffmann
- Bio21 Institute University of Melbourne Parkville Vic. Australia
| | - Madeleine J. H. Oppen
- Australian Institute of Marine Science Townsville Qld Australia
- School of BioSciences University of Melbourne Parkville Vic. Australia
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105
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Coral bacterial community structure responds to environmental change in a host-specific manner. Nat Commun 2019; 10:3092. [PMID: 31300639 PMCID: PMC6626051 DOI: 10.1038/s41467-019-10969-5] [Citation(s) in RCA: 125] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 06/12/2019] [Indexed: 01/09/2023] Open
Abstract
The global decline of coral reefs heightens the need to understand how corals respond to changing environmental conditions. Corals are metaorganisms, so-called holobionts, and restructuring of the associated bacterial community has been suggested as a means of holobiont adaptation. However, the potential for restructuring of bacterial communities across coral species in different environments has not been systematically investigated. Here we show that bacterial community structure responds in a coral host-specific manner upon cross-transplantation between reef sites with differing levels of anthropogenic impact. The coral Acropora hemprichii harbors a highly flexible microbiome that differs between each level of anthropogenic impact to which the corals had been transplanted. In contrast, the microbiome of the coral Pocillopora verrucosa remains remarkably stable. Interestingly, upon cross-transplantation to unaffected sites, we find that microbiomes become indistinguishable from back-transplanted controls, suggesting the ability of microbiomes to recover. It remains unclear whether differences to associate with bacteria flexibly reflects different holobiont adaptation mechanisms to respond to environmental change. The flexibility of corals to associate with different bacteria in different environments has not been systematically investigated. Here, the authors study bacterial community dynamics for two coral species and show that bacterial community structure responds to environmental changes in a host-specific manner.
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106
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Bernasconi R, Stat M, Koenders A, Paparini A, Bunce M, Huggett MJ. Establishment of Coral-Bacteria Symbioses Reveal Changes in the Core Bacterial Community With Host Ontogeny. Front Microbiol 2019; 10:1529. [PMID: 31338082 PMCID: PMC6629827 DOI: 10.3389/fmicb.2019.01529] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 06/18/2019] [Indexed: 12/25/2022] Open
Abstract
Bacterial communities are fundamental symbionts of corals. However, the process by which bacterial communities are acquired across the life history of corals, particularly in larval and early juvenile stages, is still poorly characterized. Here, transfer of bacteria of the Scleractinian coral Acropora digitifera from adults to spawned egg-sperm bundles was analyzed, as well as acquisition across early developmental stages (larvae and newly settled spat), and 6-month-old juveniles. Larvae were reared under manipulated environmental conditions to determine the source (maternal, seawater, or sediment) of bacteria likely to establish symbiotic relationships with the host using amplicon sequencing of the 16S rRNA gene. Maternal colonies directly transferred bacteria from the families Rhodobacteraceae, Cryomorphaceae, and Endozoicimonaceae to egg-sperm bundles. Furthermore, significant differences in the microbial community structure were identified across generations, yet the structure of the coral bacterial community across early life history stages was not impacted by different environmental rearing conditions. These data indicate that the uptake and structure of bacterial communities is developmentally, rather than environmentally, regulated. Both maternal coral colonies and ubiquitous bacteria found across environmental substrates represent a potential source of symbionts important in establishing the coral microbiome. Uniquely, we report the presence of variation with ontogeny of both the core and resident bacterial communities, supporting the hypothesis that microbial communities are likely to play specific roles within the distinct life history stages of the coral host.
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Affiliation(s)
- Rachele Bernasconi
- Centre for Marine Ecosystems Research, Edith Cowan University, Joondalup, WA, Australia
- Centre for Ecosystem Management, School of Science, Edith Cowan University, Joondalup, WA, Australia
| | - Michael Stat
- Faculty of Science, School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, Australia
| | - Annette Koenders
- Centre for Ecosystem Management, School of Science, Edith Cowan University, Joondalup, WA, Australia
| | - Andrea Paparini
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, Australia
| | - Michael Bunce
- Trace and Environmental DNA Laboratory, Department of Environment and Agriculture Curtin University, Bentley, WA, Australia
| | - Megan J. Huggett
- Centre for Marine Ecosystems Research, Edith Cowan University, Joondalup, WA, Australia
- Centre for Ecosystem Management, School of Science, Edith Cowan University, Joondalup, WA, Australia
- Faculty of Science, School of Environmental and Life Sciences, The University of Newcastle, Ourimbah, NSW, Australia
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107
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Astudillo-García C, Hermans SM, Stevenson B, Buckley HL, Lear G. Microbial assemblages and bioindicators as proxies for ecosystem health status: potential and limitations. Appl Microbiol Biotechnol 2019; 103:6407-6421. [DOI: 10.1007/s00253-019-09963-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 06/03/2019] [Accepted: 06/04/2019] [Indexed: 01/04/2023]
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108
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Zhang XH, Liu J, Liu J, Yang G, Xue CX, Curson ARJ, Todd JD. Biogenic production of DMSP and its degradation to DMS-their roles in the global sulfur cycle. SCIENCE CHINA-LIFE SCIENCES 2019; 62:1296-1319. [PMID: 31231779 DOI: 10.1007/s11427-018-9524-y] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 03/16/2019] [Indexed: 01/08/2023]
Abstract
Dimethyl sulfide (DMS) is the most abundant form of volatile sulfur in Earth's oceans, and is mainly produced by the enzymatic clevage of dimethylsulfoniopropionate (DMSP). DMS and DMSP play important roles in driving the global sulfur cycle and may affect climate. DMSP is proposed to serve as an osmolyte, a grazing deterrent, a signaling molecule, an antioxidant, a cryoprotectant and/or as a sink for excess sulfur. It was long believed that only marine eukaryotes such as phytoplankton produce DMSP. However, we recently discovered that marine heterotrophic bacteria can also produce DMSP, making them a potentially important source of DMSP. At present, one prokaryotic and two eukaryotic DMSP synthesis enzymes have been identified. Marine heterotrophic bacteria are likely the major degraders of DMSP, using two known pathways: demethylation and cleavage. Many phytoplankton and some fungi can also cleave DMSP. So far seven different prokaryotic and one eukaryotic DMSP lyases have been identified. This review describes the global distribution pattern of DMSP and DMS, the known genes for biosynthesis and cleavage of DMSP, and the physiological and ecological functions of these important organosulfur molecules, which will improve understanding of the mechanisms of DMSP and DMS production and their roles in the environment.
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Affiliation(s)
- Xiao-Hua Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| | - Ji Liu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Jingli Liu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Guipeng Yang
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao, 266071, China
| | - Chun-Xu Xue
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Andrew R J Curson
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Jonathan D Todd
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
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109
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Boza G, Worsley SF, Yu DW, Scheuring I. Efficient assembly and long-term stability of defensive microbiomes via private resources and community bistability. PLoS Comput Biol 2019; 15:e1007109. [PMID: 31150382 PMCID: PMC6576795 DOI: 10.1371/journal.pcbi.1007109] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 06/17/2019] [Accepted: 05/15/2019] [Indexed: 11/19/2022] Open
Abstract
Understanding the mechanisms that promote the assembly and maintenance of host-beneficial microbiomes is an open problem. Empirical evidence supports the idea that animal and plant hosts can combine 'private resources' with the ecological phenomenon known as 'community bistability' to favour some microbial strains over others. We briefly review evidence showing that hosts can: (i) protect the growth of beneficial strains in an isolated habitat, (ii) use antibiotics to suppress non-beneficial, competitor strains, and (iii) provide resources that only beneficial strains are able to translate into an increased rate of growth, reproduction, or antibiotic production. We then demonstrate in a spatially explicit, individual-based model that these three mechanisms act similarly by selectively promoting the initial proliferation of preferred strains, that is, by acting as a private resource. The faster early growth of preferred strains, combined with the phenomenon of 'community bistability,' allows those strains to continue to dominate the microbiome even after the private resource is withdrawn or made public. This is because after a beneficial colony reaches a sufficiently large size, it can resist invasion by parasites without further private support from the host. We further explicitly model localized microbial interactions and diffusion dynamics, and we show that an intermediate level of antibiotic diffusion is the most efficient mechanism in promoting preferred strains and that there is a wide range of parameters under which hosts can promote the assembly of a self-sustaining defensive microbiome. This in turn supports the idea that hosts readily evolve to promote host-beneficial defensive microbiomes.
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Affiliation(s)
- Gergely Boza
- Evolutionary Systems Research Group, MTA Centre for Ecological Research, Hungarian Academy of Sciences, Tihany, Hungary
- International Institute for Applied Systems Analysis (IIASA), Laxenburg, Austria
- * E-mail: , (GB); (IS)
| | - Sarah F. Worsley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Douglas W. Yu
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - István Scheuring
- Evolutionary Systems Research Group, MTA Centre for Ecological Research, Hungarian Academy of Sciences, Tihany, Hungary
- MTA-ELTE Theoretical Biology and Evolutionary Ecology Research Group, Hungarian Academy of Sciences, Budapest, Hungary
- * E-mail: , (GB); (IS)
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110
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Pollock FJ, Lamb JB, van de Water JAJM, Smith HA, Schaffelke B, Willis BL, Bourne DG. Reduced diversity and stability of coral-associated bacterial communities and suppressed immune function precedes disease onset in corals. ROYAL SOCIETY OPEN SCIENCE 2019; 6:190355. [PMID: 31312497 PMCID: PMC6599770 DOI: 10.1098/rsos.190355] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 05/08/2019] [Indexed: 05/28/2023]
Abstract
Disease is an emerging threat to coral reef ecosystems worldwide, highlighting the need to understand how environmental conditions interact with coral immune function and associated microbial communities to affect holobiont health. Increased coral disease incidence on reefs adjacent to permanently moored platforms on Australia's Great Barrier Reef provided a unique case study to investigate environment-host-microbe interactions in situ. Here, we evaluate coral-associated bacterial community (16S rRNA amplicon sequencing), immune function (protein-based prophenoloxidase-activating system), and water quality parameters before, during and after a disease event. Over the course of the study, 31% of tagged colonies adjacent to platforms developed signs of white syndrome (WS), while all control colonies on a platform-free reef remained visually healthy. Corals adjacent to platforms experienced significant reductions in coral immune function. Additionally, the corals at platform sites that remained visually healthy throughout the study had reduced bacterial diversity compared to healthy colonies at the platform-free site. Interestingly, prior to the observation of macroscopic disease, corals that would develop WS had reduced bacterial diversity and significantly greater community heterogeneity between colonies compared to healthy corals at the same location. These results suggest that activities associated with offshore marine infrastructure impacts coral immunocompetence and associated bacterial community, which affects the susceptibility of corals to disease.
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Affiliation(s)
- F. Joseph Pollock
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
- Australian Institute of Marine Science, Townsville, Queensland, Australia
- AIMS@JCU, Australian Institute of Marine Science and James Cook University, Townsville, Queensland, Australia
- Department of Ecology and Evolutionary Biology, Pennsylvania State University, University Park, PA, USA
| | - Joleah B. Lamb
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
| | - Jeroen A. J. M. van de Water
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
- Australian Institute of Marine Science, Townsville, Queensland, Australia
- AIMS@JCU, Australian Institute of Marine Science and James Cook University, Townsville, Queensland, Australia
- Centre Scientifique de Monaco, 8 Quai Antoine 1er, Monaco, Monaco
| | - Hillary A. Smith
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - Britta Schaffelke
- Australian Institute of Marine Science, Townsville, Queensland, Australia
| | - Bette L. Willis
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
- AIMS@JCU, Australian Institute of Marine Science and James Cook University, Townsville, Queensland, Australia
| | - David G. Bourne
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
- Australian Institute of Marine Science, Townsville, Queensland, Australia
- AIMS@JCU, Australian Institute of Marine Science and James Cook University, Townsville, Queensland, Australia
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111
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Huggett MJ, Apprill A. Coral microbiome database: Integration of sequences reveals high diversity and relatedness of coral-associated microbes. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:372-385. [PMID: 30094953 PMCID: PMC7379671 DOI: 10.1111/1758-2229.12686] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 08/04/2018] [Indexed: 05/10/2023]
Abstract
Coral-associated microorganisms are thought to play a fundamental role in the health and ecology of corals, but understanding of specific coral-microbial interactions are lacking. In order to create a framework to examine coral-microbial specificity, we integrated and phylogenetically compared 21,100 SSU rRNA gene Sanger-produced sequences from bacteria and archaea associated with corals from previous studies, and accompanying host, location and publication metadata, to produce the Coral Microbiome Database. From this database, we identified 39 described and candidate phyla of Bacteria and two Archaea phyla associated with corals, demonstrating that corals are one of the most phylogenetically diverse animal microbiomes. Secondly, this new phylogenetic resource shows that certain microorganisms are indeed specific to corals, including evolutionary distinct hosts. Specifically, we identified 2-37 putative monophyletic, coral-specific sequence clusters within bacterial genera associated with the greatest number of coral species (Vibrio, Endozoicomonas and Ruegeria) as well as functionally relevant microbial taxa ("Candidatus Amoebophilus", "Candidatus Nitrosopumilus" and under recognized cyanobacteria). This phylogenetic resource provides a framework for more targeted studies of corals and their specific microbial associates, which is timely given the escalated need to understand the role of the coral microbiome and its adaptability to changing ocean and reef conditions.
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Affiliation(s)
- Megan J. Huggett
- School of Environmental and Life SciencesUniversity of NewcastleOurimbahNSW, 2258Australia
- School of ScienceEdith Cowan UniversityJoondalupWAAustralia
| | - Amy Apprill
- Marine Chemistry and Geochemistry DepartmentWoods Hole Oceanographic InstitutionWoods HoleMAUSA
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112
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Zeng YX, Qiao ZY. Diversity of Dimethylsulfoniopropionate Degradation Genes Reveals the Significance of Marine Roseobacter Clade in Sulfur Metabolism in Coastal Areas of Antarctic Maxwell Bay. Curr Microbiol 2019; 76:967-974. [DOI: 10.1007/s00284-019-01709-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 05/21/2019] [Indexed: 11/24/2022]
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113
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Qin H, Wang S, Feng K, He Z, Virta MPJ, Hou W, Dong H, Deng Y. Unraveling the diversity of sedimentary sulfate-reducing prokaryotes (SRP) across Tibetan saline lakes using epicPCR. MICROBIOME 2019; 7:71. [PMID: 31054577 PMCID: PMC6500586 DOI: 10.1186/s40168-019-0688-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 04/25/2019] [Indexed: 05/07/2023]
Abstract
Sulfate reduction is an important biogeochemical process in the ecosphere; however, the major taxa of sulfate reducers have not been fully identified. Here, we used epicPCR (Emulsion, Paired Isolation, and Concatenation PCR) technology to identify the phylogeny of sulfate-reducing prokaryotes (SRP) in sediments from Tibetan Plateau saline lakes. A total of 12,519 OTUs and 883 SRP-OTUs were detected in ten lakes by sequencing of 16S rRNA gene PCR amplicons and epicPCR products of fused 16S rRNA plus dsrB gene, respectively, with Proteobacteria, Firmicutes, and Bacteroidetes being the dominant phyla in both datasets. The 120 highly abundant SRP-OTUs (> 1% in at least one sample) were affiliated with 17 described phyla, only 7 of which are widely recognized as SRP phyla. The majority of OTUs from both the whole microbial communities and the SRPs were not detected in more than one specific lake, suggesting high levels of endemism. The α-diversity of the entire microbial community and SRP sub-community showed significant positive correlations. The pH value and mean water temperature of the month prior to sampling were the environmental determinants for the whole microbial community, while the mean water temperature and total nitrogen were the major environmental drivers for the SRP sub-community. This study revealed there are still many undocumented SRP in Tibetan saline lakes, many of which could be endemic and adapted to specific environmental conditions.
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Affiliation(s)
- Huayu Qin
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Rd, Haidian, Beijing, 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shang Wang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Rd, Haidian, Beijing, 100085, China
| | - Kai Feng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Rd, Haidian, Beijing, 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhili He
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Marko P J Virta
- Department of Environmental Sciences, University of Helsinki, 00014, Helsinki, Finland
| | - Weiguo Hou
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, China
| | - Hailiang Dong
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, China
- Department of Geology and Environmental Earth Science, Miami University, Oxford, OH, United States
| | - Ye Deng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Rd, Haidian, Beijing, 100085, China.
- Institute for Marine Science and Technology, Shandong University, Qingdao, 266237, China.
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China.
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114
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Zhou Z, Zhao S, Tang J, Liu Z, Wu Y, Wang Y, Lin S. Altered Immune Landscape and Disrupted Coral- Symbiodinium Symbiosis in the Scleractinian Coral Pocillopora damicornis by Vibrio coralliilyticus Challenge. Front Physiol 2019; 10:366. [PMID: 31001143 PMCID: PMC6454040 DOI: 10.3389/fphys.2019.00366] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 03/15/2019] [Indexed: 01/07/2023] Open
Abstract
Vibrio coralliilyticus is known to cause coral diseases, especially under environmental perturbation, but its impact on coral physiology and underpinning mechanism is poorly understood. In the present study, we investigated cytological, immunological, and metatranscriptomic responses of the scleractinian coral Pocillopora damicornis to V. coralliilyticus infection. The density and chlorophyll content of symbiotic zooxanthellae decreased significantly at 12 and 24 h after Vibrio challenge. The activities of antioxidant enzymes such as superoxide dismutase and catalase, nitric oxide synthase, phenoloxidase (PO), and the activation level of caspase3 all rose significantly in P. damicornis after Vibrio challenge. In the metatranscriptomic analysis, we found 10 significantly upregulated genes in the symbionts at 24 h after the challenge, which were mostly involved in the metabolism of nucleic acid and polysaccharide, and 133 significantly down-regulated symbiont genes, which were mainly related to amino acid catabolism and transport. Meanwhile, 1432 significantly upregulated coral genes were revealed, highly overrepresented in GO terms that are mostly related to the regulation of immune response, the regulation of cytokine production, and innate immune response. Furthermore, at 24 h after Vibrio challenge, 890 coral genes were significantly downregulated, highly overrepresented in four GO terms implicated in defense response. These results in concert suggest that V. coralliilyticus infection triggered the innate immune response including the redox, PO, and apoptosis systems, but repressed the response of the complement system in the scleractinian coral P. damicornis, accompanied by symbiont density decrease and symbiosis collapse through disordering the metabolism of the symbionts. These findings shed light on the molecular regulatory processes underlying bleaching and degradation of P. damicornis resulting from the infection of V. coralliilyticus.
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Affiliation(s)
- Zhi Zhou
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou, China.,Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, China
| | - Shuimiao Zhao
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou, China
| | - Jia Tang
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou, China
| | - Zhaoqun Liu
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, China
| | - Yibo Wu
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou, China
| | - Yan Wang
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou, China
| | - Senjie Lin
- Department of Marine Sciences, University of Connecticut, Groton, CT, United States
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115
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Tipton L, Darcy JL, Hynson NA. A Developing Symbiosis: Enabling Cross-Talk Between Ecologists and Microbiome Scientists. Front Microbiol 2019; 10:292. [PMID: 30842763 PMCID: PMC6391321 DOI: 10.3389/fmicb.2019.00292] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 02/04/2019] [Indexed: 12/29/2022] Open
Abstract
Like all interactions, the success of cross-discipline collaborations relies on effective communication. Ecology offers theoretical frameworks and lexicons to study microbiomes. Yet some of the terms and concepts borrowed from ecology are being used discordantly by microbiome studies from their traditional definitions. Here we define some of the ecological terms and concepts as they are used in ecology and the study of microbiomes. Where applicable, we have provided the historical context of the terms, highlighted examples from microbiome studies, and considered the research methods involved. We divided these concepts into four sections: Biomes, Diversity, Symbiosis, and Succession. Biomes encompass the interactions within the biotic and abiotic features of an environment. This extends to the term "microbiome," derived from "biome," and includes an environment and all the microbes within it. Diversity encompasses patterns of species richness, abundance, and biogeography, all of which are important to understanding the distribution of microbiomes. Symbiosis emphasizes the relationships between organisms within a community. Symbioses are often misunderstood to be synonymous with mutualism. We discard that implication, in favor of a broader, more historically accurate definition which spans the continuum from parasitism to mutualism. Succession includes classical succession, alternative stable states, community assembly frameworks, and r/K-selection. Our hope is that as microbiome researchers continue to apply ecological terms, and as ecologists continue to gain interest in microbiomes, each will do so in a way that enables cross-talk between them. We recommend initiating these collaborations by using a common lexicon, from which new concepts can emerge.
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Affiliation(s)
- Laura Tipton
- Department of Botany, University of Hawai’i at Mānoa, Honolulu, HI, United States
| | - John L. Darcy
- Department of Botany, University of Hawai’i at Mānoa, Honolulu, HI, United States
| | - Nicole A. Hynson
- Pacific Biosciences Research Center, University of Hawai’i at Mānoa, Honolulu, HI, United States
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116
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O'Brien PA, Webster NS, Miller DJ, Bourne DG. Host-Microbe Coevolution: Applying Evidence from Model Systems to Complex Marine Invertebrate Holobionts. mBio 2019; 10:e02241-18. [PMID: 30723123 PMCID: PMC6428750 DOI: 10.1128/mbio.02241-18] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Marine invertebrates often host diverse microbial communities, making it difficult to identify important symbionts and to understand how these communities are structured. This complexity has also made it challenging to assign microbial functions and to unravel the myriad of interactions among the microbiota. Here we propose to address these issues by applying evidence from model systems of host-microbe coevolution to complex marine invertebrate microbiomes. Coevolution is the reciprocal adaptation of one lineage in response to another and can occur through the interaction of a host and its beneficial symbiont. A classic indicator of coevolution is codivergence of host and microbe, and evidence of this is found in both corals and sponges. Metabolic collaboration between host and microbe is often linked to codivergence and appears likely in complex holobionts, where microbial symbionts can interact with host cells through production and degradation of metabolic compounds. Neutral models are also useful to distinguish selected microbes against a background population consisting predominately of random associates. Enhanced understanding of the interactions between marine invertebrates and their microbial communities is urgently required as coral reefs face unprecedented local and global pressures and as active restoration approaches, including manipulation of the microbiome, are proposed to improve the health and tolerance of reef species. On the basis of a detailed review of the literature, we propose three research criteria for examining coevolution in marine invertebrates: (i) identifying stochastic and deterministic components of the microbiome, (ii) assessing codivergence of host and microbe, and (iii) confirming the intimate association based on shared metabolic function.
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Affiliation(s)
- Paul A O'Brien
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia
- Australian Institute of Marine Science, Townsville, QLD, Australia
- AIMS@JCU, Townsville, QLD, Australia
| | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, QLD, Australia
- AIMS@JCU, Townsville, QLD, Australia
- Australian Centre for Ecogenomics, University of Queensland, Brisbane, QLD, Australia
| | - David J Miller
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, Australia
| | - David G Bourne
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia
- Australian Institute of Marine Science, Townsville, QLD, Australia
- AIMS@JCU, Townsville, QLD, Australia
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117
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Liu J, Liu J, Zhang SH, Liang J, Lin H, Song D, Yang GP, Todd JD, Zhang XH. Novel Insights Into Bacterial Dimethylsulfoniopropionate Catabolism in the East China Sea. Front Microbiol 2018; 9:3206. [PMID: 30622530 PMCID: PMC6309047 DOI: 10.3389/fmicb.2018.03206] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 12/11/2018] [Indexed: 11/18/2022] Open
Abstract
The compatible solute dimethylsulfoniopropionate (DMSP), made by many marine organisms, is one of Earth's most abundant organosulfur molecules. Many marine bacteria import DMSP and can degrade it as a source of carbon and/or sulfur via DMSP cleavage or DMSP demethylation pathways, which can generate the climate active gases dimethyl sulfide (DMS) or methanthiol (MeSH), respectively. Here we used culture-dependent and -independent methods to study bacteria catabolizing DMSP in the East China Sea (ECS). Of bacterial isolates, 42.11% showed DMSP-dependent DMS (Ddd+) activity, and 12.28% produced detectable levels of MeSH. Interestingly, although most Ddd+ isolates were Alphaproteobacteria (mainly Roseobacters), many gram-positive Actinobacteria were also shown to cleave DMSP producing DMS. The mechanism by which these Actinobacteria cleave DMSP is unknown, since no known functional ddd genes have been identified in genome sequences of Ddd+Microbacterium and Agrococcus isolates or in any other sequenced Actinobacteria genomes. Gene probes to the DMSP demethylation gene dmdA and the DMSP lyase gene dddP demonstrated that these DMSP-degrading genes are abundant and widely distributed in ECS seawaters. dmdA was present in relatively high proportions in both surface (19.53% ± 6.70%) and bottom seawater bacteria (16.00% ± 8.73%). In contrast, dddP abundance positively correlated with chlorophyll a, and gradually decreased with the distance from land, which implies that the bacterial DMSP lyase gene dddP might be from bacterial groups that closely associate with phytoplankton. Bacterial community analysis showed positive correlations between Rhodobacteraceae abundance and concentrations of DMS and DMSP, further confirming the link between this abundant bacterial class and the environmental DMSP cycling.
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Affiliation(s)
- Jingli Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao, China.,School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Ji Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao, China.,School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Sheng-Hui Zhang
- College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao, China
| | - Jinchang Liang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Heyu Lin
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Delei Song
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Gui-Peng Yang
- College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jonathan D Todd
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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118
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Raimundo I, Silva SG, Costa R, Keller-Costa T. Bioactive Secondary Metabolites from Octocoral-Associated Microbes-New Chances for Blue Growth. Mar Drugs 2018; 16:E485. [PMID: 30518125 PMCID: PMC6316421 DOI: 10.3390/md16120485] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Revised: 11/25/2018] [Accepted: 11/29/2018] [Indexed: 12/14/2022] Open
Abstract
Octocorals (Cnidaria, Anthozoa Octocorallia) are magnificent repositories of natural products with fascinating and unusual chemical structures and bioactivities of interest to medicine and biotechnology. However, mechanistic understanding of the contribution of microbial symbionts to the chemical diversity of octocorals is yet to be achieved. This review inventories the natural products so-far described for octocoral-derived bacteria and fungi, uncovering a true chemical arsenal of terpenes, steroids, alkaloids, and polyketides with antibacterial, antifungal, antiviral, antifouling, anticancer, anti-inflammatory, and antimalarial activities of enormous potential for blue growth. Genome mining of 15 bacterial associates (spanning 12 genera) cultivated from Eunicella spp. resulted in the identification of 440 putative and classifiable secondary metabolite biosynthetic gene clusters (BGCs), encompassing varied terpene-, polyketide-, bacteriocin-, and nonribosomal peptide-synthase BGCs. This points towards a widespread yet uncharted capacity of octocoral-associated bacteria to synthetize a broad range of natural products. However, to extend our knowledge and foster the near-future laboratory production of bioactive compounds from (cultivatable and currently uncultivatable) octocoral symbionts, optimal blending between targeted metagenomics, DNA recombinant technologies, improved symbiont cultivation, functional genomics, and analytical chemistry are required. Such a multidisciplinary undertaking is key to achieving a sustainable response to the urgent industrial demand for novel drugs and enzyme varieties.
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Affiliation(s)
- Inês Raimundo
- Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa, 1049-001 Lisbon, Portugal.
| | - Sandra G Silva
- Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa, 1049-001 Lisbon, Portugal.
| | - Rodrigo Costa
- Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa, 1049-001 Lisbon, Portugal.
| | - Tina Keller-Costa
- Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa, 1049-001 Lisbon, Portugal.
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119
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Pratte ZA, Richardson LL. Microbiome dynamics of two differentially resilient corals. DISEASES OF AQUATIC ORGANISMS 2018; 131:213-226. [PMID: 30459293 DOI: 10.3354/dao03289] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Coral bleaching and disease are 2 common occurrences that are contributing to global coral cover decline. Understanding the interactions between the coral animal and its microbial associates, and how they may change in the presence of stressors such as warming and acidification, is a crucial component to understanding both susceptibility and resistance to disease and bleaching. The coral Diploria labyrinthiformis has been shown to be more disease resistant than its relative Pseudodiploria strigosa, providing an ideal study system for disease resistance. In this study, we examined the bacterial communities of these 2 coral species on the Florida Reef tract every 6 mo for 18 mo (in situ sampling), and under experimental (laboratory) thermal and pH manipulation. The in situ sampling encompassed wide fluctuations in temperature, including an anomalously warm summer period. The laboratory experiments involved exposure to both increased temperature (31°C) and lowered pH (7.7). The in situ bacterial communities of both coral species were highly similar in the winter, but diverged during summer, with the D. labyrinthiformis bacterial community being more stable than that of P. strigosa. Differences in the bacterial community between the 2 coral species included 29 operational taxonomic units (OTUs) that were specific to D. labyrinthiformis in all seasons, while only 2 OTUs were specific to P. strigosa. The comparative stability of the D. labyrinthiformis microbiome, in addition to harboring a more specific microbiome, may be a key component of the relative disease resistance of this coral.
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Affiliation(s)
- Zoe A Pratte
- Department of Biological Sciences, Florida International University, Miami, FL 33199, USA
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120
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Shiu JH, Ding JY, Tseng CH, Lou SP, Mezaki T, Wu YT, Wang HI, Tang SL. A Newly Designed Primer Revealed High Phylogenetic Diversity of Endozoicomonas in Coral Reefs. Microbes Environ 2018; 33:172-185. [PMID: 29760298 PMCID: PMC6031392 DOI: 10.1264/jsme2.me18054] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Accepted: 04/08/2018] [Indexed: 11/29/2022] Open
Abstract
Endozoicomonas bacteria are commonly regarded as having a potentially symbiotic relationship with their coral hosts. However, their diversity and phylogeny in samples collected from various sources remain unclear. Therefore, we designed an Endozoicomonas-specific primer paired with a bacterial universal primer to detect the 16S ribosomal RNA (rRNA) genes of this taxon and conducted an in-depth investigation of the Endozoicomonas community structure in reef-building corals. The primer had high specificity in the V3-V4 region (95.6%) and its sensitivity was high, particularly when Endozoicomonas was rare in samples (e.g., in seawater, which had a higher alpha diversity of Endozoicomonas than corals). In coral samples, predominant V3-V4 ribotypes had greater divergence than predominant V1-V2 ribotypes, and were grouped into at least 9 novel clades in a phylogenetic tree, indicating Endozoicomonas had high phylogenetic diversity. Divergence within this genus was potentially higher than that among 7 outgroup genera based on the phylogenetic distances of partial 16S rDNA sequences, suggesting that the taxonomy of this genus needs to be revised. In conclusion, dominant Endozoicomonas populations had variable phylogenies; furthermore, the newly designed primers may be useful molecular tools for the reliable detection of the Endozoicomonas community in marine environments.
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Affiliation(s)
- Jia-Ho Shiu
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia SinicaTaipeiTaiwan
- Biodiversity Research Center, Academia SinicaTaipeiTaiwan
- Graduate Institute of Biotechnology, National Chung-Hsing UniversityTaichungTaiwan
| | - Jiun-Yan Ding
- Biodiversity Research Center, Academia SinicaTaipeiTaiwan
| | - Ching-Hung Tseng
- Biodiversity Research Center, Academia SinicaTaipeiTaiwan
- Bioinformatics Program, Taiwan International Graduate Program, Academia SinicaTaipeiTaiwan
- Institute of Biomedical Informatics, National Yang-Ming UniversityTaipeiTaiwan
| | - Shueh-Ping Lou
- Biodiversity Research Center, Academia SinicaTaipeiTaiwan
| | - Takuma Mezaki
- Biological Institute on Kuroshio, Kuroshio Biological Research FoundationKochiJapan
| | - Yu-Ting Wu
- Biodiversity Research Center, Academia SinicaTaipeiTaiwan
- Department of Forestry, National Pingtung University of Science and TechnologyPingtungTaiwan
| | - Hsiang-Iu Wang
- Biodiversity Research Center, Academia SinicaTaipeiTaiwan
| | - Sen-Lin Tang
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia SinicaTaipeiTaiwan
- Biodiversity Research Center, Academia SinicaTaipeiTaiwan
- Biotechnology Center, National Chung-Hsing UniversityTaichungTaiwan
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121
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Marine Invertebrates: Underexplored Sources of Bacteria Producing Biologically Active Molecules. DIVERSITY-BASEL 2018. [DOI: 10.3390/d10030052] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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122
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van de Water JAJM, Allemand D, Ferrier-Pagès C. Host-microbe interactions in octocoral holobionts - recent advances and perspectives. MICROBIOME 2018; 6:64. [PMID: 29609655 PMCID: PMC5880021 DOI: 10.1186/s40168-018-0431-6] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 03/01/2018] [Indexed: 05/05/2023]
Abstract
Octocorals are one of the most ubiquitous benthic organisms in marine ecosystems from the shallow tropics to the Antarctic deep sea, providing habitat for numerous organisms as well as ecosystem services for humans. In contrast to the holobionts of reef-building scleractinian corals, the holobionts of octocorals have received relatively little attention, despite the devastating effects of disease outbreaks on many populations. Recent advances have shown that octocorals possess remarkably stable bacterial communities on geographical and temporal scales as well as under environmental stress. This may be the result of their high capacity to regulate their microbiome through the production of antimicrobial and quorum-sensing interfering compounds. Despite decades of research relating to octocoral-microbe interactions, a synthesis of this expanding field has not been conducted to date. We therefore provide an urgently needed review on our current knowledge about octocoral holobionts. Specifically, we briefly introduce the ecological role of octocorals and the concept of holobiont before providing detailed overviews of (I) the symbiosis between octocorals and the algal symbiont Symbiodinium; (II) the main fungal, viral, and bacterial taxa associated with octocorals; (III) the dominance of the microbial assemblages by a few microbial species, the stability of these associations, and their evolutionary history with the host organism; (IV) octocoral diseases; (V) how octocorals use their immune system to fight pathogens; (VI) microbiome regulation by the octocoral and its associated microbes; and (VII) the discovery of natural products with microbiome regulatory activities. Finally, we present our perspectives on how the field of octocoral research should move forward, and the recognition that these organisms may be suitable model organisms to study coral-microbe symbioses.
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Affiliation(s)
| | - Denis Allemand
- Centre Scientifique de Monaco, 8 Quai Antoine 1er, 98000, Monaco, Monaco
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124
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Pootakham W, Mhuantong W, Putchim L, Yoocha T, Sonthirod C, Kongkachana W, Sangsrakru D, Naktang C, Jomchai N, Thongtham N, Tangphatsornruang S. Dynamics of coral-associated microbiomes during a thermal bleaching event. Microbiologyopen 2018; 7:e00604. [PMID: 29573244 PMCID: PMC6182559 DOI: 10.1002/mbo3.604] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 12/29/2017] [Accepted: 01/17/2018] [Indexed: 02/01/2023] Open
Abstract
Coral‐associated microorganisms play an important role in their host fitness and survival. A number of studies have demonstrated connections between thermal tolerance in corals and the type/relative abundance of Symbiodinium they harbor. More recently, the shifts in coral‐associated bacterial profiles were also shown to be linked to the patterns of coral heat tolerance. Here, we investigated the dynamics of Porites lutea‐associated bacterial and algal communities throughout a natural bleaching event, using full‐length 16S rRNA and internal transcribed spacer sequences (ITS) obtained from PacBio circular consensus sequencing. We provided evidence of significant changes in the structure and diversity of coral‐associated microbiomes during thermal stress. The balance of the symbiosis shifted from a predominant association between corals and Gammaproteobacteria to a predominance of Alphaproteobacteria and to a lesser extent Betaproteobacteria following the bleaching event. On the contrary, the composition and diversity of Symbiodinium communities remained unaltered throughout the bleaching event. It appears that the switching and/or shuffling of Symbiodinium types may not be the primary mechanism used by P. lutea to cope with increasing seawater temperature. The shifts in the structure and diversity of associated bacterial communities may contribute more to the survival of the coral holobiont under heat stress.
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Affiliation(s)
- Wirulda Pootakham
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Wuttichai Mhuantong
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | | | - Thippawan Yoocha
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Chutima Sonthirod
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Wasitthee Kongkachana
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Duangjai Sangsrakru
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Chaiwat Naktang
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Nukoon Jomchai
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | | | - Sithichoke Tangphatsornruang
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
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Keller-Costa T, Eriksson D, Gonçalves JMS, Gomes NCM, Lago-Lestón A, Costa R. The gorgonian coral Eunicella labiata hosts a distinct prokaryotic consortium amenable to cultivation. FEMS Microbiol Ecol 2018; 93:4563573. [PMID: 29069352 DOI: 10.1093/femsec/fix143] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 10/20/2017] [Indexed: 11/14/2022] Open
Abstract
Microbial communities inhabiting gorgonian corals are believed to benefit their hosts through nutrient provision and chemical defence; yet much remains to be learned about their phylogenetic uniqueness and cultivability. Here, we determined the prokaryotic community structure and distinctiveness in the gorgonian Eunicella labiata by Illumina sequencing of 16S rRNA genes from gorgonian and seawater metagenomic DNA. Furthermore, we used a 'plate-wash' methodology to compare the phylogenetic diversity of the 'total' gorgonian bacteriome and its 'cultivatable' fraction. With 1016 operational taxonomic units (OTUs), prokaryotic richness was higher in seawater than in E. labiata where 603 OTUs were detected, 68 of which were host-specific. Oceanospirillales and Rhodobacterales predominated in the E. labiata communities. One Oceanospirillales OTU, classified as Endozoicomonas, was particularly dominant, and closest relatives comprised exclusively uncultured clones from other gorgonians. We cultivated a remarkable 62% of the bacterial symbionts inhabiting E. labiata: Ruegeria, Sphingorhabdus, Labrenzia, other unclassified Rhodobacteraceae, Vibrio and Shewanella ranked among the 10 most abundant genera in both the cultivation-independent and dependent samples. In conclusion, the E. labiata microbiome is diverse, distinct from seawater and enriched in (gorgonian)-specific bacterial phylotypes. In contrast to current understanding, many dominant E. labiata symbionts can, indeed, be cultivated.
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Affiliation(s)
- Tina Keller-Costa
- Instituto de Bioengenharia e Biociências (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa, 1049-001 Lisbon, Portugal
| | - Dominic Eriksson
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, 8005-139 Faro, Portugal
| | - Jorge M S Gonçalves
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, 8005-139 Faro, Portugal
| | - Newton C M Gomes
- Departamento de Biologia (CESAM), Universidade de Aveiro, 3810-193 Aveiro, Portugal
| | - Asunción Lago-Lestón
- Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), 22860 Ensenada, Mexico
| | - Rodrigo Costa
- Instituto de Bioengenharia e Biociências (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa, 1049-001 Lisbon, Portugal
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126
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Beatty DS, Clements CS, Stewart FJ, Hay ME. Intergenerational effects of macroalgae on a reef coral: major declines in larval survival but subtle changes in microbiomes. MARINE ECOLOGY PROGRESS SERIES 2018; 589:97-114. [PMID: 30505048 PMCID: PMC6261492 DOI: 10.3354/meps12465] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Tropical reefs are shifting from coral to macroalgal dominance, with macroalgae suppressing coral recovery, potentially via effects on coral microbiomes. Understanding how macroalgae affect corals and their microbiomes requires comparing algae- versus coral-dominated reefs without confounding aspects of time and geography. We compared survival, settlement, and post-settlement survival of larvae, as well as the microbiomes of larvae and adults, of the Pacific coral Pocillopora damicornis between an Marine Protected Area (MPA) dominated by corals versus an adjacent fished area dominated by macroalgae. Microbiome composition in adult coral, larval coral, and seawater did not differ between the MPA and fished area. However, microbiomes of adult coral were more variable in the fished area and Vibrionaceae bacteria, including strains most closely related to the pathogen Vibrio shilonii, were significantly enriched, but rare, in adult and larval coral from the fished area. Larvae from the macroalgae-dominated area exhibited higher pre-settlement mortality and reduced settlement compared to those from the coral-dominated area. Juveniles planted into a coral-dominated area survived better than those placed into a fished area dominated by macroalgae. Differential survival depended on whether macroalgae were immediately adjacent to juvenile coral rather than on traits of the areas per se. Contrary to our expectations, coral microbiomes were relatively uniform at the community level despite dramatic differences in macroalgal cover between the MPA (~2% cover) and fished (~90%) area. Reducing macroalgae may elicit declines in rare but potentially harmful microbes in coral and their larvae, as well as positive intergenerational effects on offspring survival.
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Affiliation(s)
- Deanna S. Beatty
- School of Biological Sciences and Aquatic Chemical Ecology Center Georgia Institute of Technology, Atlanta, GA 30332-0230
| | - Cody S. Clements
- School of Biological Sciences and Aquatic Chemical Ecology Center Georgia Institute of Technology, Atlanta, GA 30332-0230
| | - Frank J. Stewart
- School of Biological Sciences and Aquatic Chemical Ecology Center Georgia Institute of Technology, Atlanta, GA 30332-0230
| | - Mark E. Hay
- School of Biological Sciences and Aquatic Chemical Ecology Center Georgia Institute of Technology, Atlanta, GA 30332-0230
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127
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Hettiarachchi SA, Lee SJ, Lee Y, Kwon YK, Kwon KK, Yang SH, Jo E, Kang DH, Oh C. Corallibacterium pacifica gen. nov., sp. nov., a Novel Bacterium of the Family Vibrionaceae Isolated from Hard Coral. Curr Microbiol 2018; 75:835-841. [PMID: 29464363 DOI: 10.1007/s00284-018-1455-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 02/13/2018] [Indexed: 12/19/2022]
Abstract
A gram-negative, rod-shaped, motile, oxidase- and catalase-positive, non-pigmented marine bacterium, designated strain OS-11M-2T, was isolated from a coral sample collected from the Osakura coastal area in Micronesia. Phylogenetic analysis based on 16S ribosomal RNA (rRNA) gene sequences indicated that strain OS-11M-2T is a member of the family Vibrionaceae, its closest neighbors being Photobacterium damselae subsp. piscicida NCIMB 2058T (94.9%), Photobacterium damselae subsp. damselae CIP 102761T (94.75%), Grimontia marina IMCC5001T (94.5%), Enterovibrio coralii LMG 22228T (94.5%), and Grimontia celer 96-237T (94.5%). The major cellular fatty acids were summed feature 3 (21.4%), summed feature 8 (18.5%), iso-C16:0 (13.8%), and C16:0 (11.9%). The major respiratory quinone of the bacterium was ubiquinone-8 (Q-8) and its major polar lipid phosphatidylethanolamine. Six amino lipids, two phospholipids, and one polar lipid, all unidentified, were detected. The DNA G+C content was 49.7 mol%. The 16S rRNA gene sequence of OS-11M-2T was registered in GenBank under accession number MF359550. On the basis of phenotypic, genotypic, and phylogenetic analyses, strain OS-11M-2T represents a novel genus of the family Vibrionaceae, for which we propose the name Corallibacterium pacifica gen. nov., sp. nov., with the type strain of the type species being OS-11M-2T (= KCCM 43265T). The digital protologue database (DPD) taxon number for strain OS-11M-2T is GA00041.
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Affiliation(s)
- Sachithra Amarin Hettiarachchi
- Korea Institute of Ocean Science & Technology, Jeju, Jeju Province, 63349, Republic of Korea.,Department of Marine Biology, Korea University of Science and Technology, Jeju, Jeju Province, 63349, Republic of Korea
| | - Su-Jin Lee
- Korea Institute of Ocean Science & Technology, Jeju, Jeju Province, 63349, Republic of Korea
| | - Youngdeuk Lee
- Korea Institute of Ocean Science & Technology, Jeju, Jeju Province, 63349, Republic of Korea
| | - Young-Kyung Kwon
- Korea Institute of Ocean Science & Technology, Jeju, Jeju Province, 63349, Republic of Korea
| | - Kae Kyoung Kwon
- Korea Institute of Ocean Science & Technology, Busan, 49111, Republic of Korea
| | - Sung-Hyun Yang
- Korea Institute of Ocean Science & Technology, Busan, 49111, Republic of Korea
| | - Eunyoung Jo
- Korea Institute of Ocean Science & Technology, Jeju, Jeju Province, 63349, Republic of Korea
| | - Do-Hyung Kang
- Korea Institute of Ocean Science & Technology, Jeju, Jeju Province, 63349, Republic of Korea.,Department of Marine Biology, Korea University of Science and Technology, Jeju, Jeju Province, 63349, Republic of Korea
| | - Chulhong Oh
- Korea Institute of Ocean Science & Technology, Jeju, Jeju Province, 63349, Republic of Korea. .,Department of Marine Biology, Korea University of Science and Technology, Jeju, Jeju Province, 63349, Republic of Korea.
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128
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van de Water JAJM, Chaib De Mares M, Dixon GB, Raina JB, Willis BL, Bourne DG, van Oppen MJH. Antimicrobial and stress responses to increased temperature and bacterial pathogen challenge in the holobiont of a reef-building coral. Mol Ecol 2018; 27:1065-1080. [PMID: 29334418 DOI: 10.1111/mec.14489] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 12/07/2017] [Accepted: 12/08/2017] [Indexed: 12/29/2022]
Abstract
Global increases in coral disease prevalence have been linked to ocean warming through changes in coral-associated bacterial communities, pathogen virulence and immune system function. However, the interactive effects of temperature and pathogens on the coral holobiont are poorly understood. Here, we assessed three compartments of the holobiont (host, Symbiodinium and bacterial community) of the coral Montipora aequituberculata challenged with the pathogen Vibrio coralliilyticus and the commensal bacterium Oceanospirillales sp. under ambient (27°C) and elevated (29.5 and 32°C) seawater temperatures. Few visual signs of bleaching and disease development were apparent in any of the treatments, but responses were detected in the holobiont compartments. V. coralliilyticus acted synergistically and negatively impacted the photochemical efficiency of Symbiodinium at 32°C, while Oceanospirillales had no significant effect on photosynthetic efficiency. The coral, however, exhibited a minor response to the bacterial challenges, with the response towards V. coralliilyticus being significantly more pronounced, and involving the prophenoloxidase-activating system and multiple immune system-related genes. Elevated seawater temperatures did not induce shifts in the coral-associated bacterial community, but caused significant gene expression modulation in both Symbiodinium and the coral host. While Symbiodinium exhibited an antiviral response and upregulated stress response genes, M. aequituberculata showed regulation of genes involved in stress and innate immune response processes, including immune and cytokine receptor signalling, the complement system, immune cell activation and phagocytosis, as well as molecular chaperones. These observations show that M. aequituberculata is capable of maintaining a stable bacterial community under elevated seawater temperatures and thereby contributes to preventing disease development.
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Affiliation(s)
- Jeroen A J M van de Water
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, Australia.,College of Science and Engineering, James Cook University, Townsville, Qld, Australia.,AIMS@JCU, James Cook University, Townsville, Qld, Australia.,Australian Institute of Marine Science, Townsville, Qld, Australia.,Département de Biologie Marine, Centre Scientifique de Monaco, Monaco, Principauté de Monaco
| | - Maryam Chaib De Mares
- College of Science and Engineering, James Cook University, Townsville, Qld, Australia.,AIMS@JCU, James Cook University, Townsville, Qld, Australia.,Australian Institute of Marine Science, Townsville, Qld, Australia
| | - Groves B Dixon
- Section of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Jean-Baptiste Raina
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, Australia.,College of Science and Engineering, James Cook University, Townsville, Qld, Australia.,AIMS@JCU, James Cook University, Townsville, Qld, Australia.,Australian Institute of Marine Science, Townsville, Qld, Australia.,Climate Change Cluster (C3), University of Technology Sydney, Sydney, NSW, Australia
| | - Bette L Willis
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, Australia.,College of Science and Engineering, James Cook University, Townsville, Qld, Australia.,AIMS@JCU, James Cook University, Townsville, Qld, Australia
| | - David G Bourne
- College of Science and Engineering, James Cook University, Townsville, Qld, Australia.,AIMS@JCU, James Cook University, Townsville, Qld, Australia.,Australian Institute of Marine Science, Townsville, Qld, Australia
| | - Madeleine J H van Oppen
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, Australia.,AIMS@JCU, James Cook University, Townsville, Qld, Australia.,Australian Institute of Marine Science, Townsville, Qld, Australia.,School of BioSciences, The University of Melbourne, Parkville, Vic., Australia
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129
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Bonthond G, Merselis DG, Dougan KE, Graff T, Todd W, Fourqurean JW, Rodriguez-Lanetty M. Inter-domain microbial diversity within the coral holobiont Siderastrea siderea from two depth habitats. PeerJ 2018; 6:e4323. [PMID: 29441234 PMCID: PMC5808317 DOI: 10.7717/peerj.4323] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 01/13/2018] [Indexed: 12/31/2022] Open
Abstract
Corals host diverse microbial communities that are involved in acclimatization, pathogen defense, and nutrient cycling. Surveys of coral-associated microbes have been particularly directed toward Symbiodinium and bacteria. However, a holistic understanding of the total microbiome has been hindered by a lack of analyses bridging taxonomically disparate groups. Using high-throughput amplicon sequencing, we simultaneously characterized the Symbiodinium, bacterial, and fungal communities associated with the Caribbean coral Siderastrea siderea collected from two depths (17 and 27 m) on Conch reef in the Florida Keys. S. siderea hosted an exceptionally diverse Symbiodinium community, structured differently between sampled depth habitats. While dominated at 27 m by a Symbiodinium belonging to clade C, at 17 m S. siderea primarily hosted a mixture of clade B types. Most fungal operational taxonomic units were distantly related to available reference sequences, indicating the presence of a high degree of fungal novelty within the S. siderea holobiont and a lack of knowledge on the diversity of fungi on coral reefs. Network analysis showed that co-occurrence patterns in the S. siderea holobiont were prevalent among bacteria, however, also detected between fungi and bacteria. Overall, our data show a drastic shift in the associated Symbiodinium community between depths on Conch Reef, which might indicate that alteration in this community is an important mechanism facilitating local physiological adaptation of the S. siderea holobiont. In contrast, bacterial and fungal communities were not structured differently between depth habitats.
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Affiliation(s)
- Guido Bonthond
- Department of Biological Sciences, Florida International University, Miami, FL, USA.,Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Daniel G Merselis
- Department of Biological Sciences, Florida International University, Miami, FL, USA
| | - Katherine E Dougan
- Department of Biological Sciences, Florida International University, Miami, FL, USA
| | | | | | - James W Fourqurean
- Department of Biological Sciences, Florida International University, Miami, FL, USA
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130
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Rubio-Portillo E, Kersting DK, Linares C, Ramos-Esplá AA, Antón J. Biogeographic Differences in the Microbiome and Pathobiome of the Coral Cladocora caespitosa in the Western Mediterranean Sea. Front Microbiol 2018; 9:22. [PMID: 29410656 PMCID: PMC5787083 DOI: 10.3389/fmicb.2018.00022] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Accepted: 01/05/2018] [Indexed: 12/21/2022] Open
Abstract
The endemic Mediterranean zooxanthellate scleractinian reef-builder Cladocora caespitosa is among the organisms most affected by warming-related mass mortality events in the Mediterranean Sea. Corals are known to contain a diverse microbiota that plays a key role in their physiology and health. Here we report the first study that examines the microbiome and pathobiome associated with C. caespitosa in three different Mediterranean locations (i.e., Genova, Columbretes Islands, and Tabarca Island). The microbial communities associated with this species showed biogeographical differences, but shared a common core microbiome that probably plays a key role in the coral holobiont. The putatively pathogenic microbial assemblage (i.e., pathobiome) of C. caespitosa also seemed to depend on geographic location and the human footprint. In locations near the coast and with higher human influence, the pathobiome was entirely constituted by Vibrio species, including the well-known coral pathogens Vibrio coralliilyticus and V. mediterranei. However, in the Columbretes Islands, located off the coast and the most pristine of the analyzed locations, no changes among microbial communities associated to healthy and necrosed samples were detected. Hence, our results provide new insights into the microbiome of the temperate corals and its role in coral health status, highlighting its dependence on the local environmental conditions and the human footprint.
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Affiliation(s)
- Esther Rubio-Portillo
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - Diego K Kersting
- Working Group on Geobiology and Anthropocene Research, Institute of Geological Sciences, Freie Universität Berlin, Berlin, Germany.,Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Cristina Linares
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | | | - Josefa Antón
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
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131
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Corallivory and the microbial debacle in two branching scleractinians. ISME JOURNAL 2018; 12:1109-1126. [PMID: 29339825 DOI: 10.1038/s41396-017-0033-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 11/21/2017] [Accepted: 12/01/2017] [Indexed: 02/01/2023]
Abstract
The grazing activity by specific marine organisms represents a growing threat to the survival of many scleractinian species. For example, the recent proliferation of the corallivorous gastropod Drupella now constitutes a critical case in all South-East Asian waters. If the damaging effects caused by this marine snail on coral polyps are relatively well known, the indirect incidence of predation on coral microbial associates is still obscure and might also potentially impair coral health. In this study, we compared the main ecological traits of coral-associated bacterial and viral communities living in the mucus layer of Acropora formosa and Acropora millepora, of healthy and predated individuals (i.e., colonized by Drupella rugosa), in the Bay of Van Phong (Vietnam). Our results show a substantial impact of the gastropod on a variety of microbiological markers. Colonized corals harbored much more abundant and active epibiotic bacteria whose community composition shifted toward more pathogenic taxa (belonging to the Vibrionales, Clostridiales, Campylobacterales, and Alteromonadales orders), together with their specific phages. Viral epibionts were also greatly influenced by Drupella corallivory with spectacular modifications in their concentrations, life strategies, genotype richness, and diversity. Novel and abundant circular Rep-encoding ssDNA viruses (CRESS-DNA viruses) were detected and characterized in grazed corals and we propose that their occurrence may serve as indicator of the coral health status. Finally, our results reveal that corallivory can cause severe dysbiosis by altering virus-bacteria interactions in the mucus layer, and ultimately favoring the development of local opportunistic infections.
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132
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Abundance and Multilocus Sequence Analysis of Vibrio Bacteria Associated with Diseased Elkhorn Coral (Acropora palmata) of the Florida Keys. Appl Environ Microbiol 2018; 84:AEM.01035-17. [PMID: 29079623 DOI: 10.1128/aem.01035-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 10/24/2017] [Indexed: 11/20/2022] Open
Abstract
The critically endangered elkhorn coral (Acropora palmata) is affected by white pox disease (WPX) throughout the Florida Reef Tract and wider Caribbean. The bacterium Serratia marcescens was previously identified as one etiologic agent of WPX but is no longer consistently detected in contemporary outbreaks. It is now believed that multiple etiologic agents cause WPX; however, to date, no other potential pathogens have been thoroughly investigated. This study examined the association of Vibrio bacteria with WPX occurrence from August 2012 to 2014 at Looe Key Reef in the Florida Keys, USA. The concentration of cultivable Vibrio was consistently greater in WPX samples than in healthy samples. The abundance of Vibrio bacteria relative to total bacteria was four times higher in samples from WPX lesions than in adjacent apparently healthy regions of diseased corals based on quantitative PCR (qPCR). Multilocus sequence analysis (MLSA) was used to assess the diversity of 69 Vibrio isolates collected from diseased and apparently healthy A. palmata colonies and the surrounding seawater. Vibrio species with known pathogenicity to corals were detected in both apparently healthy and diseased samples. While the causative agent(s) of contemporary WPX outbreaks remains elusive, our results suggest that Vibrio spp. may be part of a nonspecific heterotrophic bacterial bloom rather than acting as primary pathogens. This study highlights the need for highly resolved temporal sampling in situ to further elucidate the role of Vibrio during WPX onset and progression.IMPORTANCE Coral diseases are increasing worldwide and are now considered a major contributor to coral reef decline. In particular, the Caribbean has been noted as a coral disease hot spot, owing to the dramatic loss of framework-building acroporid corals due to tissue loss diseases. The pathogenesis of contemporary white pox disease (WPX) outbreaks in Acropora palmata remains poorly understood. This study investigates the association of Vibrio bacteria with WPX.
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133
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How Does the Coral Microbiome Cause, Respond to, or Modulate the Bleaching Process? ECOLOGICAL STUDIES 2018. [DOI: 10.1007/978-3-319-75393-5_7] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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134
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van de Water JAJM, Voolstra CR, Rottier C, Cocito S, Peirano A, Allemand D, Ferrier-Pagès C. Seasonal Stability in the Microbiomes of Temperate Gorgonians and the Red Coral Corallium rubrum Across the Mediterranean Sea. MICROBIAL ECOLOGY 2018; 75:274-288. [PMID: 28681143 DOI: 10.1007/s00248-017-1006-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 06/02/2017] [Indexed: 06/07/2023]
Abstract
Populations of key benthic habitat-forming octocoral species have declined significantly in the Mediterranean Sea due to mass mortality events caused by microbial disease outbreaks linked to high summer seawater temperatures. Recently, we showed that the microbial communities of these octocorals are relatively structured; however, our knowledge on the seasonal dynamics of these microbiomes is still limited. To investigate their seasonal stability, we collected four soft gorgonian species (Eunicella singularis, Eunicella cavolini, Eunicella verrucosa and Leptogorgia sarmentosa) and the precious red coral (Corallium rubrum) from two coastal locations with different terrestrial impact levels in the Mediterranean Sea, and used next-generation amplicon sequencing of the 16S rRNA gene. The microbiomes of all soft gorgonian species were dominated by the same 'core microbiome' bacteria belonging to the Endozoicomonas and the Cellvibrionales clade BD1-7, whereas the red coral microbiome was primarily composed of 'core' Spirochaetes, Oceanospirillales ME2 and Parcubacteria. The associations with these bacterial taxa were relatively consistent over time at each location for each octocoral species. However, differences in microbiome composition and seasonal dynamics were observed between locations and could primarily be attributed to locally variant bacteria. Overall, our data provide further evidence of the intricate symbiotic relationships that exist between Mediterranean octocorals and their associated microbes, which are ancient and highly conserved over both space and time, and suggest regulation of the microbiome composition by the host, depending on local conditions.
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Affiliation(s)
| | - Christian R Voolstra
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Cecile Rottier
- Centre Scientifique de Monaco, 8 Quai Antoine 1er, 98000, Monaco, Monaco
| | - Silvia Cocito
- Marine Environment Research Centre, ENEA, La Spezia, Italy
| | - Andrea Peirano
- Marine Environment Research Centre, ENEA, La Spezia, Italy
| | - Denis Allemand
- Centre Scientifique de Monaco, 8 Quai Antoine 1er, 98000, Monaco, Monaco
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135
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Weynberg KD, Laffy PW, Wood-Charlson EM, Turaev D, Rattei T, Webster NS, van Oppen MJH. Coral-associated viral communities show high levels of diversity and host auxiliary functions. PeerJ 2017; 5:e4054. [PMID: 29158985 PMCID: PMC5695250 DOI: 10.7717/peerj.4054] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 10/27/2017] [Indexed: 12/19/2022] Open
Abstract
Stony corals (Scleractinia) are marine invertebrates that form the foundation and framework upon which tropical reefs are built. The coral animal associates with a diverse microbiome comprised of dinoflagellate algae and other protists, bacteria, archaea, fungi and viruses. Using a metagenomics approach, we analysed the DNA and RNA viral assemblages of seven coral species from the central Great Barrier Reef (GBR), demonstrating that tailed bacteriophages of the Caudovirales dominate across all species examined, and ssDNA viruses, notably the Microviridae, are also prevalent. Most sequences with matches to eukaryotic viruses were assigned to six viral families, including four Nucleocytoplasmic Large DNA Viruses (NCLDVs) families: Iridoviridae, Phycodnaviridae, Mimiviridae, and Poxviridae, as well as Retroviridae and Polydnaviridae. Contrary to previous findings, Herpesvirales were rare in these GBR corals. Sequences of a ssRNA virus with similarities to the dinornavirus, Heterocapsa circularisquama ssRNA virus of the Alvernaviridae that infects free-living dinoflagellates, were observed in three coral species. We also detected viruses previously undescribed from the coral holobiont, including a virus that targets fungi associated with the coral species Acropora tenuis. Functional analysis of the assembled contigs indicated a high prevalence of latency-associated genes in the coral-associated viral assemblages, several host-derived auxiliary metabolic genes (AMGs) for photosynthesis (psbA, psbD genes encoding the photosystem II D1 and D2 proteins respectively), as well as potential nematocyst toxins and antioxidants (genes encoding green fluorescent-like chromoprotein). This study expands the currently limited knowledge on coral-associated viruses by characterising viral composition and function across seven GBR coral species.
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Affiliation(s)
- Karen D Weynberg
- Australian Institute of Marine Science, Townsville, Queensland, Australia.,School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Patrick W Laffy
- Australian Institute of Marine Science, Townsville, Queensland, Australia
| | | | - Dmitrij Turaev
- Department of Microbiology and Ecosystem Science, Division of Computational Systems Biology, University of Vienna, Vienna, Austria
| | - Thomas Rattei
- Department of Microbiology and Ecosystem Science, Division of Computational Systems Biology, University of Vienna, Vienna, Austria
| | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, Queensland, Australia.,Australian Centre for Ecogenomics, University of Queensland, Brisbane, Queensland, Australia
| | - Madeleine J H van Oppen
- Australian Institute of Marine Science, Townsville, Queensland, Australia.,School of Biosciences, University of Melbourne, Melbourne, Victoria, Australia
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136
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Rädecker N, Pogoreutz C, Ziegler M, Ashok A, Barreto MM, Chaidez V, Grupstra CGB, Ng YM, Perna G, Aranda M, Voolstra CR. Assessing the effects of iron enrichment across holobiont compartments reveals reduced microbial nitrogen fixation in the Red Sea coral Pocillopora verrucosa. Ecol Evol 2017; 7:6614-6621. [PMID: 28861262 PMCID: PMC5574852 DOI: 10.1002/ece3.3293] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 07/07/2017] [Accepted: 07/09/2017] [Indexed: 11/09/2022] Open
Abstract
The productivity of coral reefs in oligotrophic tropical waters is sustained by an efficient uptake and recycling of nutrients. In reef-building corals, the engineers of these ecosystems, this nutrient recycling is facilitated by a constant exchange of nutrients between the animal host and endosymbiotic photosynthetic dinoflagellates (zooxanthellae), bacteria, and other microbes. Due to the complex interactions in this so-called coral holobiont, it has proven difficult to understand the environmental limitations of productivity in corals. Among others, the micronutrient iron has been proposed to limit primary productivity due to its essential role in photosynthesis and bacterial processes. Here, we tested the effect of iron enrichment on the physiology of the coral Pocillopora verrucosa from the central Red Sea during a 12-day experiment. Contrary to previous reports, we did not see an increase in zooxanthellae population density or gross photosynthesis. Conversely, respiration rates were significantly increased, and microbial nitrogen fixation was significantly decreased. Taken together, our data suggest that iron is not a limiting factor of primary productivity in Red Sea corals. Rather, increased metabolic demands in response to iron enrichment, as evidenced by increased respiration rates, may reduce carbon (i.e., energy) availability in the coral holobiont, resulting in reduced microbial nitrogen fixation. This decrease in nitrogen supply in turn may exacerbate the limitation of other nutrients, creating a negative feedback loop. Thereby, our results highlight that the effects of iron enrichment appear to be strongly dependent on local environmental conditions and ultimately may depend on the availability of other nutrients.
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Affiliation(s)
- Nils Rädecker
- Red Sea Research Center Division of Biological and Environmental Science and Engineering (BESE) King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia
| | - Claudia Pogoreutz
- Red Sea Research Center Division of Biological and Environmental Science and Engineering (BESE) King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia
| | - Maren Ziegler
- Red Sea Research Center Division of Biological and Environmental Science and Engineering (BESE) King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia
| | - Ananya Ashok
- Red Sea Research Center Division of Biological and Environmental Science and Engineering (BESE) King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia
| | - Marcelle M Barreto
- Red Sea Research Center Division of Biological and Environmental Science and Engineering (BESE) King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia
| | - Veronica Chaidez
- Red Sea Research Center Division of Biological and Environmental Science and Engineering (BESE) King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia
| | - Carsten G B Grupstra
- Red Sea Research Center Division of Biological and Environmental Science and Engineering (BESE) King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia
| | - Yi Mei Ng
- Red Sea Research Center Division of Biological and Environmental Science and Engineering (BESE) King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia
| | - Gabriela Perna
- Red Sea Research Center Division of Biological and Environmental Science and Engineering (BESE) King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia
| | - Manuel Aranda
- Red Sea Research Center Division of Biological and Environmental Science and Engineering (BESE) King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia
| | - Christian R Voolstra
- Red Sea Research Center Division of Biological and Environmental Science and Engineering (BESE) King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia
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137
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Damjanovic K, Blackall LL, Webster NS, van Oppen MJH. The contribution of microbial biotechnology to mitigating coral reef degradation. Microb Biotechnol 2017; 10:1236-1243. [PMID: 28696067 PMCID: PMC5609283 DOI: 10.1111/1751-7915.12769] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 06/13/2017] [Indexed: 12/14/2022] Open
Abstract
The decline of coral reefs due to anthropogenic disturbances is having devastating impacts on biodiversity and ecosystem services. Here we highlight the potential and challenges of microbial manipulation strategies to enhance coral tolerance to stress and contribute to coral reef restoration and protection.
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Affiliation(s)
- Katarina Damjanovic
- School of BioSciences, The University of Melbourne, Parkville, Vic., 3010, Australia.,Australian Institute of Marine Science, PMB No 3, Townsville MC, 4810, Qld, Australia
| | - Linda L Blackall
- School of BioSciences, The University of Melbourne, Parkville, Vic., 3010, Australia
| | - Nicole S Webster
- Australian Institute of Marine Science, PMB No 3, Townsville MC, 4810, Qld, Australia.,Australian Centre for Ecogenomics, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Madeleine J H van Oppen
- School of BioSciences, The University of Melbourne, Parkville, Vic., 3010, Australia.,Australian Institute of Marine Science, PMB No 3, Townsville MC, 4810, Qld, Australia
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138
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Roach TNF, Abieri ML, George EE, Knowles B, Naliboff DS, Smurthwaite CA, Kelly LW, Haas AF, Rohwer FL. Microbial bioenergetics of coral-algal interactions. PeerJ 2017. [PMID: 28649468 PMCID: PMC5482263 DOI: 10.7717/peerj.3423] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Human impacts are causing ecosystem phase shifts from coral- to algal-dominated reef systems on a global scale. As these ecosystems undergo transition, there is an increased incidence of coral-macroalgal interactions. Mounting evidence indicates that the outcome of these interaction events is, in part, governed by microbially mediated dynamics. The allocation of available energy through different trophic levels, including the microbial food web, determines the outcome of these interactions and ultimately shapes the benthic community structure. However, little is known about the underlying thermodynamic mechanisms involved in these trophic energy transfers. This study utilizes a novel combination of methods including calorimetry, flow cytometry, and optical oxygen measurements, to provide a bioenergetic analysis of coral-macroalgal interactions in a controlled aquarium setting. We demonstrate that the energetic demands of microbial communities at the coral-algal interaction interface are higher than in the communities associated with either of the macroorganisms alone. This was evident through higher microbial power output (energy use per unit time) and lower oxygen concentrations at interaction zones compared to areas distal from the interface. Increases in microbial power output and lower oxygen concentrations were significantly correlated with the ratio of heterotrophic to autotrophic microbes but not the total microbial abundance. These results suggest that coral-algal interfaces harbor higher proportions of heterotrophic microbes that are optimizing maximal power output, as opposed to yield. This yield to power shift offers a possible thermodynamic mechanism underlying the transition from coral- to algal-dominated reef ecosystems currently being observed worldwide. As changes in the power output of an ecosystem are a significant indicator of the current state of the system, this analysis provides a novel and insightful means to quantify microbial impacts on reef health.
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Affiliation(s)
- Ty N F Roach
- Department of Biology, San Diego State University, San Diego, CA, United States of America
| | - Maria L Abieri
- Department of Biology, San Diego State University, San Diego, CA, United States of America.,Department of Marine Biology, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Emma E George
- Department of Biology, San Diego State University, San Diego, CA, United States of America
| | - Ben Knowles
- Department of Biology, San Diego State University, San Diego, CA, United States of America
| | - Douglas S Naliboff
- Department of Biology, San Diego State University, San Diego, CA, United States of America
| | - Cameron A Smurthwaite
- Department of Biology, San Diego State University, San Diego, CA, United States of America
| | - Linda Wegley Kelly
- Department of Biology, San Diego State University, San Diego, CA, United States of America
| | - Andreas F Haas
- Department of Biology, San Diego State University, San Diego, CA, United States of America
| | - Forest L Rohwer
- Department of Biology, San Diego State University, San Diego, CA, United States of America
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139
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Pootakham W, Mhuantong W, Yoocha T, Putchim L, Sonthirod C, Naktang C, Thongtham N, Tangphatsornruang S. High resolution profiling of coral-associated bacterial communities using full-length 16S rRNA sequence data from PacBio SMRT sequencing system. Sci Rep 2017; 7:2774. [PMID: 28584301 PMCID: PMC5459821 DOI: 10.1038/s41598-017-03139-4] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 04/24/2017] [Indexed: 02/01/2023] Open
Abstract
Coral reefs are a complex ecosystem consisting of coral animals and a vast array of associated symbionts including the dinoflagellate Symbiodinium, fungi, viruses and bacteria. Several studies have highlighted the importance of coral-associated bacteria and their fundamental roles in fitness and survival of the host animal. The scleractinian coral Porites lutea is one of the dominant reef-builders in the Indo-West Pacific. Currently, very little is known about the composition and structure of bacterial communities across P. lutea reefs. The purpose of this study is twofold: to demonstrate the advantages of using PacBio circular consensus sequencing technology in microbial community studies and to investigate the diversity and structure of P. lutea-associated microbiome in the Indo-Pacific. This is the first metagenomic study of marine environmental samples that utilises the PacBio sequencing system to capture full-length 16S rRNA sequences. We observed geographically distinct coral-associated microbial profiles between samples from the Gulf of Thailand and Andaman Sea. Despite the geographical and environmental impacts on the coral-host interactions, we identified a conserved community of bacteria that were present consistently across diverse reef habitats. Finally, we demonstrated the superior performance of full-length 16S rRNA sequences in resolving taxonomic uncertainty of coral associates at the species level.
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Affiliation(s)
- Wirulda Pootakham
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand.
| | - Wuttichai Mhuantong
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Thippawan Yoocha
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Lalita Putchim
- Phuket Marine Biological Center, Phuket, 83000, Thailand
| | - Chutima Sonthirod
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Chaiwat Naktang
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | | | - Sithichoke Tangphatsornruang
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
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140
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Simon M, Scheuner C, Meier-Kolthoff JP, Brinkhoff T, Wagner-Döbler I, Ulbrich M, Klenk HP, Schomburg D, Petersen J, Göker M. Phylogenomics of Rhodobacteraceae reveals evolutionary adaptation to marine and non-marine habitats. THE ISME JOURNAL 2017; 11:1483-1499. [PMID: 28106881 PMCID: PMC5437341 DOI: 10.1038/ismej.2016.198] [Citation(s) in RCA: 194] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 10/29/2016] [Accepted: 11/19/2016] [Indexed: 12/31/2022]
Abstract
Marine Rhodobacteraceae (Alphaproteobacteria) are key players of biogeochemical cycling, comprise up to 30% of bacterial communities in pelagic environments and are often mutualists of eukaryotes. As 'Roseobacter clade', these 'roseobacters' are assumed to be monophyletic, but non-marine Rhodobacteraceae have not yet been included in phylogenomic analyses. Therefore, we analysed 106 genome sequences, particularly emphasizing gene sampling and its effect on phylogenetic stability, and investigated relationships between marine versus non-marine habitat, evolutionary origin and genomic adaptations. Our analyses, providing no unequivocal evidence for the monophyly of roseobacters, indicate several shifts between marine and non-marine habitats that occurred independently and were accompanied by characteristic changes in genomic content of orthologs, enzymes and metabolic pathways. Non-marine Rhodobacteraceae gained high-affinity transporters to cope with much lower sulphate concentrations and lost genes related to the reduced sodium chloride and organohalogen concentrations in their habitats. Marine Rhodobacteraceae gained genes required for fucoidan desulphonation and synthesis of the plant hormone indole 3-acetic acid and the compatible solutes ectoin and carnitin. However, neither plasmid composition, even though typical for the family, nor the degree of oligotrophy shows a systematic difference between marine and non-marine Rhodobacteraceae. We suggest the operational term 'Roseobacter group' for the marine Rhodobacteraceae strains.
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Affiliation(s)
- Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Carmen Scheuner
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jan P Meier-Kolthoff
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Irene Wagner-Döbler
- Helmholtz Centre for Infection Research, Research Group Microbial Communication, Braunschweig, Germany
| | - Marcus Ulbrich
- Institute of Biochemical Engineering, Technical University Braunschweig, Braunschweig, Germany
| | - Hans-Peter Klenk
- School of Biology, Newcastle University, Newcastle upon Tyne, UK
| | - Dietmar Schomburg
- Institute of Biochemical Engineering, Technical University Braunschweig, Braunschweig, Germany
| | - Jörn Petersen
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Markus Göker
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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141
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Westmoreland LS, Niemuth JN, Gracz HS, Stoskopf MK. Altered acrylic acid concentrations in hard and soft corals exposed to deteriorating water conditions. Facets (Ott) 2017. [DOI: 10.1139/facets-2016-0064] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
A reliable marker of early coral response to environmental stressors can help guide decision-making to mitigate global coral reef decline by detecting problems before the development of clinically observable disease. We document the accumulation of acrylic acid in two divergent coral taxa, stony small polyp coral ( Acropora sp.) and soft coral ( Lobophytum sp.), in response to deteriorating water quality characterized by moderately increased ammonia (0.25 ppm) and phosphate (0.15 ppm) concentrations and decreased calcium (360 ppm) concentration, using nuclear magnetic resonance spectroscopy (NMR)-based metabolomic techniques. Changes in acrylic acid concentration in polyp tissues free of zooxanthellae suggest that acrylic acid could be a product of animal metabolism and not exclusively a metabolic by-product of the osmolyte dimethylsulfoniopropionate (DMSP) in marine algae or bacteria. Our findings build on previously documented depletions of acrylic acid in wild coral potentially correlated to temperature stress and provide additional insight into approaches to further characterize the nature of the metabolic accumulation of acrylic acid under controlled experimental conditions.
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Affiliation(s)
- Lori S.H. Westmoreland
- Environmental Medicine Consortium, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607, USA
| | - Jennifer N. Niemuth
- Environmental Medicine Consortium, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607, USA
| | - Hanna S. Gracz
- Environmental Medicine Consortium, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607, USA
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27607, USA
| | - Michael K. Stoskopf
- Environmental Medicine Consortium, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607, USA
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142
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Lee MD, Walworth NG, McParland EL, Fu FX, Mincer TJ, Levine NM, Hutchins DA, Webb EA. The Trichodesmium consortium: conserved heterotrophic co-occurrence and genomic signatures of potential interactions. ISME JOURNAL 2017; 11:1813-1824. [PMID: 28440800 DOI: 10.1038/ismej.2017.49] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 12/31/2016] [Accepted: 02/16/2017] [Indexed: 11/09/2022]
Abstract
The nitrogen (N)-fixing cyanobacterium Trichodesmium is globally distributed in warm, oligotrophic oceans, where it contributes a substantial proportion of new N and fuels primary production. These photoautotrophs form macroscopic colonies that serve as relatively nutrient-rich substrates that are colonized by many other organisms. The nature of these associations may modulate ocean N and carbon (C) cycling, and can offer insights into marine co-evolutionary mechanisms. Here we integrate multiple omics-based and experimental approaches to investigate Trichodesmium-associated bacterial consortia in both laboratory cultures and natural environmental samples. These efforts have identified the conserved presence of a species of Gammaproteobacteria (Alteromonas macleodii), and enabled the assembly of a near-complete, representative genome. Interorganismal comparative genomics between A. macleodii and Trichodesmium reveal potential interactions that may contribute to the maintenance of this association involving iron and phosphorus acquisition, vitamin B12 exchange, small C compound catabolism, and detoxification of reactive oxygen species. These results identify what may be a keystone organism within Trichodesmium consortia and support the idea that functional selection has a major role in structuring associated microbial communities. These interactions, along with likely many others, may facilitate Trichodesmium's unique open-ocean lifestyle, and could have broad implications for oligotrophic ecosystems and elemental cycling.
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Affiliation(s)
- Michael D Lee
- Marine Environmental Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Nathan G Walworth
- Marine Environmental Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Erin L McParland
- Marine Environmental Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Fei-Xue Fu
- Marine Environmental Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Tracy J Mincer
- Woods Hole Oceanographic Institute, Department of Marine Chemistry and Geochemistry, Woods Hole, MA, USA
| | - Naomi M Levine
- Marine Environmental Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - David A Hutchins
- Marine Environmental Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Eric A Webb
- Marine Environmental Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
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143
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Gajigan AP, Diaz LA, Conaco C. Resilience of the prokaryotic microbial community of Acropora digitifera to elevated temperature. Microbiologyopen 2017; 6. [PMID: 28425179 PMCID: PMC5552946 DOI: 10.1002/mbo3.478] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 02/22/2017] [Accepted: 03/07/2017] [Indexed: 12/22/2022] Open
Abstract
The coral is a holobiont formed by the close interaction between the coral animal and a diverse community of microorganisms, including dinoflagellates, bacteria, archaea, fungi, and viruses. The prokaryotic symbionts of corals are important for host fitness but are also highly sensitive to changes in the environment. In this study, we used 16S ribosomal RNA (rRNA) sequencing to examine the response of the microbial community associated with the coral, Acropora digitifera, to elevated temperature. The A. digitifera microbial community is dominated by operational taxonomic unit (OTUs) affiliated with classes Alphaproteobacteria and Gammaproteobacteria. The prokaryotic community in the coral tissue is distinct from that of the mucus and the surrounding seawater. Remarkably, the overall microbial community structure of A. digitifera remained stable for 10 days of continuous exptosure at 32°C compared to corals maintained at 27°C. However, the elevated temperature regime resulted in a decrease in the abundance of OTUs affiliated with certain groups of bacteria, such as order Rhodobacterales. On the other hand, some OTUs affiliated with the orders Alteromonadales, Vibrionales, and Flavobacteriales, which are often associated with diseased and stressed corals, increased in abundance. Thus, while the A. digitifera bacterial community structure appears resilient to higher temperature, prolonged exposure and intensified stress results in changes in the abundance of specific microbial community members that may affect the overall metabolic state and health of the coral holobiont.
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Affiliation(s)
- Andrian P Gajigan
- Marine Science Institute, University of the Philippines, Diliman, Quezon City, Philippines
| | - Leomir A Diaz
- Marine Science Institute, University of the Philippines, Diliman, Quezon City, Philippines
| | - Cecilia Conaco
- Marine Science Institute, University of the Philippines, Diliman, Quezon City, Philippines
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144
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Meyer JL, Paul VJ, Raymundo LJ, Teplitski M. Comparative Metagenomics of the Polymicrobial Black Band Disease of Corals. Front Microbiol 2017; 8:618. [PMID: 28458657 PMCID: PMC5394123 DOI: 10.3389/fmicb.2017.00618] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 03/27/2017] [Indexed: 12/16/2022] Open
Abstract
Black Band Disease (BBD), the destructive microbial consortium dominated by the cyanobacterium Roseofilum reptotaenium, affects corals worldwide. While the taxonomic composition of BBD consortia has been well-characterized, substantially less is known about its functional repertoire. We sequenced the metagenomes of Caribbean and Pacific black band mats and cultured Roseofilum and obtained five metagenome-assembled genomes (MAGs) of Roseofilum, nine of Proteobacteria, and 12 of Bacteroidetes. Genomic content analysis suggests that Roseofilum is a source of organic carbon and nitrogen, as well as natural products that may influence interactions between microbes. Proteobacteria and Bacteroidetes members of the disease consortium are suited to the degradation of amino acids, proteins, and carbohydrates. The accumulation of sulfide underneath the black band mat, in part due to a lack of sulfur oxidizers, contributes to the lethality of the disease. The presence of sulfide:quinone oxidoreductase genes in all five Roseofilum MAGs and in the MAGs of several heterotrophs demonstrates that resistance to sulfide is an important characteristic for members of the BBD consortium.
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Affiliation(s)
- Julie L Meyer
- Soil and Water Science Department, University of Florida-Institute of Food and Agricultural SciencesGainesville, FL, USA
| | | | | | - Max Teplitski
- Soil and Water Science Department, University of Florida-Institute of Food and Agricultural SciencesGainesville, FL, USA.,Smithsonian Marine StationFort Pierce, FL, USA
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145
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Peixoto RS, Rosado PM, Leite DCDA, Rosado AS, Bourne DG. Beneficial Microorganisms for Corals (BMC): Proposed Mechanisms for Coral Health and Resilience. Front Microbiol 2017; 8:341. [PMID: 28326066 PMCID: PMC5339234 DOI: 10.3389/fmicb.2017.00341] [Citation(s) in RCA: 233] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 02/17/2017] [Indexed: 12/21/2022] Open
Abstract
The symbiotic association between the coral animal and its endosymbiotic dinoflagellate partner Symbiodinium is central to the success of corals. However, an array of other microorganisms associated with coral (i.e., Bacteria, Archaea, Fungi, and viruses) have a complex and intricate role in maintaining homeostasis between corals and Symbiodinium. Corals are sensitive to shifts in the surrounding environmental conditions. One of the most widely reported responses of coral to stressful environmental conditions is bleaching. During this event, corals expel Symbiodinium cells from their gastrodermal tissues upon experiencing extended seawater temperatures above their thermal threshold. An array of other environmental stressors can also destabilize the coral microbiome, resulting in compromised health of the host, which may include disease and mortality in the worst scenario. However, the exact mechanisms by which the coral microbiome supports coral health and increases resilience are poorly understood. Earlier studies of coral microbiology proposed a coral probiotic hypothesis, wherein a dynamic relationship exists between corals and their symbiotic microorganisms, selecting for the coral holobiont that is best suited for the prevailing environmental conditions. Here, we discuss the microbial-host relationships within the coral holobiont, along with their potential roles in maintaining coral health. We propose the term BMC (Beneficial Microorganisms for Corals) to define (specific) symbionts that promote coral health. This term and concept are analogous to the term Plant Growth Promoting Rhizosphere (PGPR), which has been widely explored and manipulated in the agricultural industry for microorganisms that inhabit the rhizosphere and directly or indirectly promote plant growth and development through the production of regulatory signals, antibiotics and nutrients. Additionally, we propose and discuss the potential mechanisms of the effects of BMC on corals, suggesting strategies for the use of this knowledge to manipulate the microbiome, reversing dysbiosis to restore and protect coral reefs. This may include developing and using BMC consortia as environmental "probiotics" to improve coral resistance after bleaching events and/or the use of BMC with other strategies such as human-assisted acclimation/adaption to shifting environmental conditions.
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Affiliation(s)
- Raquel S. Peixoto
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de JaneiroRio de Janeiro, Brazil
- Instituto Museu Aquário Marinho do Rio de Janeiro-AquaRio (IMAM/AquaRio) – Rio de Janeiro Marine Aquarium Research CenterRio de Janeiro, Brazil
| | - Phillipe M. Rosado
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de JaneiroRio de Janeiro, Brazil
- Instituto Museu Aquário Marinho do Rio de Janeiro-AquaRio (IMAM/AquaRio) – Rio de Janeiro Marine Aquarium Research CenterRio de Janeiro, Brazil
| | | | - Alexandre S. Rosado
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de JaneiroRio de Janeiro, Brazil
- Instituto Museu Aquário Marinho do Rio de Janeiro-AquaRio (IMAM/AquaRio) – Rio de Janeiro Marine Aquarium Research CenterRio de Janeiro, Brazil
| | - David G. Bourne
- College of Science and Engineering, James Cook University, TownsvilleQLD, Australia
- Australian Institute of Marine Science, TownsvilleQLD, Australia
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146
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Weber L, DeForce E, Apprill A. Optimization of DNA extraction for advancing coral microbiota investigations. MICROBIOME 2017; 5:18. [PMID: 28179023 PMCID: PMC5299696 DOI: 10.1186/s40168-017-0229-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 01/04/2017] [Indexed: 05/03/2023]
Abstract
BACKGROUND DNA-based sequencing approaches are commonly used to identify microorganisms and their genes and document trends in microbial community diversity in environmental samples. However, extraction of microbial DNA from complex environmental samples like corals can be technically challenging, and extraction methods may impart biases on microbial community structure. METHODS We designed a two-phase study in order to propose a comprehensive and efficient method for DNA extraction from microbial cells present in corals and investigate if extraction method influences microbial community composition. During phase I, total DNA was extracted from seven coral species in a replicated experimental design using four different MO BIO Laboratories, Inc., DNA Isolation kits: PowerSoil®, PowerPlant® Pro, PowerBiofilm®, and UltraClean® Tissue & Cells (with three homogenization permutations). Technical performance of the treatments was evaluated using DNA yield and amplification efficiency of small subunit ribosomal RNA (SSU ribosomal RNA (rRNA)) genes. During phase II, potential extraction biases were examined via microbial community analysis of SSU rRNA gene sequences amplified from the most successful DNA extraction treatments. RESULTS In phase I of the study, the PowerSoil® and PowerPlant® Pro extracts contained low DNA concentrations, amplified poorly, and were not investigated further. Extracts from PowerBiofilm® and UltraClean® Tissue and Cells permutations were further investigated in phase II, and analysis of sequences demonstrated that overall microbial community composition was dictated by coral species and not extraction treatment. Finer pairwise comparisons of sequences obtained from Orbicella faveolata, Orbicella annularis, and Acropora humilis corals revealed subtle differences in community composition between the treatments; PowerBiofilm®-associated sequences generally had higher microbial richness and the highest coverage of dominant microbial groups in comparison to the UltraClean® Tissue and Cells treatments, a result likely arising from using a combination of different beads during homogenization. CONCLUSIONS Both the PowerBiofilm® and UltraClean® Tissue and Cells treatments are appropriate for large-scale analyses of coral microbiota. However, studies interested in detecting cryptic microbial members may benefit from using the PowerBiofilm® DNA treatment because of the likely enhanced lysis efficiency of microbial cells attributed to using a variety of beads during homogenization. Consideration of the methodology involved with microbial DNA extraction is particularly important for studies investigating complex host-associated microbiota.
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Affiliation(s)
- Laura Weber
- Massachusetts Institute of Technology-Woods Hole Oceanographic Institution Joint Program in Oceanography/Applied Ocean Science and Engineering, Cambridge, MA 02139 USA
- Woods Hole Oceanographic Institution, Marine Chemistry and Geochemistry, Woods Hole, MA 02543 USA
| | | | - Amy Apprill
- Woods Hole Oceanographic Institution, Marine Chemistry and Geochemistry, Woods Hole, MA 02543 USA
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147
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Hernandez-Agreda A, Gates RD, Ainsworth TD. Defining the Core Microbiome in Corals’ Microbial Soup. Trends Microbiol 2017; 25:125-140. [DOI: 10.1016/j.tim.2016.11.003] [Citation(s) in RCA: 150] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 10/21/2016] [Accepted: 11/02/2016] [Indexed: 02/07/2023]
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148
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van de Water JAJM, Melkonian R, Voolstra CR, Junca H, Beraud E, Allemand D, Ferrier-Pagès C. Comparative Assessment of Mediterranean Gorgonian-Associated Microbial Communities Reveals Conserved Core and Locally Variant Bacteria. MICROBIAL ECOLOGY 2017; 73:466-478. [PMID: 27726033 DOI: 10.1007/s00248-016-0858-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 09/09/2016] [Indexed: 05/22/2023]
Abstract
Gorgonians are key habitat-forming species of Mediterranean benthic communities, but their populations have suffered from mass mortality events linked to high summer seawater temperatures and microbial disease. However, our knowledge on the diversity, dynamics and function of gorgonian-associated microbial communities is limited. Here, we analysed the spatial variability of the microbiomes of five sympatric gorgonian species (Eunicella singularis, Eunicella cavolini, Eunicella verrucosa, Leptogorgia sarmentosa and Paramuricea clavata), collected from the Mediterranean Sea over a scale of ∼1100 km, using next-generation amplicon sequencing of the 16S rRNA gene. The microbiomes of all gorgonian species were generally dominated by members of the genus Endozoicomonas, which were at very low abundance in the surrounding seawater. Although the composition of the core microbiome (operational taxonomic units consistently present in a species) was found to be unique for each host species, significant overlap was observed. These spatially consistent associations between gorgonians and their core bacteria suggest intricate symbiotic relationships and regulation of the microbiome composition by the host. At the same time, local variations in microbiome composition were observed. Functional predictive profiling indicated that these differences could be attributed to seawater pollution. Taken together, our data indicate that gorgonian-associated microbiomes are composed of spatially conserved bacteria (core microbiome members) and locally variant members, and that local pollution may influence these local associations, potentially impacting gorgonian health.
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Affiliation(s)
| | - Rémy Melkonian
- Centre Scientifique de Monaco, 8 Quai Antoine 1, MC 98000, Monaco, Monaco
| | - Christian R Voolstra
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Howard Junca
- Microbiomas Foundation - Division of Ecogenomics & Holobionts, Chia, Colombia
| | - Eric Beraud
- Centre Scientifique de Monaco, 8 Quai Antoine 1, MC 98000, Monaco, Monaco
| | - Denis Allemand
- Centre Scientifique de Monaco, 8 Quai Antoine 1, MC 98000, Monaco, Monaco
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149
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Alcolombri U, Lei L, Meltzer D, Vardi A, Tawfik DS. Assigning the Algal Source of Dimethylsulfide Using a Selective Lyase Inhibitor. ACS Chem Biol 2017; 12:41-46. [PMID: 28103686 DOI: 10.1021/acschembio.6b00844] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Atmospheric dimethylsulfide (DMS) is massively produced in the oceans by bacteria, algae, and corals. To enable identification of DMS sources, we developed a potent mechanism-based inhibitor of the algal Alma dimethylsulfoniopropionate lyase family that does not inhibit known bacterial lyases. Its application to coral holobiont indicates that DMS originates from Alma lyase(s). This biochemical profiling may complement meta-genomics and transcriptomics to provide better understanding of the marine sulfur cycle.
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Affiliation(s)
- Uria Alcolombri
- Department
of Biomolecular Sciences and ‡Department of Plant and Environmental
Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Lei Lei
- Department
of Biomolecular Sciences and ‡Department of Plant and Environmental
Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Diana Meltzer
- Department
of Biomolecular Sciences and ‡Department of Plant and Environmental
Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Assaf Vardi
- Department
of Biomolecular Sciences and ‡Department of Plant and Environmental
Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Dan S. Tawfik
- Department
of Biomolecular Sciences and ‡Department of Plant and Environmental
Sciences, Weizmann Institute of Science, Rehovot, Israel
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150
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Enzymology of Microbial Dimethylsulfoniopropionate Catabolism. STRUCTURAL AND MECHANISTIC ENZYMOLOGY 2017; 109:195-222. [DOI: 10.1016/bs.apcsb.2017.05.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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