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MacVittie S, Doroodian S, Alberto A, Sogin M. Microbiome depletion and recovery in the sea anemone, Exaiptasia diaphana, following antibiotic exposure. mSystems 2024; 9:e0134223. [PMID: 38757963 DOI: 10.1128/msystems.01342-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 04/19/2024] [Indexed: 05/18/2024] Open
Abstract
Microbial species that comprise host-associated microbiomes play an essential role in maintaining and mediating the health of plants and animals. While defining the role of individual or even complex communities is important toward quantifying the effect of the microbiome on host health, it is often challenging to develop causal studies that link microbial populations to changes in host fitness. Here, we investigated the impacts of reduced microbial load following antibiotic exposure on the fitness of the anemone, Exaiptasia diaphana and subsequent recovery of the host's microbiome. Anemones were exposed to two different types of antibiotic solutions for 3 weeks and subsequently held in sterilized seawater for a 3-week recovery period. Our results revealed that both antibiotic treatments reduced the overall microbial load during and up to 1 week post-treatment. The observed reduction in microbial load was coupled with reduced anemone biomass, halted asexual reproduction rates, and for one of the antibiotic treatments, the partial removal of the anemone's algal symbiont. Finally, our amplicon sequencing results of the 16S rRNA gene revealed that anemone bacterial composition only shifted in treated individuals during the recovery phase of the experiment, where we also observed a significant reduction in the overall diversity of the microbial community. Our work implies that the E. diaphana's microbiome contributes to host fitness and that the recovery of the host's microbiome following disturbance with antibiotics leads to a reduced, but stable microbial state.IMPORTANCEExaiptasia diaphana is an emerging model used to define the cellular and molecular mechanisms of coral-algal symbioses. E. diaphana also houses a diverse microbiome, consisting of hundreds of microbial partners with undefined function. Here, we applied antibiotics to quantify the impact of microbiome removal on host fitness as well as define trajectories in microbiome recovery following disturbance. We showed that reduction of the microbiome leads to negative impacts on host fitness, and that the microbiome does not recover to its original composition while held under aseptic conditions. Rather the microbiome becomes less diverse, but more consistent across individuals. Our work is important because it suggests that anemone microbiomes play a role in maintaining host fitness, that they are susceptible to disturbance events, and that it is possible to generate gnotobiotic individuals that can be leveraged in microbiome manipulation studies to investigate the role of individual species on host health.
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Affiliation(s)
- Sophie MacVittie
- Department of Molecular Cell Biology, University of California, Merced, California, USA
| | - Saam Doroodian
- Department of Molecular Cell Biology, University of California, Merced, California, USA
| | - Aaron Alberto
- Department of Molecular Cell Biology, University of California, Merced, California, USA
| | - Maggie Sogin
- Department of Molecular Cell Biology, University of California, Merced, California, USA
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2
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Lin S, Li L, Zhou Z, Yuan H, Saad OS, Tang J, Cai W, Yu K, Lin S. Higher genotypic diversity and distinct assembly mechanism of free-living Symbiodiniaceae assemblages than sympatric coral-endosymbiotic assemblages in a tropical coral reef. Microbiol Spectr 2024:e0051424. [PMID: 38874391 DOI: 10.1128/spectrum.00514-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 05/10/2024] [Indexed: 06/15/2024] Open
Abstract
While in hospite Symbiodiniaceae dinoflagellates are essential for coral health, ambient free-living counterparts are crucial for coral recruitment and resilience. Comparing free-living and in hospite Symbiodiniaceae communities can potentially provide insights into endosymbiont acquisition and recurrent recruitment in bleaching recovery. In this study, we studied coral-endosymbiotic and ambient free-living Symbiodiniaceae communities in the South China Sea. We collected samples from 183 coral and ambient plankton samples and conducted metabarcoding to investigate the diversity distribution, driving factors, and assembly mechanisms of the two groups of Symbiodiniaceae. Results revealed Cladocopium C1 and Durusdinium D1 as dominant genotypes. We detected a higher genotypic diversity in free-living than in hospite symbiodiniacean communities, but with shared dominant genotypes. This indicates a genetically diverse pool of Symbiodiniaceae available for recruitment by corals. Strikingly, we found that the cooler area had more Symbiodiniaceae thermosensitive genotypes, whereas the warmer area had more Symbiodiniaceae thermotolerant genotypes. Furthermore, in hospite and free-living Symbiodiniaceae communities were similarly affected by environmental factors, but shaped by different assembly mechanisms. The in hospite communities were controlled mainly by deterministic processes, whereas the ambient communities by stochastic processes. This study sheds light on the genetic diversity of source environmental Symbiodiniaceae and differential assembly mechanisms influencing Symbiodiniaceae inside and outside corals.IMPORTANCESymbiodiniaceae dinoflagellates play a pivotal role as key primary producers within coral reef ecosystems. Coral-endosymbiotic Symbiodiniaceae communities have been extensively studied, but relatively little work has been reported on the free-living Symbiodiniaceae community. Conducting a comparative analysis between sympatric coral-endosymbiotic and free-living Symbiodiniaceae communities can potentially enhance the understanding of how endosymbiont communities change in response to changing environments and the mechanisms driving these changes. Our findings shed light on the genetic diversity of source environmental Symbiodiniaceae and differential assembly mechanisms shaping free-living and in hospite Symbiodiniaceae communities, with implications in evaluating the adaptive and resilient capacity of corals in response to future climate change.
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Affiliation(s)
- Sitong Lin
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Ling Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Zhi Zhou
- School of Marine Science and Engineering, Hainan University, Haikou, China
| | - Huatao Yuan
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Osama S Saad
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Jia Tang
- School of Marine Science and Engineering, Hainan University, Haikou, China
| | - Wenqi Cai
- School of Marine Science and Engineering, Hainan University, Haikou, China
| | - Kefu Yu
- School of Marine Sciences, Guangxi University, Nanning, China
| | - Senjie Lin
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, USA
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3
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Chen B, Wei Y, Yu K, Liang Y, Yu X, Liao Z, Qin Z, Xu L, Bao Z. The microbiome dynamics and interaction of endosymbiotic Symbiodiniaceae and fungi are associated with thermal bleaching susceptibility of coral holobionts. Appl Environ Microbiol 2024; 90:e0193923. [PMID: 38445866 PMCID: PMC11022545 DOI: 10.1128/aem.01939-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 01/19/2024] [Indexed: 03/07/2024] Open
Abstract
The thermal bleaching percentage of coral holobionts shows interspecific differences under heat-stress conditions, which are closely related to the coral-associated microbiome. However, the ecological effects of community dynamics and interactions between Symbiodiniaceae and fungi on coral thermal bleaching susceptibility remain unclear. In this study, we analyzed the diversity, community structure, functions, and potential interaction of Symbiodiniaceae and fungi among 18 coral species from a high thermal bleaching risk atoll using next-generation sequencing. The results showed that heat-tolerant C3u sub-clade and Durusdinium dominated the Symbiodiniaceae community of corals and that there were no core amplicon sequence variants in the coral-associated fungal community. Fungal richness and the abundance of confirmed functional animal-plant pathogens were significantly positively correlated with the coral thermal bleaching percentage. Fungal indicators, including Didymellaceae, Chaetomiaceae, Schizophyllum, and Colletotrichum, were identified in corals. Each coral species had a complex Symbiodiniaceae-fungi interaction network (SFIN), which was driven by the dominant Symbiodiniaceae sub-clades. The SFINs of coral holobionts with low thermal bleaching susceptibility exhibited low complexity and high betweenness centrality. These results indicate that the extra heat tolerance of coral in Huangyan Island may be linked to the high abundance of heat-tolerant Symbiodiniaceae. Fungal communities have high interspecific flexibility, and the increase of fungal diversity and pathogen abundance was correlated with higher thermal bleaching susceptibility of corals. Moreover, fungal indicators were associated with the degrees of coral thermal bleaching susceptibility, including both high and intermediate levels. The topological properties of SFINs suggest that heat-tolerant coral have limited fungal parasitism and strong microbial network resilience.IMPORTANCEGlobal warming and enhanced marine heatwaves have led to a rapid decline in coral reef ecosystems worldwide. Several studies have focused on the impact of coral-associated microbiomes on thermal bleaching susceptibility in corals; however, the ecological functions and interactions between Symbiodiniaceae and fungi remain unclear. We investigated the microbiome dynamics and potential interactions of Symbiodiniaceae and fungi among 18 coral species in Huangyan Island. Our study found that the Symbiodiniaceae community of corals was mainly composed of heat-tolerant C3u sub-clade and Durusdinium. The increase in fungal diversity and pathogen abundance has close associations with higher coral thermal bleaching susceptibility. We first constructed an interaction network between Symbiodiniaceae and fungi in corals, which indicated that restricting fungal parasitism and strong interaction network resilience would promote heat acclimatization of corals. Accordingly, this study provides insights into the role of microorganisms and their interaction as drivers of interspecific differences in coral thermal bleaching.
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Affiliation(s)
- Biao Chen
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Yuxin Wei
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Kefu Yu
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Yanting Liang
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Xiaopeng Yu
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Zhiheng Liao
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
- Key Laboratory of Environmental Change and Resource Use in Beibu Gulf, Ministry of Education, Nanning Normal University, Nanning, China
| | - Zhenjun Qin
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Lijia Xu
- South China Institute of Environmental Sciences, MEE, Guangzhou, China
| | - Zeming Bao
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
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Wang S, Lu C, Zhang Q, He X, Wang W, Li J, Su H. Microbial community and transcriptional responses to V. coralliilyticus stress in coral Favites halicora and Pocillopora damicornis holobiont. MARINE ENVIRONMENTAL RESEARCH 2024; 196:106394. [PMID: 38340371 DOI: 10.1016/j.marenvres.2024.106394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/23/2024] [Accepted: 02/04/2024] [Indexed: 02/12/2024]
Abstract
Variability in coral hosts susceptibility to Vibrio coralliilyticus is well-documented; however, the comprehensive understanding of tolerance of response to pathogen among coral species is lacked. Herein, we investigated the microbial communities and transcriptome dynamics of two corals in response to Vibrio coralliilyticus. Favites halicora displayed greater resistance to Vibrio coralliilyticus challenge than Pocillopora damicornis. Furthermore, the relative abundances of Flavobacteriaceae, Vibrionacea, Rhodobacteraceae, and Roseobacteraceae increased significantly in Favites halicora following pathogen stress, whereas that of Akkermansiaceae increased significantly in Pocillopora damicornis, leading to bacterial community imbalance. In contrast to the previous results, pathogen infection did not have much effect on the community structures of Symbiodiniaceae and fungi, but led to a decrease in the density of Symbiodiniaceae. Transcriptome analysis indicated that Vibrio infection triggered a coral immune response, resulting in higher expression of immune-related genes, which appeared to have higher transcriptional plasticity in Favites halicora than in Pocillopora damicornis. Specifically, the upregulated genes of Favites halicora were predominantly involved in the apoptosis pathway, whereas Pocillopora damicornis were significantly enriched in the nucleotide excision repair and base excision repair pathways. These findings suggest that coral holobionts activate different mechanisms across species in response to pathogens through shifts in microbial communities and transcriptomes, which provides novel insight into assessing the future coral assemblages suffering from disease outbreaks.
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Affiliation(s)
- Shuying Wang
- Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, School of Marine Sciences, Guangxi University, Nanning, 530004, China; School of Resources, Environment and Materials, Guangxi University, Nanning, 530004, China
| | - Chunrong Lu
- Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, School of Marine Sciences, Guangxi University, Nanning, 530004, China
| | - Qi Zhang
- Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, School of Marine Sciences, Guangxi University, Nanning, 530004, China
| | - Xucong He
- Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, School of Marine Sciences, Guangxi University, Nanning, 530004, China
| | - Weihui Wang
- Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, School of Marine Sciences, Guangxi University, Nanning, 530004, China
| | - Jiani Li
- Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, School of Marine Sciences, Guangxi University, Nanning, 530004, China
| | - Hongfei Su
- Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, School of Marine Sciences, Guangxi University, Nanning, 530004, China.
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Garcias-Bonet N, Roik A, Tierney B, García FC, Villela HDM, Dungan AM, Quigley KM, Sweet M, Berg G, Gram L, Bourne DG, Ushijima B, Sogin M, Hoj L, Duarte G, Hirt H, Smalla K, Rosado AS, Carvalho S, Thurber RV, Ziegler M, Mason CE, van Oppen MJH, Voolstra CR, Peixoto RS. Horizon scanning the application of probiotics for wildlife. Trends Microbiol 2024; 32:252-269. [PMID: 37758552 DOI: 10.1016/j.tim.2023.08.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/24/2023] [Accepted: 08/28/2023] [Indexed: 09/29/2023]
Abstract
The provision of probiotics benefits the health of a wide range of organisms, from humans to animals and plants. Probiotics can enhance stress resilience of endangered organisms, many of which are critically threatened by anthropogenic impacts. The use of so-called 'probiotics for wildlife' is a nascent application, and the field needs to reflect on standards for its development, testing, validation, risk assessment, and deployment. Here, we identify the main challenges of this emerging intervention and provide a roadmap to validate the effectiveness of wildlife probiotics. We cover the essential use of inert negative controls in trials and the investigation of the probiotic mechanisms of action. We also suggest alternative microbial therapies that could be tested in parallel with the probiotic application. Our recommendations align approaches used for humans, aquaculture, and plants to the emerging concept and use of probiotics for wildlife.
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Affiliation(s)
- Neus Garcias-Bonet
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Anna Roik
- Helmholtz Institute for Functional Marine Biodiversity (HIFMB), Oldenburg, Germany; Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research (AWI), Bremerhaven, Germany
| | - Braden Tierney
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Francisca C García
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Helena D M Villela
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Ashley M Dungan
- School of Biosciences, The University of Melbourne, Parkville, VIC, Australia
| | - Kate M Quigley
- Minderoo Foundation, Perth, WA, Australia; James Cook University, Townsville, Australia
| | - Michael Sweet
- Aquatic Research Facility, Nature-based Solutions Research Centre, University of Derby, Derby, UK
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria; University of Potsdam and Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany
| | - Lone Gram
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs., Lyngby, Denmark
| | - David G Bourne
- College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia; Australian Institute of Marine Science, PMB 3, Townsville MC, Townsville, QLD 4810, Australia
| | - Blake Ushijima
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, USA
| | - Maggie Sogin
- Molecular Cell Biology, University of California, Merced, CA, USA
| | - Lone Hoj
- Australian Institute of Marine Science, PMB 3, Townsville MC, Townsville, QLD 4810, Australia
| | - Gustavo Duarte
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; IMPG, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Heribert Hirt
- Center for Desert Agriculture (CDA), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | | | - Alexandre S Rosado
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; Computational Bioscience Research Center (CBRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Susana Carvalho
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | | | - Maren Ziegler
- Department of Animal Ecology and Systematics, Justus Liebig University Giessen, Giessen, Germany
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA; WorldQuant Initiative on Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
| | - Madeleine J H van Oppen
- School of Biosciences, The University of Melbourne, Parkville, VIC, Australia; Australian Institute of Marine Science, PMB 3, Townsville MC, Townsville, QLD 4810, Australia
| | | | - Raquel S Peixoto
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; Computational Bioscience Research Center (CBRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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6
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Zou Y, Ip JCH, Xie JY, Yeung YH, Wei L, Guo Z, Zhang Y, Qiu JW. Dynamic changes in bacterial communities in three species of corals during the 2017 bleaching event in subtropical Hong Kong waters. MARINE POLLUTION BULLETIN 2024; 199:116002. [PMID: 38181470 DOI: 10.1016/j.marpolbul.2023.116002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 11/28/2023] [Accepted: 12/26/2023] [Indexed: 01/07/2024]
Abstract
Bacteria play important roles in coral health, yet little is known about the dynamics of coral-associated bacterial communities during coral bleaching. Here, we reported the dynamic changes of bacterial communities in three scleractinian corals (Montipora peltiformis, Pavona decussata and Platygyra carnosa) during and after bleaching through amplicon sequencing. Our results revealed that the bacterial composition and dominant bacteria varied among the three coral species. The higher susceptibility of M. peltiformis to bleaching corresponded to a lower bacterial community diversity, and the dominant Synechococcus shifted in abundance during the bleaching and coral recovery phases. The resilient P. decussata and P. carnosa had higher bacterial diversity and a more similar bacterial composition between the healthy and bleached conditions. Overall, our study reveals the dynamic changes in coral-associated microbial diversity under different conditions, contributing to explaining the differential susceptibility of corals to extreme climate conditions.
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Affiliation(s)
- Ying Zou
- School of Life and Health Sciences, Hainan University, Haikou, China
| | | | - James Y Xie
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Yip Hung Yeung
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Lu Wei
- School of Life and Health Sciences, Hainan University, Haikou, China
| | - Zhiqiang Guo
- School of Life and Health Sciences, Hainan University, Haikou, China
| | - Yanjie Zhang
- School of Life and Health Sciences, Hainan University, Haikou, China.
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, Hong Kong, China.
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7
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Zarate D, Gary J, Li J. Flexibility in coral-algal symbiosis is positively correlated with the host geographic range. Ecol Lett 2024; 27:e14374. [PMID: 38361467 DOI: 10.1111/ele.14374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 01/02/2024] [Accepted: 01/09/2024] [Indexed: 02/17/2024]
Abstract
Generalists are thought to adapt to broader ecological conditions compared to less flexible specialists. However, few studies have systematically tested what ecological or life-history traits are associated with organisms' ecological flexibility. Here, we used stony corals to test the relative effects of host traits and ecological factors on corals' flexibility to form photosymbioses with algae. We analysed data from 211 stony coral species to test if coral's geographic distribution, depth range, symbiont transmission mode or colony morphology predict coral-algal flexibility. We report a novel positive correlation between coral-algal flexibility and coral species' geographic range. Symbiont transmission mode was also a predictor of flexibility, albeit the result is less robust against sampling bias. Coral depth range and morphology did not show significant effects. We highlight that host-symbiont dispersal abilities, interactions and evolutionary histories likely contribute to the observed patterns. We urge conservation efforts to consider the ecological implications of coral-algal flexibility.
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Affiliation(s)
- Daniel Zarate
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado, USA
| | - Jaclyn Gary
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado, USA
| | - Jingchun Li
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado, USA
- Museum of Natural History, University of Colorado Boulder, Boulder, Colorado, USA
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Gong S, Liang J, Li G, Xu L, Tan Y, Zheng X, Jin X, Yu K, Xia X. Linking coral fluorescence phenotypes to thermal bleaching in the reef-building Galaxea fascicularis from the northern South China Sea. MARINE LIFE SCIENCE & TECHNOLOGY 2024; 6:155-167. [PMID: 38433965 PMCID: PMC10902222 DOI: 10.1007/s42995-023-00190-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 07/31/2023] [Indexed: 03/05/2024]
Abstract
Coral fluorescence phenotypes have been suggested as an adaptation to a broad range of environmental conditions, yet the mechanisms linking thermal bleaching tolerance in reef-building coral populations, associated with fluorescence phenotypes due to GFP-like proteins, remains unclear. In this study, the relationship between the thermal sensitivity and phenotypic plasticity of corals was investigated using two phenotypes of Galaxea fascicularis, green and brown. The results reveal that brown G. fascicularis was more susceptible to bleaching than green G. fascicularis when exposed to a higher growth temperature of 32 °C. Both phenotypes of G. fascicularis were associated with the thermotolerant Symbiodiniaceae symbiont, Durusdinium trenchii. However, the brown G. fascicularis showed a significant decrease in Symbiodiniaceae cell density and a significant increase in pathogenic bacteria abundance when the growth temperature was raised from 29 to 32 °C. The physiological traits and transcriptomic profiles of Symbiodiniaceae were not notably affected, but there were differences in the transcriptional levels of certain genes between the two phenotype hosts of G. fascicularis. Under heat stress of 32 °C, the gene encoding green fluorescent protein (GFP)-like and chromosome-associated proteins, as well as genes related to oxidative phosphorylation, cell growth and death showed lower transcriptional levels in the brown G. fascicularis compared to the green G. fascicularis. Overall, the results demonstrate that the green form of G. fascicularis is better able to tolerate ocean warming and defend against pathogenic bacteria, likely due to higher gene transcription levels and defense ability. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-023-00190-1.
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Affiliation(s)
- Sanqiang Gong
- Key Laboratory of Tropical Marine Bio-Resources and Ecology & Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301 China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510301 China
| | - Jiayuan Liang
- Coral Reef Research Center of China, Guangxi University, Nanning, 53004 China
| | - Gang Li
- Key Laboratory of Tropical Marine Bio-Resources and Ecology & Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301 China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510301 China
| | - Lijia Xu
- South China Institute of Environmental Sciences, The Ministry of Ecology and Environment of PRC, Guangzhou, 510530 China
| | - Yehui Tan
- Key Laboratory of Tropical Marine Bio-Resources and Ecology & Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301 China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510301 China
| | - Xinqing Zheng
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005 China
| | - Xuejie Jin
- Key Laboratory of Tropical Marine Bio-Resources and Ecology & Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301 China
| | - Kefu Yu
- Coral Reef Research Center of China, Guangxi University, Nanning, 53004 China
| | - Xiaomin Xia
- Key Laboratory of Tropical Marine Bio-Resources and Ecology & Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301 China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510301 China
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9
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Maire J, Collingro A, Horn M, van Oppen MJH. Chlamydiae in corals: shared functional potential despite broad taxonomic diversity. ISME COMMUNICATIONS 2024; 4:ycae054. [PMID: 38707840 PMCID: PMC11070183 DOI: 10.1093/ismeco/ycae054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/15/2024] [Accepted: 04/09/2024] [Indexed: 05/07/2024]
Abstract
Cnidarians, such as corals and sea anemones, associate with a wide range of bacteria that have essential functions, including nutrient cycling and the production of antimicrobial compounds. Within cnidarians, bacteria can colonize all microhabitats including the tissues. Among them are obligate intracellular bacteria of the phylum Chlamydiota (chlamydiae) whose impact on cnidarian hosts and holobionts, especially corals, remain unknown. Here, we conducted a meta-analysis of previously published 16S rRNA gene metabarcoding data from cnidarians (e.g. coral, jellyfish, and anemones), eight metagenome-assembled genomes (MAGs) of coral-associated chlamydiae, and one MAG of jellyfish-associated chlamydiae to decipher their diversity and functional potential. While the metabarcoding dataset showed an enormous diversity of cnidarian-associated chlamydiae, six out of nine MAGs were affiliated with the Simkaniaceae family. The other three MAGs were assigned to the Parasimkaniaceae, Rhabdochlamydiaceae, and Anoxychlamydiaceae, respectively. All MAGs lacked the genes necessary for an independent existence, lacking any nucleotide or vitamin and most amino acid biosynthesis pathways. Hallmark chlamydial genes, such as a type III secretion system, nucleotide transporters, and genes for host interaction, were encoded in all MAGs. Together these observations suggest an obligate intracellular lifestyle of coral-associated chlamydiae. No unique genes were found in coral-associated chlamydiae, suggesting a lack of host specificity. Additional studies are needed to understand how chlamydiae interact with their coral host, and other microbes in coral holobionts. This first study of the diversity and functional potential of coral-associated chlamydiae improves our understanding of both the coral microbiome and the chlamydial lifestyle and host range.
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Affiliation(s)
- Justin Maire
- School of BioSciences, The University of Melbourne, Parkville 3010, VIC, Australia
| | - Astrid Collingro
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna 1030, Austria
| | - Matthias Horn
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna 1030, Austria
| | - Madeleine J H van Oppen
- School of BioSciences, The University of Melbourne, Parkville 3010, VIC, Australia
- Australian Institute of Marine Science, PMB No 3, Townsville 4810, QLD, Australia
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10
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Maire J, Philip GK, Livingston J, Judd LM, Blackall LL, van Oppen MJH. Functional potential and evolutionary response to long-term heat selection of bacterial associates of coral photosymbionts. mSystems 2023; 8:e0086023. [PMID: 37909753 PMCID: PMC10746172 DOI: 10.1128/msystems.00860-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 09/28/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE Symbiotic microorganisms are crucial for the survival of corals and their resistance to coral bleaching in the face of climate change. However, the impact of microbe-microbe interactions on coral functioning is mostly unknown but could be essential factors for coral adaption to future climates. Here, we investigated interactions between cultured dinoflagellates of the Symbiodiniaceae family, essential photosymbionts of corals, and associated bacteria. By assessing the genomic potential of 49 bacteria, we found that they are likely beneficial for Symbiodiniaceae, through the production of B vitamins and antioxidants. Additionally, bacterial genes involved in host-symbiont interactions, such as secretion systems, accumulated mutations following long-term exposure to heat, suggesting symbiotic interactions may change under climate change. This highlights the importance of microbe-microbe interactions in coral functioning.
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Affiliation(s)
- Justin Maire
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Gayle K. Philip
- Melbourne Bioinformatics, The University of Melbourne, Parkville, Victoria, Australia
| | - Jadzia Livingston
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Louise M. Judd
- Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Linda L. Blackall
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Madeleine J. H. van Oppen
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
- Australian Institute of Marine Science, Townsville, Queensland, Australia
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11
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Maire J, Deore P, Jameson VJ, Sakkas M, Perez-Gonzalez A, Blackall LL, van Oppen MJH. Assessing the contribution of bacteria to the heat tolerance of experimentally evolved coral photosymbionts. Environ Microbiol 2023; 25:3298-3318. [PMID: 37849020 DOI: 10.1111/1462-2920.16521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 09/28/2023] [Indexed: 10/19/2023]
Abstract
Coral reefs are extremely vulnerable to ocean warming, which triggers coral bleaching-the loss of endosymbiotic microalgae (Symbiodiniaceae) from coral tissues, often leading to death. To enhance coral climate resilience, the symbiont, Cladocopium proliferum was experimentally evolved for >10 years under elevated temperatures resulting in increased heat tolerance. Bacterial 16S rRNA gene metabarcoding showed the composition of intra- and extracellular bacterial communities of heat-evolved strains was significantly different from that of wild-type strains, suggesting bacteria responded to elevated temperatures, and may even play a role in C. proliferum thermal tolerance. To assess whether microbiome transplantation could enhance heat tolerance of the sensitive wild-type C. proliferum, we transplanted bacterial communities from heat-evolved to the wild-type strain and subjected it to acute heat stress. Microbiome transplantation resulted in the incorporation of only 30 low-abundance strains into the microbiome of wild-type cultures, while the relative abundance of 14 pre-existing strains doubled in inoculated versus uninoculated samples. Inoculation with either wild-type or heat-evolved bacterial communities boosted C. proliferum growth, although no difference in heat tolerance was observed between the two inoculation treatments. This study provides evidence that Symbiodiniaceae-associated bacterial communities respond to heat selection and may contribute to coral adaptation to climate change.
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Affiliation(s)
- Justin Maire
- School of Biosciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Pranali Deore
- School of Biosciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Vanta J Jameson
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute of Infection and Immunity, Parkville, Victoria, Australia
- Melbourne Cytometry Platform, The University of Melbourne, Parkville, Victoria, Australia
| | - Magdaline Sakkas
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute of Infection and Immunity, Parkville, Victoria, Australia
- Melbourne Cytometry Platform, The University of Melbourne, Parkville, Victoria, Australia
| | - Alexis Perez-Gonzalez
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute of Infection and Immunity, Parkville, Victoria, Australia
- Melbourne Cytometry Platform, The University of Melbourne, Parkville, Victoria, Australia
| | - Linda L Blackall
- School of Biosciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Madeleine J H van Oppen
- School of Biosciences, The University of Melbourne, Parkville, Victoria, Australia
- Australian Institute of Marine Science, Townsville, Queensland, Australia
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12
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Dungan AM, Tandon K, Jameson V, Gotze CR, Blackall LL, van Oppen MJH. A targeted approach to enrich host-associated bacteria for metagenomic sequencing. FEMS MICROBES 2023; 5:xtad021. [PMID: 38264162 PMCID: PMC10804224 DOI: 10.1093/femsmc/xtad021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 11/02/2023] [Accepted: 11/27/2023] [Indexed: 01/25/2024] Open
Abstract
Multicellular eukaryotic organisms are hosts to communities of bacteria that reside on or inside their tissues. Often the eukaryotic members of the system contribute to high proportions of metagenomic sequencing reads, making it challenging to achieve sufficient sequencing depth to evaluate bacterial ecology. Stony corals are one such complex community; however, separation of bacterial from eukaryotic (primarily coral and algal symbiont) cells has so far not been successful. Using a combination of hybridization chain reaction fluorescence in situ hybridization and fluorescence activated cell sorting (HCR-FISH + FACS), we sorted two populations of bacteria from five genotypes of the coral Acropora loripes, targeting (i) Endozoicomonas spp, and (ii) all other bacteria. NovaSeq sequencing resulted in 67-91 M reads per sample, 55%-90% of which were identified as bacterial. Most reads were taxonomically assigned to the key coral-associated family, Endozoicomonadaceae, with Vibrionaceae also abundant. Endozoicomonadaceae were 5x more abundant in the 'Endozoicomonas' population, highlighting the success of the dual-labelling approach. This method effectively enriched coral samples for bacteria with <1% contamination from host and algal symbionts. The application of this method will allow researchers to decipher the functional potential of coral-associated bacteria. This method can also be adapted to accommodate other host-associated communities.
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Affiliation(s)
- Ashley M Dungan
- School of BioSciences, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Kshitij Tandon
- School of BioSciences, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Vanta Jameson
- Melbourne Cytometry Platform, Department of Microbiology and Immunology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Cecilie Ravn Gotze
- School of BioSciences, University of Melbourne, Melbourne, VIC 3010, Australia
- Reef Recovery, Restoration and Adaptation Program, Australian Institute of Marine Science, Townsville, QLD 4810, Australia
| | - Linda L Blackall
- School of BioSciences, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Madeleine J H van Oppen
- School of BioSciences, University of Melbourne, Melbourne, VIC 3010, Australia
- Reef Recovery, Restoration and Adaptation Program, Australian Institute of Marine Science, Townsville, QLD 4810, Australia
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Galià-Camps C, Baños E, Pascual M, Carreras C, Turon X. Multidimensional variability of the microbiome of an invasive ascidian species. iScience 2023; 26:107812. [PMID: 37744040 PMCID: PMC10514470 DOI: 10.1016/j.isci.2023.107812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/02/2023] [Accepted: 08/30/2023] [Indexed: 09/26/2023] Open
Abstract
Animals, including invasive species, are complex entities consisting of a host and its associated symbionts (holobiont). The interaction between the holobiont components is crucial for the host's survival. However, our understanding of how microbiomes of invasive species change across different tissues, localities, and ontogenetic stages, is limited. In the introduced ascidian Styela plicata, we found that its microbiome is highly distinct and specialized among compartments (tunic, gill, and gut). Smaller but significant differences were also found across harbors, suggesting local adaptation, and between juveniles and adults. Furthermore, we found a correlation between the microbiome and environmental trace element concentrations, especially in adults. Functional analyses showed that adult microbiomes possess specific metabolic pathways that may enhance fitness during the introduction process. These findings highlight the importance of integrated approaches in studying the interplay between animals and microbiomes, as a first step toward understanding how it can affect the species' invasive success.
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Affiliation(s)
- Carles Galià-Camps
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona (UB), Avinguda Diagonal 643, 08028 Barcelona, Catalonia, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Catalonia, Spain
| | - Elena Baños
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona (UB), Avinguda Diagonal 643, 08028 Barcelona, Catalonia, Spain
- Department of Marine Ecology, Centre d’Estudis Avançats de Blanes (CEAB-CSIC), Accés Cala Sant Francesc 14, 17300 Blanes, Catalonia, Spain
| | - Marta Pascual
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona (UB), Avinguda Diagonal 643, 08028 Barcelona, Catalonia, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Catalonia, Spain
| | - Carlos Carreras
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona (UB), Avinguda Diagonal 643, 08028 Barcelona, Catalonia, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Catalonia, Spain
| | - Xavier Turon
- Department of Marine Ecology, Centre d’Estudis Avançats de Blanes (CEAB-CSIC), Accés Cala Sant Francesc 14, 17300 Blanes, Catalonia, Spain
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14
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Hawthorn A, Berzins IK, Dennis MM, Kiupel M, Newton AL, Peters EC, Reyes VA, Work TM. An introduction to lesions and histology of scleractinian corals. Vet Pathol 2023; 60:529-546. [PMID: 37519147 DOI: 10.1177/03009858231189289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/01/2023]
Abstract
Stony corals (Scleractinia) are in the Phylum Cnidaria (cnidae referring to various types of stinging cells). They may be solitary or colonial, but all secrete an external, supporting aragonite skeleton. Large, colonial members of this phylum are responsible for the accretion of coral reefs in tropical and subtropical waters that form the foundations of the most biodiverse marine ecosystems. Coral reefs worldwide, but particularly in the Caribbean, are experiencing unprecedented levels of disease, resulting in reef degradation. Most coral diseases remain poorly described and lack clear case definitions, while the etiologies and pathogenesis are even more elusive. This introductory guide is focused on reef-building corals and describes basic gross and microscopic lesions in these corals in order to serve as an invitation to other veterinary pathologists to play a critical role in defining and advancing the field of coral pathology.
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Affiliation(s)
- Aine Hawthorn
- University of Wisconsin-Madison, Madison, WI
- U.S. Geological Survey, Seattle, WA
| | - Ilze K Berzins
- University of Florida, Gainesville, FL
- One Water, One Health, LLC, Golden Valley, MN
| | | | | | - Alisa L Newton
- ZooQuatic Laboratory, LLC, Baltimore, MD
- OCEARCH, Park City, UT
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15
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Doering T, Tandon K, Topa SH, Pidot SJ, Blackall LL, van Oppen MJH. Genomic exploration of coral-associated bacteria: identifying probiotic candidates to increase coral bleaching resilience in Galaxea fascicularis. MICROBIOME 2023; 11:185. [PMID: 37596630 PMCID: PMC10439622 DOI: 10.1186/s40168-023-01622-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 07/14/2023] [Indexed: 08/20/2023]
Abstract
BACKGROUND Reef-building corals are acutely threatened by ocean warming, calling for active interventions to reduce coral bleaching and mortality. Corals associate with a wide diversity of bacteria which can influence coral health, but knowledge of specific functions that may be beneficial for corals under thermal stress is scant. Under the oxidative stress theory of coral bleaching, bacteria that scavenge reactive oxygen (ROS) or nitrogen species (RNS) are expected to enhance coral thermal resilience. Further, bacterial carbon export might substitute the carbon supply from algal photosymbionts, enhance thermal resilience and facilitate bleaching recovery. To identify probiotic bacterial candidates, we sequenced the genomes of 82 pure-cultured bacteria that were isolated from the emerging coral model Galaxea fascicularis. RESULTS Genomic analyses showed bacterial isolates were affiliated with 37 genera. Isolates such as Ruegeria, Muricauda and Roseovarius were found to encode genes for the synthesis of the antioxidants mannitol, glutathione, dimethylsulfide, dimethylsulfoniopropionate, zeaxanthin and/or β-carotene. Genes involved in RNS-scavenging were found in many G. fascicularis-associated bacteria, which represents a novel finding for several genera (including Pseudophaeobacter). Transporters that are suggested to export carbon (semiSWEET) were detected in seven isolates, including Pseudovibrio and Roseibium. Further, a range of bacterial strains, including strains of Roseibium and Roseovarius, revealed genomic features that may enhance colonisation and association of bacteria with the coral host, such as secretion systems and eukaryote-like repeat proteins. CONCLUSIONS Our work provides an in-depth genomic analysis of the functional potential of G. fascicularis-associated bacteria and identifies novel combinations of traits that may enhance the coral's ability to withstand coral bleaching. Identifying and characterising bacteria that are beneficial for corals is critical for the development of effective probiotics that boost coral climate resilience. Video Abstract.
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Affiliation(s)
- Talisa Doering
- School of BioSciences, The University of Melbourne, Parkville, VIC Australia
| | - Kshitij Tandon
- School of BioSciences, The University of Melbourne, Parkville, VIC Australia
| | - Sanjida H. Topa
- School of BioSciences, The University of Melbourne, Parkville, VIC Australia
| | - Sacha J. Pidot
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, VIC Australia
| | - Linda L. Blackall
- School of BioSciences, The University of Melbourne, Parkville, VIC Australia
| | - Madeleine J. H. van Oppen
- School of BioSciences, The University of Melbourne, Parkville, VIC Australia
- Australian Institute of Marine Science, Townsville, QLD Australia
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16
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McCauley M, Goulet TL, Jackson CR, Loesgen S. Systematic review of cnidarian microbiomes reveals insights into the structure, specificity, and fidelity of marine associations. Nat Commun 2023; 14:4899. [PMID: 37580316 PMCID: PMC10425419 DOI: 10.1038/s41467-023-39876-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 06/30/2023] [Indexed: 08/16/2023] Open
Abstract
Microorganisms play essential roles in the health and resilience of cnidarians. Understanding the factors influencing cnidarian microbiomes requires cross study comparisons, yet the plethora of protocols used hampers dataset integration. We unify 16S rRNA gene sequences from cnidarian microbiome studies under a single analysis pipeline. We reprocess 12,010 cnidarian microbiome samples from 186 studies, alongside 3,388 poriferan, 370 seawater samples, and 245 cultured Symbiodiniaceae, unifying ~6.5 billion sequence reads. Samples are partitioned by hypervariable region and sequencing platform to reduce sequencing variability. This systematic review uncovers an incredible diversity of 86 archaeal and bacterial phyla associated with Cnidaria, and highlights key bacteria hosted across host sub-phylum, depth, and microhabitat. Shallow (< 30 m) water Alcyonacea and Actinaria are characterized by highly shared and relatively abundant microbial communities, unlike Scleractinia and most deeper cnidarians. Utilizing the V4 region, we find that cnidarian microbial composition, richness, diversity, and structure are primarily influenced by host phylogeny, sampling depth, and ocean body, followed by microhabitat and sampling date. We identify host and geographical generalist and specific Endozoicomonas clades within Cnidaria and Porifera. This systematic review forms a framework for understanding factors governing cnidarian microbiomes and creates a baseline for assessing stress associated dysbiosis.
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Affiliation(s)
- M McCauley
- Department of Chemistry, Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA.
- Department of Biology, University of Mississippi, University, MS, USA.
- U.S. Geological Survey, Wetland and Aquatic Research Centre, Gainesville, FL, USA.
| | - T L Goulet
- Department of Biology, University of Mississippi, University, MS, USA
| | - C R Jackson
- Department of Biology, University of Mississippi, University, MS, USA
| | - S Loesgen
- Department of Chemistry, Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA
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17
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Monti M, Giorgi A, Kemp DW, Olson JB. Spatial, temporal and network analyses provide insights into the dynamics of the bacterial communities associated with two species of Caribbean octocorals and indicate possible key taxa. Symbiosis 2023; 90:1-14. [PMID: 37360551 PMCID: PMC10238251 DOI: 10.1007/s13199-023-00923-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 05/12/2023] [Indexed: 06/28/2023]
Abstract
Despite the current decline of scleractinian coral populations, octocorals are thriving on reefs in the Caribbean Sea and western North Atlantic Ocean. These cnidarians are holobiont entities, interacting with a diverse array of microorganisms. Few studies have investigated the spatial and temporal stability of the bacterial communities associated with octocoral species and information regarding the co-occurrence and potential interactions between specific members of these bacterial communities remain sparse. To address this knowledge gap, this study investigated the stability of the bacterial assemblages associated with two common Caribbean octocoral species, Eunicea flexuosa and Antillogorgia americana, across time and geographical locations and performed network analyses to investigate potential bacterial interactions. Results demonstrated that general inferences regarding the spatial and temporal stability of octocoral-associated bacterial communities should not be made, as host-specific characteristics may influence these factors. In addition, network analyses revealed differences in the complexity of the interactions between bacteria among the octocoral species analyzed, while highlighting the presence of genera known to produce bioactive secondary metabolites in both octocorals that may play fundamental roles in structuring the octocoral-associated bacteriome. Supplementary Information The online version contains supplementary material available at 10.1007/s13199-023-00923-x.
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Affiliation(s)
- M. Monti
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487 USA
| | - A. Giorgi
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487 USA
| | - D. W. Kemp
- Department of Biology, The University of Alabama at Birmingham, Birmingham, AL 35233 USA
| | - J. B. Olson
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487 USA
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18
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Cheng K, Tong M, Cai Z, Jong MC, Zhou J, Xiao B. Prokaryotic and eukaryotic microbial communities associated with coral species have high host specificity in the South China Sea. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 867:161185. [PMID: 36581277 DOI: 10.1016/j.scitotenv.2022.161185] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 12/13/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
Reef-building corals are well known for their obligate association with Symbiodiniaceae, and an array of other microbes, including bacteria, fungi, and symbiotic algae (i.e., total microbiome), which together form the coral holobiont. The total microbiome plays an intricate part in maintaining the homeostasis of the coral holobiont and is closely associated with host health. However, the composition of the coral associated microbiome and interaction between its different members remains elusive because few analyses have bridged taxonomically disparate groups. This research gaps have prevented a holistic understanding of the total microbiome. Thus, to simultaneously characterize the bacterial, fungal and symbiotic algal communities associated with different coral species, and explore the relationship between these symbionts and coral health, healthy and bleached tissues from four coral species, Acropora muricata, Galaxea fascicularis, Platygyra daedalea, and Pavona explanulata, were collected from the Xisha Islands of the South China Sea. Using high throughput sequencing, a high degree of host-specificity was observed among bacterial, fungal, and algal groups across coral species. There were no obvious changes in the microbial community structure of apparently healthy and bleached corals, but host bleaching allowed colonization of the holobionts by diverse opportunistic microbes, resulting in a significant elevation in the α-diversity of microbial communities. In addition, co-occurrence analysis of the coral microbiota also identified more complex microbial interactions in bleached corals than in healthy ones. In summary, this study characterized the structure of coral-associated microbiomes across four coral species, and systematically studied microbiome differences between healthy and bleached corals. The findings improve our understanding of the heterogeneity of symbiotic microorganisms and the impact of coral's physiological status on its associated microbial communities composition.
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Affiliation(s)
- Keke Cheng
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China
| | - Mengmeng Tong
- Ocean College, Zhejiang University, Zhoushan 316021, PR China
| | - Zhonghua Cai
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China
| | - Mui Choo Jong
- Institute of Environment and Ecology, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China
| | - Jin Zhou
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China.
| | - Baohua Xiao
- Shenzhen Institute of Guangdong Ocean University, Shenzhen 518114, PR China.
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19
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Mohamed AR, Ochsenkühn MA, Kazlak AM, Moustafa A, Amin SA. The coral microbiome: towards an understanding of the molecular mechanisms of coral-microbiota interactions. FEMS Microbiol Rev 2023; 47:fuad005. [PMID: 36882224 PMCID: PMC10045912 DOI: 10.1093/femsre/fuad005] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 02/10/2023] [Accepted: 02/15/2023] [Indexed: 03/09/2023] Open
Abstract
Corals live in a complex, multipartite symbiosis with diverse microbes across kingdoms, some of which are implicated in vital functions, such as those related to resilience against climate change. However, knowledge gaps and technical challenges limit our understanding of the nature and functional significance of complex symbiotic relationships within corals. Here, we provide an overview of the complexity of the coral microbiome focusing on taxonomic diversity and functions of well-studied and cryptic microbes. Mining the coral literature indicate that while corals collectively harbour a third of all marine bacterial phyla, known bacterial symbionts and antagonists of corals represent a minute fraction of this diversity and that these taxa cluster into select genera, suggesting selective evolutionary mechanisms enabled these bacteria to gain a niche within the holobiont. Recent advances in coral microbiome research aimed at leveraging microbiome manipulation to increase coral's fitness to help mitigate heat stress-related mortality are discussed. Then, insights into the potential mechanisms through which microbiota can communicate with and modify host responses are examined by describing known recognition patterns, potential microbially derived coral epigenome effector proteins and coral gene regulation. Finally, the power of omics tools used to study corals are highlighted with emphasis on an integrated host-microbiota multiomics framework to understand the underlying mechanisms during symbiosis and climate change-driven dysbiosis.
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Affiliation(s)
- Amin R Mohamed
- Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
| | - Michael A Ochsenkühn
- Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
| | - Ahmed M Kazlak
- Systems Genomics Laboratory, American University in Cairo, New Cairo 11835, Egypt
- Biotechnology Graduate Program, American University in Cairo, New Cairo 11835, Egypt
| | - Ahmed Moustafa
- Systems Genomics Laboratory, American University in Cairo, New Cairo 11835, Egypt
- Biotechnology Graduate Program, American University in Cairo, New Cairo 11835, Egypt
- Department of Biology, American University in Cairo, New Cairo 11835, Egypt
| | - Shady A Amin
- Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
- Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
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20
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Doering T, Maire J, van Oppen MJH, Blackall LL. Advancing coral microbiome manipulation to build long-term climate resilience. MICROBIOLOGY AUSTRALIA 2023. [DOI: 10.1071/ma23009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023] Open
Abstract
Coral reefs house one-third of all marine species and are of high cultural and socioeconomic importance. However, coral reefs are under dire threat from climate change and other anthropogenic stressors. Climate change is causing coral bleaching, the breakdown of the symbiosis between the coral host and its algal symbionts, often resulting in coral mortality and the deterioration of these valuable ecosystems. While it is essential to counteract the root causes of climate change, it remains urgent to develop coral restoration and conservation methods that will buy time for coral reefs. The manipulation of the bacterial microbiome that is associated with corals has been suggested as one intervention to improve coral climate resilience. Early coral microbiome-manipulation studies, which are aimed at enhancing bleaching tolerance, have shown promising results, but the inoculated bacteria did generally not persist within the coral microbiome. Here, we highlight the importance of long-term incorporation of bacterial inocula into the microbiome of target corals, as repeated inoculations will be too costly and not feasible on large reef systems like the Great Barrier Reef. Therefore, coral microbiome-manipulation studies need to prioritise approaches that can provide sustained coral climate resilience.
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Zhu W, Wang H, Li X, Liu X, Zhu M, Wang A, Li X. Consistent responses of coral microbiome to acute and chronic heat stress exposures. MARINE ENVIRONMENTAL RESEARCH 2023; 185:105900. [PMID: 36731191 DOI: 10.1016/j.marenvres.2023.105900] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 01/23/2023] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
Frequent and intense heat waves lead to bleaching and even death of reef-building corals, and the thermal tolerance ultimately depends on the genetic composition of the holobiont. Here, we compared the effects of acute and chronic heat stress exposures on coral Porites cylindrica holobiont. Regardless of the temperature treatment, corals at 33 °C showed signs of bleaching and a significant decrease in photochemical efficiency (Fv/Fm). However, Symbiodiniaceae communities were relatively stable and all dominated by the same genus Cladocopium (C15). The relative abundanbce of core microbiome varied significantly, and they may provide several functions important to holobiont fitness. Both heat stress exposures induced the significant structural reorganization of coral-associated bacteria, with bacterial diversity and community heterogeneity significantly increasing with the temperature treatment. The modified stochasticity ratio (MST) revealed that stochastic processes dominated bacterial community assembly in thermally stressed corals. Certain core bacterial members that were hypothesized to fulfil functional niche decreased significantly, with the enrichment of potentially pathogenic and opportunistic bacteria in heat stress exposures. Thermally stressed corals had more positive correlation, higher network complexity and tighter associations among microbial taxa, relative to healthy corals. Overall, the coral microbiome exhibits similar responses to acute and chronic heat stress, and our study provides new insights about the deleterious impacts of complex warming oceans on coral holobiont.
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Affiliation(s)
- Wentao Zhu
- College of Ecology and Environment, Hainan University, Haikou, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Hao Wang
- College of Marine Science, Hainan University, Haikou, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Xinke Li
- College of Marine Science, Hainan University, Haikou, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Xiangbo Liu
- College of Marine Science, Hainan University, Haikou, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Ming Zhu
- College of Marine Science, Hainan University, Haikou, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Aimin Wang
- College of Marine Science, Hainan University, Haikou, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Xiubao Li
- College of Marine Science, Hainan University, Haikou, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China.
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22
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Tirichine L, Piganeau G. Editorial: Algal symbiotic relationships in freshwater and marine environments. FRONTIERS IN PLANT SCIENCE 2023; 14:1155759. [PMID: 36890883 PMCID: PMC9987335 DOI: 10.3389/fpls.2023.1155759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 02/09/2023] [Indexed: 06/18/2023]
Affiliation(s)
| | - Gwenael Piganeau
- Integrative Biology of Marine Organisms (BIOM), Sorbonne University, CNRS, Oceanological Observatory of Banyuls, Banyuls-sur-Mer, France
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23
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Paulino GVB, Félix CR, da Silva Oliveira FA, Gomez-Silvan C, Melo VMM, Andersen GL, Landell MF. Microbiota of healthy and bleached corals of the species Siderastrea stellata in response to river influx and seasonality in Brazilian northeast. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:26496-26509. [PMID: 36369436 DOI: 10.1007/s11356-022-23976-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 10/30/2022] [Indexed: 06/16/2023]
Abstract
Although coral bleaching is increasing worldwide due to warming oceans exacerbated by climate change, there has been a growing recognition that local stressors may play an additional role. Important stressors include the physicochemical and microbiological influences that are related to river runoff. Here, we investigated the microbiota associated to mucus and tissue of endemic coral Siderastrea stellata, collected from Brazilian northeast coral reefs of Barra de Santo Antônio (subject to river runoff) and Maragogi (minimal river runoff) during both the rainy and dry seasons. We sequenced the V4 region of 16S rDNA and used multiple R packages to process raw data and performed statistical analysis to reveal the microbial community structure composition and functional predictions. Major dissimilarities between microbial communities were related to seasonality, while healthy and bleached specimens were mainly associated with the enrichment of several less abundant taxa involved in specific metabolic functions, mainly related to the nitrogen cycle. We were not able to observe the dominance of groups that has been previously associated with bleachings, such as Vibrionaceae or Burkholderiaceae. The influx of freshwater appears to increase the homogeneity between individuals in Barra de Santo Antonio, especially during the rainy season. By contrast, we observed an increased homogeneity between samples in Maragogi during the dry season. Understanding the dynamics of the coral microbiota and how bleaching appears in response to specific environmental variables, in addition to determining the conditions that lead to a more robust coral microbiota, is essential for choosing the most appropriate area and conservation methods, for example.
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Affiliation(s)
- Gustavo Vasconcelos Bastos Paulino
- Universidade Federal de Alagoas, Maceió, AL, Brazil
- Programa de Pós-Graduação Em Diversidade Biológica E Conservação Nos Trópicos, Universidade Federal de Alagoas, Maceió, AL, Brazil
| | - Ciro Ramon Félix
- Universidade Federal de Alagoas, Maceió, AL, Brazil
- Programa de Pós-Graduação Em Diversidade Biológica E Conservação Nos Trópicos, Universidade Federal de Alagoas, Maceió, AL, Brazil
| | - Francisca Andréa da Silva Oliveira
- Laboratório de Ecologia Microbiana E Biotecnologia (Lembiotech), Departamento de Biologia, Universidade Federal Do Ceará, Campus Do Pici, Bloco 909, Fortaleza, CE, 60455-760, Brazil
| | - Cinta Gomez-Silvan
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Vânia M M Melo
- Laboratório de Ecologia Microbiana E Biotecnologia (Lembiotech), Departamento de Biologia, Universidade Federal Do Ceará, Campus Do Pici, Bloco 909, Fortaleza, CE, 60455-760, Brazil
| | - Gary L Andersen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Melissa Fontes Landell
- Universidade Federal de Alagoas, Maceió, AL, Brazil.
- Setor de Genética-ICBS, Universidade Federal de Alagoas, Av. Lourival Melo Mota, S/N, Tabuleiro Dos Martins, CEP: 57072-900, Maceió, AL, Brasil.
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24
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Tandon K, Ricci F, Costa J, Medina M, Kühl M, Blackall LL, Verbruggen H. Genomic view of the diversity and functional role of archaea and bacteria in the skeleton of the reef-building corals Porites lutea and Isopora palifera. Gigascience 2022; 12:giac127. [PMID: 36683362 PMCID: PMC9868349 DOI: 10.1093/gigascience/giac127] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/17/2022] [Accepted: 12/22/2022] [Indexed: 01/24/2023] Open
Abstract
At present, our knowledge on the compartmentalization of coral holobiont microbiomes is highly skewed toward the millimeter-thin coral tissue, leaving the diverse coral skeleton microbiome underexplored. Here, we present a genome-centric view of the skeleton of the reef-building corals Porites lutea and Isopora palifera, through a compendium of ∼400 high-quality bacterial and archaeal metagenome-assembled genomes (MAGs), spanning 34 phyla and 57 classes. Skeletal microbiomes harbored a diverse array of stress response genes, including dimethylsulfoniopropionate synthesis (dsyB) and metabolism (DMSP lyase). Furthermore, skeletal MAGs encoded an average of 22 ± 15 genes in P. lutea and 28 ± 23 in I. palifera with eukaryotic-like motifs thought to be involved in maintaining host association. We provide comprehensive insights into the putative functional role of the skeletal microbiome on key metabolic processes such as nitrogen fixation, dissimilatory and assimilatory nitrate, and sulfate reduction. Our study provides critical genomic resources for a better understanding of the coral skeletal microbiome and its role in holobiont functioning.
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Affiliation(s)
- Kshitij Tandon
- School of BioSciences, University of Melbourne, Parkville 3010, Australia
| | - Francesco Ricci
- School of BioSciences, University of Melbourne, Parkville 3010, Australia
- Biological, Earth and Environmental Sciences, The University of New South Wales, Kensington, NSW 2052, Australia
| | - Joana Costa
- School of BioSciences, University of Melbourne, Parkville 3010, Australia
| | - Mónica Medina
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Michael Kühl
- Marine Biological Section, Department of Biology, University of Copenhagen, DK-3000 Helsingør, Denmark
| | - Linda L Blackall
- School of BioSciences, University of Melbourne, Parkville 3010, Australia
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Parkville 3010, Australia
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Puntin G, Sweet M, Fraune S, Medina M, Sharp K, Weis VM, Ziegler M. Harnessing the Power of Model Organisms To Unravel Microbial Functions in the Coral Holobiont. Microbiol Mol Biol Rev 2022; 86:e0005322. [PMID: 36287022 PMCID: PMC9769930 DOI: 10.1128/mmbr.00053-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Stony corals build the framework of coral reefs, ecosystems of immense ecological and economic importance. The existence of these ecosystems is threatened by climate change and other anthropogenic stressors that manifest in microbial dysbiosis such as coral bleaching and disease, often leading to coral mortality. Despite a significant amount of research, the mechanisms ultimately underlying these destructive phenomena, and what could prevent or mitigate them, remain to be resolved. This is mostly due to practical challenges in experimentation on corals and the highly complex nature of the coral holobiont that also includes bacteria, archaea, protists, and viruses. While the overall importance of these partners is well recognized, their specific contributions to holobiont functioning and their interspecific dynamics remain largely unexplored. Here, we review the potential of adopting model organisms as more tractable systems to address these knowledge gaps. We draw on parallels from the broader biological and biomedical fields to guide the establishment, implementation, and integration of new and emerging model organisms with the aim of addressing the specific needs of coral research. We evaluate the cnidarian models Hydra, Aiptasia, Cassiopea, and Astrangia poculata; review the fast-evolving field of coral tissue and cell cultures; and propose a framework for the establishment of "true" tropical reef-building coral models. Based on this assessment, we also suggest future research to address key aspects limiting our ability to understand and hence improve the response of reef-building corals to future ocean conditions.
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Affiliation(s)
- Giulia Puntin
- Department of Animal Ecology and Systematics, Marine Holobiomics Lab, Justus Liebig University Giessen, Giessen, Germany
| | - Michael Sweet
- Aquatic Research Facility, Environmental Sustainability Research Centre, University of Derby, Derby, United Kingdom
| | - Sebastian Fraune
- Institute for Zoology and Organismic Interactions, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Mónica Medina
- Department of Biology, Pennsylvania State University, State College, Pennsylvania, USA
| | - Koty Sharp
- Department of Biology, Marine Biology, and Environmental Science, Roger Williams University, Bristol, Rhode Island, USA
| | - Virginia M. Weis
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon, USA
| | - Maren Ziegler
- Department of Animal Ecology and Systematics, Marine Holobiomics Lab, Justus Liebig University Giessen, Giessen, Germany
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26
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Fu JR, Zhou J, Zhang YP, Liu L. Effects of Caulerpa taxifolia on Physiological Processes and Gene Expression of Acropora hyacinthus during Thermal Stress. BIOLOGY 2022; 11:biology11121792. [PMID: 36552301 PMCID: PMC9775474 DOI: 10.3390/biology11121792] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/06/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022]
Abstract
An increasing ecological phase shift from coral-dominated reefs to macroalgae-dominated reefs as a result of anthropogenic impacts, such as eutrophication, sedimentation, and overfishing, has been observed in many reef systems around the world. Ocean warming is a universal threat to both corals and macroalgae, which may alter the outcome of competition between them. Therefore, in order to explore the effects of indirect and direct exposure to macroalgae on the physiological, biochemical, and genetic expression of corals at elevated temperature, the coral Acropora hyacinthus and highly invasive green algae Caulerpa taxifolia were chosen. Physiologically, the results exhibited that, between the control and direct contact treatments, the density and chlorophyll a content of zooxanthella decreased by 53.1% and 71.2%, respectively, when the coral indirectly contacted with the algae at an ambient temperature (27 °C). Moreover, the enzyme activities of superoxide dismutase (SOD) and catalase (CAT) in coral tissue were enhanced by interacting with algae. After an increase of 3 °C, the density and chlorophyll a content of the zooxanthella reduced by 84.4% and 93.8%, respectively, whereas the enzyme activities of SOD and CAT increased 2.3- and 3.1-fold. However, only the zooxanthellae density and pigment content decreased when Caulerpa taxifolia was co-cultured with Acropora hyacinthus at 30 °C. Molecularly, different from the control group, the differentially expressed genes (DEGs) such as Rab family, ATG family, and Casp7 genes were significantly enriched in the endocytosis, autophagy, and apoptosis pathways, regardless of whether Acropora hyacinthus was directly or indirectly exposed to Caulerpa taxifolia at 27 °C. Under thermal stress without algae interaction, the DEGs were significantly enriched in the microbial immune signal transduction pathways, such as the Toll-like receptor signaling pathway and TNF signaling pathway, while multiple cellular immunity (IFI47, TRAF family) and oxidative stress (CAT, SODC, HSP70) genes were upregulated. Inversely, compared with corals without interaction with algae at 30 °C, the DEGs of the corals that interacted with Caulerpa taxifolia at 30 °C were remarkably enriched in apoptosis and the NOD-like receptor signaling pathway, including the transcription factors such as the Casp family and TRAF family. In conclusion, the density and chlorophyll a content of zooxanthella maintained a fading tendency induced by the macroalgae at ambient temperatures. The oxidative stress and immune response levels of the coral was elevated at 30 °C, but the macroalgae alleviated the negative effects triggered by thermal stress.
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Affiliation(s)
- Jian-Rong Fu
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
| | - Jie Zhou
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
| | - Yan-Ping Zhang
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
| | - Li Liu
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
- Guangdong Laboratory of Southern Ocean Science and Engineering, Zhanjiang 524025, China
- Correspondence:
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27
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Siro G, Pipite A, Christi K, Srinivasan S, Subramani R. Marine Actinomycetes Associated with Stony Corals: A Potential Hotspot for Specialized Metabolites. Microorganisms 2022; 10:microorganisms10071349. [PMID: 35889068 PMCID: PMC9319285 DOI: 10.3390/microorganisms10071349] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/29/2022] [Accepted: 07/02/2022] [Indexed: 02/05/2023] Open
Abstract
Microbial secondary metabolites are an important source of antibiotics currently available for combating drug-resistant pathogens. These important secondary metabolites are produced by various microorganisms, including Actinobacteria. Actinobacteria have a colossal genome with a wide array of genes that code for several bioactive metabolites and enzymes. Numerous studies have reported the isolation and screening of millions of strains of actinomycetes from various habitats for specialized metabolites worldwide. Looking at the extent of the importance of actinomycetes in various fields, corals are highlighted as a potential hotspot for untapped secondary metabolites and new bioactive metabolites. Unfortunately, knowledge about the diversity, distribution and biochemistry of marine actinomycetes compared to hard corals is limited. In this review, we aim to summarize the recent knowledge on the isolation, diversity, distribution and discovery of natural compounds from marine actinomycetes associated with hard corals. A total of 11 new species of actinomycetes, representing nine different families of actinomycetes, were recovered from hard corals during the period from 2007 to 2022. In addition, this study examined a total of 13 new compounds produced by five genera of actinomycetes reported from 2017 to 2022 with antibacterial, antifungal and cytotoxic activities. Coral-derived actinomycetes have different mechanisms of action against their competitors.
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Affiliation(s)
- Galana Siro
- School of Agriculture, Geography, Environment, Ocean and Natural Sciences (SAGEONS), The University of the South Pacific, Laucala Campus, Suva, Fiji; (G.S.); (K.C.); (R.S.)
| | - Atanas Pipite
- School of Agriculture, Geography, Environment, Ocean and Natural Sciences (SAGEONS), The University of the South Pacific, Laucala Campus, Suva, Fiji; (G.S.); (K.C.); (R.S.)
- Correspondence: (A.P.); or (S.S.)
| | - Ketan Christi
- School of Agriculture, Geography, Environment, Ocean and Natural Sciences (SAGEONS), The University of the South Pacific, Laucala Campus, Suva, Fiji; (G.S.); (K.C.); (R.S.)
| | - Sathiyaraj Srinivasan
- Department of Bio & Environmental Technology, Division of Environmental & Life Science, College of Natural Science, Seoul Women’s University, 623 Hwarangno, Nowon-gu, Seoul 01797, Korea
- Correspondence: (A.P.); or (S.S.)
| | - Ramesh Subramani
- School of Agriculture, Geography, Environment, Ocean and Natural Sciences (SAGEONS), The University of the South Pacific, Laucala Campus, Suva, Fiji; (G.S.); (K.C.); (R.S.)
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28
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Microbiome Restructuring: Dominant Coral Bacterium Endozoicomonas Species Respond Differentially to Environmental Changes. mSystems 2022; 7:e0035922. [PMID: 35703535 PMCID: PMC9426584 DOI: 10.1128/msystems.00359-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Bacteria in the coral microbiome play a crucial role in determining coral health and fitness, and the coral host often restructures its microbiome composition in response to external factors. An important but often neglected factor determining this microbiome restructuring is the ability of microbiome members to respond to changes in the environment. To address this issue, we examined how the microbiome structure of Acropora muricata corals changed over 9 months following a reciprocal transplant experiment. Using a combination of metabarcoding, genomics, and comparative genomics approaches, we found that coral colonies separated by a small distance harbored different dominant Endozoicomonas-related phylotypes belonging to two different species, including a novel species, “Candidatus Endozoicomonas penghunesis” 4G, whose chromosome-level (complete) genome was also sequenced in this study. Furthermore, the two dominant Endozoicomonas species had different potentials to scavenge reactive oxygen species, suggesting potential differences in responding to the environment. Differential capabilities of dominant members of the microbiome to respond to environmental change can (i) provide distinct advantages or disadvantages to coral hosts when subjected to changing environmental conditions and (ii) have positive or negative implications for future reefs. IMPORTANCE The coral microbiome has been known to play a crucial role in host health. In recent years, we have known that the coral microbiome changes in response to external stressors and that coral hosts structure their microbiome in a host-specific manner. However, an important internal factor, the ability of microbiome members to respond to change, has been often neglected. In this study, we combine metabarcoding, culturing, and genomics to delineate the differential ability of two dominant Endozoicomonas species, including a novel “Ca. Endozoicomonas penghunesis” 4G, to respond to change in the environment following a reciprocal transplant experiment.
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29
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Jandang S, Viyakarn V, Yoshioka Y, Shinzato C, Chavanich S. The seasonal investigation of Symbiodiniaceae in broadcast spawning, Acropora humilis and brooding, Pocillopora cf. damicornis corals. PeerJ 2022; 10:e13114. [PMID: 35722256 PMCID: PMC9205303 DOI: 10.7717/peerj.13114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 02/23/2022] [Indexed: 01/12/2023] Open
Abstract
The density and diversity of Symbiodiniaceae associated with corals can be influenced by seasonal changes . This study provided the first annual investigation of Symbiodiniaceae density and diversity associated with Acropora humilis and Pocillopora cf. damicornis corals in the Gulf of Thailand using both zooxanthellae cell count and next-generation sequencing (ITS-1, ITS-2 regions) techniques, respectively. The results from this study indicated that zooxanthellae cell densities in both coral species differ significantly. The number of zooxanthellae was negatively correlated with the physical environment variable (light intensity). The diversity within A. humilis consisted of two genera, Cladocopium (Cspc_C3: 56.39%, C3w: 33.62%, C93type1: 4.42% and Cspf: 3.59%) and a small amount of Durusdinium (D1: 1.03%) whereas P. cf. damicornis was found to be 100% associated with Durusdinium (D1: 95.58%, D6: 1.01% and D10: 2.7%) suggesting that each coral species may select their appropriate genus/species of Symbiodiniaceae in response to local environmental stressors. The results of this study provided some information on the coral-Symbiodiniaceae relationship between seasons, which may be applied to predict the potential adaptation of corals in localized reef environments.
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Affiliation(s)
- Suppakarn Jandang
- Reef Biology Research Group, Department of Marine Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Voranop Viyakarn
- Reef Biology Research Group, Department of Marine Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand,Aquatic Resources Research Institute, Chulalongkorn University, Bangkok, Thailand
| | - Yuki Yoshioka
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan
| | - Chuya Shinzato
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan
| | - Suchana Chavanich
- Reef Biology Research Group, Department of Marine Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand,Aquatic Resources Research Institute, Chulalongkorn University, Bangkok, Thailand,Center of Excellence for Marine Biotechnology, Department of Marine Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
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30
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Haydon TD, Suggett DJ, Siboni N, Kahlke T, Camp EF, Seymour JR. Temporal Variation in the Microbiome of Tropical and Temperate Octocorals. MICROBIAL ECOLOGY 2022; 83:1073-1087. [PMID: 34331071 DOI: 10.1007/s00248-021-01823-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 07/15/2021] [Indexed: 06/13/2023]
Abstract
Bacterial members of the coral holobiont play an important role in determining coral fitness. However, most knowledge of the coral microbiome has come from reef-building scleractinian corals, with far less known about the nature and importance of the microbiome of octocorals (subclass Octocorallia), which contribute significantly to reef biodiversity and functional complexity. We examined the diversity and structure of the bacterial component of octocoral microbiomes over summer and winter, with a focus on two temperate (Erythropodium hicksoni, Capnella gaboensis; Sydney Harbour) and two tropical (Sinularia sp., Sarcophyton sp.; Heron Island) species common to reefs in eastern Australia. Bacterial communities associated with these octocorals were also compared to common temperate (Plesiastrea versipora) and tropical (Acropora aspera) hard corals from the same reefs. Using 16S rRNA amplicon sequencing, bacterial diversity was found to be heterogeneous among octocorals, but we observed changes in composition between summer and winter for some species (C. gaboensis and Sinularia sp.), but not for others (E. hicksoni and Sarcophyton sp.). Bacterial community structure differed significantly between all octocoral species within both the temperate and tropical environments. However, on a seasonal basis, those differences were less pronounced. The microbiomes of C. gaboensis and Sinularia sp. were dominated by bacteria belonging to the genus Endozoicomonas, which were a key conserved feature of their core microbiomes. In contrast to previous studies, our analysis revealed that Endozoicomonas phylotypes are shared across different octocoral species, inhabiting different environments. Together, our data demonstrates that octocorals harbour a broad diversity of bacterial partners, some of which comprise 'core microbiomes' that potentially impart important functional roles to their hosts.
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Affiliation(s)
- Trent D Haydon
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Ultimo, NSW, 2007, Australia.
| | - David J Suggett
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Nachshon Siboni
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Tim Kahlke
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Emma F Camp
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Justin R Seymour
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Ultimo, NSW, 2007, Australia
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31
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Deignan LK, McDougald D. Differential Response of the Microbiome of Pocillopora acuta to Reciprocal Transplantation Within Singapore. MICROBIAL ECOLOGY 2022; 83:608-618. [PMID: 34148107 PMCID: PMC8979861 DOI: 10.1007/s00248-021-01793-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 06/10/2021] [Indexed: 05/07/2023]
Abstract
As corals continue to decline globally, particularly due to climate change, it is vital to understand the extent to which their microbiome may confer an adaptive resilience against environmental stress. Corals that survive on the urban reefs of Singapore are ideal candidates to study the association of scleractinians with their microbiome, which in turn can inform reef conservation and management. In this study, we monitored differences in the microbiome of Pocillopora acuta colonies reciprocally transplanted between two reefs, Raffles and Kusu, within the Port of Singapore, where corals face intense anthropogenic impacts. Pocillopora acuta had previously been shown to host distinct microbial communities between these two reefs. Amplicon sequencing (16S rRNA) was used to assess the coral microbiomes at 1, 2, 4, and 10 days post-transplantation. Coral microbiomes responded rapidly to transplantation, becoming similar to those of the local corals at the destination reef within one day at Raffles and within two days at Kusu. Elevated nitrate concentrations were detected at Raffles for the duration of the study, potentially influencing the microbiome's response to transplantation. The persistence of corals within the port of Singapore highlights the ability of corals to adapt to stressful environments. Further, coral resilience appears to coincide with a dynamic microbiome which can undergo shifts in composition without succumbing to dysbiosis.
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Affiliation(s)
- Lindsey K Deignan
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, SBS-01N-27, Singapore, 637551, Singapore.
| | - Diane McDougald
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, SBS-01N-27, Singapore, 637551, Singapore
- The iThree Institute, University of Technology Sydney, Sydney, NSW, 2007, Australia
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Maire J, Buerger P, Chan WY, Deore P, Dungan AM, Nitschke MR, van Oppen MJH. Effects of Ocean Warming on the Underexplored Members of the Coral Microbiome. Integr Comp Biol 2022; 62:1700-1709. [PMID: 35259253 PMCID: PMC9801979 DOI: 10.1093/icb/icac005] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 03/01/2022] [Accepted: 03/05/2022] [Indexed: 01/05/2023] Open
Abstract
The climate crisis is one of the most significant threats to marine ecosystems. It is leading to severe increases in sea surface temperatures and in the frequency and magnitude of marine heatwaves. These changing conditions are directly impacting coral reef ecosystems, which are among the most biodiverse ecosystems on Earth. Coral-associated symbionts are particularly affected because summer heatwaves cause coral bleaching-the loss of endosymbiotic microalgae (Symbiodiniaceae) from coral tissues, leading to coral starvation and death. Coral-associated Symbiodiniaceae and bacteria have been extensively studied in the context of climate change, especially in terms of community diversity and dynamics. However, data on other microorganisms and their response to climate change are scarce. Here, we review current knowledge on how increasing temperatures affect understudied coral-associated microorganisms such as archaea, fungi, viruses, and protists other than Symbiodiniaceae, as well as microbe-microbe interactions. We show that the coral-microbe symbiosis equilibrium is at risk under current and predicted future climate change and argue that coral reef conservation initiatives should include microbe-focused approaches.
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Affiliation(s)
| | - Patrick Buerger
- School of BioSciences, University of Melbourne, Parkville, VIC 3010, Australia,Applied BioSciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Wing Yan Chan
- School of BioSciences, University of Melbourne, Parkville, VIC 3010, Australia
| | - Pranali Deore
- School of BioSciences, University of Melbourne, Parkville, VIC 3010, Australia
| | - Ashley M Dungan
- School of BioSciences, University of Melbourne, Parkville, VIC 3010, Australia
| | | | - Madeleine J H van Oppen
- School of BioSciences, University of Melbourne, Parkville, VIC 3010, Australia,Australian Institute of Marine Science, Townsville, QLD 4810, Australia
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33
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Chen CY, Lu TH, Liao CM. Integrated toxicokinetic/toxicodynamic assessment modeling reveals at-risk scleractinian corals under extensive microplastics impacts. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150964. [PMID: 34656596 DOI: 10.1016/j.scitotenv.2021.150964] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 10/03/2021] [Accepted: 10/09/2021] [Indexed: 06/13/2023]
Abstract
Marine microplastics (MPs)-induced threats to shallow-water scleractinian corals are a growing global concern that needs interdisciplinary studies. However, it remains uncertain to what extent the ecotoxicological effects of MPs can explain the potential health impacts on corals at the species-specific scale. Using recent datasets of multiple MPs-induced impacts on coral species, we developed an integrated ecotoxicological modeling approach to quantify the MPs-corals interaction dynamics. Toxicokinetic (TK)-based corals ingestion, egestion, and adhesion processes posed by MPs were comprehensively evaluated. Based on estimated uptake and egestion rates, we showed that corals were much likely to bioaccumulate marine MPs. We applied toxicodynamic (TD) models to appraise time- and concentration-dependent response patterns across MPs-corals systems. We found that marine MPs are highly toxic to corals with a median benchmark concentration causing 10% compromised coral health of 20-40 mg L-1 and a mean growth inhibition rate of ~2% d-1. By providing these key quantitative metrics that may inform scientists to refine existing management strategies to better understand the long-term impact of MPs on coral reef ecosystems. Our TK/TD modeling scheme can help integrating current toxicological findings to encompass a more mechanistic-, ecological-, and process-based understanding of diverse coral ecosystems that are sensitive to MPs stressor varied considerably by species and taxonomic group.
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Affiliation(s)
- Chi-Yun Chen
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taipei 10617, Taiwan, ROC
| | - Tien-Hsuan Lu
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taipei 10617, Taiwan, ROC
| | - Chung-Min Liao
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taipei 10617, Taiwan, ROC.
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34
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Dungan AM, Hartman LM, Blackall LL, van Oppen MJH. Exploring microbiome engineering as a strategy for improved thermal tolerance in Exaiptasia diaphana. J Appl Microbiol 2022; 132:2940-2956. [PMID: 35104027 PMCID: PMC9303619 DOI: 10.1111/jam.15465] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 12/08/2021] [Accepted: 01/24/2022] [Indexed: 11/28/2022]
Abstract
Aims Fourteen percent of all living coral, equivalent to more than all the coral on the Great Barrier Reef, has died in the past decade as a result of climate change‐driven bleaching. Inspired by the ‘oxidative stress theory of coral bleaching’, we investigated whether a bacterial consortium designed to scavenge free radicals could integrate into the host microbiome and improve thermal tolerance of the coral model, Exaiptasia diaphana. Methods and Results E. diaphana anemones were inoculated with a consortium of high free radical scavenging (FRS) bacteria, a consortium of congeneric low FRS bacteria, or sterile seawater as a control, then exposed to elevated temperature. Increases in the relative abundance of Labrenzia during the first 2 weeks following the last inoculation provided evidence for temporary inoculum integration into the E. diaphana microbiome. Initial uptake of other consortium members was inconsistent, and these bacteria did not persist either in E. diaphana’s microbiome over time. Given their non‐integration into the host microbiome, the ability of the FRS consortium to mitigate thermal stress could not be assessed. Importantly, there were no physiological impacts (negative or positive) of the bacterial inoculations on the holobiont. Conclusions The introduced bacteria were not maintained in the anemone microbiome over time, thus, their protective effect is unknown. Achieving long‐term integration of bacteria into cnidarian microbiomes remains a research priority. Significance and Impact of the Study Microbiome engineering strategies to mitigate coral bleaching may assist coral reefs in their persistence until climate change has been curbed. This study provides insights that will inform microbiome manipulation approaches in coral bleaching mitigation research.
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Affiliation(s)
- Ashley M Dungan
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Leon M Hartman
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia.,Swinburne University of Technology, Hawthorn, VIC, Australia
| | - Linda L Blackall
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Madeleine J H van Oppen
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia.,Australian Institute of Marine Science, Townsville, Australia
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Traylor-Knowles N, Emery M. Analysis of Spatial Gene Expression at the Cellular Level in Stony Corals. Methods Mol Biol 2022; 2450:359-371. [PMID: 35359318 PMCID: PMC9761507 DOI: 10.1007/978-1-0716-2172-1_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Scleractinians, or stony corals, are colonial animals that possess a high regenerative capacity and a highly diverse innate immune system. As such they present the opportunity to investigate the interconnection between regeneration and immunity in a colonial animal. Understanding the relationship between regeneration and immunity in stony corals is of further interest as it has major implications for coral reef health. One method for understanding the role of innate immunity in scleractinian regeneration is in situ hybridization using RNA probes. Here we describe a protocol for in situ hybridization in adult stony corals using a digoxigenin (DIG)-labeled RNA antisense probe which can be utilized to investigate the spatial expression of immune factors during regeneration.
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Affiliation(s)
- Nikki Traylor-Knowles
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, USA.
| | - Madison Emery
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, USA
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
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Dubé CE, Ziegler M, Mercière A, Boissin E, Planes S, Bourmaud CAF, Voolstra CR. Naturally occurring fire coral clones demonstrate a genetic and environmental basis of microbiome composition. Nat Commun 2021; 12:6402. [PMID: 34737272 PMCID: PMC8568919 DOI: 10.1038/s41467-021-26543-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 10/04/2021] [Indexed: 02/07/2023] Open
Abstract
Coral microbiomes are critical to holobiont functioning, but much remains to be understood about how prevailing environment and host genotype affect microbial communities in ecosystems. Resembling human identical twin studies, we examined bacterial community differences of naturally occurring fire coral clones within and between contrasting reef habitats to assess the relative contribution of host genotype and environment to microbiome structure. Bacterial community composition of coral clones differed between reef habitats, highlighting the contribution of the environment. Similarly, but to a lesser extent, microbiomes varied across different genotypes in identical habitats, denoting the influence of host genotype. Predictions of genomic function based on taxonomic profiles suggest that environmentally determined taxa supported a functional restructuring of the microbial metabolic network. In contrast, bacteria determined by host genotype seemed to be functionally redundant. Our study suggests microbiome flexibility as a mechanism of environmental adaptation with association of different bacterial taxa partially dependent on host genotype.
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Affiliation(s)
- C. E. Dubé
- grid.11642.300000 0001 2111 2608UMR 9220 ENTROPIE, UR-IRD-CNRS-UNC-IFREMER, Université de La Réunion, 15 Avenue René Cassin, CS 92003, 97744 Saint-Denis Cedex, La Réunion France ,grid.11136.340000 0001 2192 5916PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860 Perpignan, France ,Laboratoire d’Excellence “CORAIL”, 98729 Papetoai, Moorea French Polynesia ,grid.23856.3a0000 0004 1936 8390Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, G1V 0A6 Canada
| | - M. Ziegler
- grid.8664.c0000 0001 2165 8627Department of Animal Ecology and Systematics, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32 IFZ, 35392 Giessen, Germany ,grid.45672.320000 0001 1926 5090Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, 23955 Saudi Arabia
| | - A. Mercière
- grid.11136.340000 0001 2192 5916PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860 Perpignan, France ,Laboratoire d’Excellence “CORAIL”, 98729 Papetoai, Moorea French Polynesia
| | - E. Boissin
- grid.11136.340000 0001 2192 5916PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860 Perpignan, France ,Laboratoire d’Excellence “CORAIL”, 98729 Papetoai, Moorea French Polynesia
| | - S. Planes
- grid.11136.340000 0001 2192 5916PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860 Perpignan, France ,Laboratoire d’Excellence “CORAIL”, 98729 Papetoai, Moorea French Polynesia
| | - C. A. -F. Bourmaud
- grid.11642.300000 0001 2111 2608UMR 9220 ENTROPIE, UR-IRD-CNRS-UNC-IFREMER, Université de La Réunion, 15 Avenue René Cassin, CS 92003, 97744 Saint-Denis Cedex, La Réunion France ,Laboratoire d’Excellence “CORAIL”, 98729 Papetoai, Moorea French Polynesia
| | - C. R. Voolstra
- grid.45672.320000 0001 1926 5090Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, 23955 Saudi Arabia ,grid.9811.10000 0001 0658 7699Department of Biology, University of Konstanz, 78457 Konstanz, Germany
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Exploring the Diversity and Biotechnological Potential of Cultured and Uncultured Coral-Associated Bacteria. Microorganisms 2021; 9:microorganisms9112235. [PMID: 34835361 PMCID: PMC8622030 DOI: 10.3390/microorganisms9112235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 10/20/2021] [Accepted: 10/24/2021] [Indexed: 11/17/2022] Open
Abstract
Coral-associated microbes are crucial for the biology of their hosts, contributing to nutrient cycling, adaptation, mitigation of toxic compounds, and biological control of pathogens. Natural products from coral-associated micro-organisms (CAM) may possess unique traits. Despite this, the use of CAM for biotechnological purposes has not yet been adequately explored. Here, we investigated the production of commercially important enzymes by 37 strains of bacteria isolated from the coral species Mussismilia braziliensis, Millepora alcicornis, and Porites astreoides. In-vitro enzymatic assays showed that up to 56% of the isolates produced at least one of the seven enzymes screened (lipase, caseinase, keratinase, cellulase, chitinase, amylase, and gelatinase); one strain, identified as Bacillus amyloliquefaciens produced all these enzymes. Additionally, coral species-specific cultured and uncultured microbial communities were identified. The phylum Firmicutes predominated among the isolates, including the genera Exiguobacterium, Bacillus, and Halomonas, among others. Next-generation sequencing and bacteria culturing produced similar but also complementary data, with certain genera detected only by one or the other method. Our results demonstrate the importance of exploring different coral species as sources of specific micro-organisms of biotechnological and industrial interest, at the same time reinforcing the economic and ecological importance of coral reefs as reservoirs of such diversity.
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Maire J, Blackall LL, van Oppen MJH. Intracellular Bacterial Symbionts in Corals: Challenges and Future Directions. Microorganisms 2021; 9:2209. [PMID: 34835335 PMCID: PMC8619543 DOI: 10.3390/microorganisms9112209] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/21/2021] [Accepted: 10/21/2021] [Indexed: 02/07/2023] Open
Abstract
Corals are the main primary producers of coral reefs and build the three-dimensional reef structure that provides habitat to more than 25% of all marine eukaryotes. They harbor a complex consortium of microorganisms, including bacteria, archaea, fungi, viruses, and protists, which they rely on for their survival. The symbiosis between corals and bacteria is poorly studied, and their symbiotic relationships with intracellular bacteria are only just beginning to be acknowledged. In this review, we emphasize the importance of characterizing intracellular bacteria associated with corals and explore how successful approaches used to study such microorganisms in other systems could be adapted for research on corals. We propose a framework for the description, identification, and functional characterization of coral-associated intracellular bacterial symbionts. Finally, we highlight the possible value of intracellular bacteria in microbiome manipulation and mitigating coral bleaching.
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Affiliation(s)
- Justin Maire
- School of Biosciences, The University of Melbourne, Melbourne, VIC 3010, Australia; (L.L.B.); (M.J.H.v.O.)
| | - Linda L. Blackall
- School of Biosciences, The University of Melbourne, Melbourne, VIC 3010, Australia; (L.L.B.); (M.J.H.v.O.)
| | - Madeleine J. H. van Oppen
- School of Biosciences, The University of Melbourne, Melbourne, VIC 3010, Australia; (L.L.B.); (M.J.H.v.O.)
- Australian Institute of Marine Science, Townsville, QLD 4810, Australia
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Abstract
Recent human activity has profoundly transformed Earth biomes on a scale and at rates that are unprecedented. Given the central role of symbioses in ecosystem processes, functions, and services throughout the Earth biosphere, the impacts of human-driven change on symbioses are critical to understand. Symbioses are not merely collections of organisms, but co-evolved partners that arise from the synergistic combination and action of different genetic programs. They function with varying degrees of permanence and selection as emergent units with substantial potential for combinatorial and evolutionary innovation in both structure and function. Following an articulation of operational definitions of symbiosis and related concepts and characteristics of the Anthropocene, we outline a basic typology of anthropogenic change (AC) and a conceptual framework for how AC might mechanistically impact symbioses with select case examples to highlight our perspective. We discuss surprising connections between symbiosis and the Anthropocene, suggesting ways in which new symbioses could arise due to AC, how symbioses could be agents of ecosystem change, and how symbioses, broadly defined, of humans and “farmed” organisms may have launched the Anthropocene. We conclude with reflections on the robustness of symbioses to AC and our perspective on the importance of symbioses as ecosystem keystones and the need to tackle anthropogenic challenges as wise and humble stewards embedded within the system.
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Affiliation(s)
- Erik F Y Hom
- Department of Biology and Center for Biodiversity and Conservation Research, University of Mississippi, University, MS 38677 USA
| | - Alexandra S Penn
- Department of Sociology and Centre for Evaluation of Complexity Across the Nexus, University of Surrey, Guildford, Surrey, GU2 7XH UK
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40
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Abstract
Eukaryotes and their environments serve as petri dishes, hosting an abundant and a rich prokaryotic microbiome. The assemblage of a eukaryotic host and its microbiome is referred to as a holobiont. The holobiont’s microbiome interacts within itself, with the environment, and with the host at the chemical level through production of specialized metabolites resulting in homeostasis or dysbiosis. These interactions are triggered by a multitude of factors, such as community composition, age, presence of nutrients, xenobiotics, and change in physical conditions, such as temperature and oxygen. Understanding how holobionts respond and adapt to diverse triggers is necessary to uncover mechanisms of resilience or susceptibility to dysbiosis and to modulate the collective functioning of microbiome in health and disease. This article highlights the challenges associated with uncovering chemical contributions of individual holobiont members and the applicability of metabolomics-based approaches to uncover chemical signatures of microbial processes in the natural environment.
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41
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Snyder GA, Eliachar S, Connelly MT, Talice S, Hadad U, Gershoni-Yahalom O, Browne WE, Palmer CV, Rosental B, Traylor-Knowles N. Functional Characterization of Hexacorallia Phagocytic Cells. Front Immunol 2021; 12:662803. [PMID: 34381444 PMCID: PMC8350327 DOI: 10.3389/fimmu.2021.662803] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 06/03/2021] [Indexed: 11/20/2022] Open
Abstract
Phagocytosis is the cellular defense mechanism used to eliminate antigens derived from dysregulated or damaged cells, and microbial pathogens. Phagocytosis is therefore a pillar of innate immunity, whereby foreign particles are engulfed and degraded in lysolitic vesicles. In hexacorallians, phagocytic mechanisms are poorly understood, though putative anthozoan phagocytic cells (amoebocytes) have been identified histologically. We identify and characterize phagocytes from the coral Pocillopora damicornis and the sea anemone Nematostella vectensis. Using fluorescence-activated cell sorting and microscopy, we show that distinct populations of phagocytic cells engulf bacteria, fungal antigens, and beads. In addition to pathogenic antigens, we show that phagocytic cells engulf self, damaged cells. We show that target antigens localize to low pH phagolysosomes, and that degradation is occurring within them. Inhibiting actin filament rearrangement interferes with efficient particle phagocytosis but does not affect small molecule pinocytosis. We also demonstrate that cellular markers for lysolitic vesicles and reactive oxygen species (ROS) correlate with hexacorallian phagocytes. These results establish a foundation for improving our understanding of hexacorallian immune cell biology.
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Affiliation(s)
- Grace A Snyder
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, United States
| | - Shir Eliachar
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Regenerative Medicine and Stem Cell Research Center, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Michael T Connelly
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, United States
| | - Shani Talice
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Regenerative Medicine and Stem Cell Research Center, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Uzi Hadad
- Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Orly Gershoni-Yahalom
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Regenerative Medicine and Stem Cell Research Center, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - William E Browne
- Department of Biology, University of Miami, Coral Gables, FL, United States
| | - Caroline V Palmer
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, United Kingdom
| | - Benyamin Rosental
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Regenerative Medicine and Stem Cell Research Center, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Nikki Traylor-Knowles
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, United States
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42
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Dungan AM, Bulach D, Lin H, van Oppen MJH, Blackall LL. Development of a free radical scavenging bacterial consortium to mitigate oxidative stress in cnidarians. Microb Biotechnol 2021; 14:2025-2040. [PMID: 34259383 PMCID: PMC8449677 DOI: 10.1111/1751-7915.13877] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 06/13/2021] [Indexed: 12/19/2022] Open
Abstract
Corals are colonized by symbiotic microorganisms that profoundly influence the animal’s health. One noted symbiont is a single‐celled alga (in the dinoflagellate family Symbiodiniaceae), which provides the coral with most of its fixed carbon. Thermal stress increases the production of reactive oxygen species (ROS) by Symbiodiniaceae during photosynthesis. ROS can both damage the algal symbiont’s photosynthetic machinery and inhibit its repair, causing a positive feedback loop for the toxic accumulation of ROS. If not scavenged by the antioxidant network, excess ROS may trigger a signaling cascade ending with the coral host and algal symbiont disassociating in a process known as bleaching. We use Exaiptasia diaphana as a model for corals and constructed a consortium comprised of E. diaphana–associated bacteria capable of neutralizing ROS. We identified six strains with high free radical scavenging (FRS) ability belonging to the families Alteromonadaceae, Rhodobacteraceae, Flavobacteriaceae and Micrococcaceae. In parallel, we established a consortium of low FRS isolates consisting of genetically related strains. Bacterial whole genome sequences were used to identify key pathways that are known to influence ROS.
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Affiliation(s)
- Ashley M Dungan
- School of Biosciences, The University of Melbourne, Melbourne, Vic., Australia
| | - Dieter Bulach
- Melbourne Bioinformatics, The University of Melbourne, Melbourne, Vic., Australia
| | - Heyu Lin
- School of Earth Sciences, The University of Melbourne, Melbourne, Vic., Australia
| | - Madeleine J H van Oppen
- School of Biosciences, The University of Melbourne, Melbourne, Vic., Australia.,Australian Institute of Marine Science, Townsville, Qld, Australia
| | - Linda L Blackall
- School of Biosciences, The University of Melbourne, Melbourne, Vic., Australia
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Maire J, Blackall LL, van Oppen MJH. Microbiome characterization of defensive tissues in the model anemone Exaiptasia diaphana. BMC Microbiol 2021; 21:152. [PMID: 34020587 PMCID: PMC8140459 DOI: 10.1186/s12866-021-02211-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 04/29/2021] [Indexed: 01/04/2023] Open
Abstract
Background Coral reefs are among the most diverse and productive ecosystems on Earth. This success relies on the coral’s association with a wide range of microorganisms, including dinoflagellates of the family Symbiodiniaceae that provide coral hosts with most of their organic carbon requirements. While bacterial associates have long been overlooked, research on these microorganisms is gaining traction, and deciphering bacterial identity and function is greatly enhancing our understanding of cnidarian biology. Here, we investigated bacterial communities in defensive tissues (acontia) of the coral model, the sea anemone Exaiptasia diaphana. Acontia are internal filaments that are ejected upon detection of an external threat and release toxins to repel predators. Results Using culturing techniques and 16S rRNA gene metabarcoding we identified bacterial communities associated with acontia of four Great Barrier Reef-sourced E. diaphana genotypes. We show that bacterial communities are similar across genotypes, and dominated by Alteromonadaceae, Vibrionaceae, Rhodobacteraceae, and Saprospiraceae. By analyzing abundant amplicon sequence variants (ASVs) from metabarcoding data from acontia and comparing these to data from whole anemones, we identified five potentially important bacterial genera of the acontia microbiome: Vibrio, Sulfitobacter, Marivita, Alteromonas, and Lewinella. The role of these bacteria within the acontia remains uninvestigated but could entail assistance in defense processes such as toxin production. Conclusions This study provides insight into potential bacterial involvement in cnidarian defense tissues and highlights the need to study bacterial communities in individual compartments within a holobiont. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02211-4.
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Affiliation(s)
- Justin Maire
- School of Biosciences, The University of Melbourne, Melbourne, VIC, Australia.
| | - Linda L Blackall
- School of Biosciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Madeleine J H van Oppen
- School of Biosciences, The University of Melbourne, Melbourne, VIC, Australia.,Australian Institute of Marine Science, Townsville, QLD, Australia
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Bocharova EA, Kopytina NI, Slynko ЕЕ. Anti-tumour drugs of marine origin currently at various stages of clinical trials (review). REGULATORY MECHANISMS IN BIOSYSTEMS 2021. [DOI: 10.15421/022136] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Oncological diseases for a long time have remained one of the most significant health problems of modern society, which causes great losses in its labour and vital potential. Contemporary oncology still faces unsolved issues as insufficient efficacy of treatment of progressing and metastatic cancer, chemoresistance, and side-effects of the traditional therapy which lead to disabilities among or death of a high number of patients. Development of new anti-tumour preparations with a broad range of pharmaceutical properties and low toxicity is becoming increasingly relevant every year. The objective of the study was to provide a review of the recent data about anti-tumour preparations of marine origin currently being at various phases of clinical trials in order to present the biological value of marine organisms – producers of cytotoxic compounds, and the perspectives of their use in modern biomedical technologies. Unlike the synthetic oncological preparations, natural compounds are safer, have broader range of cytotoxic activity, can inhibit the processes of tumour development and metastasis, and at the same time have effects on several etiopathogenic links of carcinogenesis. Currently, practical oncology uses 12 anti-tumour preparations of marine origin (Fludarabine, Cytarabine, Midostaurin, Nelarabine, Eribulin mesylate, Brentuximab vedotin, Trabectedin, Plitidepsin, Enfortumab vedotin, Polatuzumab vedotin, Belantamab mafodotin, Lurbinectedin), 27 substances are at different stages of clinical trials. Contemporary approaches to the treatment of oncological diseases are based on targeted methods such as immune and genetic therapies, antibody-drug conjugates, nanoparticles of biopolymers, and metals. All those methods employ bioactive compounds of marine origin. Numerous literature data from recent years indicate heightened attention to the marine pharmacology and the high potential of marine organisms for the biomedicinal and pharmaceutic industries.
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Rouzé H, Galand PE, Medina M, Bongaerts P, Pichon M, Pérez-Rosales G, Torda G, Moya A, Raina JB, Hédouin L. Symbiotic associations of the deepest recorded photosynthetic scleractinian coral (172 m depth). THE ISME JOURNAL 2021; 15:1564-1568. [PMID: 33452473 PMCID: PMC8115523 DOI: 10.1038/s41396-020-00857-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 10/28/2020] [Accepted: 11/24/2020] [Indexed: 01/29/2023]
Abstract
The symbiosis between scleractinian corals and photosynthetic algae from the family Symbiodiniaceae underpins the health and productivity of tropical coral reef ecosystems. While this photosymbiotic association has been extensively studied in shallow waters (<30 m depth), we do not know how deeper corals, inhabiting large and vastly underexplored mesophotic coral ecosystems, modulate their symbiotic associations to grow in environments that receive less than 1% of surface irradiance. Here we report on the deepest photosymbiotic scleractinian corals collected to date (172 m depth), and use amplicon sequencing to identify the associated symbiotic communities. The corals, identified as Leptoseris hawaiiensis, were confirmed to host Symbiodiniaceae, predominantly of the genus Cladocopium, a single species of endolithic algae from the genus Ostreobium, and diverse communities of prokaryotes. Our results expand the reported depth range of photosynthetic scleractinian corals (0-172 m depth), and provide new insights on their symbiotic associations at the lower depth extremes of tropical coral reefs.
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Affiliation(s)
- Héloïse Rouzé
- PSL Research University, EPHE-UPVD-CNRS, USR 3278 CRIOBE, LabEx CORAIL, BP 1013 Papetoai, 98729 Moorea, French Polynesia
| | - Pierre E. Galand
- Sorbonne Université, CNRS, Laboratoire d’Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, Banyuls-sur-Mer, France
| | - Mónica Medina
- grid.29857.310000 0001 2097 4281Department of Biology, Pennsylvania State University, 208 Mueller Lab, University Park, State College, PA 16802 USA
| | - Pim Bongaerts
- grid.242287.90000 0004 0461 6769California Academy of Sciences, San Francisco, CA 94118 USA
| | - Michel Pichon
- Museum of Tropical Queensland, Townsville, QLD 4810 Australia
| | - Gonzalo Pérez-Rosales
- PSL Research University, EPHE-UPVD-CNRS, USR 3278 CRIOBE, LabEx CORAIL, BP 1013 Papetoai, 98729 Moorea, French Polynesia
| | - Gergely Torda
- grid.1011.10000 0004 0474 1797ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811 Australia
| | - Aurelie Moya
- grid.1011.10000 0004 0474 1797ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811 Australia ,grid.9811.10000 0001 0658 7699Department of Biology, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany
| | | | - Jean-Baptiste Raina
- grid.117476.20000 0004 1936 7611Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007 Australia
| | - Laetitia Hédouin
- PSL Research University, EPHE-UPVD-CNRS, USR 3278 CRIOBE, LabEx CORAIL, BP 1013 Papetoai, 98729 Moorea, French Polynesia
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Traylor-Knowles N. Unlocking the single-cell mysteries of a reef-building coral. Cell 2021; 184:2802-2804. [PMID: 34048702 DOI: 10.1016/j.cell.2021.05.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Coral reefs are one of the most important ecosystems in the world but least understood from a cellular level. In this issue of Cell, Levy et al. unravel the single-cell gene expression of the coral holobiont and open the doors to better understand the novel diversity of cell types.
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Affiliation(s)
- Nikki Traylor-Knowles
- University of Miami, Rosenstiel School of Marine and Atmospheric Sciences, Miami, FL, USA.
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Chen B, Yu K, Liao Z, Yu X, Qin Z, Liang J, Wang G, Wu Q, Jiang L. Microbiome community and complexity indicate environmental gradient acclimatisation and potential microbial interaction of endemic coral holobionts in the South China Sea. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 765:142690. [PMID: 33071127 DOI: 10.1016/j.scitotenv.2020.142690] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/31/2020] [Accepted: 09/26/2020] [Indexed: 06/11/2023]
Abstract
Regional acclimatisation and microbial interactions significantly influence the resilience of reef-building corals facing anthropogenic climate change, allowing them to adapt to environmental stresses. However, the connections between community structure and microbial interactions of the endemic coral microbiome and holobiont acclimatisation remain unclear. Herein, we used generation sequencing of internal transcribed spacer (ITS2) and 16S rRNA genes to investigate the microbiome composition (Symbiodiniaceae and bacteria) and associated potential interactions of endemic dominant coral holobionts (Pocillopora verrucosa and Turbinaria peltata) in the South China Sea (SCS). We found that shifts in Symbiodiniaceae and bacterial communities of P. verrucosa were associated with latitudinal gradient and climate zone changes, respectively. The C1 sub-clade consistently dominated the Symbiodiniaceae community in T. peltata; yet, the bacterial community structure was spatially heterogeneous. The relative abundance of the core microbiome among P. verrucosa holobionts was reduced in the biogeographical transition zone, while bacterial taxa associated with anthropogenic activity (Escherichia coli and Sphingomonas) were identified in the core microbiomes. Symbiodiniaceae and bacteria potentially interact in microbial co-occurrence networks. Further, increased bacterial, and Symbiodiniaceae α-diversity was associated with increased and decreased network complexity, respectively. Hence, Symbiodiniaceae and bacteria demonstrated different flexibility in latitudinal or climatic environmental regimes, which correlated with holobiont acclimatisation. Core microbiome analysis has indicated that the function of core bacterial microbiota might have changed in distinct environmental regimes, implying potential human activity in the coral habitats. Increased bacterial α diversity may lead to a decline in the stability of coral-microorganism symbioses, whereas rare Symbiodiniaceae may help to retain symbioses. Cladocopium, γ-proteobacteria, while α-proteobacteria may have been the primary drivers in the Symbiodiniaceae-bacterial interactions (SBIs). Our study highlights the association between microbiome shift in distinct environmental regimes and holobiont acclimatisation, while providing insights into the impact of SBIs on holobiont health and acclimatisation during climate change.
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Affiliation(s)
- Biao Chen
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning, China; Coral Reef Research Center of China, Guangxi University, Nanning, China; School of Marine Sciences, Guangxi University, Nanning, China
| | - Kefu Yu
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning, China; Coral Reef Research Center of China, Guangxi University, Nanning, China; School of Marine Sciences, Guangxi University, Nanning, China.
| | - Zhiheng Liao
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning, China; Coral Reef Research Center of China, Guangxi University, Nanning, China; School of Marine Sciences, Guangxi University, Nanning, China
| | - Xiaopeng Yu
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning, China; Coral Reef Research Center of China, Guangxi University, Nanning, China; School of Marine Sciences, Guangxi University, Nanning, China
| | - Zhenjun Qin
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning, China; Coral Reef Research Center of China, Guangxi University, Nanning, China; School of Marine Sciences, Guangxi University, Nanning, China
| | - Jiayuan Liang
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning, China; Coral Reef Research Center of China, Guangxi University, Nanning, China; School of Marine Sciences, Guangxi University, Nanning, China
| | - Guanghua Wang
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning, China; Coral Reef Research Center of China, Guangxi University, Nanning, China; School of Marine Sciences, Guangxi University, Nanning, China
| | - Qian Wu
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning, China; Coral Reef Research Center of China, Guangxi University, Nanning, China; School of Marine Sciences, Guangxi University, Nanning, China
| | - Leilei Jiang
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning, China; Coral Reef Research Center of China, Guangxi University, Nanning, China; School of Marine Sciences, Guangxi University, Nanning, China
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Intracellular bacteria are common and taxonomically diverse in cultured and in hospite algal endosymbionts of coral reefs. ISME JOURNAL 2021; 15:2028-2042. [PMID: 33558689 PMCID: PMC8245515 DOI: 10.1038/s41396-021-00902-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 01/13/2021] [Accepted: 01/19/2021] [Indexed: 02/06/2023]
Abstract
Corals house a variety of microorganisms which they depend on for their survival, including endosymbiotic dinoflagellates (Symbiodiniaceae) and bacteria. While cnidarian–microorganism interactions are widely studied, Symbiodiniaceae–bacteria interactions are only just beginning to receive attention. Here, we describe the localization and composition of the bacterial communities associated with cultures of 11 Symbiodiniaceae strains from nine species and six genera. Three-dimensional confocal laser scanning and electron microscopy revealed bacteria are present inside the Symbiodiniaceae cells as well as closely associated with their external cell surface. Bacterial pure cultures and 16S rRNA gene metabarcoding from Symbiodiniaceae cultures highlighted distinct and highly diverse bacterial communities occur intracellularly, closely associated with the Symbiodiniaceae outer cell surface and loosely associated (i.e., in the surrounding culture media). The intracellular bacteria are highly conserved across Symbiodiniaceae species, suggesting they may be involved in Symbiodiniaceae physiology. Our findings provide unique new insights into the biology of Symbiodiniaceae.
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Garcias-Bonet N, Eguíluz VM, Díaz-Rúa R, Duarte CM. Host-association as major driver of microbiome structure and composition in Red Sea seagrass ecosystems. Environ Microbiol 2020; 23:2021-2034. [PMID: 33225561 DOI: 10.1111/1462-2920.15334] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 12/16/2022]
Abstract
The role of the microbiome in sustaining seagrasses has recently been highlighted. However, our understanding of the seagrass microbiome lacks behind that of other organisms. Here, we analyse the endophytic and total bacterial communities of leaves, rhizomes, and roots of six Red Sea seagrass species and their sediments. The structure of seagrass bacterial communities revealed that the 1% most abundant OTUs accounted for 87.9% and 74.8% of the total numbers of reads in sediment and plant tissue samples, respectively. We found taxonomically distinct bacterial communities in vegetated and bare sediments. Yet, our results suggest that lifestyle (i.e. free-living or host-association) is the main driver of bacterial community composition. Seagrass bacterial communities were tissue- and species-specific and differed from those of surrounding sediments. We identified OTUs belonging to genera related to N and S cycles in roots, and members of Actinobacteria, Bacteroidetes, and Firmicutes phyla as particularly enriched in root endosphere. The finding of highly similar OTUs in well-defined sub-clusters by network analysis suggests the co-occurrence of highly connected key members within Red Sea seagrass bacterial communities. These results provide key information towards the understanding of the role of microorganisms in seagrass ecosystem functioning framed under the seagrass holobiont concept.
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Affiliation(s)
- Neus Garcias-Bonet
- Red Sea Research Centre (RSRC) and Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Víctor M Eguíluz
- Red Sea Research Centre (RSRC) and Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.,Instituto de Física Interdisciplinar y Sistemas Complejos (CSIC-UIB), Palma de Mallorca, E-07122, Spain
| | - Rubén Díaz-Rúa
- Red Sea Research Centre (RSRC) and Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Carlos M Duarte
- Red Sea Research Centre (RSRC) and Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
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50
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Vega Thurber R, Mydlarz LD, Brandt M, Harvell D, Weil E, Raymundo L, Willis BL, Langevin S, Tracy AM, Littman R, Kemp KM, Dawkins P, Prager KC, Garren M, Lamb J. Deciphering Coral Disease Dynamics: Integrating Host, Microbiome, and the Changing Environment. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.575927] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Diseases of tropical reef organisms is an intensive area of study, but despite significant advances in methodology and the global knowledge base, identifying the proximate causes of disease outbreaks remains difficult. The dynamics of infectious wildlife diseases are known to be influenced by shifting interactions among the host, pathogen, and other members of the microbiome, and a collective body of work clearly demonstrates that this is also the case for the main foundation species on reefs, corals. Yet, among wildlife, outbreaks of coral diseases stand out as being driven largely by a changing environment. These outbreaks contributed not only to significant losses of coral species but also to whole ecosystem regime shifts. Here we suggest that to better decipher the disease dynamics of corals, we must integrate more holistic and modern paradigms that consider multiple and variable interactions among the three major players in epizootics: the host, its associated microbiome, and the environment. In this perspective, we discuss how expanding the pathogen component of the classic host-pathogen-environment disease triad to incorporate shifts in the microbiome leading to dysbiosis provides a better model for understanding coral disease dynamics. We outline and discuss issues arising when evaluating each component of this trio and make suggestions for bridging gaps between them. We further suggest that to best tackle these challenges, researchers must adjust standard paradigms, like the classic one pathogen-one disease model, that, to date, have been ineffectual at uncovering many of the emergent properties of coral reef disease dynamics. Lastly, we make recommendations for ways forward in the fields of marine disease ecology and the future of coral reef conservation and restoration given these observations.
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