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Chuang PS, Wang TH, Lu CY, Tandon K, Shikina S, Tang SL. Microbiome heterogeneity in tissues of the coral, Fimbriaphyllia (Euphyllia) ancora. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13310. [PMID: 38982629 PMCID: PMC11233273 DOI: 10.1111/1758-2229.13310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 06/25/2024] [Indexed: 07/11/2024]
Abstract
Coral microbiomes differ in the mucus, soft tissue and skeleton of a coral colony, but whether variations exist in different tissues of a single polyp is unknown. In the stony coral, Fimbriaphyllia ancora, we identified 8,994 amplicon sequencing variants (ASVs) in functionally differentiated polyp tissues, i.e., tentacles, body wall, mouth and pharynx, mesenterial filaments, and gonads (testes and ovaries), with a large proportion of ASVs specific to individual tissues. However, shared ASVs comprised the majority of microbiomes from all tissues in terms of relative abundance. No tissue-specific ASVs were found, except in testes, for which there were only two samples. At the generic level, Endozoicomonas was significantly less abundant in the body wall, where calicoblastic cells reside. On the other hand, several bacterial taxa presented significantly higher abundances in the mouth. Interestingly, although without statistical confirmation, gonadal tissues showed lower ASV richness and relatively high abundances of Endozoicomonas (in ovaries) and Pseudomonas (in testes). These findings provide evidence for microbiome heterogeneity between tissues within coral polyps, suggesting a promising field for future studies of functional interactions between corals and their bacterial symbionts.
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Affiliation(s)
- Po-Shun Chuang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Tzu-Haw Wang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan
| | - Chih-Ying Lu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei, Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Kshitij Tandon
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Shinya Shikina
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung, Taiwan
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan
| | - Sen-Lin Tang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Taiwan Ocean Genome Center, National Taiwan Ocean University, Keelung, Taiwan
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Hamamoto K, Mizuyama M, Nishijima M, Maeda A, Gibu K, Poliseno A, Iguchi A, Reimer JD. Diversity, composition and potential roles of sedimentary microbial communities in different coastal substrates around subtropical Okinawa Island, Japan. ENVIRONMENTAL MICROBIOME 2024; 19:54. [PMID: 39080706 PMCID: PMC11290285 DOI: 10.1186/s40793-024-00594-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 07/08/2024] [Indexed: 08/02/2024]
Abstract
BACKGROUND Marine benthic prokaryotic communities play crucial roles in material recycling within coastal environments, including coral reefs. Coastal sedimentary microbiomes are particularly important as potential reservoirs of symbiotic, beneficial, and pathogenic bacteria in coral reef environments, and therefore presumably play a core role in local ecosystem functioning. However, there is a lack of studies comparing different environments with multiple sites on the island scale, particularly studies focusing on prokaryotic communities, as previous investigations have focused mainly on a single site or on specific environmental conditions. In our study, we collected coastal sediments from seven sites around Okinawa Island, Japan, including three different benthic types; sandy bottoms, seagrass meadows, and hard substratum with living scleractinian corals. We then used metabarcoding to identify prokaryotic compositions and estimate enzymes encoded by genes to infer their functions. RESULTS The results showed that the three substrata had significantly different prokaryotic compositions. Seagrass meadow sites exhibited significantly higher prokaryotic alpha-diversity compared to sandy bottom sites. ANCOM analysis revealed that multiple bacterial orders were differentially abundant within each substratum. At coral reef sites, putative disease- and thermal stress-related opportunistic bacteria such as Rhodobacterales, Verrucomicrobiales, and Cytophagales were comparatively abundant, while seagrass meadow sites abundantly harbored Desulfobacterales, Steroidobacterales and Chromatiales, which are common bacterial orders in seagrass meadows. According to our gene-coded enzyme analyses the numbers of differentially abundant enzymes were highest in coral reef sites. Notably, superoxide dismutase, an important enzyme for anti-oxidative stress in coral tissue, was abundant at coral sites. Our results provide a list of prokaryotes to look into in each substrate, and further emphasize the importance of considering the microbiome, especially when focusing on environmental conservation. CONCLUSION Our findings prove that prokaryotic metabarcoding is capable of capturing compositional differences and the diversity of microbial communities in three different environments. Furthermore, several taxa were suggested to be differentially more abundant in specific environments, and gene-coded enzymic compositions also showed possible differences in ecological functions. Further study, in combination with field observations and temporal sampling, is key to achieving a better understanding of the interactions between the local microbiome and the surrounding benthic community.
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Affiliation(s)
- Kohei Hamamoto
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8567, Japan.
- Molecular Invertebrate Systematics and Ecology (MISE) Laboratory, Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa, 903-0213, Japan.
| | - Masaru Mizuyama
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8567, Japan
- Department of Health Informatics, Faculty of Human Health Sciences, Meio University, Nago, Okinawa, 905-8585, Japan
| | - Miyuki Nishijima
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8567, Japan
| | - Ayumi Maeda
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, 277-8564, Japan
| | - Kodai Gibu
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8567, Japan
| | - Angelo Poliseno
- Molecular Invertebrate Systematics and Ecology (MISE) Laboratory, Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa, 903-0213, Japan
| | - Akira Iguchi
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8567, Japan.
- Research Laboratory on Environmentally-Conscious Developments and Technologies [E-code], National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8567, Japan.
| | - James Davis Reimer
- Molecular Invertebrate Systematics and Ecology (MISE) Laboratory, Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa, 903-0213, Japan
- Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, 903-0213, Japan
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Patel ZZ, Joshi H, Puvar A, Pandit R, Joshi C, Joshi M, Tipre DR. A study into the diversity of coral-associated bacteria using culture-dependent and culture-independent approaches in coral Dipsastraea favus from the Gulf of Kutch. MARINE POLLUTION BULLETIN 2024; 201:116172. [PMID: 38394797 DOI: 10.1016/j.marpolbul.2024.116172] [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: 07/20/2023] [Revised: 12/03/2023] [Accepted: 02/15/2024] [Indexed: 02/25/2024]
Abstract
Corals harbour ~25 % of the marine diversity referring to biodiversity hotspots in marine ecosystems. Global efforts to find ways to restore the coral reef ecosystem from various threats can be complemented by studying coral-associated bacteria. Coral-associated bacteria are vital components of overall coral wellbeing. We explored the bacterial diversity associated with coral Dipsastraea favus (D. favus) collected from the Gulf of Kutch, India, using both culture-dependent and metagenomic approaches. In both approaches, phylum Proteobacteria, Firmicutes, and Actinobacteria predominated, comprising the genera Vibrio, Bacillus, Shewanella, Pseudoalteromonas, Exiguobacterium and Streptomyces. Moreover, the majority of culturable isolates showed multiple antibiotic resistance index ≥0.2. In this study, specific bacterial diversity associated with coral sp. D. favus and its possible role in managing coral health was established. Almost 43 strains from the samples were successfully cultured, creating a base for exploring these microbes for their potential use in coral conservation methods.
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Affiliation(s)
- Zarna Z Patel
- Department of Microbiology and Biotechnology, School of Sciences, Gujarat University, Ahmedabad 380009, India; Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (DST), Government of Gujarat, Gandhinagar 382011, India
| | - Himanshu Joshi
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (DST), Government of Gujarat, Gandhinagar 382011, India
| | - Apurvasinh Puvar
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (DST), Government of Gujarat, Gandhinagar 382011, India
| | - Ramesh Pandit
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (DST), Government of Gujarat, Gandhinagar 382011, India
| | - Chaitanya Joshi
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (DST), Government of Gujarat, Gandhinagar 382011, India
| | - Madhvi Joshi
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (DST), Government of Gujarat, Gandhinagar 382011, India.
| | - Devayani R Tipre
- Department of Microbiology and Biotechnology, School of Sciences, Gujarat University, Ahmedabad 380009, India.
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4
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Downie AT, Cramp RL, Franklin CE. The interactive impacts of a constant reef stressor, ultraviolet radiation, with environmental stressors on coral physiology. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 907:168066. [PMID: 37890630 DOI: 10.1016/j.scitotenv.2023.168066] [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: 02/05/2023] [Revised: 07/19/2023] [Accepted: 10/21/2023] [Indexed: 10/29/2023]
Abstract
Reef-building corals create one of the most biodiverse and economically important ecosystems on the planet. Unfortunately, global coral reef ecosystems experience threats from numerous natural stressors, which are amplified by human activities. One such threat is ultraviolet radiation (UVR) from the sun; a genotoxic stressor that is a double-edged sword for corals as they rely on sunlight for energy. More intense UVR has been shown to have greater direct impacts on animal physiology, and these may be exacerbated by co-occurring stressors. The aim of this systematic literature review was to examine if the same applies to corals; that is, if the co-exposure of a constant stressor (UVR) with other stressors has a greater impact on coral physiology than if these stressors occurred separately. We reviewed the biochemical and cellular processes impacted by UVR and the defenses corals have against UVR. The main stressors investigated with UVR were temperature, nitrate, nutrient, oil, water motion, and photosynthetically active radiation (PAR). UVR generally worsened the physiological impacts of other stressors (e.g., by decreasing zooxanthellae and chlorophyll densities). There were species-specific differences in their tolerance to UVR (differences in zooxanthellae populations, sunscreen production and depth) and environmental stress (e.g., resilience to some oils), and that ambient levels of UVR were often beneficial (i.e., nullifying impacts of nitrates). We highlight areas of future investigation including examining and assessing other interacting stressors and their impacts (e.g., ocean acidification, ocean deoxygenation, toxins and pollutants), investigating impacts of multiple stressors with UVR on the coral microbiome, and elucidating the effects of multi-stressors with UVR across early-life history stages (especially larvae). UVR is a pervasive stressor to corals and can interact with other environmental conditions to compromise the resilience of corals. This environmental driver needs to be more comprehensively examined alongside climate change stressors (e.g., temperature increases, ocean acidification and hypoxia) to better understand future climate scenarios on reefs.
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Affiliation(s)
- Adam T Downie
- School of Biological Sciences, The University of Queensland, St. Lucia, Queensland 4072, Australia.
| | - Rebecca L Cramp
- School of Biological Sciences, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Craig E Franklin
- School of Biological Sciences, The University of Queensland, St. Lucia, Queensland 4072, Australia
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5
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Irudayarajan L, Ravindran C, Raveendran HP. Antimicrobial activity of coral-associated beneficial bacteria against coral disease-causing microbial pathogens. J Basic Microbiol 2024; 64:81-93. [PMID: 37726211 DOI: 10.1002/jobm.202300338] [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: 06/16/2023] [Revised: 08/27/2023] [Accepted: 09/03/2023] [Indexed: 09/21/2023]
Abstract
Microbial infection of immune-compromised corals influences disease severity, resulting in coral mortality. However, coral-associated beneficial bacteria are known to produce antimicrobial compounds that prevent the growth of potential pathogens and invading microbes. Hence, beneficial bacteria associated with coral Porites lutea were isolated and antimicrobial protein and bioactive secondary metabolites were extracted and tested for their antimicrobial activity against putative prokaryotic and eukaryotic coral pathogens. Bioactive secondary metabolites exhibited remarkable antagonism against various coral pathogens such as Serratia marcescens, Vibrio species, and Aspergillus sydowii. Besides, the metabolites of Cobetia marina, Cobetia amphilecti, Pseudoalteromonas neustonica, and Virgibacillus halodenitrificans manifested notable inhibition against the protozoan ciliates (Uronema marinum, Holosticha diademata, Cohnilembus verminus, and Euplotes vannus) and zooplankton that are known to be involved in the secondary pathogenesis in coral diseased lesion progression. Thus, the present study may benefit in understanding coral-associated beneficial bacteria for their antagonistic interactions with microbial pathogens, as well as their potential involvement in reducing coral disease severity.
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Affiliation(s)
- Lawrance Irudayarajan
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Panaji, Goa, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Chinnarajan Ravindran
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Panaji, Goa, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Haritha P Raveendran
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Panaji, Goa, India
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6
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Chuang PS, Yu SP, Liu PY, Hsu MT, Chiou YJ, Lu CY, Tang SL. A gauge of coral physiology: re-examining temporal changes in Endozoicomonas abundance correlated with natural coral bleaching. ISME COMMUNICATIONS 2024; 4:ycae001. [PMID: 38371393 PMCID: PMC10872716 DOI: 10.1093/ismeco/ycae001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/14/2023] [Accepted: 01/04/2024] [Indexed: 02/20/2024]
Abstract
Bacteria contribute to many physiological functions of coral holobionts, including responses to bleaching. The bacterial genus, Endozoicomonas, dominates the microbial flora of many coral species and its abundance appears to be correlated with coral bleaching. However, evidences for decoupling of bleaching and Endozoicomonas abundance changes have also been reported. In 2020, a severe bleaching event was recorded at reefs in Taiwan, providing a unique opportunity to re-examine bleaching-Endozoicomonas association using multiple stony corals in natural environments. In this study, we monitored tissue color and microbiome changes in three coral species (Montipora sp., Porites sp., and Stylophora pistillata) in Kenting National Park, following the bleaching event. All tagged Montipora sp. and Porites sp. recovered from bleaching within 1 year, while high mortality occurred in S. pistillata. Microbiome analysis found no correlation of Endozoicomonas relative abundance and bleaching severity during the sampling period, but found a stronger correlation when the month in which bleaching occurred was excluded. Moreover, Endozoicomonas abundance increased during recovery months in Montipora sp. and Porites sp., whereas in S. pistillata it was nearly depleted. These results suggest that Endozoicomonas abundance may represent a gauge of coral health and reflect recovery of some corals from stress. Interestingly, even though different Endozoicomonas strains predominated in the three corals, these Endozoicomonas strains were also shared among coral taxa. Meanwhile, several Endozoicomonas strains showed secondary emergence during coral recovery, suggesting possible symbiont switching in Endozoicomonas. These findings indicate that it may be possible to introduce Endozoicomonas to non-native coral hosts as a coral probiotic.
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Affiliation(s)
- Po-Shun Chuang
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Sheng-Ping Yu
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Po-Yu Liu
- School of Medicine, College of Medicine, National Sun Yat-sen University, Kaohsiung 804, Taiwan
| | - Ming-Tsung Hsu
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yu-Jing Chiou
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
- Centre for Marine Science and Innovation, School of Biological Earth and Environmental Sciences, University of New South Wales, Sydney 2052, Australia
| | - Chih-Ying Lu
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei 115, Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 402, Taiwan
| | - Sen-Lin Tang
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
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7
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Offret C, Gauthier O, Despréaux G, Bidault A, Corporeau C, Miner P, Petton B, Pernet F, Fabioux C, Paillard C, Le Blay G. Microbiota of the Digestive Glands and Extrapallial Fluids of Clams Evolve Differently Over Time Depending on the Intertidal Position. MICROBIAL ECOLOGY 2023; 85:288-297. [PMID: 35066615 DOI: 10.1007/s00248-022-01959-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 01/04/2022] [Indexed: 02/08/2023]
Abstract
The Manila clam (Ruditapes philippinarum) is the second most exploited bivalve in the world but remains threatened by diseases and global changes. Their associated microbiota play a key role in their fitness and acclimation capacities. This study aimed at better understanding the behavior of clam digestive glands and extrapallial fluids microbiota at small, but contrasting spatial and temporal scales. Results showed that environmental variations impacted clam microbiota differently according to the considered tissue. Each clam tissue presented its own microbiota and showed different dynamics according to the intertidal position and sampling period. Extrapallial fluids microbiota was modified more rapidly than digestive glands microbiota, for clams placed on the upper and lower intertidal position, respectively. Clam tissues could be considered as different microhabitats for bacteria as they presented different responses to small-scale temporal and spatial variabilities in natural conditions. These differences underlined a more stringent environmental filter capacity of the digestive glands.
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Affiliation(s)
- Clément Offret
- Univ Brest, CNRS, IRD, Ifremer, LEMAR, F-29280, Plouzané, France
| | - Olivier Gauthier
- Univ Brest, CNRS, IRD, Ifremer, LEMAR, F-29280, Plouzané, France
| | | | - Adeline Bidault
- Univ Brest, CNRS, IRD, Ifremer, LEMAR, F-29280, Plouzané, France
| | | | - Philippe Miner
- Ifremer, Univ Brest, CNRS, IRD, LEMAR, Plouzané, 29280, Brest, France
| | - Bruno Petton
- Ifremer, Univ Brest, CNRS, IRD, LEMAR, Plouzané, 29280, Brest, France
| | - Fabrice Pernet
- Ifremer, Univ Brest, CNRS, IRD, LEMAR, Plouzané, 29280, Brest, France
| | - Caroline Fabioux
- Univ Brest, CNRS, IRD, Ifremer, LEMAR, F-29280, Plouzané, France
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Wada N, Hsu MT, Tandon K, Hsiao SSY, Chen HJ, Chen YH, Chiang PW, Yu SP, Lu CY, Chiou YJ, Tu YC, Tian X, Chen BC, Lee DC, Yamashiro H, Bourne DG, Tang SL. High-resolution spatial and genomic characterization of coral-associated microbial aggregates in the coral Stylophora pistillata. SCIENCE ADVANCES 2022; 8:eabo2431. [PMID: 35857470 PMCID: PMC9258956 DOI: 10.1126/sciadv.abo2431] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 05/13/2022] [Indexed: 05/29/2023]
Abstract
Bacteria commonly form aggregates in a range of coral species [termed coral-associated microbial aggregates (CAMAs)], although these structures remain poorly characterized despite extensive efforts studying the coral microbiome. Here, we comprehensively characterize CAMAs associated with Stylophora pistillata and quantify their cell abundance. Our analysis reveals that multiple Endozoicomonas phylotypes coexist inside a single CAMA. Nanoscale secondary ion mass spectrometry imaging revealed that the Endozoicomonas cells were enriched with phosphorus, with the elemental compositions of CAMAs different from coral tissues and endosymbiotic Symbiodiniaceae, highlighting a role in sequestering and cycling phosphate between coral holobiont partners. Consensus metagenome-assembled genomes of the two dominant Endozoicomonas phylotypes confirmed their metabolic potential for polyphosphate accumulation along with genomic signatures including type VI secretion systems allowing host association. Our findings provide unprecedented insights into Endozoicomonas-dominated CAMAs and the first direct physiological and genomic linked evidence of their biological role in the coral holobiont.
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Affiliation(s)
- Naohisa Wada
- Biodiversity Research Center, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang, Taipei 11529, Taiwan
| | - Ming-Tsung Hsu
- Biodiversity Research Center, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang, Taipei 11529, Taiwan
| | - Kshitij Tandon
- Biodiversity Research Center, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang, Taipei 11529, Taiwan
| | - Silver Sung-Yun Hsiao
- Institute of Astronomy and Astrophysics, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang, Taipei 11529, Taiwan
| | - Hsing-Ju Chen
- Biodiversity Research Center, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang, Taipei 11529, Taiwan
| | - Yu-Hsiang Chen
- Biodiversity Research Center, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang, Taipei 11529, Taiwan
| | - Pei-Wen Chiang
- Biodiversity Research Center, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang, Taipei 11529, Taiwan
| | - Sheng-Ping Yu
- Biodiversity Research Center, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang, Taipei 11529, Taiwan
| | - Chih-Ying Lu
- Biodiversity Research Center, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang, Taipei 11529, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei 11529, Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan
| | - Yu-Jing Chiou
- Biodiversity Research Center, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang, Taipei 11529, Taiwan
| | - Yung-Chi Tu
- Biodiversity Research Center, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang, Taipei 11529, Taiwan
| | - Xuejiao Tian
- Research Center for Applied Sciences, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang, Taipei 11529, Taiwan
| | - Bi-Chang Chen
- Research Center for Applied Sciences, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang, Taipei 11529, Taiwan
| | - Der-Chuen Lee
- Institute of Earth Sciences, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang, Taipei 11529, Taiwan
| | - Hideyuki Yamashiro
- Sesoko Station, Tropical Biosphere Research Center, University of the Ryukyus, 3422 Sesoko, Motobu, Okinawa 905-0227, Japan
| | - David G. Bourne
- College of Science and Engineering, James Cook University, Townsville, 4811 QLD, Australia
- Australian Institute of Marine Science, Townsville, 4810 QLD, Australia
- AIMS@JCU, Townsville, 4811 QLD, Australia
| | - Sen-Lin Tang
- Biodiversity Research Center, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang, Taipei 11529, Taiwan
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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: 10] [Impact Index Per Article: 5.0] [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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Wang JT, Wang YT, Chen CA, Meng PJ, Tew KS, Chiang PW, Tang SL. Extra high superoxide dismutase in host tissue is associated with improving bleaching resistance in "thermal adapted" and Durusdinium trenchii-associating coral. PeerJ 2022; 10:e12746. [PMID: 35070504 PMCID: PMC8760857 DOI: 10.7717/peerj.12746] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 12/14/2021] [Indexed: 01/07/2023] Open
Abstract
Global warming threatens reef-building corals with large-scale bleaching events; therefore, it is important to discover potential adaptive capabilities for increasing their temperature resistance before it is too late. This study presents two coral species (Platygyra verweyi and Isopora palifera) surviving on a reef having regular hot water influxes via a nearby nuclear power plant that exhibited completely different bleaching susceptibilities to thermal stress, even though both species shared several so-called "winner" characteristics (e.g., containing Durusdinium trenchii, thick tissue, etc.). During acute heating treatment, algal density did not decline in P. verweyi corals within three days of being directly transferred from 25 to 31 °C; however, the same treatment caused I. palifera to lose < 70% of its algal symbionts within 24 h. The most distinctive feature between the two coral species was an overwhelmingly higher constitutive superoxide dismutase (ca. 10-fold) and catalase (ca. 3-fold) in P. verweyi over I. palifera. Moreover, P. verweyi also contained significantly higher saturated and lower mono-unsaturated fatty acids, especially a long-chain saturated fatty acid (C22:0), than I. palifera, and was consistently associated with the symbiotic bacteria Endozoicomonas, which was not found in I. palifera. However, antibiotic treatment and inoculation tests did not support Endozoicomonas having a direct contribution to thermal resistance. This study highlights that, besides its association with a thermally tolerable algal symbiont, a high level of constitutive antioxidant enzymes in the coral host is crucial for coral survivorship in the more fluctuating and higher temperature environments.
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Affiliation(s)
- Jih-Terng Wang
- Department of Oceanography, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Yi-Ting Wang
- Department of Oceanography, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | | | - Pei-Jei Meng
- General Education Center, National Dong Hwa University, Hualien, Taiwan,National Museum of Marine Biology and Aquarium, Pingtung, Taiwan
| | - Kwee Siong Tew
- National Museum of Marine Biology and Aquarium, Pingtung, Taiwan,Institute of Marine Biodiversity and Evolution, National Dong Hwa University, Pingtung, Taiwan
| | - Pei-Wen Chiang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Sen-Lin Tang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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11
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Yu X, Yu K, Liao Z, Chen B, Deng C, Yu J, Yao Q, Qin Z, Liang J. Seasonal fluctuations in symbiotic bacteria and their role in environmental adaptation of the scleractinian coral Acropora pruinosa in high-latitude coral reef area of the South China Sea. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 792:148438. [PMID: 34153755 DOI: 10.1016/j.scitotenv.2021.148438] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 06/09/2021] [Accepted: 06/09/2021] [Indexed: 06/13/2023]
Abstract
Coral-associated bacterial communities are paramount for coral ecosystems and holobiont health. However, the role of symbiotic bacteria in the adaptation of high-latitude corals to seasonal fluctuations remains underexplored. Therefore, we used 16S rRNA-based high-throughput sequencing to analyze the symbiotic bacterial diversity, composition, and core bacterial community in high-latitude coral and explored the seasonal fluctuation characteristics of symbiotic bacterial communities. We found that bacterial richness and α-diversity changed significantly across different seasons. Additionally, the community structure recombined seasonally, with different dominant bacterial phyla and genera in different seasons. However, the symbiotic bacterial community structures of Acropora pruinosa in winter and spring were similar. Proteobacteria were the dominant bacteria in spring, autumn, and winter. In summer, the dominant bacterial taxa were Bacteroidota and Proteobacteria. Ralstonia was the dominant bacterial genus in spring and winter, whereas in autumn, BD1-7_clade was dominant. Linear discriminant analysis effect size identified 20 abundant genera between the different groups. Core microbiome analysis revealed that 12 core bacterial operational taxonomic units were associated with A. pruinosa in all seasons, seven of which varied with the seasons, changing between dominant and rare. Distance-based redundancy and variation partitioning analyses revealed that sea surface temperature was the major contributor of variation in the microbial community structure. We hypothesized that the high diversity and abundance of symbiotic bacteria and the increase in Prosthecochloris abundance in coral in summer can help A. pruinosa maintain its physiological functions, ameliorating the negative physiological effects of the decrease in Symbiodiniaceae density under high-temperature stress. Thus, the rapid reorganization of the symbiotic bacterial community structure and core microflora in different seasons may allow the corals to adapt to large seasonal environmental fluctuations. In conclusion, seasonal variation of bacteria plays an important role in coral adaptation to large environmental fluctuations.
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Affiliation(s)
- Xiaopeng Yu
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Kefu Yu
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), China.
| | - Zhiheng Liao
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Biao Chen
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Chuanqi Deng
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Jiaoyang Yu
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Qiucui Yao
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Zhenjun Qin
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Jiayuan Liang
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
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12
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Cross-Linked Regulation of Coral-Associated Dinoflagellates and Bacteria in Pocillopora sp. during High-Temperature Stress and Recovery. Microorganisms 2021; 9:microorganisms9091972. [PMID: 34576867 PMCID: PMC8468813 DOI: 10.3390/microorganisms9091972] [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: 08/23/2021] [Revised: 09/06/2021] [Accepted: 09/15/2021] [Indexed: 11/17/2022] Open
Abstract
As the problem of ocean warming worsens, the environmental adaptation potential of symbiotic Symbiodiniaceae and bacteria is directly related to the future and fate of corals. This study aimed to analyse the comprehensive community dynamics and physiology of these two groups of organisms in the coral Pocillopora sp. through indoor simulations of heat stress (which involved manually adjusting the temperature between both 26 °C and 34 °C). Heat treatment (≥30 °C) significantly reduced the abundance of Symbiodiniaceae and bacteria by more than 70%. After the temperature was returned to 26 °C for one month, the Symbiodiniaceae density was still low, while the absolute number of bacteria quickly recovered to 55% of that of the control. At this time point, the Fv/Fm value rose to 91% of the pretemperature value. The content of chlorophyll b associated with Cyanobacteria increased by 50% compared with that under the control conditions. Moreover, analysis of the Symbiodiniaceae subclade composition suggested that the relative abundance of C1c.C45, C1, and C1ca increased during heat treatment, indicating that they might constitute heat-resistant subgroups. We suggest that the increase in the absolute number of bacteria during the recovery period could be an important indicator of coral holobiont recovery after heat stress. This study provides insight into the cross-linked regulation of key symbiotic microbes in the coral Pocillopora sp. during high-temperature stress and recovery and provides a scientific basis for exploring the mechanism underlying coral adaptation to global warming.
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13
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Tandon K, Wan MT, Yang CC, Yang SH, Baatar B, Chiu CY, Tsai JW, Liu WC, Ng CS, Tang SL. Aquatic microbial community is partially functionally redundant: Insights from an in situ reciprocal transplant experiment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 786:147433. [PMID: 33971597 DOI: 10.1016/j.scitotenv.2021.147433] [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: 03/03/2021] [Revised: 04/06/2021] [Accepted: 04/25/2021] [Indexed: 06/12/2023]
Abstract
Microbial communities are considered to be functionally redundant, but few studies have tested this hypothesis empirically. In this study, we performed an in situ reciprocal transplant experiment on the surface and bottom waters of two lakes (Tsuei-Feng (T) and Yuan-Yang (Y)) with disparate trophic states and tracked changes in their microbial community composition and functions for 6 weeks using high-throughput sequencing and functional approaches. T lake's surface (Ts) and bottom (Tb) water active bacterial community (16S rRNA gene-transcript) was dominated by Actinobacteria, Bacteroidia, and Cyanobacteria, whereas Y lake's surface (Ys) and bottom (Yb) water had Gammaproteobacteria, Alphaproteobacteria, and Bacteroidia as the dominant classes. The community composition was resistant to changes in environmental conditions following the reciprocal transplant, but their functions tended to become similar to the incubating lakes' functional profiles. A significant linear positive relationship was observed between the microbial community and functional attributes (surface: R2 = 0.5065, p < 0.0001; bottom: R2 = 0.4592, p < 0.0001), though with varying scales of similarity (1-Bray Curtis distance), suggesting partial functional redundancy. Also, the entropy-based L-divergence measure identified high divergence in community composition (surface: 1.21 ± 0.54; bottom: 1.17 ± 0.51), and relatively low divergence in functional attributes (surface: 0.04 ± 0.01; bottom: 0.04 ± 0.01) in the two lakes' surface and bottom waters, providing further support for the presence of partial functional redundancy. This study enriches our understanding of community functional relationships and establishes the presence of partial functional redundancy in freshwater ecosystems.
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Affiliation(s)
- Kshitij Tandon
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan; Bioinformatics Program, Institute of Information Science, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan; Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Min-Tao Wan
- EcoHealth Microbiology Laboratory, WanYu Co., Ltd., Chiayi 600, Taiwan
| | - Chia-Chin Yang
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Shan-Hua Yang
- Institute of Fisheries Science, National Taiwan University, Taipei 10617, Taiwan
| | | | - Chih-Yu Chiu
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Jeng-Wei Tsai
- China Medical University, Department of Biological Science and Technology, Taichung 404, Taiwan
| | - Wen-Cheng Liu
- Department of Civil and Disaster Prevention Engineering, National United University, Miao-Li, Taiwan
| | - Chen Siang Ng
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Sen-Lin Tang
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan; Bioinformatics Program, Institute of Information Science, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan.
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14
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Zhang Y, Yang Q, Zhang Y, Ahmad M, Ling J, Dong J, Wang Y. The diversity and metabolic potential of the microbial functional gene associated with Porites pukoensis. ECOTOXICOLOGY (LONDON, ENGLAND) 2021; 30:986-995. [PMID: 33991262 DOI: 10.1007/s10646-021-02419-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/28/2021] [Indexed: 06/12/2023]
Abstract
Coral reef ecosystems usually distribute in oligotrophic tropical and subtropical marine environments, but they possess great biodiversity and high productivity. It may attribute to its efficient internal nutrient cycle system. However, the knowledge of functional microbial community structure is still limited. In this study, both functional gene array (Geochip 5.0) and nifH Illumina sequencing were used to profile the overall functional genes and diazotrophic communities associated with coral Porites pukoensis. More than 7500 microbial functional genes were detected from archaea, bacteria, and fungi. Most of these genes are related to the transformation of carbon, nitrogen, sulfur, and phosphorus, providing evidence that microbes in the coral holobiont play important roles in the biogeochemical cycle of coral reef ecosystems. Our results indicated a high diversity of diazotrophs associated with corals. The dominant diazotrophic groups were related to phyla Alphaproteobacteria, Deltaproteobacteria, Cyanobacteria, and Gammaproteobacteria. And the dominant diazotrophic communities were divided into four clusters. They were affiliated with nifH sequences from genera Zymomonas, Halorhodospira, Leptolyngbya, Trichormus, and Desulfovibrio, indicating these groups may play a more important role in the nitrogen-fixing process in the coral holobiont. This study revealed functional gene diversity and suggested the roles they played in the biogeochemical cycling of the coral holobiont.
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Affiliation(s)
- Yanying Zhang
- Ocean School, Yantai University, Yantai, 264005, China.
| | - Qingsong Yang
- 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
| | - Ying Zhang
- 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
| | - Manzoor Ahmad
- 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
| | - Juan Ling
- 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
| | - Junde Dong
- 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.
- Key Laboratory of Tropical Marine Biotechnology of Hainan Province and Hainan Sanya Marine Ecosystem National Observation and Research Station, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Sanya, 572000, China.
| | - Youshao Wang
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
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15
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Mutalipassi M, Riccio G, Mazzella V, Galasso C, Somma E, Chiarore A, de Pascale D, Zupo V. Symbioses of Cyanobacteria in Marine Environments: Ecological Insights and Biotechnological Perspectives. Mar Drugs 2021; 19:227. [PMID: 33923826 PMCID: PMC8074062 DOI: 10.3390/md19040227] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/14/2021] [Accepted: 04/15/2021] [Indexed: 01/07/2023] Open
Abstract
Cyanobacteria are a diversified phylum of nitrogen-fixing, photo-oxygenic bacteria able to colonize a wide array of environments. In addition to their fundamental role as diazotrophs, they produce a plethora of bioactive molecules, often as secondary metabolites, exhibiting various biological and ecological functions to be further investigated. Among all the identified species, cyanobacteria are capable to embrace symbiotic relationships in marine environments with organisms such as protozoans, macroalgae, seagrasses, and sponges, up to ascidians and other invertebrates. These symbioses have been demonstrated to dramatically change the cyanobacteria physiology, inducing the production of usually unexpressed bioactive molecules. Indeed, metabolic changes in cyanobacteria engaged in a symbiotic relationship are triggered by an exchange of infochemicals and activate silenced pathways. Drug discovery studies demonstrated that those molecules have interesting biotechnological perspectives. In this review, we explore the cyanobacterial symbioses in marine environments, considering them not only as diazotrophs but taking into consideration exchanges of infochemicals as well and emphasizing both the chemical ecology of relationship and the candidate biotechnological value for pharmaceutical and nutraceutical applications.
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Affiliation(s)
- Mirko Mutalipassi
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (G.R.); (C.G.); (D.d.P.)
| | - Gennaro Riccio
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (G.R.); (C.G.); (D.d.P.)
| | - Valerio Mazzella
- Department of Integrated Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy;
| | - Christian Galasso
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (G.R.); (C.G.); (D.d.P.)
| | - Emanuele Somma
- Department of Life Sciences, University of Trieste, Via Licio Giorgieri, 34127 Trieste, Italy;
- Department of Marine Biotechnology, Ischia Marine Centre, Stazione Zoologica Anton Dohrn, Punta San Pietro, 80077 Naples, Italy;
| | - Antonia Chiarore
- Department of Biology, University of Naples Federico II, Via Cinthia, 80126 Naples, Italy;
| | - Donatella de Pascale
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (G.R.); (C.G.); (D.d.P.)
| | - Valerio Zupo
- Department of Marine Biotechnology, Ischia Marine Centre, Stazione Zoologica Anton Dohrn, Punta San Pietro, 80077 Naples, Italy;
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Su H, Xiao Z, Yu K, Zhang Q, Lu C, Wang G, Wang Y, Liang J, Huang W, Huang X, Wei F. High Diversity of β-Glucosidase-Producing Bacteria and Their Genes Associated with Scleractinian Corals. Int J Mol Sci 2021; 22:ijms22073523. [PMID: 33805379 PMCID: PMC8037212 DOI: 10.3390/ijms22073523] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 01/08/2023] Open
Abstract
β-Glucosidase is a microbial cellulose multienzyme that plays an important role in the regulation of the entire cellulose hydrolysis process, which is the rate-limiting step in bacterial carbon cycling in marine environments. Despite its importance in coral reefs, the diversity of β-glucosidase-producing bacteria, their genes, and enzymatic characteristics are poorly understood. In this study, 87 β-glucosidase-producing cultivable bacteria were screened from 6 genera of corals. The isolates were assigned to 21 genera, distributed among three groups: Proteobacteria, Firmicutes, and Actinobacteria. In addition, metagenomics was used to explore the genetic diversity of bacterial β-glucosidase enzymes associated with scleractinian corals, which revealed that these enzymes mainly belong to the glycosidase hydrolase family 3 (GH3). Finally, a novel recombinant β-glucosidase, referred to as Mg9373, encompassing 670 amino acids and a molecular mass of 75.2 kDa, was classified as a member of the GH3 family and successfully expressed and characterized. Mg9373 exhibited excellent tolerance to ethanol, NaCl, and glucose. Collectively, these results suggest that the diversity of β-glucosidase-producing bacteria and genes associated with scleractinian corals is high and novel, indicating great potential for applications in the food industry and agriculture.
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Affiliation(s)
- 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; (H.S.); (Z.X.); (Q.Z.); (C.L.); (G.W.); (Y.W.); (J.L.); (W.H.); (X.H.); (F.W.)
| | - Zhenlun Xiao
- 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; (H.S.); (Z.X.); (Q.Z.); (C.L.); (G.W.); (Y.W.); (J.L.); (W.H.); (X.H.); (F.W.)
| | - Kefu Yu
- 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; (H.S.); (Z.X.); (Q.Z.); (C.L.); (G.W.); (Y.W.); (J.L.); (W.H.); (X.H.); (F.W.)
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai 519080, China
- Correspondence:
| | - 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; (H.S.); (Z.X.); (Q.Z.); (C.L.); (G.W.); (Y.W.); (J.L.); (W.H.); (X.H.); (F.W.)
| | - 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; (H.S.); (Z.X.); (Q.Z.); (C.L.); (G.W.); (Y.W.); (J.L.); (W.H.); (X.H.); (F.W.)
| | - Guanghua 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; (H.S.); (Z.X.); (Q.Z.); (C.L.); (G.W.); (Y.W.); (J.L.); (W.H.); (X.H.); (F.W.)
| | - Yinghui 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; (H.S.); (Z.X.); (Q.Z.); (C.L.); (G.W.); (Y.W.); (J.L.); (W.H.); (X.H.); (F.W.)
| | - Jiayuan Liang
- 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; (H.S.); (Z.X.); (Q.Z.); (C.L.); (G.W.); (Y.W.); (J.L.); (W.H.); (X.H.); (F.W.)
| | - Wen Huang
- 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; (H.S.); (Z.X.); (Q.Z.); (C.L.); (G.W.); (Y.W.); (J.L.); (W.H.); (X.H.); (F.W.)
| | - Xueyong Huang
- 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; (H.S.); (Z.X.); (Q.Z.); (C.L.); (G.W.); (Y.W.); (J.L.); (W.H.); (X.H.); (F.W.)
| | - Fen Wei
- 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; (H.S.); (Z.X.); (Q.Z.); (C.L.); (G.W.); (Y.W.); (J.L.); (W.H.); (X.H.); (F.W.)
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17
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Tandon K, Baatar B, Chiang PW, Dashdondog N, Oyuntsetseg B, Tang SL. A Large-Scale Survey of the Bacterial Communities in Lakes of Western Mongolia with Varying Salinity Regimes. Microorganisms 2020; 8:E1729. [PMID: 33158252 PMCID: PMC7716208 DOI: 10.3390/microorganisms8111729] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/02/2020] [Accepted: 11/03/2020] [Indexed: 12/12/2022] Open
Abstract
In recent years, climate change coupled with anthropogenic activities has led to monumental changes in saline lakes which are rapidly drying up across the globe and particularly in Central Asia. The landlocked country of Mongolia is rich in lakes which have remained primarily undisturbed by human impact, and many of these lakes have varying salinity regimes and are located across various geographical landscapes. In this study, we sampled 18 lakes with varying salinity regimes (hyperhaline, mesohaline, oligohaline, and polyhaline) covering 7000 km of western Mongolia and its various geographical landscapes (Gobi Desert, forests, and steppe). We identified that the bacterial communities that dominate these lakes are significantly influenced by salinity (p < 0.001) and geographical landscape (p < 0.001). Further, only five zOTUs were shared in all the lakes across the salinity regimes, providing evidence that both local and regional factors govern the community assembly and composition. Furthermore, the bacterial communities of hyperhaline lakes were significantly positively correlated with salinity (ANOVA, p < 0.001) and arsenic concentrations (ANOVA, p < 0.001), whereas bacterial communities of mesohaline and polyhaline lakes situated in forest and steppe landscapes were positively correlated with temperature (ANOVA, p < 0.001) and altitude (ANOVA, p < 0.001), respectively. Functional predictions based on the 16S rRNA gene indicated enrichment of KEGG Ontology terms related to transporters for osmoprotection and -regulation. Overall, our study provides a comprehensive view of the bacterial diversity and community composition present in these lakes, which might be lost in the future.
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Affiliation(s)
- Kshitij Tandon
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan; (K.T.); (B.B.); (P.-W.C.)
- Bioinformatics Program, Institute of Information Science, Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Bayanmunkh Baatar
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan; (K.T.); (B.B.); (P.-W.C.)
- School of Arts and Sciences, National University of Mongolia, Ulaanbaatar 14201, Mongolia;
| | - Pei-Wen Chiang
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan; (K.T.); (B.B.); (P.-W.C.)
| | - Narangarvuu Dashdondog
- School of Arts and Sciences, National University of Mongolia, Ulaanbaatar 14201, Mongolia;
| | - Bolormaa Oyuntsetseg
- School of Arts and Sciences, National University of Mongolia, Ulaanbaatar 14201, Mongolia;
| | - Sen-Lin Tang
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan; (K.T.); (B.B.); (P.-W.C.)
- Bioinformatics Program, Institute of Information Science, Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan
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18
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Yang SH, Tseng CH, Lo HP, Chiang PW, Chen HJ, Shiu JH, Lai HC, Tandon K, Isomura N, Mezaki T, Yamamoto H, Tang SL. Locality Effect of Coral-Associated Bacterial Community in the Kuroshio Current From Taiwan to Japan. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.569107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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19
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Jain SS, Afiq-Rosli L, Feldman B, Levy O, Phua JW, Wainwright BJ, Huang D. Homogenization of Endosymbiont Communities Hosted by Equatorial Corals during the 2016 Mass Bleaching Event. Microorganisms 2020; 8:microorganisms8091370. [PMID: 32906741 PMCID: PMC7564173 DOI: 10.3390/microorganisms8091370] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/31/2020] [Accepted: 09/04/2020] [Indexed: 01/08/2023] Open
Abstract
Thermal stress drives the bleaching of reef corals, during which the endosymbiotic relationship between Symbiodiniaceae microalgae and the host breaks down. The endosymbiont communities are known to shift in response to environmental disturbances, but how they respond within and between colonies during and following bleaching events remains unclear. In 2016, a major global-scale bleaching event hit countless tropical reefs. Here, we investigate the relative abundances of Cladocopium LaJeunesse & H.J.Jeong, 2018 and Durusdinium LaJeunesse, 2018 within and among Pachyseris speciosa colonies in equatorial Singapore that are known to host both these Symbiodiniaceae clades. Bleached and unbleached tissues from bleaching colonies, as well as healthy colonies, during and following the bleaching event were sampled and analyzed for comparison. The nuclear ribosomal internal transcribed spacer (ITS) regions were separately amplified and quantified using a SYBR Green-based quantitative polymerase chain reaction (qPCR) method and Illumina high-throughput sequencing. We found Cladocopium to be highly abundant relative to Durusdinium. The relative abundance of Durusdinium, known to be thermally tolerant, was highest in post-bleaching healthy colonies, while bleached and unbleached tissues from bleaching colonies as well as tissue from healthy colonies during the event had depressed proportions of Durusdinium. Given the importance of Durusdinium for thermal tolerance and stress response, it is surprising that bleached tissue showed limited change over healthy tissue during the bleaching event. Moreover, colonies were invariably dominated by Cladocopium during bleaching, but a minority of colonies were Durusdinium-dominant during non-bleaching times. The detailed characterization of Symbiodiniaceae in specific colonies during stress and recovery will provide insights into this crucial symbiosis, with implications for their responses during major bleaching events.
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Affiliation(s)
- Sudhanshi S. Jain
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore; (L.A.-R.); (J.W.P.)
- Correspondence: (S.S.J.); (D.H.)
| | - Lutfi Afiq-Rosli
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore; (L.A.-R.); (J.W.P.)
- Tropical Marine Science Institute, National University of Singapore, 18 Kent Ridge Road, Singapore 119227, Singapore
| | - Bar Feldman
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel; (B.F.); (O.L.)
| | - Oren Levy
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel; (B.F.); (O.L.)
| | - Jun Wei Phua
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore; (L.A.-R.); (J.W.P.)
| | - Benjamin J. Wainwright
- Yale-NUS College, National University of Singapore, 16 College Avenue West, Singapore 138527, Singapore;
| | - Danwei Huang
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore; (L.A.-R.); (J.W.P.)
- Tropical Marine Science Institute, National University of Singapore, 18 Kent Ridge Road, Singapore 119227, Singapore
- Correspondence: (S.S.J.); (D.H.)
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20
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Marchioro GM, Glasl B, Engelen AH, Serrão EA, Bourne DG, Webster NS, Frade PR. Microbiome dynamics in the tissue and mucus of acroporid corals differ in relation to host and environmental parameters. PeerJ 2020; 8:e9644. [PMID: 32874778 PMCID: PMC7439960 DOI: 10.7717/peerj.9644] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 07/10/2020] [Indexed: 12/19/2022] Open
Abstract
Corals are associated with diverse microbial assemblages; however, the spatial-temporal dynamics of intra-species microbial interactions are poorly understood. The coral-associated microbial community varies substantially between tissue and mucus microhabitats; however, the factors controlling the occurrence, abundance, and distribution of microbial taxa over time have rarely been explored for different coral compartments simultaneously. Here, we test (1) differentiation in microbiome diversity and composition between coral compartments (surface mucus and tissue) of two Acropora hosts (A. tenuis and A. millepora) common along inshore reefs of the Great Barrier Reef, as well as (2) the potential linkage between shifts in individual coral microbiome families and underlying host and environmental parameters. Amplicon based 16S ribosomal RNA gene sequencing of 136 samples collected over 14 months, revealed significant differences in bacterial richness, diversity and community structure among mucus, tissue and the surrounding seawater. Seawater samples were dominated by members of the Synechococcaceae and Pelagibacteraceae bacterial families. The mucus microbiome of Acropora spp. was dominated by members of Flavobacteriaceae, Synechococcaceae and Rhodobacteraceae and the tissue was dominated by Endozoicimonaceae. Mucus microbiome in both Acropora species was primarily correlated with seawater parameters including levels of chlorophyll a, ammonium, particulate organic carbon and the sum of nitrate and nitrite. In contrast, the correlation of the tissue microbiome to the measured environmental (i.e., seawater parameters) and host health physiological factors differed between host species, suggesting host-specific modulation of the tissue-associated microbiome to intrinsic and extrinsic factors. Furthermore, the correlation between individual coral microbiome members and environmental factors provides novel insights into coral microbiome-by-environment dynamics and hence has potential implications for current reef restoration and management efforts (e.g. microbial monitoring and observatory programs).
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Affiliation(s)
- Giulia M Marchioro
- University of Algarve, Faro, Portugal.,CCMAR - Centre of Marine Sciences, University of Algarve, Faro, Portugal.,AIMS@JCU, Townsville, Queensland, Australia
| | - Bettina Glasl
- AIMS@JCU, Townsville, Queensland, Australia.,Australian Institute of Marine Science, Townsville, Queensland, Australia.,College of Science and Engineering, James Cook University, Queensland, Townsville, Australia
| | - Aschwin H Engelen
- CCMAR - Centre of Marine Sciences, University of Algarve, Faro, Portugal
| | - Ester A Serrão
- CCMAR - Centre of Marine Sciences, University of Algarve, Faro, Portugal
| | - David G Bourne
- AIMS@JCU, Townsville, Queensland, Australia.,Australian Institute of Marine Science, Townsville, Queensland, Australia.,College of Science and Engineering, James Cook University, Queensland, Townsville, Australia
| | - Nicole S Webster
- AIMS@JCU, Townsville, Queensland, Australia.,Australian Institute of Marine Science, Townsville, Queensland, Australia.,Australian Centre for Ecogenomics, University of Queensland, Brisbane, Queensland, Australia
| | - Pedro R Frade
- CCMAR - Centre of Marine Sciences, University of Algarve, Faro, Portugal
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21
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Shiu JH, Yu SP, Fong CL, Ding JY, Tan CJ, Fan TY, Lu CY, Tang SL. Shifting in the Dominant Bacterial Group Endozoicomonas Is Independent of the Dissociation With Coral Symbiont Algae. Front Microbiol 2020; 11:1791. [PMID: 32849407 PMCID: PMC7412130 DOI: 10.3389/fmicb.2020.01791] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 07/08/2020] [Indexed: 11/13/2022] Open
Abstract
The coral-associated Endozoicomonas are dominant bacteria in the coral holobiont. Their relative abundance usually decreases with heat-induced coral bleaching and is proposed to be positively correlated with Symbiodiniaceae abundance. It remains unclear whether this phenomenon of decreased Endozoicomonas abundance is caused by temperature stress or a decreased abundance of Symbiodiniaceae. This study induced bleaching in the coral Euphyllia glabrescens using a dark treatment over 15 weeks. We examined shifts in Endozoicomonas abundance and experimentally reduced Symbiodiniaceae density. 16S rRNA gene amplicon sequencing was used to characterize the changes in bacterial community (incl. Endozoicomonas) over time, and the 16S rRNA gene copy number of Endozoicomonas was quantified by qPCR. We detected a high abundance of Endozoicomonas in E. glabrescens that underwent dark-induced bleaching. The results reveal that changes in the relative abundance of Endozoicomonas are unrelated to Symbiodiniaceae abundance, indicating that Endozoicomonas can be independent of Symbiodiniaceae in the coral holobiont.
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Affiliation(s)
- Jia-Ho Shiu
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan, and National Chung-Hsing University, Taichung, Taiwan.,Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.,Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung, Taiwan
| | - Sheng-Ping Yu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Chia-Ling Fong
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Jiun-Yan Ding
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Chih-Jui Tan
- National Museum of Marine Biology and Aquarium, Pingtung, Taiwan.,Department of Oceanography, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Tung-Yung Fan
- National Museum of Marine Biology and Aquarium, Pingtung, Taiwan
| | - Chih-Ying Lu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Sen-Lin Tang
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan, and National Chung-Hsing University, Taichung, Taiwan.,Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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22
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Claar DC, McDevitt-Irwin JM, Garren M, Vega Thurber R, Gates RD, Baum JK. Increased diversity and concordant shifts in community structure of coral-associated Symbiodiniaceae and bacteria subjected to chronic human disturbance. Mol Ecol 2020; 29:2477-2491. [PMID: 32495958 DOI: 10.1111/mec.15494] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 05/16/2020] [Accepted: 05/28/2020] [Indexed: 12/27/2022]
Abstract
Both coral-associated bacteria and endosymbiotic algae (Symbiodiniaceae spp.) are vitally important for the biological function of corals. Yet little is known about their co-occurrence within corals, how their diversity varies across coral species, or how they are impacted by anthropogenic disturbances. Here, we sampled coral colonies (n = 472) from seven species, encompassing a range of life history traits, across a gradient of chronic human disturbance (n = 11 sites on Kiritimati [Christmas] atoll) in the central equatorial Pacific, and quantified the sequence assemblages and community structure of their associated Symbiodiniaceae and bacterial communities. Although Symbiodiniaceae alpha diversity did not vary with chronic human disturbance, disturbance was consistently associated with higher bacterial Shannon diversity and richness, with bacterial richness by sample almost doubling from sites with low to very high disturbance. Chronic disturbance was also associated with altered microbial beta diversity for Symbiodiniaceae and bacteria, including changes in community structure for both and increased variation (dispersion) of the Symbiodiniaceae communities. We also found concordance between Symbiodiniaceae and bacterial community structure, when all corals were considered together, and individually for two massive species, Hydnophora microconos and Porites lobata, implying that symbionts and bacteria respond similarly to human disturbance in these species. Finally, we found that the dominant Symbiodiniaceae ancestral lineage in a coral colony was associated with differential abundances of several distinct bacterial taxa. These results suggest that increased beta diversity of Symbiodiniaceae and bacterial communities may be a reliable indicator of stress in the coral microbiome, and that there may be concordant responses to chronic disturbance between these communities at the whole-ecosystem scale.
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Affiliation(s)
- Danielle C Claar
- Department of Biology, University of Victoria, Victoria, BC, Canada.,School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA
| | - Jamie M McDevitt-Irwin
- Department of Biology, University of Victoria, Victoria, BC, Canada.,Department of Biology, Stanford University, Stanford, CA, USA
| | - Melissa Garren
- School of Natural Sciences, California State University Monterey Bay, Seaside, CA, USA
| | | | - Ruth D Gates
- Hawai`i Institute of Marine Biology, University of Hawai`i, Honolulu, HI, USA
| | - Julia K Baum
- Department of Biology, University of Victoria, Victoria, BC, Canada.,Hawai`i Institute of Marine Biology, University of Hawai`i, Honolulu, HI, USA
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23
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O'Brien PA, Webster NS, Miller DJ, Bourne DG. Host-Microbe Coevolution: Applying Evidence from Model Systems to Complex Marine Invertebrate Holobionts. mBio 2019; 10:e02241-18. [PMID: 30723123 PMCID: PMC6428750 DOI: 10.1128/mbio.02241-18] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Marine invertebrates often host diverse microbial communities, making it difficult to identify important symbionts and to understand how these communities are structured. This complexity has also made it challenging to assign microbial functions and to unravel the myriad of interactions among the microbiota. Here we propose to address these issues by applying evidence from model systems of host-microbe coevolution to complex marine invertebrate microbiomes. Coevolution is the reciprocal adaptation of one lineage in response to another and can occur through the interaction of a host and its beneficial symbiont. A classic indicator of coevolution is codivergence of host and microbe, and evidence of this is found in both corals and sponges. Metabolic collaboration between host and microbe is often linked to codivergence and appears likely in complex holobionts, where microbial symbionts can interact with host cells through production and degradation of metabolic compounds. Neutral models are also useful to distinguish selected microbes against a background population consisting predominately of random associates. Enhanced understanding of the interactions between marine invertebrates and their microbial communities is urgently required as coral reefs face unprecedented local and global pressures and as active restoration approaches, including manipulation of the microbiome, are proposed to improve the health and tolerance of reef species. On the basis of a detailed review of the literature, we propose three research criteria for examining coevolution in marine invertebrates: (i) identifying stochastic and deterministic components of the microbiome, (ii) assessing codivergence of host and microbe, and (iii) confirming the intimate association based on shared metabolic function.
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Affiliation(s)
- Paul A O'Brien
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia
- Australian Institute of Marine Science, Townsville, QLD, Australia
- AIMS@JCU, Townsville, QLD, Australia
| | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, QLD, Australia
- AIMS@JCU, Townsville, QLD, Australia
- Australian Centre for Ecogenomics, University of Queensland, Brisbane, QLD, Australia
| | - David J Miller
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, Australia
| | - David G Bourne
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia
- Australian Institute of Marine Science, Townsville, QLD, Australia
- AIMS@JCU, Townsville, QLD, Australia
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24
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Yang SH, Tandon K, Lu CY, Wada N, Shih CJ, Hsiao SSY, Jane WN, Lee TC, Yang CM, Liu CT, Denis V, Wu YT, Wang LT, Huang L, Lee DC, Wu YW, Yamashiro H, Tang SL. Metagenomic, phylogenetic, and functional characterization of predominant endolithic green sulfur bacteria in the coral Isopora palifera. MICROBIOME 2019; 7:3. [PMID: 30609942 PMCID: PMC6320609 DOI: 10.1186/s40168-018-0616-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 12/21/2018] [Indexed: 05/13/2023]
Abstract
BACKGROUND Endolithic microbes in coral skeletons are known to be a nutrient source for the coral host. In addition to aerobic endolithic algae and Cyanobacteria, which are usually described in the various corals and form a green layer beneath coral tissues, the anaerobic photoautotrophic green sulfur bacteria (GSB) Prosthecochloris is dominant in the skeleton of Isopora palifera. However, due to inherent challenges in studying anaerobic microbes in coral skeleton, the reason for its niche preference and function are largely unknown. RESULTS This study characterized a diverse and dynamic community of endolithic microbes shaped by the availability of light and oxygen. In addition, anaerobic bacteria isolated from the coral skeleton were cultured for the first time to experimentally clarify the role of these GSB. This characterization includes GSB's abundance, genetic and genomic profiles, organelle structure, and specific metabolic functions and activity. Our results explain the advantages endolithic GSB receive from living in coral skeletons, the potential metabolic role of a clade of coral-associated Prosthecochloris (CAP) in the skeleton, and the nitrogen fixation ability of CAP. CONCLUSION We suggest that the endolithic microbial community in coral skeletons is diverse and dynamic and that light and oxygen are two crucial factors for shaping it. This study is the first to demonstrate the ability of nitrogen uptake by specific coral-associated endolithic bacteria and shed light on the role of endolithic bacteria in coral skeletons.
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Affiliation(s)
- Shan-Hua Yang
- Biodiversity Research Center, Academia Sinica, Taipei, 11529 Taiwan
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, 905-0227 Japan
- Department of Life Science, Tunghai University, Taichung, 40704 Taiwan
- Center for Ecology and Environment, Tunghai University, Taichung, 40704 Taiwan
| | - Kshitij Tandon
- Biodiversity Research Center, Academia Sinica, Taipei, 11529 Taiwan
- Bioinformatics Program, Institute of Information Science, Taiwan International Graduate Program, Academia Sinica, Taipei, 11529 Taiwan
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013 Taiwan
| | - Chih-Ying Lu
- Biodiversity Research Center, Academia Sinica, Taipei, 11529 Taiwan
| | - Naohisa Wada
- Biodiversity Research Center, Academia Sinica, Taipei, 11529 Taiwan
| | - Chao-Jen Shih
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, 30062 Taiwan
| | - Silver Sung-Yun Hsiao
- Institute of Earth Sciences, Academia Sinica, Taipei, 11529 Taiwan
- Institute of Astronomy and Astrophysics, Academia Sinica, Taipei, 11529 Taiwan
| | - Wann-Neng Jane
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529 Taiwan
| | - Tzan-Chain Lee
- Biodiversity Research Center, Academia Sinica, Taipei, 11529 Taiwan
| | - Chi-Ming Yang
- Biodiversity Research Center, Academia Sinica, Taipei, 11529 Taiwan
| | - Chi-Te Liu
- Institute of Biotechnology, National Taiwan University, Taipei, 10672 Taiwan
| | - Vianney Denis
- Institute of Oceanography, National Taiwan University, Taipei, 10617 Taiwan
| | - Yu-Ting Wu
- Department of Forestry, National Pingtung University of Science and Technology, Pintung, 91201 Taiwan
| | - Li-Ting Wang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, 30062 Taiwan
| | - Lina Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, 30062 Taiwan
| | - Der-Chuen Lee
- Institute of Earth Sciences, Academia Sinica, Taipei, 11529 Taiwan
| | - Yu-Wei Wu
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, 11031 Taiwan
| | - Hideyuki Yamashiro
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, 905-0227 Japan
| | - Sen-Lin Tang
- Biodiversity Research Center, Academia Sinica, Taipei, 11529 Taiwan
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25
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Neave MJ, Apprill A, Aeby G, Miyake S, Voolstra CR. Microbial Communities of Red Sea Coral Reefs. CORAL REEFS OF THE RED SEA 2019. [DOI: 10.1007/978-3-030-05802-9_4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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26
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Pratte ZA, Richardson LL. Microbiome dynamics of two differentially resilient corals. DISEASES OF AQUATIC ORGANISMS 2018; 131:213-226. [PMID: 30459293 DOI: 10.3354/dao03289] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Coral bleaching and disease are 2 common occurrences that are contributing to global coral cover decline. Understanding the interactions between the coral animal and its microbial associates, and how they may change in the presence of stressors such as warming and acidification, is a crucial component to understanding both susceptibility and resistance to disease and bleaching. The coral Diploria labyrinthiformis has been shown to be more disease resistant than its relative Pseudodiploria strigosa, providing an ideal study system for disease resistance. In this study, we examined the bacterial communities of these 2 coral species on the Florida Reef tract every 6 mo for 18 mo (in situ sampling), and under experimental (laboratory) thermal and pH manipulation. The in situ sampling encompassed wide fluctuations in temperature, including an anomalously warm summer period. The laboratory experiments involved exposure to both increased temperature (31°C) and lowered pH (7.7). The in situ bacterial communities of both coral species were highly similar in the winter, but diverged during summer, with the D. labyrinthiformis bacterial community being more stable than that of P. strigosa. Differences in the bacterial community between the 2 coral species included 29 operational taxonomic units (OTUs) that were specific to D. labyrinthiformis in all seasons, while only 2 OTUs were specific to P. strigosa. The comparative stability of the D. labyrinthiformis microbiome, in addition to harboring a more specific microbiome, may be a key component of the relative disease resistance of this coral.
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Affiliation(s)
- Zoe A Pratte
- Department of Biological Sciences, Florida International University, Miami, FL 33199, USA
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27
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Goldsmith DB, Kellogg CA, Morrison CL, Gray MA, Stone RP, Waller RG, Brooke SD, Ross SW. Comparison of microbiomes of cold-water corals Primnoa pacifica and Primnoa resedaeformis, with possible link between microbiome composition and host genotype. Sci Rep 2018; 8:12383. [PMID: 30120375 PMCID: PMC6098105 DOI: 10.1038/s41598-018-30901-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 08/08/2018] [Indexed: 12/26/2022] Open
Abstract
Cold-water corals provide critical habitats for a multitude of marine species, but are understudied relative to tropical corals. Primnoa pacifica is a cold-water coral prevalent throughout Alaskan waters, while another species in the genus, Primnoa resedaeformis, is widely distributed in the Atlantic Ocean. This study examined the V4-V5 region of the 16S rRNA gene after amplifying and pyrosequencing bacterial DNA from samples of these species. Key differences between the two species' microbiomes included a robust presence of bacteria belonging to the Chlamydiales order in most of the P. pacifica samples, whereas no more than 2% of any microbial community from P. resedaeformis comprised these bacteria. Microbiomes of P. resedaeformis exhibited higher diversity than those of P. pacifica, and the two species largely clustered separately in a principal coordinate analysis. Comparison of P. resedaeformis microbiomes from samples collected in two submarine canyons revealed a significant difference between locations. This finding mirrored significant genetic differences among the P. resedaeformis from the two canyons based upon population genetic analysis of microsatellite loci. This study presents the first report of microbiomes associated with these two coral species.
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Affiliation(s)
- Dawn B Goldsmith
- St. Petersburg Coastal and Marine Science Center, US Geological Survey, St. Petersburg, FL, United States of America
| | - Christina A Kellogg
- St. Petersburg Coastal and Marine Science Center, US Geological Survey, St. Petersburg, FL, United States of America.
| | - Cheryl L Morrison
- Leetown Science Center, US Geological Survey, Kearneysville, WV, United States of America
| | - Michael A Gray
- St. Petersburg Coastal and Marine Science Center, US Geological Survey, St. Petersburg, FL, United States of America
| | - Robert P Stone
- Auke Bay Laboratories, Alaska Fisheries Science Center, NOAA Fisheries, 17109, Point Lena Loop Road, Juneau, AK, United States of America
| | - Rhian G Waller
- Darling Marine Center, University of Maine, Walpole, ME, United States of America
| | - Sandra D Brooke
- Coastal and Marine Laboratory, Florida State University, St. Teresa, FL, United States of America
| | - Steve W Ross
- Center for Marine Science, University of North Carolina at Wilmington, Wilmington, NC, United States of America
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28
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Shelyakin PV, Garushyants SK, Nikitin MA, Mudrova SV, Berumen M, Speksnijder AGCL, Hoeksema BW, Fontaneto D, Gelfand MS, Ivanenko VN. Microbiomes of gall-inducing copepod crustaceans from the corals Stylophora pistillata (Scleractinia) and Gorgonia ventalina (Alcyonacea). Sci Rep 2018; 8:11563. [PMID: 30069039 PMCID: PMC6070567 DOI: 10.1038/s41598-018-29953-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 07/18/2018] [Indexed: 12/31/2022] Open
Abstract
Corals harbor complex and diverse microbial communities that strongly impact host fitness and resistance to diseases, but these microbes themselves can be influenced by stresses, like those caused by the presence of macroscopic symbionts. In addition to directly influencing the host, symbionts may transmit pathogenic microbial communities. We analyzed two coral gall-forming copepod systems by using 16S rRNA gene metagenomic sequencing: (1) the sea fan Gorgonia ventalina with copepods of the genus Sphaerippe from the Caribbean and (2) the scleractinian coral Stylophora pistillata with copepods of the genus Spaniomolgus from the Saudi Arabian part of the Red Sea. We show that bacterial communities in these two systems were substantially different with Actinobacteria, Alphaproteobacteria, and Betaproteobacteria more prevalent in samples from Gorgonia ventalina, and Gammaproteobacteria in Stylophora pistillata. In Stylophora pistillata, normal coral microbiomes were enriched with the common coral symbiont Endozoicomonas and some unclassified bacteria, while copepod and gall-tissue microbiomes were highly enriched with the family ME2 (Oceanospirillales) or Rhodobacteraceae. In Gorgonia ventalina, no bacterial group had significantly different prevalence in the normal coral tissues, copepods, and injured tissues. The total microbiome composition of polyps injured by copepods was different. Contrary to our expectations, the microbial community composition of the injured gall tissues was not directly affected by the microbiome of the gall-forming symbiont copepods.
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Affiliation(s)
- Pavel V Shelyakin
- Kharkevich Institute for Information Transmission Problems RAS, B. Karetny per. 19, Moscow, 127051, Russia.,Vavilov Institute of General Genetics RAS, Gubkina str. 3, Moscow, 119333, Russia
| | - Sofya K Garushyants
- Kharkevich Institute for Information Transmission Problems RAS, B. Karetny per. 19, Moscow, 127051, Russia.,Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Nobel str. 1, Moscow, 121205, Russia
| | - Mikhail A Nikitin
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Sofya V Mudrova
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955, Saudi Arabia
| | - Michael Berumen
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955, Saudi Arabia
| | | | - Bert W Hoeksema
- Naturalis Biodiversity Center, Leiden, 2332 AA, The Netherlands
| | - Diego Fontaneto
- National Research Council, Institute of Ecosystem Study, Verbania, 28922, Italy
| | - Mikhail S Gelfand
- Kharkevich Institute for Information Transmission Problems RAS, B. Karetny per. 19, Moscow, 127051, Russia.,Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Nobel str. 1, Moscow, 121205, Russia.,Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119992, Russia.,Faculty of Computer Science, Higher School of Economics, Kochnovsky pr. 3, Moscow, 125319, Russia
| | - Viatcheslav N Ivanenko
- Naturalis Biodiversity Center, Leiden, 2332 AA, The Netherlands. .,Department of Invertebrate Zoology, Biological Faculty, Lomonosov Moscow State University, Moscow, 119992, Russia.
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29
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Shiu JH, Ding JY, Tseng CH, Lou SP, Mezaki T, Wu YT, Wang HI, Tang SL. A Newly Designed Primer Revealed High Phylogenetic Diversity of Endozoicomonas in Coral Reefs. Microbes Environ 2018; 33:172-185. [PMID: 29760298 PMCID: PMC6031392 DOI: 10.1264/jsme2.me18054] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Accepted: 04/08/2018] [Indexed: 11/29/2022] Open
Abstract
Endozoicomonas bacteria are commonly regarded as having a potentially symbiotic relationship with their coral hosts. However, their diversity and phylogeny in samples collected from various sources remain unclear. Therefore, we designed an Endozoicomonas-specific primer paired with a bacterial universal primer to detect the 16S ribosomal RNA (rRNA) genes of this taxon and conducted an in-depth investigation of the Endozoicomonas community structure in reef-building corals. The primer had high specificity in the V3-V4 region (95.6%) and its sensitivity was high, particularly when Endozoicomonas was rare in samples (e.g., in seawater, which had a higher alpha diversity of Endozoicomonas than corals). In coral samples, predominant V3-V4 ribotypes had greater divergence than predominant V1-V2 ribotypes, and were grouped into at least 9 novel clades in a phylogenetic tree, indicating Endozoicomonas had high phylogenetic diversity. Divergence within this genus was potentially higher than that among 7 outgroup genera based on the phylogenetic distances of partial 16S rDNA sequences, suggesting that the taxonomy of this genus needs to be revised. In conclusion, dominant Endozoicomonas populations had variable phylogenies; furthermore, the newly designed primers may be useful molecular tools for the reliable detection of the Endozoicomonas community in marine environments.
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Affiliation(s)
- Jia-Ho Shiu
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia SinicaTaipeiTaiwan
- Biodiversity Research Center, Academia SinicaTaipeiTaiwan
- Graduate Institute of Biotechnology, National Chung-Hsing UniversityTaichungTaiwan
| | - Jiun-Yan Ding
- Biodiversity Research Center, Academia SinicaTaipeiTaiwan
| | - Ching-Hung Tseng
- Biodiversity Research Center, Academia SinicaTaipeiTaiwan
- Bioinformatics Program, Taiwan International Graduate Program, Academia SinicaTaipeiTaiwan
- Institute of Biomedical Informatics, National Yang-Ming UniversityTaipeiTaiwan
| | - Shueh-Ping Lou
- Biodiversity Research Center, Academia SinicaTaipeiTaiwan
| | - Takuma Mezaki
- Biological Institute on Kuroshio, Kuroshio Biological Research FoundationKochiJapan
| | - Yu-Ting Wu
- Biodiversity Research Center, Academia SinicaTaipeiTaiwan
- Department of Forestry, National Pingtung University of Science and TechnologyPingtungTaiwan
| | - Hsiang-Iu Wang
- Biodiversity Research Center, Academia SinicaTaipeiTaiwan
| | - Sen-Lin Tang
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia SinicaTaipeiTaiwan
- Biodiversity Research Center, Academia SinicaTaipeiTaiwan
- Biotechnology Center, National Chung-Hsing UniversityTaichungTaiwan
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30
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Bednarz VN, Naumann MS, Cardini U, van Hoytema N, Rix L, Al-Rshaidat MMD, Wild C. Contrasting seasonal responses in dinitrogen fixation between shallow and deep-water colonies of the model coral Stylophora pistillata in the northern Red Sea. PLoS One 2018; 13:e0199022. [PMID: 29902263 PMCID: PMC6002246 DOI: 10.1371/journal.pone.0199022] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 05/30/2018] [Indexed: 01/08/2023] Open
Abstract
Tropical corals are often associated with dinitrogen (N2)-fixing bacteria (diazotrophs), and seasonal changes in key environmental parameters, such as dissolved inorganic nitrogen (DIN) availability and seawater temperature, are known to affect N2 fixation in coral-microbial holobionts. Despite, then, such potential for seasonal and depth-related changes in N2 fixation in reef corals, such variation has not yet been investigated. Therefore, this study quantified seasonal (winter vs. summer) N2 fixation rates associated with the reef-building coral Stylophora pistillata collected from depths of 5, 10 and 20 m in the northern Gulf of Aqaba (Red Sea). Findings revealed that corals from all depths exhibited the highest N2 fixation rates during the oligotrophic summer season, when up to 11% of their photo-metabolic nitrogen demand (CPND) could be met by N2 fixation. While N2 fixation remained seasonally stable for deep corals (20 m), it significantly decreased for the shallow corals (5 and 10 m) during the DIN-enriched winter season, accounting for less than 2% of the corals’ CPND. This contrasting seasonal response in N2 fixation across corals of different depths could be driven by 1) release rates of coral-derived organic matter, 2) the community composition of the associated diazotrophs, and/or 3) nutrient acquisition by the Symbiodinium community.
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Affiliation(s)
- Vanessa N. Bednarz
- Coral Reef Ecology Group, Leibniz Centre for Tropical Marine Research (ZMT), Bremen, Germany
- Marine Department, Centre Scientifique de Monaco, Principality of Monaco
- * E-mail:
| | - Malik S. Naumann
- Coral Reef Ecology Group, Leibniz Centre for Tropical Marine Research (ZMT), Bremen, Germany
| | - Ulisse Cardini
- Coral Reef Ecology Group, Leibniz Centre for Tropical Marine Research (ZMT), Bremen, Germany
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, Italy
| | - Nanne van Hoytema
- Coral Reef Ecology Group, Leibniz Centre for Tropical Marine Research (ZMT), Bremen, Germany
| | - Laura Rix
- Coral Reef Ecology Group, Leibniz Centre for Tropical Marine Research (ZMT), Bremen, Germany
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Mamoon M. D. Al-Rshaidat
- Laboratory for Molecular Microbial Ecology, Marine Science Station, Aqaba, Jordan
- Molecular and Microbial Ecology, Department of Biological Sciences, The University of Jordan, Amman, Jordan
| | - Christian Wild
- Coral Reef Ecology Group, Leibniz Centre for Tropical Marine Research (ZMT), Bremen, Germany
- Marine Ecology Group, Faculty of Biology and Chemistry, University of Bremen, Bremen, Germany
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31
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Tandon K, Yang SH, Wan MT, Yang CC, Baatar B, Chiu CY, Tsai JW, Liu WC, Tang SL. Bacterial Community in Water and Air of Two Sub-Alpine Lakes in Taiwan. Microbes Environ 2018; 33:120-126. [PMID: 29681561 PMCID: PMC6031399 DOI: 10.1264/jsme2.me17148] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Very few studies have attempted to profile the microbial communities in the air above freshwater bodies, such as lakes, even though freshwater sources are an important part of aquatic ecosystems and airborne bacteria are the most dispersible microorganisms on earth. In the present study, we investigated microbial communities in the waters of two high mountain sub-alpine montane lakes—located 21 km apart and with disparate trophic characteristics—and the air above them. Although bacteria in the lakes had locational differences, their community compositions remained constant over time. However, airborne bacterial communities were diverse and displayed spatial and temporal variance. Proteobacteria, Actinobacteria, Bacteroidetes, and Cyanobacteria were dominant in both lakes, with different relative abundances between lakes, and Parcubacteria (OD1) was dominant in air samples for all sampling times, except two. We also identified certain shared taxa between lake water and the air above it. The results obtained on these communities in the present study provide putative candidates to study how airborne communities shape lake water bacterial compositions and vice versa.
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Affiliation(s)
- Kshitij Tandon
- Biodiversity Research Center, Academia Sinica.,Bioinformatics Program, Institute of Information Science, Taiwan International Graduate Program, Academia Sinica.,Institute of Bioinformatics and Structural Biology, National Tsing Hua University
| | | | - Min-Tao Wan
- EcoHealth Microbiology Laboratory, WanYu Co., Ltd
| | | | | | | | - Jeng-Wei Tsai
- China Medical University, Department of Biological Science and Technology
| | - Wen-Cheng Liu
- Department of Civil and Disaster Prevention Engineering, National United University
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32
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Season structures prokaryotic partners but not algal symbionts in subtropical hard corals. Appl Microbiol Biotechnol 2018; 102:4963-4973. [PMID: 29637293 DOI: 10.1007/s00253-018-8909-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Revised: 02/12/2018] [Accepted: 02/28/2018] [Indexed: 01/03/2023]
Abstract
Coral reef ecosystems have great economic, social, and ecological value. The ecological success of coral reef ecosystems critically depends on coral-algal symbiosis and coral-prokaryotic partnership. However, seasonal changes underlying these relationships in subtropical hard corals of Hong Kong are poorly studied. Here, we compared the community changes of algal symbionts and prokaryotic partners in Platygyra carnosa and Galaxea fascicularis from Hong Kong collected at two seasonal time points of winter and summer via massively parallel sequencing of genetic markers and multivariate analysis. The results indicated that algal symbionts showed no significant changes between the two seasonal time points but prokaryotic partners changed substantially. Prokaryotic partners putatively involved in photosynthesis, nitrogen fixation, and sulfur oxidation increased significantly from winter to summer, while prokaryotic partners potentially associated with chemosynthesis, ammonia oxidation, and nitrite oxidation decreased significantly from winter to summer. Dissolved oxygen and pH served as the main contributors influencing prokaryotic partners in winter, while temperature, turbidity, and salinity played a dominant role in shaping prokaryotic partners in summer. The findings of the present study suggest that season structures prokaryotic partners but not algal symbionts in subtropical hard corals.
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33
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Brener-Raffalli K, Clerissi C, Vidal-Dupiol J, Adjeroud M, Bonhomme F, Pratlong M, Aurelle D, Mitta G, Toulza E. Thermal regime and host clade, rather than geography, drive Symbiodinium and bacterial assemblages in the scleractinian coral Pocillopora damicornis sensu lato. MICROBIOME 2018; 6:39. [PMID: 29463295 PMCID: PMC5819220 DOI: 10.1186/s40168-018-0423-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 02/11/2018] [Indexed: 05/17/2023]
Abstract
BACKGROUND Although the term holobiont has been popularized in corals with the advent of the hologenome theory of evolution, the underlying concepts are still a matter of debate. Indeed, the relative contribution of host and environment and especially thermal regime in shaping the microbial communities should be examined carefully to evaluate the potential role of symbionts for holobiont adaptation in the context of global changes. We used the sessile, long-lived, symbiotic and environmentally sensitive reef-building coral Pocillopora damicornis to address these issues. RESULTS We sampled Pocillopora damicornis colonies corresponding to two different mitochondrial lineages in different geographic areas displaying different thermal regimes: Djibouti, French Polynesia, New Caledonia, and Taiwan. The community composition of bacteria and the algal endosymbiont Symbiodinium were characterized using high-throughput sequencing of 16S rRNA gene and internal transcribed spacer, ITS2, respectively. Bacterial microbiota was very diverse with high prevalence of Endozoicomonas, Arcobacter, and Acinetobacter in all samples. While Symbiodinium sub-clade C1 was dominant in Taiwan and New Caledonia, D1 was dominant in Djibouti and French Polynesia. Moreover, we also identified a high background diversity (i.e., with proportions < 1%) of A1, C3, C15, and G Symbiodinum sub-clades. Using redundancy analyses, we found that the effect of geography was very low for both communities and that host genotypes and temperatures differently influenced Symbiodinium and bacterial microbiota. Indeed, while the constraint of host haplotype was higher than temperatures on bacterial composition, we showed for the first time a strong relationship between the composition of Symbiodinium communities and minimal sea surface temperatures. CONCLUSION Because Symbiodinium assemblages are more constrained by the thermal regime than bacterial communities, we propose that their contribution to adaptive capacities of the holobiont to temperature changes might be higher than the influence of bacterial microbiota. Moreover, the link between Symbiodinium community composition and minimal temperatures suggests low relative fitness of clade D at lower temperatures. This observation is particularly relevant in the context of climate change, since corals will face increasing temperatures as well as much frequent abnormal cold episodes in some areas of the world.
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Affiliation(s)
- Kelly Brener-Raffalli
- IHPE, UMR 5244, University of Perpignan Via Domitia, CNRS, IFREMER, University of Montpellier, Perpignan, France
| | - Camille Clerissi
- IHPE, UMR 5244, University of Perpignan Via Domitia, CNRS, IFREMER, University of Montpellier, Perpignan, France
| | - Jeremie Vidal-Dupiol
- IHPE, UMR 5244, University of Perpignan Via Domitia, CNRS, IFREMER, University of Montpellier, Perpignan, France
| | - Mehdi Adjeroud
- ENTROPIE, UMR 9220 & Laboratoire d’Excellence CORAIL, IRD, University of Perpignan Via Domitia, Perpignan, France
| | - François Bonhomme
- ISEM, UMR 5554, CNRS, University of Montpellier, IRD, EPHE, Sète, France
| | - Marine Pratlong
- IMBE, UMR 7263, Aix Marseille University, CNRS, IRD, Avignon University, Marseille, France
| | - Didier Aurelle
- IMBE, UMR 7263, Aix Marseille University, CNRS, IRD, Avignon University, Marseille, France
| | - Guillaume Mitta
- IHPE, UMR 5244, University of Perpignan Via Domitia, CNRS, IFREMER, University of Montpellier, Perpignan, France
| | - Eve Toulza
- IHPE, UMR 5244, University of Perpignan Via Domitia, CNRS, IFREMER, University of Montpellier, Perpignan, France
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Exploring coral microbiome assemblages in the South China Sea. Sci Rep 2018; 8:2428. [PMID: 29402898 PMCID: PMC5799258 DOI: 10.1038/s41598-018-20515-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 01/18/2018] [Indexed: 12/29/2022] Open
Abstract
Coral reefs are significant ecosystems. The ecological success of coral reefs relies on not only coral-algal symbiosis but also coral-microbial partnership. However, microbiome assemblages in the South China Sea corals remain largely unexplored. Here, we compared the microbiome assemblages of reef-building corals Galaxea (G. fascicularis) and Montipora (M. venosa, M. peltiformis, M. monasteriata) collected from five different locations in the South China Sea using massively-parallel sequencing of 16S rRNA gene and multivariate analysis. The results indicated that microbiome assemblages for each coral species were unique regardless of location and were different from the corresponding seawater. Host type appeared to drive the coral microbiome assemblages rather than location and seawater. Network analysis was employed to explore coral microbiome co-occurrence patterns, which revealed 61 and 80 co-occurring microbial species assembling the Galaxea and Montipora microbiomes, respectively. Most of these co-occurring microbial species were commonly found in corals and were inferred to play potential roles in host nutrient metabolism; carbon, nitrogen, sulfur cycles; host detoxification; and climate change. These findings suggest that the co-occurring microbial species explored might be essential to maintain the critical coral-microbial partnership. The present study provides new insights into coral microbiome assemblages in the South China Sea.
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Grottoli AG, Dalcin Martins P, Wilkins MJ, Johnston MD, Warner ME, Cai WJ, Melman TF, Hoadley KD, Pettay DT, Levas S, Schoepf V. Coral physiology and microbiome dynamics under combined warming and ocean acidification. PLoS One 2018; 13:e0191156. [PMID: 29338021 PMCID: PMC5770069 DOI: 10.1371/journal.pone.0191156] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 01/01/2018] [Indexed: 11/23/2022] Open
Abstract
Rising seawater temperature and ocean acidification threaten the survival of coral reefs. The relationship between coral physiology and its microbiome may reveal why some corals are more resilient to these global change conditions. Here, we conducted the first experiment to simultaneously investigate changes in the coral microbiome and coral physiology in response to the dual stress of elevated seawater temperature and ocean acidification expected by the end of this century. Two species of corals, Acropora millepora containing the thermally sensitive endosymbiont C21a and Turbinaria reniformis containing the thermally tolerant endosymbiont Symbiodinium trenchi, were exposed to control (26.5°C and pCO2 of 364 μatm) and treatment (29.0°C and pCO2 of 750 μatm) conditions for 24 days, after which we measured the microbial community composition. These microbial findings were interpreted within the context of previously published physiological measurements from the exact same corals in this study (calcification, organic carbon flux, ratio of photosynthesis to respiration, photosystem II maximal efficiency, total lipids, soluble animal protein, soluble animal carbohydrates, soluble algal protein, soluble algal carbohydrate, biomass, endosymbiotic algal density, and chlorophyll a). Overall, dually stressed A. millepora had reduced microbial diversity, experienced large changes in microbial community composition, and experienced dramatic physiological declines in calcification, photosystem II maximal efficiency, and algal carbohydrates. In contrast, the dually stressed coral T. reniformis experienced a stable and more diverse microbiome community with minimal physiological decline, coupled with very high total energy reserves and particulate organic carbon release rates. Thus, the microbiome changed and microbial diversity decreased in the physiologically sensitive coral with the thermally sensitive endosymbiotic algae but not in the physiologically tolerant coral with the thermally tolerant endosymbiont. Our results confirm recent findings that temperature-stress tolerant corals have a more stable microbiome, and demonstrate for the first time that this is also the case under the dual stresses of ocean warming and acidification. We propose that coral with a stable microbiome are also more physiologically resilient and thus more likely to persist in the future, and shape the coral species diversity of future reef ecosystems.
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Affiliation(s)
- Andréa G. Grottoli
- School of Earth Sciences, The Ohio State University, Columbus, OH, United States of America
- * E-mail:
| | - Paula Dalcin Martins
- Department of Microbiology, The Ohio State University, Columbus, OH, United States of America
| | - Michael J. Wilkins
- School of Earth Sciences, The Ohio State University, Columbus, OH, United States of America
- Department of Microbiology, The Ohio State University, Columbus, OH, United States of America
| | - Michael D. Johnston
- School of Earth Sciences, The Ohio State University, Columbus, OH, United States of America
| | - Mark E. Warner
- School of Marine Science and Policy, University of Delaware, Lewes, DE, United States of America
| | - Wei-Jun Cai
- School of Marine Science and Policy, University of Delaware, Lewes, DE, United States of America
| | - Todd F. Melman
- Reef Systems Coral Farm, New Albany, OH, United States of America
| | - Kenneth D. Hoadley
- School of Marine Science and Policy, University of Delaware, Lewes, DE, United States of America
| | - D. Tye Pettay
- School of Marine Science and Policy, University of Delaware, Lewes, DE, United States of America
| | - Stephen Levas
- School of Earth Sciences, The Ohio State University, Columbus, OH, United States of America
| | - Verena Schoepf
- School of Earth Sciences, The Ohio State University, Columbus, OH, United States of America
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van de Water JAJM, Voolstra CR, Rottier C, Cocito S, Peirano A, Allemand D, Ferrier-Pagès C. Seasonal Stability in the Microbiomes of Temperate Gorgonians and the Red Coral Corallium rubrum Across the Mediterranean Sea. MICROBIAL ECOLOGY 2018; 75:274-288. [PMID: 28681143 DOI: 10.1007/s00248-017-1006-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 06/02/2017] [Indexed: 06/07/2023]
Abstract
Populations of key benthic habitat-forming octocoral species have declined significantly in the Mediterranean Sea due to mass mortality events caused by microbial disease outbreaks linked to high summer seawater temperatures. Recently, we showed that the microbial communities of these octocorals are relatively structured; however, our knowledge on the seasonal dynamics of these microbiomes is still limited. To investigate their seasonal stability, we collected four soft gorgonian species (Eunicella singularis, Eunicella cavolini, Eunicella verrucosa and Leptogorgia sarmentosa) and the precious red coral (Corallium rubrum) from two coastal locations with different terrestrial impact levels in the Mediterranean Sea, and used next-generation amplicon sequencing of the 16S rRNA gene. The microbiomes of all soft gorgonian species were dominated by the same 'core microbiome' bacteria belonging to the Endozoicomonas and the Cellvibrionales clade BD1-7, whereas the red coral microbiome was primarily composed of 'core' Spirochaetes, Oceanospirillales ME2 and Parcubacteria. The associations with these bacterial taxa were relatively consistent over time at each location for each octocoral species. However, differences in microbiome composition and seasonal dynamics were observed between locations and could primarily be attributed to locally variant bacteria. Overall, our data provide further evidence of the intricate symbiotic relationships that exist between Mediterranean octocorals and their associated microbes, which are ancient and highly conserved over both space and time, and suggest regulation of the microbiome composition by the host, depending on local conditions.
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Affiliation(s)
| | - Christian R Voolstra
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Cecile Rottier
- Centre Scientifique de Monaco, 8 Quai Antoine 1er, 98000, Monaco, Monaco
| | - Silvia Cocito
- Marine Environment Research Centre, ENEA, La Spezia, Italy
| | - Andrea Peirano
- Marine Environment Research Centre, ENEA, La Spezia, Italy
| | - Denis Allemand
- Centre Scientifique de Monaco, 8 Quai Antoine 1er, 98000, Monaco, Monaco
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Shiu JH, Keshavmurthy S, Chiang PW, Chen HJ, Lou SP, Tseng CH, Justin Hsieh H, Allen Chen C, Tang SL. Dynamics of coral-associated bacterial communities acclimated to temperature stress based on recent thermal history. Sci Rep 2017; 7:14933. [PMID: 29097716 PMCID: PMC5668310 DOI: 10.1038/s41598-017-14927-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 10/13/2017] [Indexed: 11/08/2022] Open
Abstract
Seasonal variation in temperature fluctuations may provide corals and their algal symbionts varying abilities to acclimate to changing temperatures. We hypothesized that different temperature ranges between seasons may promote temperature-tolerance of corals, which would increase stability of a bacterial community following thermal stress. Acropora muricata coral colonies were collected in summer and winter (water temperatures were 23.4-30.2 and 12.1-23.1 °C, respectively) from the Penghu Archipelago in Taiwan, then exposed to 6 temperature treatments (10-33 °C). Changes in coral-associated bacteria were determined after 12, 24, and 48 h. Based on 16S rRNA gene amplicons and Illumina sequencing, bacterial communities differed between seasons and treatments altered the dominant bacteria. Cold stress caused slower shifts in the bacterial community in winter than in summer, whereas a more rapid shift occurred under heat stress in both seasons. Results supported our hypothesis that bacterial community composition of corals in winter are more stable in cold temperatures but changed rapidly in hot temperatures, with opposite results for the bacterial communities in summer. We infer that the thermal tolerance ranges of coral-associated bacteria, with a stable community composition, are associated with their short-term (3 mo) seawater thermal history. Therefore, seasonal acclimation may increase tolerance of coral-associated bacteria to temperature fluctuations.
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Affiliation(s)
- Jia-Ho Shiu
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan, and National Chung-Hsing University, Taichung, Taiwan
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung, Taiwan
| | | | - Pei-Wen Chiang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Hsing-Ju Chen
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Shueh-Ping Lou
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | | | - Hernyi Justin Hsieh
- Penghu Marine Biology Research Center, Fishery Research Institute, Council of Agriculture, Magong, Penghu, 880, Taiwan
| | | | - Sen-Lin Tang
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan, and National Chung-Hsing University, Taichung, Taiwan.
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.
- Biotechnology Center, National Chung-Hsing University, Taichung, Taiwan.
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38
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Woo S, Yang SH, Chen HJ, Tseng YF, Hwang SJ, De Palmas S, Denis V, Imahara Y, Iwase F, Yum S, Tang SL. Geographical variations in bacterial communities associated with soft coral Scleronephthya gracillimum. PLoS One 2017; 12:e0183663. [PMID: 28859111 PMCID: PMC5578639 DOI: 10.1371/journal.pone.0183663] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 08/08/2017] [Indexed: 01/17/2023] Open
Abstract
Environmental impacts can alter relationships between a coral and its symbiotic microbial community. Furthermore, changes in the microbial community associated with increased seawater temperatures can cause opportunistic infections, coral disease and death. Interactions between soft corals and their associated microbes are not well understood. The species Scleronephthya gracillimum is distributed in tropical to temperate zones in coral assemblages along the Kuroshio Current region. In this study we collected S. gracillimum from various sites at different latitudes, and compared composition of their bacterial communities using Next Generation Sequencing. Coral samples from six geographically distinct areas (two sites each in Taiwan, Japan, and Korea) had considerable variation in their associated bacterial communities and diversity. Endozoicimonaceae was the dominant group in corals from Korea and Japan, whereas Mycoplasma was dominant in corals from Taiwan corals. Interestingly, the latter corals had lower relative abundance of Endozoicimonaceae, but greater diversity. These biogeographic differences in bacterial composition may have been due to varying environmental conditions among study locations, or because of host responses to prevailing environmental conditions. This study provided a baseline for future studies of soft coral microbiomes, and assessment of functions of host metabolites and soft coral holobionts.
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Affiliation(s)
- Seonock Woo
- Korea Institute of Ocean Science & Technology, Geoje, Republic of Korea
- Faculty of Marine Environmental Science, University of Science and Technology (UST), Geoje, Republic of Korea
| | - Shan-Hua Yang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Hsing-Ju Chen
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Yu-Fang Tseng
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Sung-Jin Hwang
- Department of Eco-Biological Science, Woosuk University, Jincheon, Republic of Korea
| | - Stephane De Palmas
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Vianney Denis
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan
| | - Yukimitsu Imahara
- Wakayama Laboratory, Biological Institute on Kuroshio, Wakayama City, Wakayama, Japan
| | - Fumihito Iwase
- Shikoku Marine Life Laboratory, Otsuki-Town, Kochi, Japan
| | - Seungshic Yum
- Korea Institute of Ocean Science & Technology, Geoje, Republic of Korea
- Faculty of Marine Environmental Science, University of Science and Technology (UST), Geoje, Republic of Korea
| | - Sen-Lin Tang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- * E-mail:
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39
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Metagenomic analysis reveals a green sulfur bacterium as a potential coral symbiont. Sci Rep 2017; 7:9320. [PMID: 28839161 PMCID: PMC5571212 DOI: 10.1038/s41598-017-09032-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 07/20/2017] [Indexed: 01/27/2023] Open
Abstract
Coral reefs are ecologically significant habitats. Coral-algal symbiosis confers ecological success on coral reefs and coral-microbial symbiosis is also vital to coral reefs. However, current understanding of coral-microbial symbiosis on a genomic scale is largely unknown. Here we report a potential microbial symbiont in corals revealed by metagenomics-based genomic study. Microbial cells in coral were enriched for metagenomic analysis and a high-quality draft genome of “Candidatus Prosthecochloris korallensis” was recovered by metagenome assembly and genome binning. Phylogenetic analysis shows “Ca. P. korallensis” belongs to the Prosthecochloris clade and is clustered with two Prosthecochloris clones derived from Caribbean corals. Genomic analysis reveals “Ca. P. korallensis” has potentially important ecological functions including anoxygenic photosynthesis, carbon fixation via the reductive tricarboxylic acid (rTCA) cycle, nitrogen fixation, and sulfur oxidization. Core metabolic pathway analysis suggests “Ca. P. korallensis” is a green sulfur bacterium capable of photoautotrophy or mixotrophy. Potential host-microbial interaction reveals a symbiotic relationship: “Ca. P. korallensis” might provide organic and nitrogenous nutrients to its host and detoxify sulfide for the host; the host might provide “Ca. P. korallensis” with an anaerobic environment for survival, carbon dioxide and acetate for growth, and hydrogen sulfide as an electron donor for photosynthesis.
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40
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Yang SH, Tseng CH, Huang CR, Chen CP, Tandon K, Lee STM, Chiang PW, Shiu JH, Chen CA, Tang SL. Long-Term Survey Is Necessary to Reveal Various Shifts of Microbial Composition in Corals. Front Microbiol 2017; 8:1094. [PMID: 28659905 PMCID: PMC5468432 DOI: 10.3389/fmicb.2017.01094] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 05/30/2017] [Indexed: 11/13/2022] Open
Abstract
The coral holobiont is the assemblage of coral host and its microbial symbionts, which functions as a unit and is responsive to host species and environmental factors. Although monitoring surveys have been done to determine bacteria associated with coral, none have persisted for >1 year. Therefore, potential variations in minor or dominant community members that occur over extended intervals have not been characterized. In this study, 16S rRNA gene amplicon pyrosequencing was used to investigate the relationship between bacterial communities in healthy Stylophora pistillata in tropical and subtropical Taiwan over 2 years, apparently one of the longest surveys of coral-associated microbes. Dominant bacterial genera in S. pistillata had disparate changes in different geographical setups, whereas the constitution of minor bacteria fluctuated in abundance over time. We concluded that dominant bacteria (Acinetobacter, Propionibacterium, and Pseudomonas) were stable in composition, regardless of seasonal and geographical variations, whereas Endozoicomonas had a geographical preference. In addition, by combining current data with previous studies, we concluded that a minor bacteria symbiont, Ralstonia, was a keystone species in coral. Finally, we concluded that long-term surveys for coral microbial communities were necessary to detect compositional shifts, especially for minor bacterial members in corals.
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Affiliation(s)
- Shan-Hua Yang
- Biodiversity Research Center, Academia SinicaTaipei, Taiwan
| | | | | | | | - Kshitij Tandon
- Biodiversity Research Center, Academia SinicaTaipei, Taiwan.,Bioinformatics Program, Institute of Information Science, Taiwan International Graduate Program, Academia SinicaTaipei, Taiwan.,Institute of Bioinformatics and Structural Biology, National Tsing Hua UniversityHsinchu, Taiwan
| | - Sonny T M Lee
- Section of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Chicago Medicine, ChicagoIL, United States
| | - Pei-Wen Chiang
- Biodiversity Research Center, Academia SinicaTaipei, Taiwan
| | - Jia-Ho Shiu
- Biodiversity Research Center, Academia SinicaTaipei, Taiwan.,Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia SinicaTaipei, Taiwan.,Graduate Institute of Biotechnology, National Chung Hsing UniversityTaichung, Taiwan
| | - Chaolun A Chen
- Biodiversity Research Center, Academia SinicaTaipei, Taiwan
| | - Sen-Lin Tang
- Biodiversity Research Center, Academia SinicaTaipei, Taiwan
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41
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Liang J, Yu K, Wang Y, Huang X, Huang W, Qin Z, Pan Z, Yao Q, Wang W, Wu Z. Distinct Bacterial Communities Associated with Massive and Branching Scleractinian Corals and Potential Linkages to Coral Susceptibility to Thermal or Cold Stress. Front Microbiol 2017. [PMID: 28642738 PMCID: PMC5462945 DOI: 10.3389/fmicb.2017.00979] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
It is well known that different coral species have different tolerances to thermal or cold stress, which is presumed to be related to the density of Symbiodinium. However, the intrinsic factors between stress-tolerant characteristics and coral-associated bacteria are rarely studied. In this study, 16 massive coral and 9 branching coral colonies from 6 families, 10 genera, and 18 species were collected at the same time and location (Xinyi Reef) in the South China Sea to investigate the bacterial communities. The results of an alpha diversity analysis showed that bacterial diversities associated with massive corals were generally higher than those with branching corals at different taxonomic levels (phylum, class, order, and so on). In addition, hierarchical clustering tree and PCoA analyses showed that coral species were clustered into two large groups according to the similarity of bacterial communities. Group I consisted of massive Goniastrea, Plesiastrea, Leptastrea, Platygyra, Echinopora, Porites, and Leptoria, and group II consisted of branching Acropora and Pocillopora. These findings suggested that both massive corals and branching corals have their own preference for the choice of associated bacteria, which may be involved in observed differences in thermal/cold tolerances. Further analysis found that 55 bacterial phyla, including 43 formally described phyla and 12 candidate phyla, were detected in these coral species. Among them, 52 phyla were recovered from the massive coral group, and 46 phyla were recovered from the branching coral group. Formally described coral pathogens have not been detected in these coral species, suggesting that they are less likely to be threatened by disease in this geographic area. This study highlights a clear relationship between the high complexity of bacterial community associated with coral, skeletal morphology of coral and potentially tolerances to thermal or cold stress.
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Affiliation(s)
- Jiayuan Liang
- Coral Reef Research Center of China, Guangxi UniversityNanning, China.,Guangxi Laboratory on the Study of Coral Reefs in the South China SeaNanning, China.,School of Marine Sciences, Guangxi UniversityNanning, China
| | - Kefu Yu
- Coral Reef Research Center of China, Guangxi UniversityNanning, China.,Guangxi Laboratory on the Study of Coral Reefs in the South China SeaNanning, China.,School of Marine Sciences, Guangxi UniversityNanning, China
| | - Yinghui Wang
- Coral Reef Research Center of China, Guangxi UniversityNanning, China.,Guangxi Laboratory on the Study of Coral Reefs in the South China SeaNanning, China.,School of Marine Sciences, Guangxi UniversityNanning, China
| | - Xueyong Huang
- Coral Reef Research Center of China, Guangxi UniversityNanning, China.,Guangxi Laboratory on the Study of Coral Reefs in the South China SeaNanning, China.,School of Marine Sciences, Guangxi UniversityNanning, China
| | - Wen Huang
- Coral Reef Research Center of China, Guangxi UniversityNanning, China.,Guangxi Laboratory on the Study of Coral Reefs in the South China SeaNanning, China.,School of Marine Sciences, Guangxi UniversityNanning, China
| | - Zhenjun Qin
- Coral Reef Research Center of China, Guangxi UniversityNanning, China.,Guangxi Laboratory on the Study of Coral Reefs in the South China SeaNanning, China.,School of Marine Sciences, Guangxi UniversityNanning, China
| | - Ziliang Pan
- Coral Reef Research Center of China, Guangxi UniversityNanning, China.,Guangxi Laboratory on the Study of Coral Reefs in the South China SeaNanning, China.,School of Marine Sciences, Guangxi UniversityNanning, China
| | - Qiucui Yao
- Coral Reef Research Center of China, Guangxi UniversityNanning, China.,Guangxi Laboratory on the Study of Coral Reefs in the South China SeaNanning, China.,School of Marine Sciences, Guangxi UniversityNanning, China
| | - Wenhuan Wang
- Coral Reef Research Center of China, Guangxi UniversityNanning, China.,Guangxi Laboratory on the Study of Coral Reefs in the South China SeaNanning, China.,School of Marine Sciences, Guangxi UniversityNanning, China
| | - Zhengchao Wu
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of SciencesGuangzhou, China
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Water flow buffers shifts in bacterial community structure in heat-stressed Acropora muricata. Sci Rep 2017; 7:43600. [PMID: 28240318 PMCID: PMC5327421 DOI: 10.1038/srep43600] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 01/25/2017] [Indexed: 11/16/2022] Open
Abstract
Deterioration of coral health and associated change in the coral holobiont’s bacterial community are often a result of different environmental stressors acting synergistically. There is evidence that water flow is important for a coral’s resistance to elevated seawater temperature, but there is no information on how water flow affects the coral-associated bacterial community under these conditions. In a laboratory cross-design experiment, Acropora muricata nubbins were subjected to interactive effects of seawater temperature (27 °C to 31 °C) and water flow (0.20 m s−1 and 0.03 m s−1). In an in situ experiment, water flow manipulation was conducted with three colonies of A. muricata during the winter and summer, by partially enclosing each colony in a clear plastic mesh box. 16S rRNA amplicon pyrosequencing showed an increase in the relative abundance of Flavobacteriales and Rhodobacterales in the laboratory experiment, and Vibrio spp. in the in situ experiment when corals were exposed to elevated temperature and slow water flow. In contrast, corals that were exposed to faster water flow under laboratory and in situ conditions had a stable bacterial community. These findings indicate that water flow plays an important role in the maintenance of specific coral-bacteria associations during times of elevated thermal stress.
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43
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Hernandez-Agreda A, Gates RD, Ainsworth TD. Defining the Core Microbiome in Corals’ Microbial Soup. Trends Microbiol 2017; 25:125-140. [DOI: 10.1016/j.tim.2016.11.003] [Citation(s) in RCA: 150] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 10/21/2016] [Accepted: 11/02/2016] [Indexed: 02/07/2023]
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Zhang Y, Yang Q, Ling J, Van Nostrand JD, Shi Z, Zhou J, Dong J. The Shifts of Diazotrophic Communities in Spring and Summer Associated with Coral Galaxea astreata, Pavona decussata, and Porites lutea. Front Microbiol 2016; 7:1870. [PMID: 27920768 PMCID: PMC5118425 DOI: 10.3389/fmicb.2016.01870] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 11/07/2016] [Indexed: 11/13/2022] Open
Abstract
The coral holobiont often resides in oligotrophic waters; both coral cells and their symbiotic dinoflagellates possess ammonium assimilation enzymes and potentially benefit from the nitrogen fixation of coral-associated diazotrophs. However, the seasonal dynamics of coral-associated diazotrophs are not well characterized. Here, the seasonal variations of diazotrophic communities associated with three corals, Galaxea astreata, Pavona decussata, and Porites lutea, were studied using nifH gene amplicon pyrosequencing techniques. Our results revealed a great diversity of coral-associated diazotrophs. nifH sequences related to Alphaproteobacteria, Deltaproteobacteria, and Gammaproteobacteria were ubiquitous and dominant in all corals in two seasons. In contrast with the coral P. decussata, both G. astreata and P. lutea showed significant seasonal changes in the diazotrophic communities and nifH gene abundance. Variable diazotroph groups accounted for a range from 11 to 49% within individual coral samples. Most of the variable diazotrophic groups from P. decussata were species-specific, however, the majority of overlapping variable groups in G. astreata and P. lutea showed the same seasonal variation characteristics. Rhodopseudomonas palustris- and Gluconacetobacter diazotrophicus-affiliated sequences were relatively abundant in the summer, whereas a nifH sequence related to Halorhodospira halophila was relatively abundant in spring G. astreata and P. lutea. The seasonal variations of all diazotrophic communities were significantly correlated with the seasonal shifts of ammonium and nitrate, suggesting that diazotrophs play an important role in the nitrogen cycle of the coral holobiont.
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Affiliation(s)
- Yanying Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of SciencesGuangzhou, China; Tropical Marine Biological Research Station in Hainan, South China Sea Institute of Oceanology, Chinese Academy of SciencesSanya, China; Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, NormanOK, USA
| | - Qingsong Yang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou, China
| | - Juan Ling
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou, China
| | - Joy D Van Nostrand
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman OK, USA
| | - Zhou Shi
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman OK, USA
| | - Jizhong Zhou
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman OK, USA
| | - Junde Dong
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of SciencesGuangzhou, China; Tropical Marine Biological Research Station in Hainan, South China Sea Institute of Oceanology, Chinese Academy of SciencesSanya, China
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Hernández-Zulueta J, Araya R, Vargas-Ponce O, Díaz-Pérez L, Rodríguez-Troncoso AP, Ceh J, Ríos-Jara E, Rodríguez-Zaragoza FA. First deep screening of bacterial assemblages associated with corals of the Tropical Eastern Pacific. FEMS Microbiol Ecol 2016; 92:fiw196. [DOI: 10.1093/femsec/fiw196] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/11/2016] [Indexed: 11/12/2022] Open
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46
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Bacterial Community Associated with Organs of Shallow Hydrothermal Vent Crab Xenograpsus testudinatus near Kuishan Island, Taiwan. PLoS One 2016; 11:e0150597. [PMID: 26934591 PMCID: PMC4774926 DOI: 10.1371/journal.pone.0150597] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 02/16/2016] [Indexed: 01/21/2023] Open
Abstract
Shallow-water hydrothermal vents off Kueishan Island (northeastern Taiwan) provide a unique, sulfur-rich, highly acidic (pH 1.75-4.6) and variable-temperature environment. In this species-poor habitat, the crab Xenograpsus testudinatus is dominant, as it mainly feeds on zooplankton killed by sulfurous plumes. In this study, 16S ribosomal RNA gene amplicon pyrosequencing was used to investigate diversity and composition of bacteria residing in digestive gland, gill, stomach, heart, and mid-gut of X. testudinatus, as well as in surrounding seawater. Dominant bacteria were Gamma- and Epsilonproteobacteria that might be capable of autotrophic growth by oxidizing reduced sulfur compounds and are usually resident in deep-sea hydrothermal systems. Dominant bacterial OTUs in X. testudinatus had both host and potential organ specificities, consistent with a potential trophic symbiotic relationship (nutrient transfer between host and bacteria). We inferred that versatile ways to obtain nutrients may provide an adaptive advantage for X. testudinatus in this demanding environment. To our knowledge, this is the first study of bacterial communities in various organs/tissues of a crustacean in a shallow-water hydrothermal system, and as such, may be a convenient animal model for studying these systems.
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Baatar B, Chiang PW, Rogozin DY, Wu YT, Tseng CH, Yang CY, Chiu HH, Oyuntsetseg B, Degermendzhy AG, Tang SL. Bacterial Communities of Three Saline Meromictic Lakes in Central Asia. PLoS One 2016; 11:e0150847. [PMID: 26934492 PMCID: PMC4775032 DOI: 10.1371/journal.pone.0150847] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 02/19/2016] [Indexed: 12/20/2022] Open
Abstract
Meromictic lakes located in landlocked steppes of central Asia (~2500 km inland) have unique geophysiochemical characteristics compared to other meromictic lakes. To characterize their bacteria and elucidate relationships between those bacteria and surrounding environments, water samples were collected from three saline meromictic lakes (Lakes Shira, Shunet and Oigon) in the border between Siberia and the West Mongolia, near the center of Asia. Based on in-depth tag pyrosequencing, bacterial communities were highly variable and dissimilar among lakes and between oxic and anoxic layers within individual lakes. Proteobacteria, Bacteroidetes, Cyanobacteria, Actinobacteria and Firmicutes were the most abundant phyla, whereas three genera of purple sulfur bacteria (a novel genus, Thiocapsa and Halochromatium) were predominant bacterial components in the anoxic layer of Lake Shira (~20.6% of relative abundance), Lake Shunet (~27.1%) and Lake Oigon (~9.25%), respectively. However, few known green sulfur bacteria were detected. Notably, 3.94% of all sequencing reads were classified into 19 candidate divisions, which was especially high (23.12%) in the anoxic layer of Lake Shunet. Furthermore, several hydro-parameters (temperature, pH, dissolved oxygen, H2S and salinity) were associated (P< 0.05) with variations in dominant bacterial groups. In conclusion, based on highly variable bacterial composition in water layers or lakes, we inferred that the meromictic ecosystem was characterized by high diversity and heterogenous niches.
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Affiliation(s)
- Bayanmunkh Baatar
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung, Taiwan
| | - Pei-Wen Chiang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | | | - Yu-Ting Wu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- National Pingtung University of Science and Technology, Pingtung, Taiwan
| | | | - Cheng-Yu Yang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Hsiu-Hui Chiu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Bolormaa Oyuntsetseg
- School of Art and Sciences, National University of Mongolia, Ulaanbaatar 14201, Mongolia
| | | | - Sen-Lin Tang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Biotechnology Center, National Chung-Hsing University, Taichung, Taiwan
- * E-mail:
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48
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Webster NS, Negri AP, Botté ES, Laffy PW, Flores F, Noonan S, Schmidt C, Uthicke S. Host-associated coral reef microbes respond to the cumulative pressures of ocean warming and ocean acidification. Sci Rep 2016; 6:19324. [PMID: 26758800 PMCID: PMC4725835 DOI: 10.1038/srep19324] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 12/11/2015] [Indexed: 12/20/2022] Open
Abstract
Key calcifying reef taxa are currently threatened by thermal stress associated with elevated sea surface temperatures (SST) and reduced calcification linked to ocean acidification (OA). Here we undertook an 8 week experimental exposure to near-future climate change conditions and explored the microbiome response of the corals Acropora millepora and Seriatopora hystrix, the crustose coralline algae Hydrolithon onkodes, the foraminifera Marginopora vertebralis and Heterostegina depressa and the sea urchin Echinometra sp. Microbial communities of all taxa were tolerant of elevated pCO2/reduced pH, exhibiting stable microbial communities between pH 8.1 (pCO2 479–499 μatm) and pH 7.9 (pCO2 738–835 μatm). In contrast, microbial communities of the CCA and foraminifera were sensitive to elevated seawater temperature, with a significant microbial shift involving loss of specific taxa and appearance of novel microbial groups occurring between 28 and 31 °C. An interactive effect between stressors was also identified, with distinct communities developing under different pCO2 conditions only evident at 31 °C. Microbiome analysis of key calcifying coral reef species under near-future climate conditions highlights the importance of assessing impacts from both increased SST and OA, as combinations of these global stressors can amplify microbial shifts which may have concomitant impacts for coral reef structure and function.
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Affiliation(s)
- N S Webster
- Australian Institute of Marine Science, Townsville Qld Australia
| | - A P Negri
- Australian Institute of Marine Science, Townsville Qld Australia
| | - E S Botté
- Australian Institute of Marine Science, Townsville Qld Australia
| | - P W Laffy
- Australian Institute of Marine Science, Townsville Qld Australia
| | - F Flores
- Australian Institute of Marine Science, Townsville Qld Australia
| | - S Noonan
- Australian Institute of Marine Science, Townsville Qld Australia
| | - C Schmidt
- Australian Institute of Marine Science, Townsville Qld Australia
| | - S Uthicke
- Australian Institute of Marine Science, Townsville Qld Australia
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Stable and sporadic symbiotic communities of coral and algal holobionts. ISME JOURNAL 2015; 10:1157-69. [PMID: 26555246 PMCID: PMC5029208 DOI: 10.1038/ismej.2015.190] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 09/09/2015] [Accepted: 09/22/2015] [Indexed: 12/26/2022]
Abstract
Coral and algal holobionts are assemblages of macroorganisms and microorganisms, including viruses, Bacteria, Archaea, protists and fungi. Despite a decade of research, it remains unclear whether these associations are spatial–temporally stable or species-specific. We hypothesized that conflicting interpretations of the data arise from high noise associated with sporadic microbial symbionts overwhelming signatures of stable holobiont members. To test this hypothesis, the bacterial communities associated with three coral species (Acropora rosaria, Acropora hyacinthus and Porites lutea) and two algal guilds (crustose coralline algae and turf algae) from 131 samples were analyzed using a novel statistical approach termed the Abundance-Ubiquity (AU) test. The AU test determines whether a given bacterial species would be present given additional sampling effort (that is, stable) versus those species that are sporadically associated with a sample. Using the AU test, we show that coral and algal holobionts have a high-diversity group of stable symbionts. Stable symbionts are not exclusive to one species of coral or algae. No single bacterial species was ubiquitously associated with one host, showing that there is not strict heredity of the microbiome. In addition to the stable symbionts, there was a low-diversity community of sporadic symbionts whose abundance varied widely across individual holobionts of the same species. Identification of these two symbiont communities supports the holobiont model and calls into question the hologenome theory of evolution.
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50
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The functional gene composition and metabolic potential of coral-associated microbial communities. Sci Rep 2015; 5:16191. [PMID: 26536917 PMCID: PMC4633650 DOI: 10.1038/srep16191] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 10/12/2015] [Indexed: 11/24/2022] Open
Abstract
The phylogenetic diversity of coral-associated microbes has been extensively examined, but some contention remains regarding whether coral-associated microbial communities are species-specific or site-specific. It is suggested that corals may associate with microbes in terms of function, although little is known about the differences in coral-associated microbial functional gene composition and metabolic potential among coral species. Here, 16S rRNA Illumina sequencing and functional gene array (GeoChip 5.0) were used to assess coral-associated microbial communities. Our results indicate that both host species and environmental variables significantly correlate with shifts in the microbial community structure and functional potential. Functional genes related to key biogeochemical cycles including carbon, nitrogen, sulfur and phosphorus cycling, metal homeostasis, organic remediation, antibiotic resistance and secondary metabolism were shown to significantly vary between and among the four study corals (Galaxea astreata, Porites lutea, Porites andrewsi and Pavona decussata). Genes specific for anammox were also detected for the first time in the coral holobiont and positively correlated with ammonium. This study reveals that variability in the functional potential of coral-associated microbial communities is largely driven by changes in environmental factors and further demonstrates the importance of linking environmental parameters with genomic data in complex environmental systems.
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