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Reigel AM, Easson CG, Apprill A, Freeman CJ, Bartley MM, Fiore CL. Sponge-derived matter is assimilated by coral holobionts. Commun Biol 2024; 7:146. [PMID: 38308082 PMCID: PMC10837432 DOI: 10.1038/s42003-024-05836-z] [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: 03/20/2023] [Accepted: 01/19/2024] [Indexed: 02/04/2024] Open
Abstract
Coral reef biodiversity is maintained by a complex network of nutrient recycling among organisms. Sponges assimilate nutrients produced by other organisms like coral and algae, releasing them as particulate and dissolved matter, but to date, only a single trophic link between sponge-derived dissolved matter and a macroalgae has been identified. We sought to determine if sponge-coral nutrient exchange is reciprocal using a stable isotope 'pulse-chase' experiment to trace the uptake of 13C and 15N sponge-derived matter by the coral holobiont for three coral species (Acropora cervicornis, Orbicella faveolata, and Eunicea flexuosa). Coral holobionts incorporated 2.3-26.8x more 15N than 13C from sponge-derived matter and A. cervicornis incorporated more of both C and N than the other corals. Differential isotopic incorporation among coral species aligns with their ecophysiological characteristics (e.g., morphology, Symbiodiniaceae density). Our results elucidate a recycling pathway on coral reefs that has implications for improving coral aquaculture and management approaches.
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Affiliation(s)
| | - Cole G Easson
- Middle Tennessee State University, Murfreesboro, TN, USA
| | - Amy Apprill
- Woods Hole Oceanographic Institution, Woods Hole, RI, USA
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Chiou YJ, Chan YF, Yu SP, Lu CY, Hsiao SSY, Chiang PW, Hsu TC, Liu PY, Wada N, Lee Y, Jane WN, Lee DC, Huang YW, Tang SL. Similar but different: Characterization of dddD gene-mediated DMSP metabolism among coral-associated Endozoicomonas. SCIENCE ADVANCES 2023; 9:eadk1910. [PMID: 37992165 PMCID: PMC10664990 DOI: 10.1126/sciadv.adk1910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 10/20/2023] [Indexed: 11/24/2023]
Abstract
Endozoicomonas are often predominant bacteria and prominently important in coral health. Their role in dimethylsulfoniopropionate (DMSP) degradation has been a subject of discussion for over a decade. A previous study found that Endozoicomonas degraded DMSP through the dddD pathway. This process releases dimethyl sulfide, which is vital for corals coping with thermal stress. However, little is known about the related gene regulation and metabolic abilities of DMSP metabolism in Endozoicomonadaceae. In this study, we isolated a novel Endozoicomonas DMSP degrader and observed a distinct DMSP metabolic trend in two phylogenetically close dddD-harboring Endozoicomonas species, confirmed genetically by comparative transcriptomic profiling and visualization of the change of DMSP stable isotopes in bacterial cells using nanoscale secondary ion spectrometry. Furthermore, we found that DMSP cleavage enzymes are ubiquitous in coral Endozoicomonas with a preference for having DddD lyase. We speculate that harboring DMSP degrading genes enables Endozoicomonas to successfully colonize various coral species across the globe.
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Affiliation(s)
- Yu-Jing Chiou
- Institute of Oceanography, National Taiwan University, Taipei 106, Taiwan
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Ya-Fan Chan
- Department of Microbiology, Soochow University, Taipei 111, Taiwan
| | - Sheng-Ping Yu
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - 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
| | | | - Pei-Wen Chiang
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Ting-Chang Hsu
- 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
| | - Naohisa Wada
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yu Lee
- Department of Chemistry, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Wann-Neng Jane
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115, Taiwan
| | - Der-Chuen Lee
- Institute of Astronomy and Astrophysics, Academia Sinica, Taipei 115, Taiwan
| | - Yu-Wen Huang
- Department of Chemistry, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Sen-Lin Tang
- Institute of Oceanography, National Taiwan University, Taipei 106, Taiwan
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
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3
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Rodríguez-Barreras R, Dominicci-Maura A, Tosado-Rodríguez EL, Godoy-Vitorino F. The Epibiotic Microbiota of Wild Caribbean Sea Urchin Spines Is Species Specific. Microorganisms 2023; 11:391. [PMID: 36838357 PMCID: PMC9966300 DOI: 10.3390/microorganisms11020391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 02/05/2023] Open
Abstract
Caribbean sea urchins are marine invertebrates that have experienced a decline over the years. Studies on sea urchins have focused primarily on the microbiome of the coelomic fluid or the gut microbiota. In this study, the epibiota community associated with four wild Caribbean sea urchin species, Lytechinus variegatus, Echinometra lucunter, Tripneustes ventricosus, and Diadema antillarum, was characterized for the first time. Using 57 sea urchin animal samples, we evaluated the influence of animal species, trophic niches, and geographical location on the composition of the epibiotic microbiota. We found significant differences in the bacterial biota among species and trophic niches, but not among geographical locations. L. variegatus exhibited the highest alpha diversity with high dominance of Fusobacteria, Planctomycetes, and Cyanobacteria, whereas T. ventricosus and D. antillarum were dominated by Firmicutes. T. ventricosus inhabiting the seagrass biotope dominated by Thalassia testudinum meadows had mostly Endozoicomonas. In contrast, samples located in the reef (dominated by corals and other reef builders) had a higher abundance of Kistimonas and Photobacterium. Our findings confirm that the epibiotic microbiota is species-specific, but also niche-dependent, revealing the trophic networks emerging from the organic matter being recycled in the seagrass and reef niches. As echinoids are important grazers of benthic communities, their microbiota will likely influence ecosystem processes.
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Affiliation(s)
- Ruber Rodríguez-Barreras
- Department of Biology, University of Puerto Rico, Mayagüez Campus, P.O. Box 9000, Mayagüez 00681-9000, Puerto Rico
| | - Anelisse Dominicci-Maura
- Department of Microbiology, University of Puerto Rico School of Medicine, Guillermo Arbona Main Building, San Juan 00936-5067, Puerto Rico
| | - Eduardo L. Tosado-Rodríguez
- Department of Microbiology, University of Puerto Rico School of Medicine, Guillermo Arbona Main Building, San Juan 00936-5067, Puerto Rico
| | - Filipa Godoy-Vitorino
- Department of Microbiology, University of Puerto Rico School of Medicine, Guillermo Arbona Main Building, San Juan 00936-5067, Puerto Rico
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Ide K, Nishikawa Y, Maruyama T, Tsukada Y, Kogawa M, Takeda H, Ito H, Wagatsuma R, Miyaoka R, Nakano Y, Kinjo K, Ito M, Hosokawa M, Yura K, Suda S, Takeyama H. Targeted single-cell genomics reveals novel host adaptation strategies of the symbiotic bacteria Endozoicomonas in Acropora tenuis coral. MICROBIOME 2022; 10:220. [PMID: 36503599 PMCID: PMC9743535 DOI: 10.1186/s40168-022-01395-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 10/13/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Endozoicomonas bacteria symbiosis with various marine organisms is hypothesized as a potential indicator of health in corals. Although many amplicon analyses using 16S rRNA gene have suggested the diversity of Endozoicomonas species, genome analysis has been limited due to contamination of host-derived sequences and difficulties in culture and metagenomic analysis. Therefore, the evolutionary and functional potential of individual Endozoicomonas species symbiotic with the same coral species remains unresolved. RESULTS In this study, we applied a novel single-cell genomics technique using droplet microfluidics to obtain single-cell amplified genomes (SAGs) for uncultured coral-associated Endozoicomonas spp. We obtained seven novel Endozoicomonas genomes and quantitative bacterial composition from Acropora tenuis corals at four sites in Japan. Our quantitative 16S rRNA gene and comparative genomic analysis revealed that these Endozoicomonas spp. belong to different lineages (Clade A and Clade B), with widely varying abundance among individual corals. Furthermore, each Endozoicomonas species possessed various eukaryotic-like genes in clade-specific genes. It was suggested that these eukaryotic-like genes might have a potential ability of different functions in each clade, such as infection of the host coral or suppression of host immune pathways. These Endozoicomonas species may have adopted different host adaptation strategies despite living symbiotically on the same coral. CONCLUSIONS This study suggests that coral-associated Endozoicomonas spp. on the same species of coral have different evolutional strategies and functional potentials in each species and emphasizes the need to analyze the genome of each uncultured strain in future coral-Endozoicomonas relationships studies. Video Abstract.
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Affiliation(s)
- Keigo Ide
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
- Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan
| | - Yohei Nishikawa
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
- Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan
| | - Toru Maruyama
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Yuko Tsukada
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Masato Kogawa
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
- Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan
| | - Hiroki Takeda
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Haruka Ito
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Ryota Wagatsuma
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Rimi Miyaoka
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Yoshikatsu Nakano
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
- Marine Science Section, Research Support Division, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | | | - Michihiro Ito
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Masahito Hosokawa
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
- Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Tokyo, Japan
| | - Kei Yura
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
- Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan
- Graduate School of Humanities and Sciences, Ochanomizu University, Tokyo, Japan
| | - Shoichiro Suda
- Faculty of Science, University of the Ryukyus, Okinawa, Japan
| | - Haruko Takeyama
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan.
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, Tokyo, Japan.
- Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan.
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Tokyo, Japan.
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Coral holobiont cues prime Endozoicomonas for a symbiotic lifestyle. THE ISME JOURNAL 2022; 16:1883-1895. [PMID: 35444262 PMCID: PMC9296628 DOI: 10.1038/s41396-022-01226-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 02/23/2022] [Accepted: 03/14/2022] [Indexed: 12/11/2022]
Abstract
Endozoicomonas are prevalent, abundant bacterial associates of marine animals, including corals. Their role in holobiont health and functioning, however, remains poorly understood. To identify potential interactions within the coral holobiont, we characterized the novel isolate Endozoicomonas marisrubri sp. nov. 6c and assessed its transcriptomic and proteomic response to tissue extracts of its native host, the Red Sea coral Acropora humilis. We show that coral tissue extracts stimulated differential expression of genes putatively involved in symbiosis establishment via the modulation of the host immune response by E. marisrubri 6c, such as genes for flagellar assembly, ankyrins, ephrins, and serpins. Proteome analyses revealed that E. marisrubri 6c upregulated vitamin B1 and B6 biosynthesis and glycolytic processes in response to holobiont cues. Our results suggest that the priming of Endozoicomonas for a symbiotic lifestyle involves the modulation of host immunity and the exchange of essential metabolites with other holobiont members. Consequently, Endozoicomonas may play an important role in holobiont nutrient cycling and may therefore contribute to coral health, acclimatization, and adaptation.
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Cowen LJ, Putnam HM. Bioinformatics of Corals: Investigating Heterogeneous Omics Data from Coral Holobionts for Insight into Reef Health and Resilience. Annu Rev Biomed Data Sci 2022; 5:205-231. [PMID: 35537462 DOI: 10.1146/annurev-biodatasci-122120-030732] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Coral reefs are home to over two million species and provide habitat for roughly 25% of all marine animals, but they are being severely threatened by pollution and climate change. A large amount of genomic, transcriptomic, and other omics data is becoming increasingly available from different species of reef-building corals, the unicellular dinoflagellates, and the coral microbiome (bacteria, archaea, viruses, fungi, etc.). Such new data present an opportunity for bioinformatics researchers and computational biologists to contribute to a timely, compelling, and urgent investigation of critical factors that influence reef health and resilience. Expected final online publication date for the Annual Review of Biomedical Data Science, Volume 5 is August 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Lenore J Cowen
- Department of Computer Science, Tufts University, Medford, Massachusetts, USA;
| | - Hollie M Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, USA;
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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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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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Bennion M, Ross P, Howells J, McDonald IR, Lane H. Characterisation and distribution of the bacterial genus Endozoicomonas in a threatened surf clam. DISEASES OF AQUATIC ORGANISMS 2021; 146:91-105. [PMID: 34617515 DOI: 10.3354/dao03626] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The toheroa Paphies ventricosa is a large Aotearoa New Zealand (ANZ) endemic surf clam of cultural importance to many Māori, the Indigenous people of ANZ. Extensive commercial and recreational harvesting in the 20th century dramatically reduced populations, leading to the collapse and closure of the fishery. Despite being protected for >40 yr, toheroa have inexplicably failed to recover. In 2017, intracellular microcolonies (IMCs) of bacteria were detected in 'sick' toheroa in northern ANZ. Numerous mass mortality events (MMEs) have recently been recorded in ANZ shellfish, with many events linked by the presence of IMCs resembling Rickettsia-like organisms (RLOs). While similar IMCs have been implicated in MMEs in surf clams elsewhere, the impact of these IMCs on the health or recovery of toheroa is unknown. A critical first step towards understanding the significance of a pathogen in a host population is pathogen identification and characterisation. To begin this process, we examined 16S rRNA gene sequences of the putative IMCs from 4 toheroa populations that showed 97% homology to Endozoicomonas spp. sequences held in GenBank. Phylogenetic analysis identified closely related Endozoicomonas strains from the North and South Island, ANZ, and in situ hybridization, using 16S rRNA gene probes, confirmed the presence of the sequenced IMC gene in the gill and digestive gland tissues of toheroa. Quantitative PCR revealed site-specific and seasonal abundance patterns of Endozoicomonas spp. in toheroa populations. Although implicated in disease outbreaks elsewhere, the role of Endozoicomonas spp. within the ANZ shellfish mortality landscape remains uncertain.
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Affiliation(s)
- Matthew Bennion
- Environmental Research Institute, University of Waikato, Tauranga 3110, New Zealand
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10
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Qian Y, Gao Z, Wang J, Wang C, Li G, Fu F, Guo J, Shan Y. Safety Evaluation and Whole Genome Sequencing of Aspergillus japonicas PJ01 Reveal Its Potential to Degrade Citrus Segments in Juice Processing. Foods 2021; 10:foods10081736. [PMID: 34441514 PMCID: PMC8391945 DOI: 10.3390/foods10081736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/23/2021] [Accepted: 07/23/2021] [Indexed: 11/20/2022] Open
Abstract
Aspergillus japonicas PJ01 (A. japonicas PJ01) is a strain isolated from the rotten branches. In previ-ous studies, it was shown that it can produce complex enzymes to degrade polysaccharide com-ponents. In this study, we evaluated the safety of its crude enzyme solution. Acute oral toxicity, subchronic toxicity, micronucleus and sperm malformation tests all validated the high biologi-cal safety for the crude enzymes. Secondly, we carried out the citrus segment degradation ex-periment of crude enzyme solution. Compared with the control group, the crude enzyme solu-tion of A. japonicas PJ01 can completely degrade the segments in 50 min, which provides the basis for enzymatic peeling during juice processing. The whole genome sequencing showed that the genome of A. japonicus PJ01 has a GC content of 51.37% with a size of 36204647 bp, and encoded 10070 genes. GO, COG, KEGG and CAZy databases were used in gene annotation analyses. Pathway enrichment showed many genes related to carbohydrate metabolism, rich in genes re-lated to pectinase, xylanase and carboxylcellulase. Therefore, the complex enzyme produced by A. japonicus PJ01 can be used in gizzard juice processing to achieve efficient enzymatic decapsu-lation.
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Affiliation(s)
- Yujiao Qian
- Longping Branch, Graduate School of Hunan University, Changsha 410125, China; (Y.Q.); (J.W.); (C.W.); (G.L.); (F.F.)
- International Joint Lab on Fruits & Vegetables Processing, Quality and Safety, Hunan Key Lab of Fruits & Vegetables Storage, Processing, Quality and Safety, Hunan Agriculture Product Processing Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Zhipeng Gao
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China;
| | - Jieyi Wang
- Longping Branch, Graduate School of Hunan University, Changsha 410125, China; (Y.Q.); (J.W.); (C.W.); (G.L.); (F.F.)
| | - Chen Wang
- Longping Branch, Graduate School of Hunan University, Changsha 410125, China; (Y.Q.); (J.W.); (C.W.); (G.L.); (F.F.)
| | - Gaoyang Li
- Longping Branch, Graduate School of Hunan University, Changsha 410125, China; (Y.Q.); (J.W.); (C.W.); (G.L.); (F.F.)
- International Joint Lab on Fruits & Vegetables Processing, Quality and Safety, Hunan Key Lab of Fruits & Vegetables Storage, Processing, Quality and Safety, Hunan Agriculture Product Processing Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Fuhua Fu
- Longping Branch, Graduate School of Hunan University, Changsha 410125, China; (Y.Q.); (J.W.); (C.W.); (G.L.); (F.F.)
- International Joint Lab on Fruits & Vegetables Processing, Quality and Safety, Hunan Key Lab of Fruits & Vegetables Storage, Processing, Quality and Safety, Hunan Agriculture Product Processing Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Jiajing Guo
- Longping Branch, Graduate School of Hunan University, Changsha 410125, China; (Y.Q.); (J.W.); (C.W.); (G.L.); (F.F.)
- International Joint Lab on Fruits & Vegetables Processing, Quality and Safety, Hunan Key Lab of Fruits & Vegetables Storage, Processing, Quality and Safety, Hunan Agriculture Product Processing Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
- Correspondence: (Y.S.); (J.G.)
| | - Yang Shan
- Longping Branch, Graduate School of Hunan University, Changsha 410125, China; (Y.Q.); (J.W.); (C.W.); (G.L.); (F.F.)
- International Joint Lab on Fruits & Vegetables Processing, Quality and Safety, Hunan Key Lab of Fruits & Vegetables Storage, Processing, Quality and Safety, Hunan Agriculture Product Processing Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
- Correspondence: (Y.S.); (J.G.)
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11
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Pupier CA, Grover R, Fine M, Rottier C, van de Water JAJM, Ferrier-Pagès C. Dissolved Nitrogen Acquisition in the Symbioses of Soft and Hard Corals With Symbiodiniaceae: A Key to Understanding Their Different Nutritional Strategies? Front Microbiol 2021; 12:657759. [PMID: 34149646 PMCID: PMC8211778 DOI: 10.3389/fmicb.2021.657759] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 04/23/2021] [Indexed: 11/13/2022] Open
Abstract
Nitrogen is one of the limiting nutrients for coral growth and primary productivity. Therefore, the capacity of different associations between corals and their algal symbionts (Symbiodiniaceae) to efficiently exploit the available nitrogen sources will influence their distribution and abundance. Recent studies have advanced our understanding of nitrogen assimilation in reef-building scleractinian (hard) coral-Symbiodiniaceae symbioses. However, the nutrient metabolism of other coral taxa, such as Alcyoniina (soft corals), remains underexplored. Using stable isotope labeling, we investigated the assimilation of dissolved nitrogen (i.e., ammonium, nitrate, and free amino acids) by multiple species of soft and hard corals sampled in the Gulf of Aqaba in shallow (8-10 m) and mesophotic (40-50 m) reefs. Our results show that dissolved nitrogen assimilation rates per tissue biomass were up to 10-fold higher in hard than in soft coral symbioses for all sources of nitrogen. Although such differences in assimilation rates could be linked to the Symbiodiniaceae density, Symbiodiniaceae species, or the C:N ratio of the host and algal symbiont fractions, none of these parameters were different between the two coral taxa. Instead, the lower assimilation rates in soft coral symbioses might be explained by their different nutritional strategy: whereas soft corals may obtain most of their nitrogen via the capture of planktonic prey by the coral host (heterotrophic feeding), hard corals may rely more on dissolved nitrogen assimilation by their algal symbionts to fulfill their needs. This study highlights different nutritional strategies in soft and hard coral symbioses. A higher reliance on heterotrophy may help soft corals to grow in reefs with higher turbidity, which have a high concentration of particles in suspension in seawater. Further, soft corals may benefit from lower dissolved nitrogen assimilation rates in areas with low water quality.
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Affiliation(s)
- Chloé A. Pupier
- Marine Department, Centre Scientifique de Monaco, Monaco, Monaco
- Collège Doctoral, Sorbonne Université, Paris, France
| | - Renaud Grover
- Marine Department, Centre Scientifique de Monaco, Monaco, Monaco
| | - Maoz Fine
- The Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
- The Interuniversity Institute for Marine Science in Eilat, Eilat, Israel
| | - Cécile Rottier
- Marine Department, Centre Scientifique de Monaco, Monaco, Monaco
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12
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Pootakham W, Mhuantong W, Yoocha T, Sangsrakru D, Kongkachana W, Sonthirod C, Naktang C, Jomchai N, U-Thoomporn S, Yeemin T, Pengsakun S, Sutthacheep M, Tangphatsornruang S. Taxonomic profiling of Symbiodiniaceae and bacterial communities associated with Indo-Pacific corals in the Gulf of Thailand using PacBio sequencing of full-length ITS and 16S rRNA genes. Genomics 2021; 113:2717-2729. [PMID: 34089786 DOI: 10.1016/j.ygeno.2021.06.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 04/28/2021] [Accepted: 06/01/2021] [Indexed: 11/15/2022]
Abstract
Corals live with complex assemblages of microbes including bacteria, the dinoflagellate Symbiodiniaceae, fungi and viruses in a coral holobiont. These coral-associated microorganisms play an important role in their host fitness and survival. Here, we investigated the structure and diversity of algal and bacterial communities associated with five Indo-Pacific coral species, using full-length 16S rRNA and internal transcribed spacer sequences. While the dinoflagellate communities associated with Poriteslutea were dominated with Symbiodiniaceae genus Cladocopium, the other four coral hosts were associated mainly with members of the Durusdinium genus, suggesting that host species was one of the underlying factors influencing the structure and composition of dinoflagellate communities associated with corals in the Gulf of Thailand. Alphaproteobacteria dominated the microbiomes of Pocillopora spp. while Pavonafrondifera and P. lutea were associated primarily with Gammaproteobacteria. Finally, we demonstrated a superior performance of full-length 16S rRNA sequences in achieving species-resolution taxonomic classification of coral-associated microbiota.
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Affiliation(s)
- Wirulda Pootakham
- National Omics Center (NOC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand.
| | - Wuttichai Mhuantong
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Thippawan Yoocha
- National Omics Center (NOC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Duangjai Sangsrakru
- National Omics Center (NOC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Wasitthee Kongkachana
- National Omics Center (NOC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Chutima Sonthirod
- National Omics Center (NOC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Chaiwat Naktang
- National Omics Center (NOC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Nukoon Jomchai
- National Omics Center (NOC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Sonicha U-Thoomporn
- National Omics Center (NOC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Thammasak Yeemin
- Marine Biodiversity Research Group, Faculty of Science, Ramkhamhaeng University, Bangkok, Thailand
| | - Sittiporn Pengsakun
- Marine Biodiversity Research Group, Faculty of Science, Ramkhamhaeng University, Bangkok, Thailand
| | - Makamas Sutthacheep
- Marine Biodiversity Research Group, Faculty of Science, Ramkhamhaeng University, Bangkok, Thailand
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13
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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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14
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Cleary DFR, Polónia ARM, Reijnen BT, Berumen ML, de Voogd NJ. Prokaryote Communities Inhabiting Endemic and Newly Discovered Sponges and Octocorals from the Red Sea. MICROBIAL ECOLOGY 2020; 80:103-119. [PMID: 31932882 DOI: 10.1007/s00248-019-01465-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 11/14/2019] [Indexed: 06/10/2023]
Abstract
In the present study, we assessed prokaryotic communities of demosponges, a calcareous sponge, octocorals, sediment and seawater in coral reef habitat of the central Red Sea, including endemic species and species new to science. Goals of the study were to compare the prokaryotic communities of demosponges with the calcareous sponge and octocorals and to assign preliminary high microbial abundance (HMA) or low microbial abundance (LMA) status to the sponge species based on compositional trait data. Based on the compositional data, we were able to assign preliminary LMA or HMA status to all sponge species. Certain species, however, had traits of both LMA and HMA species. For example, the sponge Ectyoplasia coccinea, which appeared to be a LMA species, had traits, including a relatively high abundance of Chloroflexi members, that were more typical of HMA species. This included dominant OTUs assigned to two different classes within the Chloroflexi. The calcareous sponge clustered together with seawater, the known LMA sponge Stylissa carteri and other presumable LMA species. The two dominant OTUs of this species were assigned to the Deltaproteobacteria and had no close relatives in the GenBank database. The octocoral species in the present study had prokaryotic communities that were distinct from sediment, seawater and all sponge species. These were characterised by OTUs assigned to the orders Rhodospirillales, Cellvibrionales, Spirochaetales and the genus Endozoicomonas, which were rare or absent in samples from other biotopes.
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Affiliation(s)
- D F R Cleary
- Department of Biology & CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal.
| | - A R M Polónia
- Department of Biology & CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - B T Reijnen
- Marine Biodiversity, Naturalis Biodiversity Center, Leiden, The Netherlands
| | - M L Berumen
- Red Sea Research Center, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - N J de Voogd
- Marine Biodiversity, Naturalis Biodiversity Center, Leiden, The Netherlands
- Institute of Environmental Sciences, Environmental Biology Department, Leiden University, Leiden, The Netherlands
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15
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Tandon K, Lu CY, Chiang PW, Wada N, Yang SH, Chan YF, Chen PY, Chang HY, Chiou YJ, Chou MS, Chen WM, Tang SL. Comparative genomics: Dominant coral-bacterium Endozoicomonas acroporae metabolizes dimethylsulfoniopropionate (DMSP). THE ISME JOURNAL 2020; 14:1290-1303. [PMID: 32055028 PMCID: PMC7174347 DOI: 10.1038/s41396-020-0610-x] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 01/30/2020] [Accepted: 02/04/2020] [Indexed: 01/24/2023]
Abstract
Dominant coral-associated Endozoicomonas bacteria species are hypothesized to play a role in the coral sulfur cycle by metabolizing dimethylsulfoniopropionate (DMSP) into dimethylsulfide (DMS); however, no sequenced genome to date harbors genes for this process. In this study, we assembled high-quality (>95% complete) draft genomes of strains of the recently added species Endozoicomonas acroporae (Acr-14T, Acr-1, and Acr-5) isolated from the coral Acropora sp. and performed a comparative genomic analysis on the genus Endozoicomonas. We identified DMSP CoA-transferase/lyase-a dddD gene homolog in all sequenced genomes of E. acroporae strains-and functionally characterized bacteria capable of metabolizing DMSP into DMS via the DddD cleavage pathway using RT-qPCR and gas chromatography (GC). Furthermore, we demonstrated that E. acroporae strains can use DMSP as a carbon source and have genes arranged in an operon-like manner to link DMSP metabolism to the central carbon cycle. This study confirms the role of Endozoicomonas in the coral sulfur cycle.
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Affiliation(s)
- Kshitij Tandon
- Biodiversity Research Center, Academia Sinica, Taipei, 115, Taiwan
- 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
| | - Chih-Ying Lu
- Biodiversity Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Pei-Wen Chiang
- Biodiversity Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Naohisa Wada
- Biodiversity Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Shan-Hua Yang
- Institute of Fisheries Science, National Taiwan University, Taipei, 10617, Taiwan
| | - Ya-Fan Chan
- Biodiversity Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Ping-Yun Chen
- Institute of Environmental Engineering, National Sun Yat-sen University, Kaohsiung, 80424, Taiwan
| | - Hsiao-Yu Chang
- Institute of Environmental Engineering, National Sun Yat-sen University, Kaohsiung, 80424, Taiwan
| | - Yu-Jing Chiou
- Biodiversity Research Center, Academia Sinica, Taipei, 115, Taiwan
- Institute of Oceanography, National Taiwan University, Taipei, 10617, Taiwan
| | - Ming-Shean Chou
- Institute of Environmental Engineering, National Sun Yat-sen University, Kaohsiung, 80424, Taiwan
| | - Wen-Ming Chen
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung Marine University, No. 142, Hai-Chuan Rd, Nan-Tzu, Kaohsiung City, 811, Taiwan
| | - Sen-Lin Tang
- Biodiversity Research Center, Academia Sinica, Taipei, 115, Taiwan.
- Bioinformatics Program, Institute of Information Science, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan.
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16
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Epstein HE, Smith HA, Cantin NE, Mocellin VJL, Torda G, van Oppen MJH. Temporal Variation in the Microbiome of Acropora Coral Species Does Not Reflect Seasonality. Front Microbiol 2019; 10:1775. [PMID: 31474944 PMCID: PMC6706759 DOI: 10.3389/fmicb.2019.01775] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 07/18/2019] [Indexed: 12/22/2022] Open
Abstract
The coral microbiome is known to fluctuate in response to environmental variation and has been suggested to vary seasonally. However, most studies to date, particularly studies on bacterial communities, have examined temporal variation over a time frame of less than 1 year, which is insufficient to establish if microbiome variations are indeed seasonal in nature. The present study focused on expanding our understanding of long-term variability in microbial community composition using two common coral species, Acropora hyacinthus, and Acropora spathulata, at two mid-shelf reefs on the Great Barrier Reef. By sampling over a 2-year time period, this study aimed to determine whether temporal variations reflect seasonal cycles. Community composition of both bacteria and Symbiodiniaceae was characterized through 16S rRNA gene and ITS2 rDNA metabarcoding. We observed significant variations in community composition of both bacteria and Symbiodiniaceae among time points for A. hyacinthus and A. spathulata. However, there was no evidence to suggest that temporal variations were cyclical in nature and represented seasonal variation. Clear evidence for differences in the microbial communities found between reefs suggests that reef location and coral species play a larger role than season in driving microbial community composition in corals. In order to identify the basis of temporal patterns in coral microbial community composition, future studies should employ longer time series of sampling at sufficient temporal resolution to identify the environmental correlates of microbiome variation.
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Affiliation(s)
- Hannah E. Epstein
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, Australia
- AIMS@JCU, James Cook University, Townsville, QLD, Australia
- Australian Institute of Marine Science, Townsville, QLD, Australia
| | - Hillary A. Smith
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia
| | - Neal E. Cantin
- Australian Institute of Marine Science, Townsville, QLD, Australia
| | | | - Gergely Torda
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, Australia
- Australian Institute of Marine Science, Townsville, QLD, Australia
| | - Madeleine J. H. van Oppen
- Australian Institute of Marine Science, Townsville, QLD, Australia
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia
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17
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Ziegler M, Roik A, Röthig T, Wild C, Rädecker N, Bouwmeester J, Voolstra CR. Ecophysiology of Reef-Building Corals in the Red Sea. ACTA ACUST UNITED AC 2019. [DOI: 10.1007/978-3-030-05802-9_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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18
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Akarsu H, Bordes P, Mansour M, Bigot DJ, Genevaux P, Falquet L. TASmania: A bacterial Toxin-Antitoxin Systems database. PLoS Comput Biol 2019; 15:e1006946. [PMID: 31022176 PMCID: PMC6504116 DOI: 10.1371/journal.pcbi.1006946] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 05/07/2019] [Accepted: 03/11/2019] [Indexed: 11/30/2022] Open
Abstract
Bacterial Toxin-Antitoxin systems (TAS) are involved in key biological functions including plasmid maintenance, defense against phages, persistence and virulence. They are found in nearly all phyla and classified into 6 different types based on the mode of inactivation of the toxin, with the type II TAS being the best characterized so far. We have herein developed a new in silico discovery pipeline named TASmania, which mines the >41K assemblies of the EnsemblBacteria database for known and uncharacterized protein components of type I to IV TAS loci. Our pipeline annotates the proteins based on a list of curated HMMs, which leads to >2.106 loci candidates, including orphan toxins and antitoxins, and organises the candidates in pseudo-operon structures in order to identify new TAS candidates based on a guilt-by-association strategy. In addition, we classify the two-component TAS with an unsupervised method on top of the pseudo-operon (pop) gene structures, leading to 1567 “popTA” models offering a more robust classification of the TAs families. These results give valuable clues in understanding the toxin/antitoxin modular structures and the TAS phylum specificities. Preliminary in vivo work confirmed six putative new hits in Mycobacterium tuberculosis as promising candidates. The TASmania database is available on the following server https://shiny.bioinformatics.unibe.ch/apps/tasmania/. TASmania offers an extensive annotation of TA loci in a very large database of bacterial genomes, which represents a resource of crucial importance for the microbiology community. TASmania supports i) the discovery of new TA families; ii) the design of a robust experimental strategy by taking into account potential interferences in trans; iii) the comparative analysis between TA loci content, phylogeny and/or phenotypes (pathogenicity, persistence, stress resistance, associated host types) by providing a vast repertoire of annotated assemblies. Our database contains TA annotations of a given strain not only mapped to its core genome but also to its plasmids, whenever applicable.
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Affiliation(s)
- Hatice Akarsu
- Department of Biology, University of Fribourg & Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | - Patricia Bordes
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Moise Mansour
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Donna-Joe Bigot
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Pierre Genevaux
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Laurent Falquet
- Department of Biology, University of Fribourg & Swiss Institute of Bioinformatics, Fribourg, Switzerland
- * E-mail:
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19
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Jaspers C, Fraune S, Arnold AE, Miller DJ, Bosch TCG, Voolstra CR. Resolving structure and function of metaorganisms through a holistic framework combining reductionist and integrative approaches. ZOOLOGY 2019; 133:81-87. [PMID: 30979392 DOI: 10.1016/j.zool.2019.02.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 02/20/2019] [Accepted: 02/27/2019] [Indexed: 02/07/2023]
Abstract
Current research highlights the importance of associated microbes in contributing to the functioning, health, and even adaptation of their animal, plant, and fungal hosts. As such, we are witnessing a shift in research that moves away from focusing on the eukaryotic host sensu stricto to research into the complex conglomerate of the host and its associated microorganisms (i.e., microbial eukaryotes, archaea, bacteria, and viruses), the so-called metaorganism, as the biological entity. While recent research supports and encourages the adoption of such an integrative view, it must be understood that microorganisms are not involved in all host processes and not all associated microorganisms are functionally important. As such, our intention here is to provide a critical review and evaluation of perspectives and limitations relevant to studying organisms in a metaorganism framework and the functional toolbox available to do so. We note that marker gene-guided approaches that primarily characterize microbial diversity are a first step in delineating associated microbes but are not sufficient to establish proof of their functional relevance. More sophisticated tools and experiments are necessary to reveal the specific functions of associated microbes. This can be accomplished through the study of metaorganisms in less complex environments, the targeted manipulation of microbial associates, or work at the mechanistic level with the toolbox available in model systems. We conclude that the metaorganism framework is a powerful new concept to help provide answers to longstanding biological questions such as the evolution and ecology of organismal complexity and the importance of organismal symbioses to ecosystem functioning. The intricacy of the metaorganism requires a holistic framework combining reductionist and integrative approaches to resolve the structure and function of its member species and to disclose the various roles that microorganisms play in the biology of their hosts.
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Affiliation(s)
- Cornelia Jaspers
- GEOMAR - Helmholtz Centre for Ocean Research Kiel, Evolutionary Ecology of Marine Fishes, Düsternbrooker Weg 20, 24105 Kiel, Germany; National Institute of Aquatic Resources, Technical University of Denmark, DTU Aqua, Kemitorvet, Building 202, 2800 Kgs. Lyngby, Denmark
| | - Sebastian Fraune
- Zoological Institute, Kiel University, Am Botanischen Garten 9, 24118 Kiel, Germany
| | - A Elizabeth Arnold
- School of Plant Sciences and the Department of Ecology and Evolutionary Biology, The University of Arizona, Tucson, AZ 85719, USA
| | - David J Miller
- ARC Centre of Excellence for Coral Reef Studies and Department of Molecular and Cell Biology, James Cook University, Townsville, Queensland 4811, Australia
| | - Thomas C G Bosch
- Zoological Institute, Kiel University, Am Botanischen Garten 9, 24118 Kiel, Germany
| | - Christian R Voolstra
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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20
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Qi W, Cascarano MC, Schlapbach R, Katharios P, Vaughan L, Seth-Smith HMB. Ca. Endozoicomonas cretensis: A Novel Fish Pathogen Characterized by Genome Plasticity. Genome Biol Evol 2018; 10:1363-1374. [PMID: 29726925 PMCID: PMC6007542 DOI: 10.1093/gbe/evy092] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/02/2018] [Indexed: 02/06/2023] Open
Abstract
Endozoicomonas bacteria are generally beneficial symbionts of diverse marine invertebrates including reef-building corals, sponges, sea squirts, sea slugs, molluscs, and Bryozoans. In contrast, the recently reported Ca. Endozoicomonas cretensis was identified as a vertebrate pathogen, causing epitheliocystis in fish larvae resulting in massive mortality. Here, we described the Ca. E. cretensis draft genome, currently undergoing genome decay as evidenced by massive insertion sequence (IS element) expansion and pseudogene formation. Many of the insertion sequences are also predicted to carry outward-directed promoters, implying that they may be able to modulate the expression of neighbouring coding sequences (CDSs). Comparative genomic analysis has revealed many Ca. E. cretensis-specific CDSs, phage integration and novel gene families. Potential virulence related CDSs and machineries were identified in the genome, including secretion systems and related effector proteins, and systems related to biofilm formation and directed cell movement. Mucin degradation would be of importance to a fish pathogen, and many candidate CDSs associated with this pathway have been identified. The genome may reflect a bacterium in the process of changing niche from symbiont to pathogen, through expansion of virulence genes and some loss of metabolic capacity.
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Affiliation(s)
- Weihong Qi
- Functional Genomics Center Zurich, University of Zurich, Switzerland
| | - Maria Chiara Cascarano
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, Greece
| | - Ralph Schlapbach
- Functional Genomics Center Zurich, University of Zurich, Switzerland
| | - Pantelis Katharios
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, Greece
| | - Lloyd Vaughan
- Institute for Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Switzerland.,Pathovet AG, Tagelswangen, Switzerland
| | - Helena M B Seth-Smith
- Functional Genomics Center Zurich, University of Zurich, Switzerland.,Institute for Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Switzerland
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21
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Draft Genome Sequence of Endozoicomonas acroporae Strain Acr-14 T, Isolated from Acropora Coral. GENOME ANNOUNCEMENTS 2018; 6:6/6/e01576-17. [PMID: 29439049 PMCID: PMC5805887 DOI: 10.1128/genomea.01576-17] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
A lacuna exists in our understanding of the genetic makeup of Endozoicomonas bacteria, due to scarcity of genome sequences. We report here the first draft genome sequence of Endozoicomonas acroporae Acr-14, a type strain isolated from the coral Acropora. This sequence will foster an understanding of the genetic makeup and role of hosts in shaping gene repertoires.
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22
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Molecular Characterization of an Endozoicomonas-Like Organism Causing Infection in the King Scallop (Pecten maximus L.). Appl Environ Microbiol 2018; 84:AEM.00952-17. [PMID: 29150518 PMCID: PMC5772249 DOI: 10.1128/aem.00952-17] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Accepted: 11/10/2017] [Indexed: 11/20/2022] Open
Abstract
One of the fastest growing fisheries in the UK is the king scallop (Pecten maximus L.), also currently rated as the second most valuable fishery. Mass mortality events in scallops have been reported worldwide, often with the causative agent(s) remaining uncharacterized. In May 2013 and 2014, two mass mortality events affecting king scallops were recorded in the Lyme Bay marine protected area (MPA) in Southwest England. Histopathological examination showed gill epithelial tissues infected with intracellular microcolonies (IMCs) of bacteria resembling Rickettsia-like organisms (RLOs), often with bacteria released in vascular spaces. Large colonies were associated with cellular and tissue disruption of the gills. Ultrastructural examination confirmed the intracellular location of these organisms in affected epithelial cells. The 16S rRNA gene sequences of the putative IMCs obtained from infected king scallop gill samples, collected from both mortality events, were identical and had a 99.4% identity to 16S rRNA gene sequences obtained from “Candidatus Endonucleobacter bathymodioli” and 95% with Endozoicomonas species. In situ hybridization assays using 16S rRNA gene probes confirmed the presence of the sequenced IMC gene in the gill tissues. Additional DNA sequences of the bacterium were obtained using high-throughput (Illumina) sequencing, and bioinformatic analysis identified over 1,000 genes with high similarity to protein sequences from Endozoicomonas spp. (ranging from 77 to 87% identity). Specific PCR assays were developed and applied to screen for the presence of IMC 16S rRNA gene sequences in king scallop gill tissues collected at the Lyme Bay MPA during 2015 and 2016. There was 100% prevalence of the IMCs in these gill tissues, and the 16S rRNA gene sequences identified were identical to the sequence found during the previous mortality event. IMPORTANCE Molluscan mass mortalities associated with IMCs have been reported worldwide for many years; however, apart from histological and ultrastructural characterization, characterization of the etiological agents is limited. In the present work, we provide detailed molecular characterization of an Endozoicomonas-like organism (ELO) associated with an important commercial scallop species.
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23
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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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24
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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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25
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Pootakham W, Mhuantong W, Yoocha T, Putchim L, Sonthirod C, Naktang C, Thongtham N, Tangphatsornruang S. High resolution profiling of coral-associated bacterial communities using full-length 16S rRNA sequence data from PacBio SMRT sequencing system. Sci Rep 2017; 7:2774. [PMID: 28584301 PMCID: PMC5459821 DOI: 10.1038/s41598-017-03139-4] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 04/24/2017] [Indexed: 02/01/2023] Open
Abstract
Coral reefs are a complex ecosystem consisting of coral animals and a vast array of associated symbionts including the dinoflagellate Symbiodinium, fungi, viruses and bacteria. Several studies have highlighted the importance of coral-associated bacteria and their fundamental roles in fitness and survival of the host animal. The scleractinian coral Porites lutea is one of the dominant reef-builders in the Indo-West Pacific. Currently, very little is known about the composition and structure of bacterial communities across P. lutea reefs. The purpose of this study is twofold: to demonstrate the advantages of using PacBio circular consensus sequencing technology in microbial community studies and to investigate the diversity and structure of P. lutea-associated microbiome in the Indo-Pacific. This is the first metagenomic study of marine environmental samples that utilises the PacBio sequencing system to capture full-length 16S rRNA sequences. We observed geographically distinct coral-associated microbial profiles between samples from the Gulf of Thailand and Andaman Sea. Despite the geographical and environmental impacts on the coral-host interactions, we identified a conserved community of bacteria that were present consistently across diverse reef habitats. Finally, we demonstrated the superior performance of full-length 16S rRNA sequences in resolving taxonomic uncertainty of coral associates at the species level.
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Affiliation(s)
- Wirulda Pootakham
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand.
| | - Wuttichai Mhuantong
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Thippawan Yoocha
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Lalita Putchim
- Phuket Marine Biological Center, Phuket, 83000, Thailand
| | - Chutima Sonthirod
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Chaiwat Naktang
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | | | - Sithichoke Tangphatsornruang
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
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26
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Endozoicomonas genomes reveal functional adaptation and plasticity in bacterial strains symbiotically associated with diverse marine hosts. Sci Rep 2017; 7:40579. [PMID: 28094347 PMCID: PMC5240137 DOI: 10.1038/srep40579] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 12/07/2016] [Indexed: 01/22/2023] Open
Abstract
Endozoicomonas bacteria are globally distributed and often abundantly associated with diverse marine hosts including reef-building corals, yet their function remains unknown. In this study we generated novel Endozoicomonas genomes from single cells and metagenomes obtained directly from the corals Stylophora pistillata, Pocillopora verrucosa, and Acropora humilis. We then compared these culture-independent genomes to existing genomes of bacterial isolates acquired from a sponge, sea slug, and coral to examine the functional landscape of this enigmatic genus. Sequencing and analysis of single cells and metagenomes resulted in four novel genomes with 60–76% and 81–90% genome completeness, respectively. These data also confirmed that Endozoicomonas genomes are large and are not streamlined for an obligate endosymbiotic lifestyle, implying that they have free-living stages. All genomes show an enrichment of genes associated with carbon sugar transport and utilization and protein secretion, potentially indicating that Endozoicomonas contribute to the cycling of carbohydrates and the provision of proteins to their respective hosts. Importantly, besides these commonalities, the genomes showed evidence for differential functional specificity and diversification, including genes for the production of amino acids. Given this metabolic diversity of Endozoicomonas we propose that different genotypes play disparate roles and have diversified in concert with their hosts.
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27
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Distinguishing between Microbial Habitats Unravels Ecological Complexity in Coral Microbiomes. mSystems 2016; 1:mSystems00143-16. [PMID: 27822559 PMCID: PMC5080407 DOI: 10.1128/msystems.00143-16] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 09/26/2016] [Indexed: 01/07/2023] Open
Abstract
The diverse prokaryotic communities associated with reef-building corals may provide important ecological advantages to their threatened hosts. The consistency of relationships between corals and specific prokaryotes, however, is debated, and the locations where microbially mediated processes occur in the host are not resolved. Here, we examined how the prokaryotic associates of five common Caribbean corals with different evolutionary and ecological traits differ across mucus and tissue habitats. We used physical and chemical separation of coral mucus and tissue and sequencing of partial small-subunit rRNA genes of bacteria and archaea from these samples to demonstrate that coral tissue and mucus harbor unique reservoirs of prokaryotes, with 23 to 49% and 31 to 56% of sequences exclusive to the tissue and mucus habitats, respectively. Across all coral species, we found that 46 tissue- and 22 mucus-specific microbial members consistently associated with the different habitats. Sequences classifying as "Candidatus Amoebophilus," Bacteroidetes-affiliated intracellular symbionts of amoebae, emerged as previously unrecognized tissue associates of three coral species. This study demonstrates how coral habitat differentiation enables highly resolved examination of ecological interactions between corals and their associated microorganisms and identifies previously unrecognized tissue and mucus associates of Caribbean corals for future targeted study. IMPORTANCE This study demonstrates that coral tissue or mucus habitats structure the microbiome of corals and that separation of these habitats facilitates identification of consistent microbial associates. Using this approach, we demonstrated that sequences related to "Candidatus Amoebophilus," recognized intracellular symbionts of amoebae, were highly associated with the tissues of Caribbean corals and possibly endosymbionts of a protistan host within corals, adding a further degree of intricacy to coral holobiont symbioses. Examining specific habitats within complex hosts such as corals is useful for targeting important microbial associations that may otherwise be masked by the sheer microbial diversity associated with all host habitats.
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28
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Parris DJ, Brooker RM, Morgan MA, Dixson DL, Stewart FJ. Whole gut microbiome composition of damselfish and cardinalfish before and after reef settlement. PeerJ 2016; 4:e2412. [PMID: 27635360 PMCID: PMC5012416 DOI: 10.7717/peerj.2412] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 08/04/2016] [Indexed: 12/17/2022] Open
Abstract
The Pomacentridae (damselfish) and Apogonidae (cardinalfish) are among the most common fish families on coral reefs and in the aquarium trade. Members of both families undergo a pelagic larvae phase prior to settlement on the reef, where adults play key roles in benthic habitat structuring and trophic interactions. Fish-associated microbial communities (microbiomes) significantly influence fish health and ecology, yet little is known of how microbiomes change with life stage. We quantified the taxonomic (16S rRNA gene) composition of whole gut microbiomes from ten species of damselfish and two species of cardinalfish from Lizard Island, Australia, focusing specifically on comparisons between pelagic larvae prior to settlement on the reef versus post-settlement juvenile and adult individuals. On average, microbiome phylogenetic diversity increased from pre- to post-settlement, and was unrelated to the microbial composition in the surrounding water column. However, this trend varied among species, suggesting stochasticity in fish microbiome assembly. Pre-settlement fish were enriched with bacteria of the Endozoicomonaceae, Shewanellaceae, and Fusobacteriaceae, whereas settled fish harbored higher abundances of Vibrionaceae and Pasteurellaceae. Several individual operational taxonomic units, including ones related to Vibrio harveyi, Shewanella sp., and uncultured Endozoicomonas bacteria, were shared between both pre and post-settlement stages and may be of central importance in the intestinal niche across development. Richness of the core microbiome shared among pre-settlement fish was comparable to that of settled individuals, suggesting that changes in diversity with adulthood are due to the acquisition or loss of host-specific microbes. These results identify a key transition in microbiome structure across host life stage, suggesting changes in the functional contribution of microbiomes over development in two ecologically dominant reef fish families.
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Affiliation(s)
- Darren J Parris
- School of Biology, Georgia Institute of Technology , Atlanta , GA , United States
| | - Rohan M Brooker
- School of Marine Science and Policy, University of Delaware , Newark , DE , United States
| | - Michael A Morgan
- School of Biology, Georgia Institute of Technology , Atlanta , GA , United States
| | - Danielle L Dixson
- School of Marine Science and Policy, University of Delaware , Newark , DE , United States
| | - Frank J Stewart
- School of Biology, Georgia Institute of Technology , Atlanta , GA , United States
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29
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Neave MJ, Apprill A, Ferrier-Pagès C, Voolstra CR. Diversity and function of prevalent symbiotic marine bacteria in the genus Endozoicomonas. Appl Microbiol Biotechnol 2016; 100:8315-24. [PMID: 27557714 PMCID: PMC5018254 DOI: 10.1007/s00253-016-7777-0] [Citation(s) in RCA: 150] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Revised: 07/29/2016] [Accepted: 08/01/2016] [Indexed: 02/01/2023]
Abstract
Endozoicomonas bacteria are emerging as extremely diverse and flexible symbionts of numerous marine hosts inhabiting oceans worldwide. Their hosts range from simple invertebrate species, such as sponges and corals, to complex vertebrates, such as fish. Although widely distributed, the functional role of Endozoicomonas within their host microenvironment is not well understood. In this review, we provide a summary of the currently recognized hosts of Endozoicomonas and their global distribution. Next, the potential functional roles of Endozoicomonas, particularly in light of recent microscopic, genomic, and genetic analyses, are discussed. These analyses suggest that Endozoicomonas typically reside in aggregates within host tissues, have a free-living stage due to their large genome sizes, show signs of host and local adaptation, participate in host-associated protein and carbohydrate transport and cycling, and harbour a high degree of genomic plasticity due to the large proportion of transposable elements residing in their genomes. This review will finish with a discussion on the methodological tools currently employed to study Endozoicomonas and host interactions and review future avenues for studying complex host-microbial symbioses.
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Affiliation(s)
- Matthew J Neave
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.,Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Amy Apprill
- Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | | | - Christian R Voolstra
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
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30
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Chu ND, Vollmer SV. Caribbean corals house shared and host-specific microbial symbionts over time and space. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:493-500. [PMID: 27083502 DOI: 10.1111/1758-2229.12412] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The rise of coral diseases has triggered a surge of interest in coral microbial communities. But to fully understand how the coral microbiome may cause or respond to disease, we must first understand structure and variation in the healthy coral microbiome. We used 16S rRNA sequencing to characterize the microbiomes of 100 healthy coral colonies from six Caribbean coral species (Acropora cervicornis, A. palmata, Diploria labyrinthiformis, Diploria strigosa, Porites astreoides and P. furcata) across four reefs and three time points over 1 year. We found host species to be the strongest driver of coral microbiome structure across site and time. Analysis of the core microbiome revealed remarkable similarity in the bacterial taxa represented across coral hosts and many bacterial phylotypes shared across all corals sampled. Some of these widespread bacterial taxa have been identified in Pacific corals, indicating that a core coral microbiome may extend across oceans. Core bacterial phylotypes that were unique to each coral were taxonomically diverse, suggesting that different coral hosts provide persistent, divergent niches for bacteria.
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Affiliation(s)
- Nathaniel D Chu
- Marine Science Center, Northeastern University, 430 Nahant Road, Nahant, MA, 01908, USA
- Smithsonian Tropical Research Institute, Bocas del Toro, Panama
- Microbiology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Steven V Vollmer
- Marine Science Center, Northeastern University, 430 Nahant Road, Nahant, MA, 01908, USA
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31
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Bourne DG, Morrow KM, Webster NS. Insights into the Coral Microbiome: Underpinning the Health and Resilience of Reef Ecosystems. Annu Rev Microbiol 2016; 70:317-40. [PMID: 27482741 DOI: 10.1146/annurev-micro-102215-095440] [Citation(s) in RCA: 346] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Corals are fundamental ecosystem engineers, creating large, intricate reefs that support diverse and abundant marine life. At the core of a healthy coral animal is a dynamic relationship with microorganisms, including a mutually beneficial symbiosis with photosynthetic dinoflagellates (Symbiodinium spp.) and enduring partnerships with an array of bacterial, archaeal, fungal, protistan, and viral associates, collectively termed the coral holobiont. The combined genomes of this coral holobiont form a coral hologenome, and genomic interactions within the hologenome ultimately define the coral phenotype. Here we integrate contemporary scientific knowledge regarding the ecological, host-specific, and environmental forces shaping the diversity, specificity, and distribution of microbial symbionts within the coral holobiont, explore physiological pathways that contribute to holobiont fitness, and describe potential mechanisms for holobiont homeostasis. Understanding the role of the microbiome in coral resilience, acclimation, and environmental adaptation is a new frontier in reef science that will require large-scale collaborative research efforts.
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Affiliation(s)
- David G Bourne
- Marine Biology and Aquaculture, College of Science and Engineering, James Cook University, Townsville, Queensland, Australia 4811; .,Australian Institute of Marine Science, Townsville, Queensland, Australia 4810
| | - Kathleen M Morrow
- Australian Institute of Marine Science, Townsville, Queensland, Australia 4810.,Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire 03824
| | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, Queensland, Australia 4810
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32
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Neave MJ, Rachmawati R, Xun L, Michell CT, Bourne DG, Apprill A, Voolstra CR. Differential specificity between closely related corals and abundant Endozoicomonas endosymbionts across global scales. ISME JOURNAL 2016; 11:186-200. [PMID: 27392086 PMCID: PMC5335547 DOI: 10.1038/ismej.2016.95] [Citation(s) in RCA: 137] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Revised: 04/19/2016] [Accepted: 06/07/2016] [Indexed: 01/20/2023]
Abstract
Reef-building corals are well regarded not only for their obligate association with endosymbiotic algae, but also with prokaryotic symbionts, the specificity of which remains elusive. To identify the central microbial symbionts of corals, their specificity across species and conservation over geographic regions, we sequenced partial SSU ribosomal RNA genes of Bacteria and Archaea from the common corals Stylophora pistillata and Pocillopora verrucosa across 28 reefs within seven major geographical regions. We demonstrate that both corals harbor Endozoicomonas bacteria as their prevalent symbiont. Importantly, catalyzed reporter deposition–fluorescence in situ hybridization (CARD–FISH) with Endozoicomonas-specific probes confirmed their residence as large aggregations deep within coral tissues. Using fine-scale genotyping techniques and single-cell genomics, we demonstrate that P. verrucosa harbors the same Endozoicomonas, whereas S. pistillata associates with geographically distinct genotypes. This specificity may be shaped by the different reproductive strategies of the hosts, potentially uncovering a pattern of symbiont selection that is linked to life history. Spawning corals such as P. verrucosa acquire prokaryotes from the environment. In contrast, brooding corals such as S. pistillata release symbiont-packed planula larvae, which may explain a strong regional signature in their microbiome. Our work contributes to the factors underlying microbiome specificity and adds detail to coral holobiont functioning.
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Affiliation(s)
- Matthew J Neave
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Rita Rachmawati
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Liping Xun
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Craig T Michell
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - David G Bourne
- Australian Institute of Marine Science and College of Science and Engineering, James Cook University Townsville, Townsville, Queensland, Australia
| | - Amy Apprill
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Christian R Voolstra
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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33
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McCauley EP, Haltli B, Correa H, Kerr RG. Spatial and temporal investigation of the microbiome of the Caribbean octocoral Erythropodium caribaeorum. FEMS Microbiol Ecol 2016; 92:fiw147. [PMID: 27381833 DOI: 10.1093/femsec/fiw147] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/29/2016] [Indexed: 11/13/2022] Open
Abstract
The octocoral Erythropodium caribaeorum is an important species in the Caribbean coral reef community and a source of the cytotoxic natural product desmethyleleutherobin. We utilized 16S small subunit rRNA gene amplicon pyrosequencing to characterize the microbiome of E. caribaeorum collected from Florida, USA and San Salvador, The Bahamas at multiple time points. This coral was found to have a very high microbial richness with an average Chao1 estimated richness of 1464 ± 707 operational taxonomic units and average Shannon diversity index of 4.26 ± 1.65. The taxonomic class Gammaproteobacteria was a dominant member in all samples and the genus Endozoicomonas accounted for an average of 37.7% ± 30.0% of the total sequence reads. One Endozoicomonas sp. was found to be a stable member of all E. caribaeorum sequence libraries regardless of location or time of collection and accounted for 30.1% of all sequence reads. This is the first report characterizing the microbiome associated with the encrusting octocoral E. caribaeorum.
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Affiliation(s)
- Erin P McCauley
- Department of Biomedical Sciences, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada
| | - Brad Haltli
- Department of Biomedical Sciences, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada Department of Chemistry, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada
| | - Hebelin Correa
- Department of Chemistry, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada
| | - Russell G Kerr
- Department of Biomedical Sciences, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada Department of Chemistry, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada
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34
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Ding JY, Shiu JH, Chen WM, Chiang YR, Tang SL. Genomic Insight into the Host-Endosymbiont Relationship of Endozoicomonas montiporae CL-33(T) with its Coral Host. Front Microbiol 2016; 7:251. [PMID: 27014194 PMCID: PMC4781883 DOI: 10.3389/fmicb.2016.00251] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 02/15/2016] [Indexed: 11/13/2022] Open
Abstract
The bacterial genus Endozoicomonas was commonly detected in healthy corals in many coral-associated bacteria studies in the past decade. Although, it is likely to be a core member of coral microbiota, little is known about its ecological roles. To decipher potential interactions between bacteria and their coral hosts, we sequenced and investigated the first culturable endozoicomonal bacterium from coral, the E. montiporae CL-33(T). Its genome had potential sign of ongoing genome erosion and gene exchange with its host. Testosterone degradation and type III secretion system are commonly present in Endozoicomonas and may have roles to recognize and deliver effectors to their hosts. Moreover, genes of eukaryotic ephrin ligand B2 are present in its genome; presumably, this bacterium could move into coral cells via endocytosis after binding to coral's Eph receptors. In addition, 7,8-dihydro-8-oxoguanine triphosphatase and isocitrate lyase are possible type III secretion effectors that might help coral to prevent mitochondrial dysfunction and promote gluconeogenesis, especially under stress conditions. Based on all these findings, we inferred that E. montiporae was a facultative endosymbiont that can recognize, translocate, communicate and modulate its coral host.
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Affiliation(s)
- Jiun-Yan Ding
- Biodiversity Research Center, Academia Sinica Taipei, Taiwan
| | - Jia-Ho Shiu
- Biodiversity Research Center, Academia Sinica Taipei, Taiwan
| | - Wen-Ming Chen
- Department of Seafood Science, Laboratory of Microbiology, National Kaohsiung Marine University Kaohsiung, Taiwan
| | - Yin-Ru Chiang
- Biodiversity Research Center, Academia Sinica Taipei, Taiwan
| | - Sen-Lin Tang
- Biodiversity Research Center, Academia Sinica Taipei, Taiwan
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Appolinario LR, Tschoeke DA, Rua CPJ, Venas T, Campeão ME, Amaral GRS, Leomil L, de Oliveira L, Vieira VV, Otsuki K, Swings J, Thompson FL, Thompson CC. Description of Endozoicomonas arenosclerae sp. nov. using a genomic taxonomy approach. Antonie van Leeuwenhoek 2016; 109:431-8. [PMID: 26786501 DOI: 10.1007/s10482-016-0649-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 01/11/2016] [Indexed: 11/28/2022]
Abstract
The taxonomic position of strains Ab112(T) (CBAS 572(T)) and Ab227_MC (CBAS 573) was evaluated by means of genomic taxonomy. These isolates represent the dominant flora cultured from the healthy marine sponge Arenosclera brasiliensis, endemic to Rio de Janeiro. Strains CBAS 572(T) and CBAS 573 shared >98 % 16S rRNA sequence identity with Endozoicomonas numazuensis and Endozoicomonas montiporae. In silico DNA-DNA Hybridization, i.e. genome-to-genome distance (GGD), amino acid identity (AAI) and average nucleotide identity (ANI) further showed that these strains had <70 %, at maximum 71.1 and 78 % of identity, respectively, to their closest neighbours E. numazuensis and E. montiporae. The DNA G+C content of CBAS 572(T) and CBAS 573 were 47.6 and 47.7 mol%, respectively. Phenotypic and chemotaxonomic features also allowed a separation from the type strains of their phylogenetic neighbours. Useful phenotypic features for discriminating CBAS 572(T) and CBAS 573 from E. numazuensis and E. montiporae species include C8 esterase, N-acetyl-β-glucosaminidase, citric acid, uridine and siderophore. The species Endozoicomonas arenosclerae sp. nov. is proposed to harbour the new isolates. The type strain is CBAS 572(T) (=Ab112(T)).
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Affiliation(s)
- Luciana R Appolinario
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio De Janeiro, RJ, Brazil
| | - Diogo A Tschoeke
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio De Janeiro, RJ, Brazil
| | - Cintia P J Rua
- Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos, SP, Brazil
| | - Tainá Venas
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio De Janeiro, RJ, Brazil
| | - Mariana E Campeão
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio De Janeiro, RJ, Brazil
| | - Gilda R S Amaral
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio De Janeiro, RJ, Brazil
| | - Luciana Leomil
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio De Janeiro, RJ, Brazil
| | - Louisi de Oliveira
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio De Janeiro, RJ, Brazil
| | | | - Koko Otsuki
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio De Janeiro, RJ, Brazil
| | - Jean Swings
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio De Janeiro, RJ, Brazil.,Laboratory for Microbiology, Ghent University, Ghent, Belgium
| | - Fabiano L Thompson
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio De Janeiro, RJ, Brazil.,SAGE-COPPE, Federal University of Rio de Janeiro, Rio De Janeiro, RJ, Brazil
| | - Cristiane C Thompson
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio De Janeiro, RJ, Brazil.
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Environmental marine pathogen isolation using mesocosm culture of sharpsnout seabream: striking genomic and morphological features of novel Endozoicomonas sp. Sci Rep 2015; 5:17609. [PMID: 26639610 PMCID: PMC4671022 DOI: 10.1038/srep17609] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 11/02/2015] [Indexed: 11/09/2022] Open
Abstract
Aquaculture is a burgeoning industry, requiring diversification into new farmed species, which are often at risk from infectious disease. We used a mesocosm technique to investigate the susceptibility of sharpsnout seabream (Diplodus puntazzo) larvae to potential environmental pathogens in seawater compared to control borehole water. Fish exposed to seawater succumbed to epitheliocystis from 21 days post hatching, causing mortality in a quarter of the hosts. The pathogen responsible was not chlamydial, as is often found in epitheliocystis, but a novel species of the γ-proteobacterial genus Endozoicomonas. Detailed characterisation of this pathogen within the infectious lesions using high resolution fluorescent and electron microscopy showed densely packed rod shaped bacteria. A draft genome sequence of this uncultured bacterium was obtained from preserved material. Comparison with the genome of the Endozoicomonas elysicola type strain shows that the genome of Ca. Endozoicomonas cretensis is undergoing decay through loss of functional genes and insertion sequence expansion, often indicative of adaptation to a new niche or restriction to an alternative lifestyle. These results demonstrate the advantage of mesocosm studies for investigating the effect of environmental bacteria on susceptible hosts and provide an important insight into the genome dynamics of a novel fish pathogen.
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37
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Meyer JL, Dillard BA, Rodgers JM, Ritchie KB, Paul VJ, Teplitski M. Draft genome sequence of Halomonas meridiana R1t3 isolated from the surface microbiota of the Caribbean Elkhorn coral Acropora palmata. Stand Genomic Sci 2015; 10:75. [PMID: 26451236 PMCID: PMC4597393 DOI: 10.1186/s40793-015-0069-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 09/28/2015] [Indexed: 11/24/2022] Open
Abstract
Members of the gammaproteobacterial genus Halomonas are common in marine environments. Halomonas and other members of the Oceanospirillales have recently been identified as prominent members of the surface microbiota of reef-building corals. Halomonas meridiana strain R1t3 was isolated from the surface mucus layer of the scleractinian coral Acropora palmata in 2005 from the Florida Keys. This strain was chosen for genome sequencing to provide insight into the role of commensal heterotrophic bacteria in the coral holobiont. The draft genome consists of 290 scaffolds, totaling 3.5 Mbp in length and contains 3397 protein-coding genes.
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Affiliation(s)
- Julie L Meyer
- Soil and Water Science Department, University of Florida-Institute of Food and Agricultural Sciences, Gainesville, FL USA
| | - Brian A Dillard
- Soil and Water Science Department, University of Florida-Institute of Food and Agricultural Sciences, Gainesville, FL USA
| | - John M Rodgers
- Soil and Water Science Department, University of Florida-Institute of Food and Agricultural Sciences, Gainesville, FL USA
| | | | | | - Max Teplitski
- Soil and Water Science Department, University of Florida-Institute of Food and Agricultural Sciences, Gainesville, FL USA ; Smithsonian Marine Station, Fort Pierce, FL USA
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38
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Har JY, Helbig T, Lim JH, Fernando SC, Reitzel AM, Penn K, Thompson JR. Microbial diversity and activity in the Nematostella vectensis holobiont: insights from 16S rRNA gene sequencing, isolate genomes, and a pilot-scale survey of gene expression. Front Microbiol 2015; 6:818. [PMID: 26388838 PMCID: PMC4557100 DOI: 10.3389/fmicb.2015.00818] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Accepted: 07/27/2015] [Indexed: 01/08/2023] Open
Abstract
We have characterized the molecular and genomic diversity of the microbiota of the starlet sea anemone Nematostella vectensis, a cnidarian model for comparative developmental and functional biology and a year-round inhabitant of temperate salt marshes. Molecular phylogenetic analysis of 16S rRNA gene clone libraries revealed four ribotypes associated with N. vectensis at multiple locations and times. These associates include two novel ribotypes within the ε-Proteobacterial order Campylobacterales and the Spirochetes, respectively, each sharing <85% identity with cultivated strains, and two γ-Proteobacterial ribotypes sharing >99% 16S rRNA identity with Endozoicomonas elysicola and Pseudomonas oleovorans, respectively. Species-specific PCR revealed that these populations persisted in N. vectensis asexually propagated under laboratory conditions. cDNA indicated expression of the Campylobacterales and Endozoicomonas 16S rRNA in anemones from Sippewissett Marsh, MA. A collection of bacteria from laboratory raised N. vectensis was dominated by isolates from P. oleovorans and Rhizobium radiobacter. Isolates from field-collected anemones revealed an association with Limnobacter and Stappia isolates. Genomic DNA sequencing was carried out on 10 cultured bacterial isolates representing field- and laboratory-associates, i.e., Limnobacter spp., Stappia spp., P. oleovorans and R. radiobacter. Genomes contained multiple genes identified as virulence (host-association) factors while S. stellulata and L. thiooxidans genomes revealed pathways for mixotrophic sulfur oxidation. A pilot metatranscriptome of laboratory-raised N. vectensis was compared to the isolate genomes and indicated expression of ORFs from L. thiooxidans with predicted functions of motility, nutrient scavenging (Fe and P), polyhydroxyalkanoate synthesis for carbon storage, and selective permeability (porins). We hypothesize that such activities may mediate acclimation and persistence of bacteria in a N. vectensis holobiont defined by both internal and external gradients of chemicals and nutrients in a dynamic coastal habitat.
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Affiliation(s)
- Jia Y Har
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology Cambridge, MA, USA
| | - Tim Helbig
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology Cambridge, MA, USA
| | - Ju H Lim
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology Cambridge, MA, USA
| | - Samodha C Fernando
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology Cambridge, MA, USA
| | - Adam M Reitzel
- Department of Biological Sciences, University of North Carolina at Charlotte Charlotte, NC, USA
| | - Kevin Penn
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology Cambridge, MA, USA
| | - Janelle R Thompson
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology Cambridge, MA, USA
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39
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Roder C, Bayer T, Aranda M, Kruse M, Voolstra CR. Microbiome structure of the fungid coral Ctenactis echinata aligns with environmental differences. Mol Ecol 2015; 24:3501-11. [PMID: 26018191 PMCID: PMC4736464 DOI: 10.1111/mec.13251] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 05/07/2015] [Accepted: 05/22/2015] [Indexed: 12/31/2022]
Abstract
The significance of bacteria for eukaryotic functioning is increasingly recognized. Coral reef ecosystems critically rely on the relationship between coral hosts and their intracellular photosynthetic dinoflagellates, but the role of the associated bacteria remains largely theoretical. Here, we set out to relate coral‐associated bacterial communities of the fungid host species Ctenactis echinata to environmental settings (geographic location, substrate cover, summer/winter, nutrient and suspended matter concentrations) and coral host abundance. We show that bacterial diversity of C. echinata aligns with ecological differences between sites and that coral colonies sampled at the species’ preferred habitats are primarily structured by one bacterial taxon (genus Endozoicomonas) representing more than 60% of all bacteria. In contrast, host microbiomes from lower populated coral habitats are less structured and more diverse. Our study demonstrates that the content and structure of the coral microbiome aligns with environmental differences and denotes habitat adequacy. Availability of a range of coral host habitats might be important for the conservation of distinct microbiome structures and diversity.
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Affiliation(s)
- Cornelia Roder
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Till Bayer
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia.,GEOMAR Helmholtz Centre for Ocean Research, Kiel, 24105, Germany
| | - Manuel Aranda
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Maren Kruse
- Leibniz Center for Tropical Marine Ecology, Bremen, 28359, Germany
| | - Christian R Voolstra
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
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40
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Tout J, Siboni N, Messer LF, Garren M, Stocker R, Webster NS, Ralph PJ, Seymour JR. Increased seawater temperature increases the abundance and alters the structure of natural Vibrio populations associated with the coral Pocillopora damicornis. Front Microbiol 2015; 6:432. [PMID: 26042096 PMCID: PMC4435422 DOI: 10.3389/fmicb.2015.00432] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 04/22/2015] [Indexed: 12/22/2022] Open
Abstract
Rising seawater temperature associated with global climate change is a significant threat to coral health and is linked to increasing coral disease and pathogen-related bleaching events. We performed heat stress experiments with the coral Pocillopora damicornis, where temperature was increased to 31°C, consistent with the 2–3°C predicted increase in summer sea surface maxima. 16S rRNA amplicon sequencing revealed a large shift in the composition of the bacterial community at 31°C, with a notable increase in Vibrio, including known coral pathogens. To investigate the dynamics of the naturally occurring Vibrio community, we performed quantitative PCR targeting (i) the whole Vibrio community and (ii) the coral pathogen Vibrio coralliilyticus. At 31°C, Vibrio abundance increased by 2–3 orders of magnitude and V. coralliilyticus abundance increased by four orders of magnitude. Using a Vibrio-specific amplicon sequencing assay, we further demonstrated that the community composition shifted dramatically as a consequence of heat stress, with significant increases in the relative abundance of known coral pathogens. Our findings provide quantitative evidence that the abundance of potential coral pathogens increases within natural communities of coral-associated microbes as a consequence of rising seawater temperature and highlight the potential negative impacts of anthropogenic climate change on coral reef ecosystems.
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Affiliation(s)
- Jessica Tout
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, NSW, Australia
| | - Nachshon Siboni
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, NSW, Australia
| | - Lauren F Messer
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, NSW, Australia
| | - Melissa Garren
- Ralph M. Parsons Laboratory, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology Cambridge, MA, USA
| | - Roman Stocker
- Ralph M. Parsons Laboratory, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology Cambridge, MA, USA
| | - Nicole S Webster
- Australian Institute of Marine Science Townsville, QLD, Australia
| | - Peter J Ralph
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, NSW, Australia
| | - Justin R Seymour
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, NSW, Australia
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41
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Thompson JR, Rivera HE, Closek CJ, Medina M. Microbes in the coral holobiont: partners through evolution, development, and ecological interactions. Front Cell Infect Microbiol 2015; 4:176. [PMID: 25621279 PMCID: PMC4286716 DOI: 10.3389/fcimb.2014.00176] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 12/04/2014] [Indexed: 01/18/2023] Open
Abstract
In the last two decades, genetic and genomic studies have revealed the astonishing diversity and ubiquity of microorganisms. Emergence and expansion of the human microbiome project has reshaped our thinking about how microbes control host health-not only as pathogens, but also as symbionts. In coral reef environments, scientists have begun to examine the role that microorganisms play in coral life history. Herein, we review the current literature on coral-microbe interactions within the context of their role in evolution, development, and ecology. We ask the following questions, first posed by McFall-Ngai et al. (2013) in their review of animal evolution, with specific attention to how coral-microbial interactions may be affected under future environmental conditions: (1) How do corals and their microbiome affect each other's genomes? (2) How does coral development depend on microbial partners? (3) How is homeostasis maintained between corals and their microbial symbionts? (4) How can ecological approaches deepen our understanding of the multiple levels of coral-microbial interactions? Elucidating the role that microorganisms play in the structure and function of the holobiont is essential for understanding how corals maintain homeostasis and acclimate to changing environmental conditions.
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Affiliation(s)
- Janelle R. Thompson
- Civil and Environmental Engineering Department, Massachusetts Institute of TechnologyCambridge, MA, USA
| | - Hanny E. Rivera
- Civil and Environmental Engineering Department, Massachusetts Institute of TechnologyCambridge, MA, USA
- Department of Biology, Woods Hole Oceanographic InstitutionWoods Hole, MA, USA
| | - Collin J. Closek
- Department of Biology, Pennsylvania State UniversityUniversity Park, PA, USA
| | - Mónica Medina
- Department of Biology, Pennsylvania State UniversityUniversity Park, PA, USA
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