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Hill LJ, Messias CSMDA, Vilela CLS, Garritano AN, Villela HDM, do Carmo FL, Thomas T, Peixoto RS. Bacteria associated with the in hospite Symbiodiniaceae's phycosphere. iScience 2024; 27:109531. [PMID: 38585661 PMCID: PMC10995889 DOI: 10.1016/j.isci.2024.109531] [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: 05/16/2023] [Revised: 12/23/2023] [Accepted: 03/16/2024] [Indexed: 04/09/2024] Open
Abstract
Symbiotic interactions between Symbiodiniaceae and bacteria are still poorly explored, especially those in hospite. Here, we adapted a technique that allows for the enrichment of intact and metabolically active in hospite Symbiodiniaceae cells (ihSC) and their associated bacteria from the tissue of the model coral Pocillopora damicornis, using a discontinuous gradient of solution of isotonic Percoll (SIP). The ihSC were concentrated in the 50% SIP fraction, as determined by microscopy. The presence of bacteria associated with ihSC was confirmed by fluorescence in situ hybridization, while microbiome analysis indicated that bacteria of the families Halieaceae, Flavobacteriaceae, and Alcanivoraceae are significantly associated with ihSC. Extracellular vesicles that could be exuding molecules were detected on the symbiosome membranes. Our technique and data contribute to elucidate ihSC-bacteria interactions.
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Affiliation(s)
- Lilian Jorge Hill
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | | | - Caren Leite Spindola Vilela
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | - Alessandro N Garritano
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Helena Dias Muller Villela
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955, Kingdom of Saudi Arabia
| | - Flavia Lima do Carmo
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | - Torsten Thomas
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Raquel S. Peixoto
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955, Kingdom of Saudi Arabia
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Shoguchi E. Gene clusters for biosynthesis of mycosporine-like amino acids in dinoflagellate nuclear genomes: Possible recent horizontal gene transfer between species of Symbiodiniaceae (Dinophyceae). JOURNAL OF PHYCOLOGY 2022; 58:1-11. [PMID: 34699617 PMCID: PMC9298759 DOI: 10.1111/jpy.13219] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 10/01/2021] [Accepted: 10/12/2021] [Indexed: 05/12/2023]
Abstract
Global warming increases the temperature of the ocean surface, which can disrupt dinoflagellate-coral symbioses and result in coral bleaching. Photosynthetic dinoflagellates of the family Symbiodiniaceae include bleaching-tolerant and bleaching-sensitive coral symbionts. Therefore, understanding the molecular mechanisms for changing symbiont diversity is potentially useful to assist recovery of coral holobionts (corals and their associated microbes, including multiple species of Symbiodiniaceae), although sexual reproduction has not been observed in the Symbiodiniaceae. Recent molecular phylogenetic analyses estimate that the Symbiodiniaceae appeared 160 million years ago and diversified into 15 groups, five genera of which now have available draft genomes (i.e., Symbiodinium, Durusdinium, Breviolum, Fugacium, and Cladocopium). Comparative genomic analyses have suggested that crown groups have fewer gene families than early-diverging groups, although many genes that were probably acquired via gene duplications and horizontal gene transfers (HGTs) have been found in each decoded genome. Because UV stress is likely a contributor to coral bleaching, and because the highly conserved gene cluster for mycosporine-like amino acid (MAA) biosynthesis has been found in thermal-tolerant symbiont genomes, I reviewed genomic features of the Symbiodiniaceae, focusing on possible acquisition of a biosynthetic gene cluster for MAAs, which absorb UV radiation. On the basis of highly conserved noncoding sequences, I hypothesized that HGTs have occurred among members of the Symbiodiniaceae and have contributed to the diversification of Symbiodiniaceae-host relationships. Finally, I proposed that bleaching tolerance may be strengthened by multiple MAAs from both symbiotic dinoflagellates and corals.
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Affiliation(s)
- Eiichi Shoguchi
- Marine Genomics UnitOkinawa Institute of Science and Technology Graduate UniversityOnnaOkinawa904‐0495Japan
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Varasteh T, Tschoeke D, Silva-Lima AW, Thompson C, Thompson F. Transcriptome of the coral Mussismilia braziliensis symbiont Sargassococcus simulans. Mar Genomics 2021; 61:100912. [PMID: 34710723 DOI: 10.1016/j.margen.2021.100912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 10/11/2021] [Accepted: 10/12/2021] [Indexed: 10/20/2022]
Abstract
A transcriptomic profile of Sargassococcus simulans 103B3, isolated from the coral Mussismilia braziliensis in Abrolhos, Brazil, is presented. A total of 631.3 Mbp transcriptomic sequences were obtained. The transcriptomic analysis disclosed transcripts coding for enzymes relevant for holobiont health including genes involved in I. Light harvesting complex (LHC), II. Organic matter utilization and III. Oxidative stress and microbial defense (Oxidoreductases) enzymes. The isolate exhibited transcripts for uptake and utilization of a variety of carbon sources, such as sugars, oligopeptides, and amino acids by ATP-binding cassette (ABC) and tripartite ATP-independent periplasmic (TRAP) type transporters. Collectively, these enzymes indicate a mixotrophic metabolism in S. simulans with metabolic capabilities for the degradation of an array of organic carbon compounds in the coral Mussismilia and light harvesting within the low-light environments of Abrolhos.
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Affiliation(s)
- Tooba Varasteh
- Institute of Biology and Sage-Coppe, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
| | - Diogo Tschoeke
- Institute of Biology and Sage-Coppe, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Arthur W Silva-Lima
- Institute of Biology and Sage-Coppe, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Cristiane Thompson
- Institute of Biology and Sage-Coppe, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Fabiano Thompson
- Institute of Biology and Sage-Coppe, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
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Yuyama I, Ugawa N, Hashimoto T. Transcriptome Analysis of Durusdinium Associated with the Transition from Free-Living to Symbiotic. Microorganisms 2021; 9:microorganisms9081560. [PMID: 34442639 PMCID: PMC8399598 DOI: 10.3390/microorganisms9081560] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/23/2021] [Accepted: 07/12/2021] [Indexed: 12/20/2022] Open
Abstract
To detect the change during coral-dinoflagellate endosymbiosis establishment, we compared transcriptome data derived from free-living and symbiotic Durusdinium, a coral symbiont genus. We detected differentially expressed genes (DEGs) using two statistical methods (edgeR using raw read data and the Student's t-test using bootstrap resampling read data) and detected 1214 DEGs between the symbiotic and free-living states, which we subjected to gene ontology (GO) analysis. Based on the representative GO terms and 50 DEGs with low false discovery rates, changes in Durusdinium during endosymbiosis were predicted. The expression of genes related to heat-shock proteins and microtubule-related proteins tended to decrease, and those of photosynthesis genes tended to increase. In addition, a phylogenetic analysis of dapdiamide A (antibiotics) synthase, which was upregulated among the 50 DEGs, confirmed that two genera in the Symbiodiniaceae family, Durusdinium and Symbiodinium, retain dapdiamide A synthase. This antibiotic synthase-related gene may contribute to the high stress tolerance documented in Durusdinium species, and its increased expression during endosymbiosis suggests increased antibacterial activity within the symbiotic complex.
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Affiliation(s)
- Ikuko Yuyama
- Graduate School of Science and Technology for Innovation, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8512, Japan
- Correspondence: ; Tel.: +81-83-933-5835
| | - Naoto Ugawa
- Faculty of Life and Environmental Sciences, University of Tsukuba, 111 Tennodai, Tsukuba, Ibaraki 305-8577, Japan; (N.U.); (T.H.)
| | - Tetsuo Hashimoto
- Faculty of Life and Environmental Sciences, University of Tsukuba, 111 Tennodai, Tsukuba, Ibaraki 305-8577, Japan; (N.U.); (T.H.)
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Zhou L, Wu S, Gu W, Wang L, Wang J, Gao S, Wang G. Photosynthesis acclimation under severely fluctuating light conditions allows faster growth of diatoms compared with dinoflagellates. BMC PLANT BIOLOGY 2021; 21:164. [PMID: 33794787 PMCID: PMC8015109 DOI: 10.1186/s12870-021-02902-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 02/11/2021] [Indexed: 05/20/2023]
Abstract
BACKGROUND Diatoms contribute 20% of the global primary production and are adaptable in dynamic environments. Diatoms always bloom earlier in the annual phytoplankton succession instead of dinoflagellates. However, how diatoms acclimate to a dynamic environment, especially under changing light conditions, remains unclear. RESULTS We compared the growth and photosynthesis under fluctuating light conditions of red tide diatom Skeletonema costatum, red tide dinoflagellate Amphidinium carterae, Prorocentrum donghaiense, Karenia mikimotoi, model diatom Phaeodactylum tricornutum, Thalassiosira pseudonana and model dinoflagellate Dinophycae Symbiodinium. Diatoms grew faster and maintained a consistently higher level of photosynthesis. Diatoms were sensitive to the specific inhibitor of Proton Gradient Regulation 5 (PGR5) depending photosynthetic electron flow, which is a crucial mechanism to protect their photosynthetic apparatus under fluctuating light. In contrast, the dinoflagellates were not sensitive to this inhibitor. Therefore, we investigate how PGR5 functions under light fluctuations in the model diatom P. tricornutum by knocking down and overexpressing PGR5. Overexpression of PGR5 reduced the photosystem I acceptor side limitation (Y (NA)) and increased growth rate under severely fluctuating light in contrast to the knockdown of PGR5. CONCLUSION Diatoms acclimatize to fluctuating light conditions better than dinoflagellates. PGR5 in diatoms can regulate their photosynthetic electron flow and accelerate their growth under severe light fluctuation, supporting fast biomass accumulation under dynamic environments in pioneer blooms.
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Affiliation(s)
- Lu Zhou
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- College of Earth Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Songcui Wu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Wenhui Gu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Lijun Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Jing Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Shan Gao
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| | - Guangce Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
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Liu T, Cui Y, Jia X, Zhang J, Li R, Yu Y, Jia S, Qu J, Wang X. OGDA: a comprehensive organelle genome database for algae. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2020:6008697. [PMID: 33247934 PMCID: PMC7698662 DOI: 10.1093/database/baaa097] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 09/27/2020] [Accepted: 11/16/2020] [Indexed: 11/20/2022]
Abstract
Algae are the oldest taxa on Earth, with an evolutionary relationship that spans prokaryotes (Cyanobacteria) and eukaryotes. A long evolutionary history has led to high algal diversity. Their organelle DNAs are characterized by uniparental inheritance and a compact genome structure compared with nuclear genomes; thus, they are efficient molecular tools for the analysis of gene structure, genome structure, organelle function and evolution. However, an integrated organelle genome database for algae, which could enable users to both examine and use relevant data, has not previously been developed. Therefore, to provide an organelle genome platform for algae, we have developed a user-friendly database named Organelle Genome Database for Algae (OGDA, http://ogda.ytu.edu.cn/). OGDA contains organelle genome data either retrieved from several public databases or sequenced in our laboratory (Laboratory of Genetics and Breeding of Marine Organism [MOGBL]), which are continuously updated. The first release of OGDA contains 1055 plastid genomes and 755 mitochondrial genomes. Additionally, a variety of applications have been integrated into this platform to analyze the structural characteristics, collinearity and phylogeny of organellar genomes for algae. This database represents a useful tool for users, enabling the rapid retrieval and analysis of information related to organellar genomes for biological discovery.
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Affiliation(s)
- Tao Liu
- College of Life Sciences, Yantai University, No.30 Qingquan Road, Laishan District, Yantai, 264005, Shandong, P.R. China.,College of Marine Life Sciences, Ocean University of China, No.5 Yushan Road, Shinan District, Qingdao 266003, Shandong, P.R. China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), No.9 Jintang Road, Xiangzhou District, Zhuhai 519000, Guangdong, P.R. China
| | - Yutong Cui
- College of Life Sciences, Yantai University, No.30 Qingquan Road, Laishan District, Yantai, 264005, Shandong, P.R. China
| | - Xuli Jia
- College of Marine Life Sciences, Ocean University of China, No.5 Yushan Road, Shinan District, Qingdao 266003, Shandong, P.R. China
| | - Jing Zhang
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), No.3501 Daxue Road, Changqing District, Jinan 250353, Shandong, P.R. China and
| | - Ruoran Li
- College of Life Sciences, Yantai University, No.30 Qingquan Road, Laishan District, Yantai, 264005, Shandong, P.R. China
| | - Yahui Yu
- College of Marine Life Sciences, Ocean University of China, No.5 Yushan Road, Shinan District, Qingdao 266003, Shandong, P.R. China
| | - Shangang Jia
- College of Grassland Science and Technology, China Agricultural University, No.2 Yuanmingyuan Xi Road, Haidian District, Beijing, 100193, P.R. China
| | - Jiangyong Qu
- College of Life Sciences, Yantai University, No.30 Qingquan Road, Laishan District, Yantai, 264005, Shandong, P.R. China
| | - Xumin Wang
- College of Life Sciences, Yantai University, No.30 Qingquan Road, Laishan District, Yantai, 264005, Shandong, P.R. China
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