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Matthews JL, Ueland M, Bartels N, Lawson CA, Lockwood TE, Wu Y, Camp EF. Multi-Chemical Omics Analysis of the Symbiodiniaceae Durusdinium trenchii under Heat Stress. Microorganisms 2024; 12:317. [PMID: 38399721 PMCID: PMC10893086 DOI: 10.3390/microorganisms12020317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 01/22/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
The urgency of responding to climate change for corals necessitates the exploration of innovative methods to swiftly enhance our understanding of crucial processes. In this study, we employ an integrated chemical omics approach, combining elementomics, metabolomics, and volatilomics methodologies to unravel the biochemical pathways associated with the thermal response of the coral symbiont, Symbiodiniaceae Durusdinium trenchii. We outline the complimentary sampling approaches and discuss the standardised data corrections used to allow data integration and comparability. Our findings highlight the efficacy of individual methods in discerning differences in the biochemical response of D. trenchii under both control and stress-inducing temperatures. However, a deeper insight emerges when these methods are integrated, offering a more comprehensive understanding, particularly regarding oxidative stress pathways. Employing correlation network analysis enhanced the interpretation of volatile data, shedding light on the potential metabolic origins of volatiles with undescribed functions and presenting promising candidates for further exploration. Elementomics proves to be less straightforward to integrate, likely due to no net change in elements but rather elements being repurposed across compounds. The independent and integrated data from this study informs future omic profiling studies and recommends candidates for targeted research beyond Symbiodiniaceae biology. This study highlights the pivotal role of omic integration in advancing our knowledge, addressing critical gaps, and guiding future research directions in the context of climate change and coral reef preservation.
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Affiliation(s)
- Jennifer L. Matthews
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Maiken Ueland
- Centre for Forensic Sciences, School of Mathematical and Physical Sciences, University of Technology Sydney, Ultimo, NSW 2007, Australia
- Hyphenated Mass Spectrometry Laboratory, School of Mathematical and Physical Sciences, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Natasha Bartels
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Caitlin A. Lawson
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007, Australia
- School of Environmental and Life Sciences, University of Newcastle, Ourimbah, NSW 2258, Australia
| | - Thomas E. Lockwood
- Hyphenated Mass Spectrometry Laboratory, School of Mathematical and Physical Sciences, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Yida Wu
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Emma F. Camp
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007, Australia
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Haydon TD, Matthews JL, Seymour JR, Raina JB, Seymour JE, Chartrand K, Camp EF, Suggett DJ. Metabolomic signatures of corals thriving across extreme reef habitats reveal strategies of heat stress tolerance. Proc Biol Sci 2023; 290:20221877. [PMID: 36750192 PMCID: PMC9904954 DOI: 10.1098/rspb.2022.1877] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 01/11/2023] [Indexed: 02/09/2023] Open
Abstract
Anthropogenic stressors continue to escalate worldwide, driving unprecedented declines in reef environmental conditions and coral health. One approach to better understand how corals can function in the future is to examine coral populations that thrive within present day naturally extreme habitats. We applied untargeted metabolomics (gas chromatography-mass spectrometry (GC-MS)) to contrast metabolite profiles of Pocillopora acuta colonies from hot, acidic and deoxygenated mangrove environments versus those from adjacent reefs. Under ambient temperatures, P. acuta predominantly associated with endosymbionts of the genera Cladocopium (reef) or Durusdinium (mangrove), exhibiting elevated metabolism in mangrove through energy-generating and biosynthesis pathways compared to reef populations. Under transient heat stress, P. acuta endosymbiont associations were unchanged. Reef corals bleached and exhibited extensive shifts in symbiont metabolic profiles (whereas host metabolite profiles were unchanged). By contrast, mangrove populations did not bleach and solely the host metabolite profiles were altered, including cellular responses in inter-partner signalling, antioxidant capacity and energy storage. Thus mangrove P. acuta populations resist periodically high-temperature exposure via association with thermally tolerant endosymbionts coupled with host metabolic plasticity. Our findings highlight specific metabolites that may be biomarkers of heat tolerance, providing novel insight into adaptive coral resilience to elevated temperatures.
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Affiliation(s)
- Trent D. Haydon
- Center for Genomics and Systems Biology, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, UAE
- Faculty of Science, Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales 2007, Australia
| | - Jennifer L. Matthews
- Faculty of Science, Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales 2007, Australia
| | - Justin R. Seymour
- Faculty of Science, Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales 2007, Australia
| | - Jean-Baptiste Raina
- Faculty of Science, Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales 2007, Australia
| | - Jamie E. Seymour
- Division of Tropical Health and Medicine, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD 4811, Australia
| | - Kathryn Chartrand
- Centre for tropical Water and Aquatic Ecosystem Research, James Cook University, Cairns, QLD 4811, Australia
| | - Emma F. Camp
- Faculty of Science, Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales 2007, Australia
| | - David J. Suggett
- Faculty of Science, Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales 2007, Australia
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Davies SW, Gamache MH, Howe-Kerr LI, Kriefall NG, Baker AC, Banaszak AT, Bay LK, Bellantuono AJ, Bhattacharya D, Chan CX, Claar DC, Coffroth MA, Cunning R, Davy SK, del Campo J, Díaz-Almeyda EM, Frommlet JC, Fuess LE, González-Pech RA, Goulet TL, Hoadley KD, Howells EJ, Hume BCC, Kemp DW, Kenkel CD, Kitchen SA, LaJeunesse TC, Lin S, McIlroy SE, McMinds R, Nitschke MR, Oakley CA, Peixoto RS, Prada C, Putnam HM, Quigley K, Reich HG, Reimer JD, Rodriguez-Lanetty M, Rosales SM, Saad OS, Sampayo EM, Santos SR, Shoguchi E, Smith EG, Stat M, Stephens TG, Strader ME, Suggett DJ, Swain TD, Tran C, Traylor-Knowles N, Voolstra CR, Warner ME, Weis VM, Wright RM, Xiang T, Yamashita H, Ziegler M, Correa AMS, Parkinson JE. Building consensus around the assessment and interpretation of Symbiodiniaceae diversity. PeerJ 2023; 11:e15023. [PMID: 37151292 PMCID: PMC10162043 DOI: 10.7717/peerj.15023] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 02/17/2023] [Indexed: 05/09/2023] Open
Abstract
Within microeukaryotes, genetic variation and functional variation sometimes accumulate more quickly than morphological differences. To understand the evolutionary history and ecology of such lineages, it is key to examine diversity at multiple levels of organization. In the dinoflagellate family Symbiodiniaceae, which can form endosymbioses with cnidarians (e.g., corals, octocorals, sea anemones, jellyfish), other marine invertebrates (e.g., sponges, molluscs, flatworms), and protists (e.g., foraminifera), molecular data have been used extensively over the past three decades to describe phenotypes and to make evolutionary and ecological inferences. Despite advances in Symbiodiniaceae genomics, a lack of consensus among researchers with respect to interpreting genetic data has slowed progress in the field and acted as a barrier to reconciling observations. Here, we identify key challenges regarding the assessment and interpretation of Symbiodiniaceae genetic diversity across three levels: species, populations, and communities. We summarize areas of agreement and highlight techniques and approaches that are broadly accepted. In areas where debate remains, we identify unresolved issues and discuss technologies and approaches that can help to fill knowledge gaps related to genetic and phenotypic diversity. We also discuss ways to stimulate progress, in particular by fostering a more inclusive and collaborative research community. We hope that this perspective will inspire and accelerate coral reef science by serving as a resource to those designing experiments, publishing research, and applying for funding related to Symbiodiniaceae and their symbiotic partnerships.
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Affiliation(s)
- Sarah W. Davies
- Department of Biology, Boston University, Boston, MA, United States
| | - Matthew H. Gamache
- Department of Integrative Biology, University of South Florida, Tampa, FL, United States
| | | | | | - Andrew C. Baker
- Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL, United States
| | - Anastazia T. Banaszak
- Unidad Académica de Sistemas Arrecifales, Universidad Nacional Autónoma de México, Puerto Morelos, Mexico
| | - Line Kolind Bay
- Australian Institute of Marine Science, Townsville, Australia
| | - Anthony J. Bellantuono
- Department of Biological Sciences, Florida International University, Miami, FL, United States
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, United States
| | - Cheong Xin Chan
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Danielle C. Claar
- Nearshore Habitat Program, Washington State Department of Natural Resources, Olympia, WA, USA
| | | | - Ross Cunning
- Daniel P. Haerther Center for Conservation and Research, John G. Shedd Aquarium, Chicago, IL, United States
| | - Simon K. Davy
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Javier del Campo
- Institut de Biologia Evolutiva (CSIC - Universitat Pompeu Fabra), Barcelona, Catalonia, Spain
| | | | - Jörg C. Frommlet
- Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
| | - Lauren E. Fuess
- Department of Biology, Texas State University, San Marcos, TX, United States
| | - Raúl A. González-Pech
- Department of Integrative Biology, University of South Florida, Tampa, FL, United States
- Department of Biology, Pennsylvania State University, State College, PA, United States
| | - Tamar L. Goulet
- Department of Biology, University of Mississippi, University, MS, United States
| | - Kenneth D. Hoadley
- Department of Biological Sciences, University of Alabama—Tuscaloosa, Tuscaloosa, AL, United States
| | - Emily J. Howells
- National Marine Science Centre, Faculty of Science and Engineering, Southern Cross University, Coffs Harbour, NSW, Australia
| | | | - Dustin W. Kemp
- Department of Biology, University of Alabama—Birmingham, Birmingham, Al, United States
| | - Carly D. Kenkel
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Sheila A. Kitchen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
| | - Todd C. LaJeunesse
- Department of Biology, Pennsylvania State University, University Park, PA, United States
| | - Senjie Lin
- Department of Marine Sciences, University of Connecticut, Mansfield, CT, United States
| | - Shelby E. McIlroy
- Swire Institute of Marine Science, School of Biological Sciences, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Ryan McMinds
- Center for Global Health and Infectious Disease Research, University of South Florida, Tampa, FL, United States
| | | | - Clinton A. Oakley
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Raquel S. Peixoto
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Carlos Prada
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, United States
| | - Hollie M. Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, United States
| | | | - Hannah G. Reich
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, United States
| | - James Davis Reimer
- Department of Biology, Chemistry and Marine Sciences, Faculty of Science, University of the Ryukyus, Nishihara, Okinawa, Japan
| | | | - Stephanie M. Rosales
- The Cooperative Institute For Marine and Atmospheric Studies, Miami, FL, United States
| | - Osama S. Saad
- Department of Biological Oceanography, Red Sea University, Port-Sudan, Sudan
| | - Eugenia M. Sampayo
- School of Biological Sciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Scott R. Santos
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, United States
| | - Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Edward G. Smith
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Michael Stat
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, Australia
| | - Timothy G. Stephens
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, United States
| | - Marie E. Strader
- Department of Biology, Texas A&M University, College Station, TX, United States
| | - David J. Suggett
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Timothy D. Swain
- Department of Marine and Environmental Science, Nova Southeastern University, Dania Beach, FL, United States
| | - Cawa Tran
- Department of Biology, University of San Diego, San Diego, CA, United States
| | - Nikki Traylor-Knowles
- Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL, United States
| | | | - Mark E. Warner
- School of Marine Science and Policy, University of Delaware, Lewes, DE, United States
| | - Virginia M. Weis
- Department of Integrative Biology, Oregon State University, Corvallis, OR, United States
| | - Rachel M. Wright
- Department of Biological Sciences, Southern Methodist University, Dallas, TX, United States
| | - Tingting Xiang
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Hiroshi Yamashita
- Fisheries Technology Institute, Japan Fisheries Research and Education Agency, Ishigaki, Okinawa, Japan
| | - Maren Ziegler
- Department of Animal Ecology & Systematics, Justus Liebig University Giessen (Germany), Giessen, Germany
| | | | - John Everett Parkinson
- Department of Integrative Biology, University of South Florida, Tampa, FL, United States
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Proteome metabolome and transcriptome data for three Symbiodiniaceae under ambient and heat stress conditions. Sci Data 2022; 9:153. [PMID: 35383179 PMCID: PMC8983644 DOI: 10.1038/s41597-022-01258-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 03/14/2022] [Indexed: 12/12/2022] Open
Abstract
The Symbiodiniaceae are a taxonomically and functionally diverse family of marine dinoflagellates. Their symbiotic relationship with invertebrates such as scleractinian corals has made them the focus of decades of research to resolve the underlying biology regulating their sensitivity to stressors, particularly thermal stress. Research to-date suggests that Symbiodiniaceae stress sensitivity is governed by a complex interplay between phylogenetic dependent and independent traits (diversity of characteristics of a species). Consequently, there is a need for datasets that simultaneously broadly resolve molecular and physiological processes under stressed and non-stressed conditions. Therefore, we provide a dataset simultaneously generating transcriptome, metabolome, and proteome data for three ecologically important Symbiodiniaceae isolates under nutrient replete growth conditions and two temperature treatments (ca. 26 °C and 32 °C). Elevated sea surface temperature is primarily responsible for coral bleaching events that occur when the coral-Symbiodiniaceae relationship has been disrupted. Symbiodiniaceae can strongly influence their host's response to thermal stress and consequently it is necessary to resolve drivers of Symbiodiniaceae heat stress tolerance. We anticipate these datasets to expand our understanding on the key genotypic and functional properties that influence the sensitivities of Symbiodiniaceae to thermal stress.
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5
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Abstract
Pseudo random and true random sequence generators are important components in many scientific and technical fields, playing a fundamental role in the application of the Monte Carlo methods and stochastic simulation. Unfortunately, the quality of the sequences produced by these generators are not always ideal in terms of randomness for many applications. We present a new nonlinear filter design that improves the output sequences of common pseudo random generators in terms of statistical randomness. Taking inspiration from techniques employed in symmetric ciphers, it is based on four seed-dependent substitution boxes, an evolving internal state register, and the combination of different types of operations with the aim of diffusing nonrandom patterns in the input sequence. For statistical analysis we employ a custom initial battery of tests and well-regarded comprehensive packages such as TestU01 and PractRand. Analysis results show that our proposal achieves excellent randomness characteristics and can even transform nonrandom sources (such as a simple counter generator) into perfectly usable pseudo random sequences. Furthermore, performance is excellent while storage consumption is moderate, enabling its implementation in embedded or low power computational platforms.
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Suescún-Bolívar LP, Thomé PE. The specific inhibition of glycerol synthesis and the phosphorylation of a putative MAPK give insight into the mechanism of osmotic sensing in a dinoflagellate symbiont. J Eukaryot Microbiol 2021; 69:e12883. [PMID: 34936156 DOI: 10.1111/jeu.12883] [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: 09/22/2021] [Revised: 12/03/2021] [Accepted: 12/14/2021] [Indexed: 11/30/2022]
Abstract
Signaling pathways are fundamental for the establishment and maintenance of diverse symbioses. The symbiosis of cnidarians and dinoflagellate algae is the foundation for the ecological success of coral reefs, involving the transfer of photosynthetic products from symbiont to host. However, signal transduction pathways for this symbiosis remain uncharacterized. Cultured and natural cnidarian symbionts can produce glycerol, one of the main translocated photosynthates. Here, we investigate whether a signal transduction pathway may be involved in inducing glycerol synthesis in cultured symbionts under an osmotic stress model. We evaluated the effect of specific inhibitors of the main transduction pathways, p38, JNK, and ERK 1/2 in Brevolium minutum, the symbiont of the Aiptasia model system. We found that glycerol production and the specific activity of the enzyme Gpdh were selectively inhibited by a p38 MAPK inhibitor. Additionally, the phosphorylation of a putative p38-like protein was rapidly detected. Finally, we studied the presence of each of the components of the p38 MAPK pathway in silico, in genomes and transcriptomes reported up to date for different symbiont types. We propose a model for the arrangement of this pathway in the family of dinoflagellate symbionts known as Symbiodiniaceae.
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Affiliation(s)
- L P Suescún-Bolívar
- Universidad Nacional Autónoma de México Instituto de Ciencias del Mar y Limnología Unidad Académica de Sistemas Arrecifales Puerto Morelos, Puerto Morelos, Mexico
| | - P E Thomé
- Universidad Nacional Autónoma de México Instituto de Ciencias del Mar y Limnología Unidad Académica de Sistemas Arrecifales Puerto Morelos, Puerto Morelos, Mexico
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Affiliation(s)
- Todd C. LaJeunesse
- Department of Biology, 208 Mueller Laboratory Penn State University Park Pennsylvania 16802 USA
| | - Matthew R. Nitschke
- School of Biological Sciences Victoria University of Wellington, Kelburn Parade Wellington 6012 New Zealand
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Shoguchi E, Beedessee G, Hisata K, Tada I, Narisoko H, Satoh N, Kawachi M, Shinzato C. A New Dinoflagellate Genome Illuminates a Conserved Gene Cluster Involved in Sunscreen Biosynthesis. Genome Biol Evol 2020; 13:5955767. [PMID: 33146374 PMCID: PMC7875005 DOI: 10.1093/gbe/evaa235] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/28/2020] [Indexed: 12/18/2022] Open
Abstract
Photosynthetic dinoflagellates of the Family Symbiodiniaceae live symbiotically with many organisms that inhabit coral reefs and are currently classified into fifteen groups, including seven genera. Draft genomes from four genera, Symbiodinium, Breviolum, Fugacium, and Cladocopium, which have been isolated from corals, have been reported. However, no genome is available from the genus Durusdinium, which occupies an intermediate phylogenetic position in the Family Symbiodiniaceae and is well known for thermal tolerance (resistance to bleaching). We sequenced, assembled, and annotated the genome of Durusdinium trenchii, isolated from the coral, Favia speciosa, in Okinawa, Japan. Assembled short reads amounted to 670 Mb with ∼47% GC content. This GC content was intermediate among taxa belonging to the Symbiodiniaceae. Approximately 30,000 protein-coding genes were predicted in the D. trenchii genome, fewer than in other genomes from the Symbiodiniaceae. However, annotations revealed that the D. trenchii genome encodes a cluster of genes for synthesis of mycosporine-like amino acids, which absorb UV radiation. Interestingly, a neighboring gene in the cluster encodes a glucose-methanol-choline oxidoreductase with a flavin adenine dinucleotide domain that is also found in Symbiodinium tridacnidorum. This conservation seems to partially clarify an ancestral genomic structure in the Symbiodiniaceae and its loss in late-branching lineages, including Breviolum and Cladocopium, after splitting from the Durusdinium lineage. Our analysis suggests that approximately half of the taxa in the Symbiodiniaceae may maintain the ability to synthesize mycosporine-like amino acids. Thus, this work provides a significant genomic resource for understanding the genomic diversity of Symbiodiniaceae in corals.
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Affiliation(s)
- Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Girish Beedessee
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Kanako Hisata
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Ipputa Tada
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan.,Department of Genetics, The Graduate University for Advanced Studies, SOKENDAI, Mishima, Shizuoka, Japan
| | - Haruhi Narisoko
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Masanobu Kawachi
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, Tsukuba, Ibaraki, Japan
| | - Chuya Shinzato
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan.,Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
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Kumar G, Shekh A, Jakhu S, Sharma Y, Kapoor R, Sharma TR. Bioengineering of Microalgae: Recent Advances, Perspectives, and Regulatory Challenges for Industrial Application. Front Bioeng Biotechnol 2020; 8:914. [PMID: 33014997 PMCID: PMC7494788 DOI: 10.3389/fbioe.2020.00914] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 07/15/2020] [Indexed: 01/14/2023] Open
Abstract
Microalgae, due to their complex metabolic capacity, are being continuously explored for nutraceuticals, pharmaceuticals, and other industrially important bioactives. However, suboptimal yield and productivity of the bioactive of interest in local and robust wild-type strains are of perennial concerns for their industrial applications. To overcome such limitations, strain improvement through genetic engineering could play a decisive role. Though the advanced tools for genetic engineering have emerged at a greater pace, they still remain underused for microalgae as compared to other microorganisms. Pertaining to this, we reviewed the progress made so far in the development of molecular tools and techniques, and their deployment for microalgae strain improvement through genetic engineering. The recent availability of genome sequences and other omics datasets form diverse microalgae species have remarkable potential to guide strategic momentum in microalgae strain improvement program. This review focuses on the recent and significant improvements in the omics resources, mutant libraries, and high throughput screening methodologies helpful to augment research in the model and non-model microalgae. Authors have also summarized the case studies on genetically engineered microalgae and highlight the opportunities and challenges that are emerging from the current progress in the application of genome-editing to facilitate microalgal strain improvement. Toward the end, the regulatory and biosafety issues in the use of genetically engineered microalgae in commercial applications are described.
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Affiliation(s)
- Gulshan Kumar
- Agricultural Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), Sahibzada Ajit Singh Nagar, India
| | - Ajam Shekh
- Plant Cell Biotechnology Department, CSIR-Central Food Technological Research Institute (CFTRI), Mysuru, India
| | - Sunaina Jakhu
- Agricultural Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), Sahibzada Ajit Singh Nagar, India
| | - Yogesh Sharma
- Agricultural Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), Sahibzada Ajit Singh Nagar, India
| | - Ritu Kapoor
- Agricultural Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), Sahibzada Ajit Singh Nagar, India
| | - Tilak Raj Sharma
- Division of Crop Science, Indian Council of Agricultural Research, New Delhi, India
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Morgans CA, Hung JY, Bourne DG, Quigley KM. Symbiodiniaceae probiotics for use in bleaching recovery. Restor Ecol 2020. [DOI: 10.1111/rec.13069] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Carys A. Morgans
- College of Science and EngineeringJames Cook University Townsville Queensland 4814 Australia
| | - Julia Y. Hung
- College of Science and EngineeringJames Cook University Townsville Queensland 4814 Australia
| | - David G. Bourne
- College of Science and EngineeringJames Cook University Townsville Queensland 4814 Australia
- Australian Institute of Marine Science Townsville Queensland 4816 Australia
| | - Kate M. Quigley
- College of Science and EngineeringJames Cook University Townsville Queensland 4814 Australia
- Australian Institute of Marine Science Townsville Queensland 4816 Australia
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A Review: The Role of Reactive Oxygen Species in Mass Coral Bleaching. PHOTOSYNTHESIS IN ALGAE: BIOCHEMICAL AND PHYSIOLOGICAL MECHANISMS 2020. [DOI: 10.1007/978-3-030-33397-3_17] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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12
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Omics Analysis for Dinoflagellates Biology Research. Microorganisms 2019; 7:microorganisms7090288. [PMID: 31450827 PMCID: PMC6780300 DOI: 10.3390/microorganisms7090288] [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: 07/09/2019] [Revised: 08/20/2019] [Accepted: 08/21/2019] [Indexed: 01/13/2023] Open
Abstract
Dinoflagellates are important primary producers for marine ecosystems and are also responsible for certain essential components in human foods. However, they are also notorious for their ability to form harmful algal blooms, and cause shellfish poisoning. Although much work has been devoted to dinoflagellates in recent decades, our understanding of them at a molecular level is still limited owing to some of their challenging biological properties, such as large genome size, permanently condensed liquid-crystalline chromosomes, and the 10-fold lower ratio of protein to DNA than other eukaryotic species. In recent years, omics technologies, such as genomics, transcriptomics, proteomics, and metabolomics, have been applied to the study of marine dinoflagellates and have uncovered many new physiological and metabolic characteristics of dinoflagellates. In this article, we review recent application of omics technologies in revealing some of the unusual features of dinoflagellate genomes and molecular mechanisms relevant to their biology, including the mechanism of harmful algal bloom formations, toxin biosynthesis, symbiosis, lipid biosynthesis, as well as species identification and evolution. We also discuss the challenges and provide prospective further study directions and applications of dinoflagellates.
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13
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Lin MF, Takahashi S, Forêt S, Davy SK, Miller DJ. Transcriptomic analyses highlight the likely metabolic consequences of colonization of a cnidarian host by native or non-native Symbiodinium species. Biol Open 2019; 8:bio.038281. [PMID: 30814067 PMCID: PMC6451341 DOI: 10.1242/bio.038281] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Reef-building corals and some other cnidarians form symbiotic relationships with members of the dinoflagellate family Symbiodinaceae. As Symbiodinaceae is a highly diverse taxon, the physiological interactions between its members and their hosts are assumed to differ between associations. The presence of different symbiont types is known to affect expression levels of specific host genes, but knowledge of the effects on the transcriptome more broadly remains limited. In the present study, transcriptome profiling was conducted on the tropical corallimorpharian, Ricordea yuma, following the establishment of symbiosis with either the ‘homologous’ symbiont Symbiodinium goreaui (also known as Cladocopium goreaui; ITS2 type C1) or ‘heterologous’ symbionts (predominantly S. trenchii, which is also known as Durusdinium trenchii; ITS2 type D1a) isolated from a different corallimorpharian host (Rhodactis indosinensis). Transcriptomic analyses showed that genes encoding host glycogen biosynthesis pathway components are more highly induced during colonization by the homologous symbiont than by the heterologous symbiont. Similar patterns were also observed for several other genes thought to facilitate symbiotic nutrient exchange, including those involved in lipid translocation/storage and metabolite transport. The gene expression results presented here imply that colonization by homologous or heterologous Symbiodinium types may have very different metabolic consequences for the Ricordea host, supporting the notion that even though some cnidarians may be able to form novel symbioses after bleaching, the metabolic performance of these may be compromised. This article has an associated First Person interview with the first author of the paper. Summary: Colonization by the homologous symbiont, Symbiodinium goreaui, resulted in greater glycogen synthesis and ammonium assimilation capacity in the host than when it was colonized by a heterologous symbiont (S. trenchii).
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Affiliation(s)
- Mei-Fang Lin
- Molecular and Cell Biology, James Cook University, Townsville, QLD 4811, Australia.,ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811, Australia.,Evolutionary Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Shunichi Takahashi
- Division of Environmental Photobiology, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki 444-8585, Japan
| | - Sylvain Forêt
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811, Australia.,Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
| | - Simon K Davy
- School of Biological Sciences, Victoria University of Wellington, Kelburn Parade, Wellington 6140, New Zealand
| | - David J Miller
- Molecular and Cell Biology, James Cook University, Townsville, QLD 4811, Australia .,ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811, Australia
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14
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Beedessee G, Hisata K, Roy MC, Van Dolah FM, Satoh N, Shoguchi E. Diversified secondary metabolite biosynthesis gene repertoire revealed in symbiotic dinoflagellates. Sci Rep 2019; 9:1204. [PMID: 30718591 PMCID: PMC6361889 DOI: 10.1038/s41598-018-37792-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 12/13/2018] [Indexed: 11/09/2022] Open
Abstract
Symbiodiniaceae dinoflagellates possess smaller nuclear genomes than other dinoflagellates and produce structurally specialized, biologically active, secondary metabolites. Till date, little is known about the evolution of secondary metabolism in dinoflagellates as comparative genomic approaches have been hampered by their large genome sizes. Here, we overcome this challenge by combining genomic and metabolomics approaches to investigate how chemical diversity arises in three decoded Symbiodiniaceae genomes (clades A3, B1 and C). Our analyses identify extensive diversification of polyketide synthase and non-ribosomal peptide synthetase genes from two newly decoded genomes of Symbiodinium tridacnidorum (A3) and Cladocopium sp. (C). Phylogenetic analyses indicate that almost all the gene families are derived from lineage-specific gene duplications in all three clades, suggesting divergence for environmental adaptation. Few metabolic pathways are conserved among the three clades and we detect metabolic similarity only in the recently diverged clades, B1 and C. We establish that secondary metabolism protein architecture guides substrate specificity and that gene duplication and domain shuffling have resulted in diversification of secondary metabolism genes.
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Affiliation(s)
- Girish Beedessee
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan.
| | - Kanako Hisata
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Michael C Roy
- Instrumental Analysis Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Frances M Van Dolah
- College of Charleston, School of Sciences and Mathematics, 66 George St., Charleston, South Carolina, 29424, USA
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan.
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15
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Lohr KE, Camp EF, Kuzhiumparambil U, Lutz A, Leggat W, Patterson JT, Suggett DJ. Resolving coral photoacclimation dynamics through coupled photophysiological and metabolomic profiling. J Exp Biol 2019; 222:jeb.195982. [DOI: 10.1242/jeb.195982] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 03/11/2019] [Indexed: 11/20/2022]
Abstract
Corals continuously adjust to short term variation in light availability on shallow reefs. Long-term light alterations can also occur due to natural and anthropogenic stressors, as well as management interventions such as coral transplantation. Although short term photophysiological responses are relatively well-understood in corals, little information is available regarding photoacclimation dynamics over weeks of altered light availability. We coupled photophysiology and metabolomic profiling to explore changes that accompany longer-term photoacclimation in a key Great Barrier Reef coral species (Acropora muricata). High (HL) and low light (LL) acclimated corals were collected from the reef and reciprocally exposed to high and low light ex situ. Rapid light curves using Pulse Amplitude Modulation (PAM) fluorometry revealed photophysiological acclimation of LL to HL and HL to LL shifted corals within 21 days. A subset of colonies sampled at 7 and 21 days for untargeted LC-MS and GC-MS metabolomic profiling revealed metabolic reorganization before acclimation was detected using PAM fluorometry. Metabolomic shifts were more pronounced for LL to HL treated corals than their HL to LL counterparts. Compounds driving metabolomic separation between HL-exposed and LL control colonies included amino acids, organic acids, fatty acids and sterols. Reduced glycerol and campesterol suggest decreased translocation of photosynthetic products from symbiont to host in LL to HL shifted corals, with concurrent increases in fatty acid abundance indicating reliance on stored lipids for energy. We discuss how these data provide novel insight into environmental regulation of metabolism and implications for management strategies that drive rapid changes in light availability.
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Affiliation(s)
- Kathryn E. Lohr
- Program in Fisheries and Aquatic Sciences, School of Forest Resources and Conservation, University of Florida, Gainesville, FL, USA
| | - Emma F. Camp
- Climate Change Cluster (C3), University of Technology Sydney, Ultimo, NSW, Australia
| | | | - Adrian Lutz
- Metabolomics Australia, University of Melbourne, Parkville, VIC, Australia
| | - William Leggat
- School of Environmental and Life Sciences, University of Newcastle, Ourimbah, NSW, Australia
| | - Joshua T. Patterson
- Program in Fisheries and Aquatic Sciences, School of Forest Resources and Conservation, University of Florida, Gainesville, FL, USA
- Center for Conservation, The Florida Aquarium, Apollo Beach, FL, USA
| | - David J. Suggett
- Climate Change Cluster (C3), University of Technology Sydney, Ultimo, NSW, Australia
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16
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Matthews JL, Oakley CA, Lutz A, Hillyer KE, Roessner U, Grossman AR, Weis VM, Davy SK. Partner switching and metabolic flux in a model cnidarian-dinoflagellate symbiosis. Proc Biol Sci 2018; 285:20182336. [PMID: 30487315 PMCID: PMC6283946 DOI: 10.1098/rspb.2018.2336] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 11/02/2018] [Indexed: 11/12/2022] Open
Abstract
Metabolite exchange is fundamental to the viability of the cnidarian-Symbiodiniaceae symbiosis and survival of coral reefs. Coral holobiont tolerance to environmental change might be achieved through changes in Symbiodiniaceae species composition, but differences in the metabolites supplied by different Symbiodiniaceae species could influence holobiont fitness. Using 13C stable-isotope labelling coupled to gas chromatography-mass spectrometry, we characterized newly fixed carbon fate in the model cnidarian Exaiptasia pallida (Aiptasia) when experimentally colonized with either native Breviolum minutum or non-native Durusdinium trenchii Relative to anemones containing B. minutum, D. trenchii-colonized hosts exhibited a 4.5-fold reduction in 13C-labelled glucose and reduced abundance and diversity of 13C-labelled carbohydrates and lipogenesis precursors, indicating symbiont species-specific modifications to carbohydrate availability and lipid storage. Mapping carbon fate also revealed significant alterations to host molecular signalling pathways. In particular, D. trenchii-colonized hosts exhibited a 40-fold reduction in 13C-labelled scyllo-inositol, a potential interpartner signalling molecule in symbiosis specificity. 13C-labelling also highlighted differential antioxidant- and ammonium-producing pathway activities, suggesting physiological responses to different symbiont species. Such differences in symbiont metabolite contribution and host utilization may limit the proliferation of stress-driven symbioses; this contributes valuable information towards future scenarios that select in favour of less-competent symbionts in response to environmental change.
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Affiliation(s)
- Jennifer L Matthews
- School of Biological Sciences, Victoria University of Wellington, Wellington 6140, New Zealand
| | - Clinton A Oakley
- School of Biological Sciences, Victoria University of Wellington, Wellington 6140, New Zealand
| | - Adrian Lutz
- Metabolomics Australia, School of Botany, The University of Melbourne, Parkville 3052, Victoria, Australia
| | - Katie E Hillyer
- School of Biological Sciences, Victoria University of Wellington, Wellington 6140, New Zealand
| | - Ute Roessner
- Metabolomics Australia, School of Botany, The University of Melbourne, Parkville 3052, Victoria, Australia
| | - Arthur R Grossman
- Department of Plant Biology, The Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Virginia M Weis
- Department of Integrative Biology, Oregon State University, 3029 Cordley Hall, Corvallis, OR 97331, USA
| | - Simon K Davy
- School of Biological Sciences, Victoria University of Wellington, Wellington 6140, New Zealand
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17
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Shoguchi E, Beedessee G, Tada I, Hisata K, Kawashima T, Takeuchi T, Arakaki N, Fujie M, Koyanagi R, Roy MC, Kawachi M, Hidaka M, Satoh N, Shinzato C. Two divergent Symbiodinium genomes reveal conservation of a gene cluster for sunscreen biosynthesis and recently lost genes. BMC Genomics 2018; 19:458. [PMID: 29898658 PMCID: PMC6001144 DOI: 10.1186/s12864-018-4857-9] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 06/06/2018] [Indexed: 11/10/2022] Open
Abstract
Background The marine dinoflagellate, Symbiodinium, is a well-known photosynthetic partner for coral and other diverse, non-photosynthetic hosts in subtropical and tropical shallows, where it comprises an essential component of marine ecosystems. Using molecular phylogenetics, the genus Symbiodinium has been classified into nine major clades, A-I, and one of the reported differences among phenotypes is their capacity to synthesize mycosporine-like amino acids (MAAs), which absorb UV radiation. However, the genetic basis for this difference in synthetic capacity is unknown. To understand genetics underlying Symbiodinium diversity, we report two draft genomes, one from clade A, presumed to have been the earliest branching clade, and the other from clade C, in the terminal branch. Results The nuclear genome of Symbiodinium clade A (SymA) has more gene families than that of clade C, with larger numbers of organelle-related genes, including mitochondrial transcription terminal factor (mTERF) and Rubisco. While clade C (SymC) has fewer gene families, it displays specific expansions of repeat domain-containing genes, such as leucine-rich repeats (LRRs) and retrovirus-related dUTPases. Interestingly, the SymA genome encodes a gene cluster for MAA biosynthesis, potentially transferred from an endosymbiotic red alga (probably of bacterial origin), while SymC has completely lost these genes. Conclusions Our analysis demonstrates that SymC appears to have evolved by losing gene families, such as the MAA biosynthesis gene cluster. In contrast to the conservation of genes related to photosynthetic ability, the terminal clade has suffered more gene family losses than other clades, suggesting a possible adaptation to symbiosis. Overall, this study implies that Symbiodinium ecology drives acquisition and loss of gene families. Electronic supplementary material The online version of this article (10.1186/s12864-018-4857-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan.
| | - Girish Beedessee
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Ipputa Tada
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan.,Present address: Department of Genetics, School of Life Science, The Graduate University for Advanced Studies, 1111, Yata, Mishima-shi, Shizuoka, 411-8540, Japan
| | - Kanako Hisata
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Takeshi Kawashima
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan.,Present address: Center for Information Biology, National Institute of Genetics, Mishima, 411-8540, Japan
| | - Takeshi Takeuchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Nana Arakaki
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Manabu Fujie
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Ryo Koyanagi
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Michael C Roy
- Instrumental Analysis Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Masanobu Kawachi
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, Tsukuba, 305-8506, Japan
| | - Michio Hidaka
- Department of Chemistry, Biology and Marine Science, University of the Ryukyus, Nishihara, Okinawa, 903-0213, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Chuya Shinzato
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan. .,Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwanoha, Kashiwa, 277-8564, Japan.
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18
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Farag MA, Meyer A, Ali SE, Salem MA, Giavalisco P, Westphal H, Wessjohann LA. Comparative Metabolomics Approach Detects Stress-Specific Responses during Coral Bleaching in Soft Corals. J Proteome Res 2018; 17:2060-2071. [PMID: 29671321 DOI: 10.1021/acs.jproteome.7b00929] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Chronic exposure to ocean acidification and elevated sea-surface temperatures pose significant stress to marine ecosystems. This in turn necessitates costly acclimation responses in corals in both the symbiont and host, with a reorganization of cell metabolism and structure. A large-scale untargeted metabolomics approach comprising gas chromatography mass spectrometry (GC-MS) and ultraperformance liquid chromatography coupled to high resolution mass spectrometry (UPLC-MS) was applied to profile the metabolite composition of the soft coral Sarcophyton ehrenbergi and its dinoflagellate symbiont. Metabolite profiling compared ambient conditions with response to simulated climate change stressors and with the sister species, S. glaucum. Among ∼300 monitored metabolites, 13 metabolites were modulated. Incubation experiments providing four selected upregulated metabolites (alanine, GABA, nicotinic acid, and proline) in the culturing water failed to subside the bleaching response at temperature-induced stress, despite their known ability to mitigate heat stress in plants or animals. Thus, the results hint to metabolite accumulation (marker) during heat stress. This study provides the first detailed map of metabolic pathways transition in corals in response to different environmental stresses, accounting for the superior thermal tolerance of S. ehrenbergi versus S. glaucum, which can ultimately help maintain a viable symbiosis and mitigate against coral bleaching.
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Affiliation(s)
- Mohamed A Farag
- Pharmacognosy Department, College of Pharmacy , Cairo University , Kasr el Aini st. P.B. , 11562 Cairo , Egypt.,Department of Chemistry, School of Sciences & Engineering , The American University in Cairo (AUC) , New Cairo 11835 , Egypt
| | - Achim Meyer
- Leibniz Centre for Tropical Marine Research (ZMT), Fahrenheit Str. 6 , D-28359 Bremen , Germany
| | - Sara E Ali
- Department of Pharmaceutical Biology, Faculty of Pharmacy & Biotechnology , The German University in Cairo , New Cairo 11432 , Egypt
| | - Mohamed A Salem
- Pharmacognosy Department, College of Pharmacy , Cairo University , Kasr el Aini st. P.B. , 11562 Cairo , Egypt.,Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1 , Golm, Potsdam 14476 , Germany
| | - Patrick Giavalisco
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1 , Golm, Potsdam 14476 , Germany
| | - Hildegard Westphal
- Leibniz Centre for Tropical Marine Research (ZMT), Fahrenheit Str. 6 , D-28359 Bremen , Germany.,Department of Geosciences , University of Bremen , 28359 Bremen , Germany
| | - Ludger A Wessjohann
- Department of Bioorganic Chemistry , Leibniz Institute of Plant Biochemistry , Weinberg 3 , D-06120 Halle (Saale) , Germany
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19
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20
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Comparative growth rates of cultured marine dinoflagellates in the genus Symbiodinium and the effects of temperature and light. PLoS One 2017; 12:e0187707. [PMID: 29186143 PMCID: PMC5706665 DOI: 10.1371/journal.pone.0187707] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 10/24/2017] [Indexed: 02/04/2023] Open
Abstract
Many dinoflagellate microalgae of the genus Symbiodinium form successful symbioses with a large group of metazoans and selected protists. Yet knowledge of growth kinetics of these endosymbionts and their ecological and evolutionary implications is limited. We used a Bayesian biphasic generalized logistic model to estimate key parameters of the growth of five strains of cultured Symbiodinium, S. microadriaticum (cp-type A194; strain 04–503), S. microadriaticum (cp-type A194; strain CassKB8), S. minutum (cp-type B184; strain Mf 1.05b.01.SCI.01), S. psygmophilum (cp-type B224; strain Mf 11.05b.01) and S. trenchii (cp-type D206; strain Mf 2.2b), grown in four different combinations of temperature and light. Growth kinetics varied among Symbiodinium strains and across treatments. Biphasic growth was especially evident for S. minutum and S. psygmophilum across all treatments. Monophasic growth was more common when final asymptotic densities were relatively low (~ 200 million cells ml-1). All species tended to grow faster and / or reached a higher asymptote at 26°C than at 18°C. The fastest growth was exhibited by S. minutum, with an approximate four-fold increase in estimated cell density after 60 days. The strongest effect of light was seen in S. trenchii, in which increasing light levels resulted in a decrease in initial growth rate, and an increase in asymptotic density, time when growth rate was at its maximum, final growth rate, and maximum growth rate. Results suggest that Symbiodinium species have different photokinetic and thermal optima, which may affect their growth-related nutritional physiology and allow them to modify their response to environmental changes.
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21
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Kinney MJ, Kacev D, Kohin S, Eguchi T. An analytical approach to sparse telemetry data. PLoS One 2017; 12:e0188660. [PMID: 29182675 PMCID: PMC5705164 DOI: 10.1371/journal.pone.0188660] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 11/11/2017] [Indexed: 11/18/2022] Open
Abstract
Horizontal behavior of highly migratory marine species is difficult to decipher because animals are wide-ranging, spend minimal time at the ocean surface, and utilize remote habitats. Satellite telemetry enables researchers to track individual movements, but population level inferences are rare due to data limitations that result from difficulty of capture and sporadic tag reporting. We introduce a Bayesian modeling framework to address population level questions with satellite telemetry data when data are sparse. We also outline an approach for identifying informative variables for use within the model. We tested our modeling approach using a large telemetry dataset for Shortfin Makos (Isurus oxyrinchus), which allowed us to assess the effects of various degrees of data paucity. First, a permuted Random Forest analysis is implemented to determine which variables are most informative. Next, a generalized additive mixed model is used to help define the relationship of each remaining variable with the response variable. Using jags and rjags for the analysis of Bayesian hierarchical models using Markov Chain Monte Carlo simulation, we then developed a movement model to generate parameter estimates for each of the variables of interest. By randomly reducing the tagging dataset by 25, 50, 75, and 90 percent and recalculating the parameter estimates, we demonstrate that the proposed Bayesian approach can be applied in data-limited situations. We also demonstrate how two commonly used linear mixed models with maximum likelihood estimation (MLE) can be similarly applied. Additionally, we simulate data from known parameter values to test each model’s ability to recapture those values. Despite performing similarly, we advocate using the Bayesian over the MLE approach due to the ability for later studies to easily utilize results of past study to inform working models, and the ability to use prior knowledge via informed priors in systems where such information is available.
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Affiliation(s)
- Michael J. Kinney
- Ocean Associates; Under Contract to Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, San Diego, California, United States of America
- * E-mail:
| | - David Kacev
- Ocean Associates; Under Contract to Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, San Diego, California, United States of America
| | - Suzanne Kohin
- Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, San Diego, California, United States of America
| | - Tomoharu Eguchi
- Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, San Diego, California, United States of America
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22
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Sogin EM, Putnam HM, Nelson CE, Anderson P, Gates RD. Correspondence of coral holobiont metabolome with symbiotic bacteria, archaea and Symbiodinium communities. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:310-315. [PMID: 28464532 DOI: 10.1111/1758-2229.12541] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 01/25/2017] [Accepted: 03/12/2017] [Indexed: 06/07/2023]
Abstract
Microbial symbiotic partners, such as those associated with Scleractinian corals, mediate biochemical transformations that influence host performance and survival. While evidence suggests microbial community composition partly accounts for differences in coral physiology, how these symbionts affect metabolic pathways remains underexplored. We aimed to assess functional implications of variation among coral-associated microbial partners in hospite. To this end, we characterized and compared metabolomic profiles and microbial community composition from nine reef-building coral species. These data demonstrate metabolite profiles and microbial communities are species-specific and are correlated to one another. Using Porites spp. as a case study, we present evidence that the relative abundance of different sub-clades of Symbiodinium and bacterial/archaeal families are linked to positive and negative metabolomic signatures. Our data suggest that while some microbial partners benefit the union, others are more opportunistic with potential detriment to the host. Consequently, coral partner choice likely influences cellular metabolic activities and, therefore, holobiont nutrition.
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Affiliation(s)
- Emilia M Sogin
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, USA
| | - Hollie M Putnam
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, USA
| | - Craig E Nelson
- Department of Oceanography and Sea Grant College Program, Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - Paul Anderson
- Department of Computer Science, College of Charleston, Charleston, NC, USA
| | - Ruth D Gates
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, USA
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23
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Hillyer KE, Dias DA, Lutz A, Roessner U, Davy SK. Mapping carbon fate during bleaching in a model cnidarian symbiosis: the application of 13 C metabolomics. THE NEW PHYTOLOGIST 2017; 214:1551-1562. [PMID: 28272836 DOI: 10.1111/nph.14515] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 02/05/2017] [Indexed: 06/06/2023]
Abstract
Coral bleaching is a major threat to the persistence of coral reefs. Yet we lack detailed knowledge of the metabolic interactions that determine symbiosis function and bleaching-induced change. We mapped autotrophic carbon fate within the free metabolite pools of both partners of a model cnidarian-dinoflagellate symbiosis (Aiptasia-Symbiodinium) during exposure to thermal stress via the stable isotope tracer (13 C bicarbonate), coupled to GC-MS. Symbiont photodamage and pronounced bleaching coincided with substantial increases in the turnover of non13 C-labelled pools in the dinoflagellate (lipid and starch store catabolism). However, 13 C enrichment of multiple compounds associated with ongoing carbon fixation and de novo biosynthesis pathways was maintained (glucose, fatty acid and lipogenesis intermediates). Minimal change was also observed in host pools of 13 C-enriched glucose (a major symbiont-derived mobile product). However, host pathways downstream showed altered carbon fate and/or pool composition, with accumulation of compatible solutes and nonenzymic antioxidant precursors. In hospite symbionts continue to provide mobile products to the host, but at a significant cost to themselves, necessitating the mobilization of energy stores. These data highlight the need to further elucidate the role of metabolic interactions between symbiotic partners, during the process of thermal acclimation and coral bleaching.
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Affiliation(s)
- Katie E Hillyer
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, 6140, New Zealand
| | - Daniel A Dias
- School of Health and Biomedical Sciences, RMIT University, PO Box 71, Bundoora, 3083, Vic, Australia
| | - Adrian Lutz
- Metabolomics Australia, School of BioSciences, The University of Melbourne, Parkville, Vic, 3010, Australia
| | - Ute Roessner
- Metabolomics Australia, School of BioSciences, The University of Melbourne, Parkville, Vic, 3010, Australia
| | - Simon K Davy
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, 6140, New Zealand
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24
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McIlroy SE, Gillette P, Cunning R, Klueter A, Capo T, Baker AC, Coffroth MA. The effects of Symbiodinium (Pyrrhophyta) identity on growth, survivorship, and thermal tolerance of newly settled coral recruits. JOURNAL OF PHYCOLOGY 2016; 52:1114-1124. [PMID: 27690269 DOI: 10.1111/jpy.12471] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 08/23/2016] [Indexed: 05/23/2023]
Abstract
For many coral species, the obligate association with phylogenetically diverse algal endosymbiont species is dynamic in time and space. Here, we used controlled laboratory inoculations of newly settled, aposymbiotic corals (Orbicella faveolata) with two cultured species of algal symbiont (Symbiodinium microadriaticum and S. minutum) to examine the role of symbiont identity on growth, survivorship, and thermal tolerance of the coral holobiont. We evaluated these data in the context of Symbiodinium photophysiology for 9 months post-settlement and also during a 5-d period of elevated temperatures Our data show that recruits that were inoculated with S. minutum grew significantly slower than those inoculated with S. microadriaticum (occasionally co-occurring with S. minutum), but that there was no difference in survivorship of O. faveolata polyps infected with Symbiodinium. However, photophysiological metrics (∆Fv/F'm, the efficiency with which available light is used to drive photosynthesis and α, the maximum light utilization coefficient) were higher in those slower growing recruits containing S. minutum. These findings suggest that light use (i.e., photophysiology) and carbon acquisition by the coral host (i.e., host growth) are decoupled, but did not distinguish the source of this difference. Neither Symbiodinium treatment demonstrated a significant negative effect of a 5-d exposure to temperatures as high as 32°C under low light conditions similar to those measured at settlement habitats.
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Affiliation(s)
- Shelby E McIlroy
- Graduate Program in Evolution, Ecology, and Behavior, University at Buffalo, 126 Cooke Hall, Buffalo, New York, 14260, USA
| | - Phillip Gillette
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Csy, Miami, Florida, 33149, USA
| | - Ross Cunning
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Csy, Miami, Florida, 33149, USA
| | - Anke Klueter
- Department of Geology, University at Buffalo, 126 Cooke Hall, Buffalo, New York, 14260, USA
| | - Tom Capo
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Csy, Miami, Florida, 33149, USA
| | - Andrew C Baker
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Csy, Miami, Florida, 33149, USA
| | - Mary Alice Coffroth
- Graduate Program in Evolution, Ecology, and Behavior, University at Buffalo, 126 Cooke Hall, Buffalo, New York, 14260, USA
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Putnam HM, Davidson JM, Gates RD. Ocean acidification influences host DNA methylation and phenotypic plasticity in environmentally susceptible corals. Evol Appl 2016; 9:1165-1178. [PMID: 27695524 PMCID: PMC5039329 DOI: 10.1111/eva.12408] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 06/27/2016] [Indexed: 12/13/2022] Open
Abstract
As climate change challenges organismal fitness by creating a phenotype-environment mismatch, phenotypic plasticity generated by epigenetic mechanisms (e.g., DNA methylation) can provide a temporal buffer for genetic adaptation. Epigenetic mechanisms may be crucial for sessile benthic marine organisms, such as reef-building corals, where ocean acidification (OA) and warming reflect in strong negative responses. We tested the potential for scleractinian corals to exhibit phenotypic plasticity associated with a change in DNA methylation in response to OA. Clonal coral fragments of the environmentally sensitive Pocillopora damicornis and more environmentally robust Montipora capitata were exposed to fluctuating ambient pH (7.9-7.65) and low pH (7.6-7.35) conditions in common garden tanks for ~6 weeks. M. capitata responded weakly, or acclimated more quickly, to OA, with no difference in calcification, minimal separation of metabolomic profiles, and no change in DNA methylation between treatments. Conversely, P. damicornis exhibited diminished calcification at low pH, stronger separation in metabolomic profiles, and responsiveness of DNA methylation to treatment. Our data suggest corals differ in their temporal dynamics and sensitivity for environmentally triggered real-time epigenetic reprogramming. The generation of potentially heritable plasticity via environmental induction of DNA methylation provides an avenue for assisted evolution applications in corals under rapid climate change.
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Affiliation(s)
- Hollie M. Putnam
- Hawaii Institute of Marine BiologyUniversity of HawaiiKaneoheHIUSA
| | | | - Ruth D. Gates
- Hawaii Institute of Marine BiologyUniversity of HawaiiKaneoheHIUSA
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26
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Anesi A, Obertegger U, Hansen G, Sukenik A, Flaim G, Guella G. Comparative Analysis of Membrane Lipids in Psychrophilic and Mesophilic Freshwater Dinoflagellates. FRONTIERS IN PLANT SCIENCE 2016; 7:524. [PMID: 27148341 PMCID: PMC4837943 DOI: 10.3389/fpls.2016.00524] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 04/04/2016] [Indexed: 06/05/2023]
Abstract
Here we report the lipid profiles of ten dinoflagellate species originating from different freshwater habitats and grown at 4, 13, or 20°C akin to their natural occurrence. Lipids were determined by High Performance Liquid Chromatography-ElectroSpray Ionization-Mass Spectrometry in positive and negative ion modes. Besides the well-studied monogalactosyldiacylglycerol (MGDG) and digalactosyldiacylglycerol (DGDG) lipids, our study revealed the presence of intact molecular lipid species of trigalactosyldiacylglycerols, betaine diacylglyceryl-carboxyhydroxymethylcholine, sulfolipid sulfoquinovosyldiacylglycerols (SQDG) and phospholipids, in particular phosphatidylcholine, phosphatidylethanolamine and phosphatidylglycerol. In multivariate ordination, the freshwater dinoflagellates studied could be distinguished into two groups based on their lipid profiles. Peridinium aciculiferum, Borghiella dodgei, B. tenuissima and Tovellia coronata belonged to group 1 while Ceratium cornutum, Gymnodinium palustre, Jadwigia applanata, P. cinctum, P. willei, and P. gatunense belonged to group 2. Indicator species analysis evidenced that group 1 was characterized by 36:9 MGDG and 36:9 DGDG and group 2 by 38:9 and 38:10 MGDG, 38:9 and 38:10 DGDG and 34:1 SQDG. We suggest that the grouping of dinoflagellates indicated their range of temperature tolerance. Furthermore, non-thylakoid lipids were linked to dinoflagellate phylogeny based on the large ribosomal sub-unit (28S LSU) rather than their temperature tolerance. Thus certain lipids better reflected habitat adaptation while other lipids better reflected genetic diversity.
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Affiliation(s)
- Andrea Anesi
- Bioorganic Chemistry Laboratory, Department of Physics, University of TrentoTrento, Italy
| | | | - Gert Hansen
- Department of Biology, University of CopenhagenCopenhagen, Denmark
| | - Assaf Sukenik
- Kinneret Limnological Laboratory, Israel Oceanographic and Limnological ResearchMigdal, Israel
| | - Giovanna Flaim
- Fondazione Edmund Mach, Research and Innovation CentreTrento, Italy
| | - Graziano Guella
- Bioorganic Chemistry Laboratory, Department of Physics, University of TrentoTrento, Italy
- Biophysical Institute, Consiglio Nazionale delle RicerchePovo, Italy
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27
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Bertucci A, Forêt S, Ball EE, Miller DJ. Transcriptomic differences between day and night in Acropora millepora provide new insights into metabolite exchange and light-enhanced calcification in corals. Mol Ecol 2015. [PMID: 26198296 DOI: 10.1111/mec.13328] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The evolutionary success of reef-building corals is often attributed to their symbiotic relationship with photosynthetic dinoflagellates of the genus Symbiodinium, but metabolic interactions between the partners and the molecular bases of light-enhanced calcification (LEC) are not well understood. Here, the metabolic bases of the interaction between the coral Acropora millepora and its dinoflagellate symbiont were investigated by comparing gene expression levels under light and dark conditions at the whole transcriptome level. Among the 497 differentially expressed genes identified, a suite of genes involved in cholesterol transport was found to be upregulated under light conditions, confirming the significance of this compound in the coral symbiosis. Although ion transporters likely to have roles in calcification were not differentially expressed in this study, expression levels of many genes associated with skeletal organic matrix composition and organization were higher in light conditions. This implies that the rate of organic matrix synthesis is one factor limiting calcification at night. Thus, LEC during the day is likely to be a consequence of increases in both matrix synthesis and the supply of precursor molecules as a result of photosynthetic activity.
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Affiliation(s)
- A Bertucci
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, 4811, Australia
| | - S Forêt
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, 4811, Australia.,Evolution, Ecology and Genetics, Research School of Biology, Australian National University, Bldg. 46, Canberra, ACT, 0200, Australia
| | - E E Ball
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, 4811, Australia.,Evolution, Ecology and Genetics, Research School of Biology, Australian National University, Bldg. 46, Canberra, ACT, 0200, Australia
| | - D J Miller
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, 4811, Australia.,Comparative Genomics Centre and Department of Molecular and Cell Biology, James Cook University, Townsville, Qld, 4811, Australia
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