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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Parkinson JE, Tang SL, Denis V. Editorial: Variance matters: Individual differences and their consequences for natural selection within and among coral holobionts. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.977844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Fujiwara Y, Kawamura I, Reimer JD, Parkinson JE. Zoantharian Endosymbiont Community Dynamics During a Stress Event. Front Microbiol 2021; 12:674026. [PMID: 34122387 PMCID: PMC8193574 DOI: 10.3389/fmicb.2021.674026] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 04/28/2021] [Indexed: 11/13/2022] Open
Abstract
Coral reefs are complex ecosystems composed of many interacting species. One ecologically important group consists of zoantharians, which are closely related to reef-building corals. Like corals, zoantharians form mutualistic symbioses with dinoflagellate micro-algae (family Symbiodiniaceae), but their associations remain underexplored. To examine the degree to which zoantharians exhibit altered symbiont dynamics under changing environmental conditions, we reciprocally transplanted colonies of Zoanthus sansibaricus between intertidal (2 m) and subtidal (26 m) depths within a reef in Okinawa, Japan. At this location, Z. sansibaricus can associate with three Symbiodiniaceae species from two genera distributed along a light and depth gradient. We developed species-specific molecular assays and sampled colonies pre- and post-transplantation to analyze symbiont community diversity. Despite large environmental differences across depths, we detected few symbiont compositional changes resulting from transplantation stress. Colonies sourced from the intertidal zone associated with mixtures of a "shallow" Symbiodinium sp. and a "shallow" Cladocopium sp. independent of whether they were transplanted to shallow or deep waters. Colonies sourced from the subtidal zone were dominated by a "deep" Cladocopium sp. regardless of transplant depth. Subtidal colonies brought to shallow depths did not transition to the presumably high-light adapted shallow symbionts present in the new environment, but rather bleached and died. These patterns mirror observations of highly stable coral-algal associations subjected to depth transplantation. Our results indicate that Zoanthus-Symbiodiniaceae symbioses remain stable despite stress, suggesting these important reef community members have relatively low capacity to shuffle to more stress-tolerant micro-algae in response to ongoing climate change.
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Affiliation(s)
- Yu Fujiwara
- Molecular Invertebrate Systematics and Ecology Laboratory, Department of Chemistry, Biology, and Marine Science, Faculty of Science, University of the Ryukyus, Nishihara, Japan.,Nakajima Suisan Co. Ltd., Tokyo, Japan
| | - Iori Kawamura
- Molecular Invertebrate Systematics and Ecology Laboratory, Department of Chemistry, Biology, and Marine Science, Faculty of Science, University of the Ryukyus, Nishihara, Japan
| | - James Davis Reimer
- Molecular Invertebrate Systematics and Ecology Laboratory, Department of Chemistry, Biology, and Marine Science, Faculty of Science, University of the Ryukyus, Nishihara, Japan.,Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Japan
| | - John Everett Parkinson
- Molecular Invertebrate Systematics and Ecology Laboratory, Department of Chemistry, Biology, and Marine Science, Faculty of Science, University of the Ryukyus, Nishihara, Japan.,Department of Integrative Biology, University of South Florida, Tampa, FL, United States
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Tivey TR, Parkinson JE, Mandelare PE, Adpressa DA, Peng W, Dong X, Mechref Y, Weis VM, Loesgen S. N-Linked Surface Glycan Biosynthesis, Composition, Inhibition, and Function in Cnidarian-Dinoflagellate Symbiosis. Microb Ecol 2020; 80:223-236. [PMID: 31982929 DOI: 10.1007/s00248-020-01487-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 01/08/2020] [Indexed: 06/10/2023]
Abstract
The success of symbioses between cnidarian hosts (e.g., corals and sea anemones) and micro-algal symbionts hinges on the molecular interactions that govern the establishment and maintenance of intracellular mutualisms. As a fundamental component of innate immunity, glycan-lectin interactions impact the onset of marine endosymbioses, but our understanding of the effects of cell surface glycome composition on symbiosis establishment remains limited. In this study, we examined the canonical N-glycan biosynthesis pathway in the genome of the dinoflagellate symbiont Breviolum minutum (family Symbiodiniaceae) and found it to be conserved with the exception of the transferase GlcNAc-TII (MGAT2). Using coupled liquid chromatography-mass spectrometry (LC-MS/MS), we characterized the cell surface N-glycan content of B. minutum, providing the first insight into the molecular composition of surface glycans in dinoflagellates. We then used the biosynthesis inhibitors kifunensine and swainsonine to alter the glycan composition of B. minutum. Successful high-mannose enrichment via kifunensine treatment resulted in a significant decrease in colonization of the model sea anemone Aiptasia (Exaiptasia pallida) by B. minutum. Hybrid glycan enrichment via swainsonine treatment, however, could not be confirmed and did not impact colonization. We conclude that functional Golgi processing of N-glycans is critical for maintaining appropriate cell surface glycan composition and for ensuring colonization success by B. minutum.
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Affiliation(s)
- Trevor R Tivey
- Department of Integrative Biology, Oregon State University, Corvallis, OR, USA.
- Department of Entomology, Cornell University, Ithaca, NY, USA.
| | - John Everett Parkinson
- Department of Integrative Biology, Oregon State University, Corvallis, OR, USA
- Department of Integrative Biology, University of South Florida, Tampa, FL, USA
| | - Paige E Mandelare
- Department of Chemistry, Oregon State University, Corvallis, OR, USA
- Whitney Laboratory for Marine Bioscience and Department of Chemistry, University of Florida, St. Augustine, FL, USA
| | - Donovon A Adpressa
- Department of Chemistry, Oregon State University, Corvallis, OR, USA
- Analytical Research & Development, Merck & Co. Inc., Boston, MA, USA
| | - Wenjing Peng
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Xue Dong
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Virginia M Weis
- Department of Integrative Biology, Oregon State University, Corvallis, OR, USA
| | - Sandra Loesgen
- Department of Chemistry, Oregon State University, Corvallis, OR, USA.
- Whitney Laboratory for Marine Bioscience and Department of Chemistry, University of Florida, St. Augustine, FL, USA.
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5
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Parkinson JE, Baker AC, Baums IB, Davies SW, Grottoli AG, Kitchen SA, Matz MV, Miller MW, Shantz AA, Kenkel CD. Molecular tools for coral reef restoration: Beyond biomarker discovery. Conserv Lett 2019. [DOI: 10.1111/conl.12687] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- John Everett Parkinson
- SECORE International Miami Florida
- Department of Integrative BiologyUniversity of South Florida Tampa Florida
| | - Andrew C. Baker
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric ScienceUniversity of Miami Miami Florida
| | - Iliana B. Baums
- Department of BiologyPennsylvania State University University Park Pennsylvania
| | | | | | - Sheila A. Kitchen
- Department of BiologyPennsylvania State University University Park Pennsylvania
| | - Mikhail V. Matz
- Department of Integrative BiologyUniversity of Texas at Austin Austin Texas
| | | | - Andrew A. Shantz
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric ScienceUniversity of Miami Miami Florida
| | - Carly D. Kenkel
- Department of Biological SciencesUniversity of Southern California Los Angeles California
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Gabay Y, Parkinson JE, Wilkinson SP, Weis VM, Davy SK. Inter-partner specificity limits the acquisition of thermotolerant symbionts in a model cnidarian-dinoflagellate symbiosis. ISME J 2019; 13:2489-2499. [PMID: 31186513 DOI: 10.1038/s41396-019-0429-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 02/07/2019] [Accepted: 04/10/2019] [Indexed: 01/19/2023]
Abstract
The ability of corals and other cnidarians to survive climate change depends partly on the composition of their endosymbiont communities. The dinoflagellate family Symbiodiniaceae is genetically and physiologically diverse, and one proposed mechanism for cnidarians to acclimate to rising temperatures is to acquire more thermally tolerant symbionts. However, cnidarian-dinoflagellate associations vary in their degree of specificity, which may limit their capacity to alter symbiont communities. Here, we inoculated symbiont-free polyps of the sea anemone Exaiptasia pallida (commonly referred to as 'Aiptasia'), a model system for the cnidarian-dinoflagellate symbiosis, with simultaneous or sequential mixtures of thermally tolerant and thermally sensitive species of Symbiodiniaceae. We then monitored symbiont success (relative proportional abundance) at normal and elevated temperatures across two to four weeks. All anemones showed signs of bleaching at high temperature. During simultaneous inoculations, the native, thermally sensitive Breviolum minutum colonized polyps most successfully regardless of temperature when paired against the non-native but more thermally tolerant Symbiodinium microadriaticum or Durusdinium trenchii. Furthermore, anemones initially colonized with B. minutum and subsequently exposed to S. microadriaticum failed to acquire the new symbiont. These results highlight how partner specificity may place strong limitations on the ability of certain cnidarians to acquire more thermally tolerant symbionts, and hence their adaptive potential under climate change.
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Affiliation(s)
- Yasmin Gabay
- School of Biological Sciences, Victoria University of Wellington, Kelburn Parade, Wellington, 6140, New Zealand
| | - John Everett Parkinson
- Department of Integrative Biology, Oregon State University, Corvallis, OR, 97331, USA.,Department of Integrative Biology, University of South Florida, Tampa, FL, 33620, USA
| | - Shaun P Wilkinson
- School of Biological Sciences, Victoria University of Wellington, Kelburn Parade, Wellington, 6140, New Zealand
| | - Virginia M Weis
- Department of Integrative Biology, Oregon State University, Corvallis, OR, 97331, USA
| | - Simon K Davy
- School of Biological Sciences, Victoria University of Wellington, Kelburn Parade, Wellington, 6140, New Zealand.
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LaJeunesse TC, Parkinson JE, Gabrielson PW, Jeong HJ, Reimer JD, Voolstra CR, Santos SR. Systematic Revision of Symbiodiniaceae Highlights the Antiquity and Diversity of Coral Endosymbionts. Curr Biol 2018; 28:2570-2580.e6. [PMID: 30100341 DOI: 10.1016/j.cub.2018.07.008] [Citation(s) in RCA: 620] [Impact Index Per Article: 103.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 06/08/2018] [Accepted: 07/03/2018] [Indexed: 11/18/2022]
Abstract
The advent of molecular data has transformed the science of organizing and studying life on Earth. Genetics-based evidence provides fundamental insights into the diversity, ecology, and origins of many biological systems, including the mutualisms between metazoan hosts and their micro-algal partners. A well-known example is the dinoflagellate endosymbionts ("zooxanthellae") that power the growth of stony corals and coral reef ecosystems. Once assumed to encompass a single panmictic species, genetic evidence has revealed a divergent and rich diversity within the zooxanthella genus Symbiodinium. Despite decades of reporting on the significance of this diversity, the formal systematics of these eukaryotic microbes have not kept pace, and a major revision is long overdue. With the consideration of molecular, morphological, physiological, and ecological data, we propose that evolutionarily divergent Symbiodinium "clades" are equivalent to genera in the family Symbiodiniaceae, and we provide formal descriptions for seven of them. Additionally, we recalibrate the molecular clock for the group and amend the date for the earliest diversification of this family to the middle of the Mesozoic Era (∼160 mya). This timing corresponds with the adaptive radiation of analogs to modern shallow-water stony corals during the Jurassic Period and connects the rise of these symbiotic dinoflagellates with the emergence and evolutionary success of reef-building corals. This improved framework acknowledges the Symbiodiniaceae's long evolutionary history while filling a pronounced taxonomic gap. Its adoption will facilitate scientific dialog and future research on the physiology, ecology, and evolution of these important micro-algae.
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Affiliation(s)
- Todd C LaJeunesse
- Department of Biology, The Pennsylvania State University, 208 Mueller Laboratory, University Park, PA 16802, USA.
| | - John Everett Parkinson
- Department of Integrative Biology, Oregon State University, 3029 Cordley Hall, Corvallis, OR 97331, USA.
| | - Paul W Gabrielson
- Herbarium and Biology Department, University of North Carolina-Chapel Hill, Coker Hall, CB 3280, Chapel Hill, NC 27599, USA
| | - Hae Jin Jeong
- School of Earth and Environmental Sciences, College of Natural Sciences, Seoul National University, Seoul 151-747, Republic of Korea; Advanced Institutes of Convergence Technology, Suwon, Gyeonggi-do 16229, Republic of Korea
| | - James Davis Reimer
- Molecular Invertebrate Systematics and Ecology Laboratory, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213, Japan
| | - Christian R Voolstra
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Scott R Santos
- Department of Biological Sciences and Molette Laboratory for Climate Change and Environmental Studies, Auburn University, 101 Rouse Life Sciences Building, Auburn, AL 36849, USA
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Parkinson JE, Bartels E, Devlin‐Durante MK, Lustic C, Nedimyer K, Schopmeyer S, Lirman D, LaJeunesse TC, Baums IB. Extensive transcriptional variation poses a challenge to thermal stress biomarker development for endangered corals. Mol Ecol 2018; 27:1103-1119. [DOI: 10.1111/mec.14517] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Revised: 12/29/2017] [Accepted: 01/16/2018] [Indexed: 12/11/2022]
Affiliation(s)
- John Everett Parkinson
- Department of Biology Pennsylvania State University State College PA USA
- Department of Integrative Biology Oregon State University Corvallis OR USA
| | - Erich Bartels
- Center for Coral Reef Research Mote Marine Laboratory Summerland Key FL USA
| | | | - Caitlin Lustic
- The Nature Conservancy Florida Keys Office Summerland Key FL USA
| | | | - Stephanie Schopmeyer
- Rosenstiel School of Marine and Atmospheric Science University of Miami Miami FL USA
| | - Diego Lirman
- Rosenstiel School of Marine and Atmospheric Science University of Miami Miami FL USA
| | - Todd C. LaJeunesse
- Department of Biology Pennsylvania State University State College PA USA
| | - Iliana B. Baums
- Department of Biology Pennsylvania State University State College PA USA
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9
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Noda H, Parkinson JE, Yang SY, Reimer JD. A preliminary survey of zoantharian endosymbionts shows high genetic variation over small geographic scales on Okinawa-jima Island, Japan. PeerJ 2017; 5:e3740. [PMID: 29018596 PMCID: PMC5629959 DOI: 10.7717/peerj.3740] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 08/05/2017] [Indexed: 12/03/2022] Open
Abstract
Symbiotic dinoflagellates (genus Symbiodinium) shape the responses of their host reef organisms to environmental variability and climate change. To date, the biogeography of Symbiodinium has been investigated primarily through phylogenetic analyses of the ribosomal internal transcribed spacer 2 region. Although the marker can approximate species-level diversity, recent work has demonstrated that faster-evolving genes can resolve otherwise hidden species and population lineages, and that this diversity is often distributed over much finer geographical and environmental scales than previously recognized. Here, we use the noncoding region of the chloroplast psbA gene (psbAncr) to examine genetic diversity among clade C Symbiodinium associating with the common reef zoantharian Palythoa tuberculosa on Okinawa-jima Island, Japan. We identify four closely related Symbiodinium psbAncr lineages including one common generalist and two potential specialists that appear to be associated with particular microhabitats. The sea surface temperature differences that distinguish these habitats are smaller than those usually investigated, suggesting that future biogeographic surveys of Symbiodinium should incorporate fine scale environmental information as well as fine scale molecular data to accurately determine species diversity and their distributions.
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Affiliation(s)
- Hatsuko Noda
- Molecular Invertebrate Systematics and Ecology Laboratory, Department of Biology, Chemistry and Marine Sciences, Faculty of Science, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - John Everett Parkinson
- Molecular Invertebrate Systematics and Ecology Laboratory, Department of Biology, Chemistry and Marine Sciences, Faculty of Science, University of the Ryukyus, Nishihara, Okinawa, Japan.,Department of Integrative Biology, Oregon State University, Corvallis, OR, USA
| | - Sung-Yin Yang
- Molecular Invertebrate Systematics and Ecology Laboratory, Department of Biology, Chemistry and Marine Sciences, Faculty of Science, University of the Ryukyus, Nishihara, Okinawa, Japan.,Microbiology and Biochemistry of Secondary Metabolites Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan.,Biodiversity Research Center, Academia Sinica, Nankang, Taipei, Taiwan
| | - James Davis Reimer
- Molecular Invertebrate Systematics and Ecology Laboratory, Department of Biology, Chemistry and Marine Sciences, Faculty of Science, University of the Ryukyus, Nishihara, Okinawa, Japan.,Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, Japan
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Parkinson JE, Yang SY, Kawamura I, Byron G, Todd PA, Reimer JD. A citizen science approach to monitoring bleaching in the zoantharian Palythoa tuberculosa. PeerJ 2016; 4:e1815. [PMID: 27069784 PMCID: PMC4824907 DOI: 10.7717/peerj.1815] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 02/24/2016] [Indexed: 11/25/2022] Open
Abstract
Coral reef bleaching events are expected to become more frequent and severe in the near future as climate changes. The zoantharian Palythoa tuberculosa bleaches earlier than many scleractinian corals and may serve as an indicator species. Basic monitoring of such species could help to detect and even anticipate bleaching events, especially in areas where more sophisticated approaches that rely on buoy or satellite measurements of sea surface temperature are unavailable or too coarse. One simple and inexpensive monitoring method involves training volunteers to record observations of host color as a proxy for symbiosis quality. Here, we trained university students to take the 'color fingerprint' of a reef by assessing the color of multiple randomly selected colonies of P. tuberculosa at one time point in Okinawa Island, Japan. We tested the reliability of the students' color scores and whether they matched expectations based on previous monthly monitoring of tagged colonies at the same locations. We also measured three traditional metrics of symbiosis quality for comparison: symbiont morphological condition, cell density, and chlorophyll a content. We found that P. tuberculosa color score, although highly correlated among observers, provided little predictive power for the other variables. This was likely due to inherent variation in colony color among generally healthy zoantharians in midwinter, as well as low sample size and brief training owing to the course structure. Despite certain limitations of P. tuberculosa as a focal organism, the citizen science approach to color monitoring has promise, and we outline steps that could improve similar efforts in the future.
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Affiliation(s)
- John Everett Parkinson
- Molecular Invertebrate Systematics and Ecology Laboratory, Department of Chemistry, Biology, and Marine Science, Faculty of Science, University of the Ryukyus , Nishihara, Okinawa , Japan
| | - Sung-Yin Yang
- Molecular Invertebrate Systematics and Ecology Laboratory, Department of Chemistry, Biology, and Marine Science, Faculty of Science, University of the Ryukyus, Nishihara, Okinawa, Japan; Microbiology and Biochemistry of Secondary Metabolites Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Iori Kawamura
- Molecular Invertebrate Systematics and Ecology Laboratory, Department of Chemistry, Biology, and Marine Science, Faculty of Science, University of the Ryukyus , Nishihara, Okinawa , Japan
| | - Gordon Byron
- Molecular Invertebrate Systematics and Ecology Laboratory, Department of Chemistry, Biology, and Marine Science, Faculty of Science, University of the Ryukyus, Nishihara, Okinawa, Japan; Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Peter Alan Todd
- Experimental Marine Ecology Laboratory, National University of Singapore , Republic of Singapore
| | - James Davis Reimer
- Molecular Invertebrate Systematics and Ecology Laboratory, Department of Chemistry, Biology, and Marine Science, Faculty of Science, University of the Ryukyus, Nishihara, Okinawa, Japan; Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, Japan
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Parkinson JE, Coffroth MA, LaJeunesse TC. New species of Clade B Symbiodinium (Dinophyceae) from the greater Caribbean belong to different functional guilds: S. aenigmaticum sp. nov., S. antillogorgium sp. nov., S. endomadracis sp. nov., and S. pseudominutum sp. nov. J Phycol 2015; 51:850-858. [PMID: 26986882 DOI: 10.1111/jpy.12340] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 07/24/2015] [Indexed: 06/05/2023]
Abstract
Molecular approaches have begun to supersede traditional morphometrics in the species delineation of micro-eukaryotes. In addition to fixed differences in DNA sequences, recent genetics-based descriptions within the dinoflagellate genus Symbiodinium have incorporated confirmatory morphological, physiological, and ecological evidence when possible. However, morphological and physiological data are difficult to collect from species that have not been cultured, while the natural ecologies of many cultured species remain unknown. Here, we rely on genetic evidence-the only data consistently available among all taxa investigated-to describe four new Clade B Symbiodinium species. The 'host-specialized' species (S. antillogorgium sp. nov. and S. endomadracis sp. nov.) engage in mutualisms with specific cnidarian hosts, but exhibit differences in our ability to culture them in vitro. The ecologically 'cryptic' species (S. aenigmaticum sp. nov. and S. pseudominutum sp. nov.) thrive in culture, but their roles or functions in the ecosystem (i.e., niches) are yet to be documented. These new species call further attention to the spectrum of ecological guilds among Symbiodinium.
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Affiliation(s)
- John Everett Parkinson
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | - Mary Alice Coffroth
- Graduate Program in Evolution, Ecology and Behavior and Department of Geological Sciences, State University of New York at Buffalo, Buffalo, New York, 14260, USA
| | - Todd C LaJeunesse
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, 16802, USA
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Sanderson CM, Parkinson JE, Hollinshead M, Smith GL. Overexpression of the vaccinia virus A38L integral membrane protein promotes Ca2+ influx into infected cells. J Virol 1996; 70:905-14. [PMID: 8551630 PMCID: PMC189894 DOI: 10.1128/jvi.70.2.905-914.1996] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The vaccinia virus Western Reserve A38L protein is a hydrophobic integral membrane glycoprotein with amino acid similarity to mammalian integrin-associated protein. The protein has an N-terminal immunoglobulin superfamily domain, followed by five membrane-spanning domains and a short cytoplasmic tail. Deletion of the protein reduces virus plaque size but does not affect virus virulence (J. E. Parkinson, C. M. Sanderson, and G. L. Smith, Virology, in press). In this study, we have used a recombinant vaccinia virus in which the A38L gene may be inducibly overexpressed by addition of isopropyl-beta-D-thiogalactopyranoside (IPTG), to demonstrate that overexpression of the vaccinia virus A38L gene produces drastic changes in the morphology, permeability, and adhesion of infected cells. In particular, A38L overexpression caused swelling of cells, marginalization of nuclear chromatin, and vacuolization of the endoplasmic reticulum, features characteristic of cell necrosis. By 18 h postinfection, cells become permeable and lytic as defined by the free entry of propidium iodide and loss of the cytoplasmic enzyme lactate dehydrogenase. Chelation of extracellular Ca2+ 22 h postinfection inhibited further release of lactate dehydrogenase, showing that Ca2+ influx was required for A38L-induced lysis. Direct measurement of 45Ca2+ influx showed that the rate of Ca2+ uptake was directly related to the period of A38L induction. The A38L protein, therefore, promotes the formation of pores within the plasma membrane of cells, and these pores facilitate Ca2+ entry and induce necrosis. Addition of rifampin inhibited virus assembly but not the ability of A38L to induce necrosis, indicating that pore formation is independent of viral morphogenesis. Finally, overexpression of the A38L protein resulted in a reduced plaque size and a threefold decrease in production of infective particles in vitro. The A38L protein represents the first example of a virus protein which directly or indirectly promotes the influx of extracellular Ca2+.
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Affiliation(s)
- C M Sanderson
- Sir William Dunn School of Pathology, University of Oxford, United Kingdom
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Abstract
The vaccinia virus gene A38L encodes a highly hydrophobic protein with amino acid similarity to mammalian integrin-associated protein (IAP). In this report we have identified the A38L protein of strain Western Reserve (WR), defined its membrane topology, and analyzed its role in virus production and virulence. An antiserum raised against an A38L peptide identified the A38L gene product as a 33-kDa protein which is expressed at low levels during virus infection. A serum from a rabbit previously infected with WR virus recognized the A38L protein, thus confirming that the A38L gene is expressed in vivo. Using a coupled in vitro-translation/membrane-translocation system the 33-kDa protein was shown to be a membrane-associated and glycosylated form of a 29-kDa polypeptide precursor. The membrane topology of the A38L protein was defined by its glycosylation and protease sensitivity when associated with microsomal membranes. The N-terminal immunoglobulin-like variable domain was protected from exogenous protease and was therefore in the lumen of the vesicle, whereas the C-terminus was sensitive and therefore cytoplasmic. A38L deletion and revertant viruses were constructed and were used to study the involvement of A38L in virus assembly, release, and virulence. Deletion of the A38L gene caused a slight reduction in virus plaque size but did not affect the production of intracellular mature virus or extracellular enveloped virus particles in tissue culture cells nor the virulence of the virus in the murine intranasal model. The A38L protein therefore possesses similar sequence and membrane topology to the mammalian IAP protein but is not required for virus particle production or virulence.
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Affiliation(s)
- J E Parkinson
- Sir William Dunn School of Pathology, University of Oxford, United Kingdom
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Abstract
A characterization of vaccinia virus strain Western Reserve (WR) open reading frame (ORF) A36R is described. This ORF is predicted to encode a 221-amino-acid protein (M(r) 25.1 K) with an amino-terminal hydrophobic sequence, seven potential sites for attachment of N-linked carbohydrate, but no carboxy-terminal transmembrane anchor. It is identical in vaccinia strain Copenhagen and shares 94.6% amino acid identity with the corresponding ORF in variola virus strains Harvey, India-1967, and Bangladesh-1975. RNA analyses detected a 600-nucleotide, early transcript that initiated 10-13 nucleotides upstream of the A36R ORF, and heterogeneously sized late transcripts running across the ORF. A rabbit antiserum raised against an Escherichia coli glutathione S-transferase fusion protein identified M(r) 43-50 K proteins that accumulated late during vaccinia virus infection and fractionated as integral membrane proteins during Triton X-114 partitioning. Similar polypeptides were expressed by vaccinia virus strains Tian Tan, Tashkent, Lister, Wyeth, Copenhagen, and IHD-J and by rabbitpox virus and cowpox virus (strain Brighton Red). Immunoblot analysis of purified and protease-digested intracellular mature virus (IMV) and extracellular enveloped virus (EEV) showed that the A36R proteins were present on the surface of EEV with type II membrane topology, but were absent from IMV. A WR deletion mutant lacking the A36R ORF (delta A36R) had a small plaque phenotype on all cell lines tested. IMV formation by delta A36R was unaltered but EEV formation was reduced approximately fivefold compared to wild-type (WT) when measured either by density gradient analysis of isotopically labeled virions or by infectivity assays. Thus the loss of the A36R protein from the EEV surface did not reduce EEV specific infectivity in vitro. Despite this, delta A36R showed striking attenuation compared with WT in a murine intranasal model. Finally, a revertant virus in which the A36R ORF was restored showed WT plaque size, EEV formation, and virulence, demonstrating that all the phenotypic differences of delta A36R were attributable to loss of the A36R gene and not to other mutations acquired during its construction.
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Affiliation(s)
- J E Parkinson
- Sir William Dunn School of Pathology, University of Oxford, United Kingdom
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