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Krueger-Hadfield SA. Let's talk about sex: Why reproductive systems matter for understanding algae. JOURNAL OF PHYCOLOGY 2024; 60:581-597. [PMID: 38743848 DOI: 10.1111/jpy.13462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 04/23/2024] [Accepted: 04/24/2024] [Indexed: 05/16/2024]
Abstract
Sex is a crucial process that has molecular, genetic, cellular, organismal, and population-level consequences for eukaryotic evolution. Eukaryotic life cycles are composed of alternating haploid and diploid phases but are constrained by the need to accommodate the phenotypes of these different phases. Critical gaps in our understanding of evolutionary drivers of the diversity in algae life cycles include how selection acts to stabilize and change features of the life cycle. Moreover, most eukaryotes are partially clonal, engaging in both sexual and asexual reproduction. Yet, our understanding of the variation in their reproductive systems is largely based on sexual reproduction in animals or angiosperms. The relative balance of sexual versus asexual reproduction not only controls but also is in turn controlled by standing genetic variability, thereby shaping evolutionary trajectories. Thus, we must quantitatively assess the consequences of the variation in life cycles on reproductive systems. Algae are a polyphyletic group spread across many of the major eukaryotic lineages, providing powerful models by which to resolve this knowledge gap. There is, however, an alarming lack of data about the population genetics of most algae and, therefore, the relative frequency of sexual versus asexual processes. For many algae, the occurrence of sexual reproduction is unknown, observations have been lost in overlooked papers, or data on population genetics do not yet exist. This greatly restricts our ability to forecast the consequences of climate change on algal populations inhabiting terrestrial, aquatic, and marine ecosystems. This perspective summarizes our extant knowledge and provides some future directions to pursue broadly across micro- and macroalgal species.
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2
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Gomez-Campo K, Sanchez R, Martínez-Rugerio I, Yang X, Maher T, Osborne CC, Enriquez S, Baums IB, Mackenzie SA, Iglesias-Prieto R. Phenotypic plasticity for improved light harvesting, in tandem with methylome repatterning in reef-building corals. Mol Ecol 2024; 33:e17246. [PMID: 38153177 PMCID: PMC10922902 DOI: 10.1111/mec.17246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 11/24/2023] [Accepted: 11/30/2023] [Indexed: 12/29/2023]
Abstract
Acclimatization through phenotypic plasticity represents a more rapid response to environmental change than adaptation and is vital to optimize organisms' performance in different conditions. Generally, animals are less phenotypically plastic than plants, but reef-building corals exhibit plant-like properties. They are light dependent with a sessile and modular construction that facilitates rapid morphological changes within their lifetime. We induced phenotypic changes by altering light exposure in a reciprocal transplant experiment and found that coral plasticity is a colony trait emerging from comprehensive morphological and physiological changes within the colony. Plasticity in skeletal features optimized coral light harvesting and utilization and paralleled significant methylome and transcriptome modifications. Network-associated responses resulted in the identification of hub genes and clusters associated to the change in phenotype: inter-partner recognition and phagocytosis, soft tissue growth and biomineralization. Furthermore, we identified hub genes putatively involved in animal photoreception-phototransduction. These findings fundamentally advance our understanding of how reef-building corals repattern the methylome and adjust a phenotype, revealing an important role of light sensing by the coral animal to optimize photosynthetic performance of the symbionts.
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Affiliation(s)
- Kelly Gomez-Campo
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Robersy Sanchez
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | | | - Xiaodong Yang
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Tom Maher
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - C. Cornelia Osborne
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Susana Enriquez
- Unidad Académica de Sistemas Arrecifales Puerto Morelos, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, 77580, México
| | - Iliana B. Baums
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Sally A. Mackenzie
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Plant Science, The Pennsylvania State University, University Park, PA 16802, USA
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3
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Armstrong EJ, Lê-Hoang J, Carradec Q, Aury JM, Noel B, Hume BCC, Voolstra CR, Poulain J, Belser C, Paz-García DA, Cruaud C, Labadie K, Da Silva C, Moulin C, Boissin E, Bourdin G, Iwankow G, Romac S, Agostini S, Banaigs B, Boss E, Bowler C, de Vargas C, Douville E, Flores M, Forcioli D, Furla P, Galand PE, Gilson E, Lombard F, Pesant S, Reynaud S, Sullivan MB, Sunagawa S, Thomas OP, Troublé R, Thurber RV, Zoccola D, Planes S, Allemand D, Wincker P. Host transcriptomic plasticity and photosymbiotic fidelity underpin Pocillopora acclimatization across thermal regimes in the Pacific Ocean. Nat Commun 2023; 14:3056. [PMID: 37264036 DOI: 10.1038/s41467-023-38610-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 05/10/2023] [Indexed: 06/03/2023] Open
Abstract
Heat waves are causing declines in coral reefs globally. Coral thermal responses depend on multiple, interacting drivers, such as past thermal exposure, endosymbiont community composition, and host genotype. This makes the understanding of their relative roles in adaptive and/or plastic responses crucial for anticipating impacts of future warming. Here, we extracted DNA and RNA from 102 Pocillopora colonies collected from 32 sites on 11 islands across the Pacific Ocean to characterize host-photosymbiont fidelity and to investigate patterns of gene expression across a historical thermal gradient. We report high host-photosymbiont fidelity and show that coral and microalgal gene expression respond to different drivers. Differences in photosymbiotic association had only weak impacts on host gene expression, which was more strongly correlated with the historical thermal environment, whereas, photosymbiont gene expression was largely determined by microalgal lineage. Overall, our results reveal a three-tiered strategy of thermal acclimatization in Pocillopora underpinned by host-photosymbiont specificity, host transcriptomic plasticity, and differential photosymbiotic association under extreme warming.
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Affiliation(s)
- Eric J Armstrong
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France.
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France.
- PSL Université Paris: EPHE-UPVD-CNRS, UAR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan Cedex, France.
| | - Julie Lê-Hoang
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Quentin Carradec
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France.
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France.
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Benjamin Noel
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Benjamin C C Hume
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | | | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Caroline Belser
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - David A Paz-García
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Av. IPN 195, La Paz, Baja California Sur, 23096, México
| | - Corinne Cruaud
- Genoscope, Institut François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Karine Labadie
- Genoscope, Institut François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Corinne Da Silva
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Clémentine Moulin
- Fondation Tara Océan, Base Tara, 8 rue de Prague, 75 012, Paris, France
| | - Emilie Boissin
- PSL Université Paris: EPHE-UPVD-CNRS, UAR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan Cedex, France
| | - Guillaume Bourdin
- School of Marine Sciences, University of Maine, Orono, 04469, ME, USA
| | - Guillaume Iwankow
- PSL Université Paris: EPHE-UPVD-CNRS, UAR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan Cedex, France
| | - Sarah Romac
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, 29680, Roscoff, France
| | - Sylvain Agostini
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1, Shimoda, Shizuoka, Japan
| | - Bernard Banaigs
- PSL Université Paris: EPHE-UPVD-CNRS, UAR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan Cedex, France
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, 04469, ME, USA
| | - Chris Bowler
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
- Ecole Normale Supérieure, PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, 46 rue d'Ulm, F-75005, Paris, France
| | - Colomban de Vargas
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, 29680, Roscoff, France
| | - Eric Douville
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, F-91191, Gif-sur-Yvette, France
| | - Michel Flores
- Weizmann Institute of Science, Department of Earth and Planetary Sciences, 76100, Rehovot, Israel
| | - Didier Forcioli
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Medical School, Nice, France
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco, Principality of Monaco, Monaco
| | - Paola Furla
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Medical School, Nice, France
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco, Principality of Monaco, Monaco
| | - Pierre E Galand
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, 66650, Banyuls sur mer, France
| | - Eric Gilson
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Medical School, Nice, France
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco, Principality of Monaco, Monaco
- Department of Medical Genetics, CHU, Nice, France
| | - Fabien Lombard
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
- Sorbonne Université, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, F-06230, Villefranche-sur-Mer, France
| | - Stéphane Pesant
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Stéphanie Reynaud
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco, Principality of Monaco, Monaco
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, MC-98000, Principality of Monaco, Monaco
| | - Matthew B Sullivan
- Departments of Microbiology and Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH, 43210, USA
| | - Shinichi Sunagawa
- Institute of Microbiology, Department of Biology, Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
| | - Olivier P Thomas
- School of Biological and Chemical Sciences, Ryan institute, University of Galway, University Road H91TK33, Galway, Ireland
| | - Romain Troublé
- Fondation Tara Océan, Base Tara, 8 rue de Prague, 75 012, Paris, France
| | - Rebecca Vega Thurber
- Oregon State University, Department of Microbiology, 220 Nash Hall, 97331, Corvallis, OR, USA
| | - Didier Zoccola
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco, Principality of Monaco, Monaco
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, MC-98000, Principality of Monaco, Monaco
| | - Serge Planes
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 66860, Perpignan Cedex, France
| | - Denis Allemand
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco, Principality of Monaco, Monaco
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, MC-98000, Principality of Monaco, Monaco
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
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4
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Riley AB, Grillo MA, Epstein B, Tiffin P, Heath KD. Discordant population structure among rhizobium divided genomes and their legume hosts. Mol Ecol 2023; 32:2646-2659. [PMID: 36161739 DOI: 10.1111/mec.16704] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 09/15/2022] [Accepted: 09/20/2022] [Indexed: 11/29/2022]
Abstract
Symbiosis often occurs between partners with distinct life history characteristics and dispersal mechanisms. Many bacterial symbionts have genomes comprising multiple replicons with distinct rates of evolution and horizontal transmission. Such differences might drive differences in population structure between hosts and symbionts and among the elements of the divided genomes of bacterial symbionts. These differences might, in turn, shape the evolution of symbiotic interactions and bacterial evolution. Here we use whole genome resequencing of a hierarchically structured sample of 191 strains of Sinorhizobium meliloti collected from 21 locations in southern Europe to characterize population structures of this bacterial symbiont, which forms a root nodule symbiosis with the host plant Medicago truncatula. S. meliloti genomes showed high local (within-site) variation and little isolation by distance. This was particularly true for the two symbiosis elements, pSymA and pSymB, which have population structures that are similar to each other, but distinct from both the bacterial chromosome and the host plant. Given limited recombination on the chromosome, compared to the symbiosis elements, distinct population structures may result from differences in effective gene flow. Alternatively, positive or purifying selection, with little recombination, may explain distinct geographical patterns at the chromosome. Discordant population structure between hosts and symbionts indicates that geographically and genetically distinct host populations in different parts of the range might interact with genetically similar symbionts, potentially minimizing local specialization.
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Affiliation(s)
- Alex B Riley
- Department of Plant Biology, University of Illinois, Urbana, Illinois, USA
| | - Michael A Grillo
- Department of Biology, Loyola University Chicago, Chicago, Illinois, USA
| | - Brendan Epstein
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - Peter Tiffin
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - Katy D Heath
- Department of Plant Biology, University of Illinois, Urbana, Illinois, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois, USA
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5
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Elder H, Million WC, Bartels E, Krediet CJ, Muller EM, Kenkel CD. Long-term maintenance of a heterologous symbiont association in Acropora palmata on natural reefs. THE ISME JOURNAL 2023; 17:486-489. [PMID: 36510006 PMCID: PMC9938269 DOI: 10.1038/s41396-022-01349-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 11/24/2022] [Accepted: 11/29/2022] [Indexed: 12/14/2022]
Abstract
The sensitivity of reef-building coral to elevated temperature is a function of their symbiosis with dinoflagellate algae in the family Symbiodiniaceae. Changes in the composition of the endosymbiont community in response to thermal stress can increase coral thermal tolerance. Consequently, this mechanism is being investigated as a human-assisted intervention for rapid acclimation of coral in the face of climate change. Successful establishment of novel symbioses that increase coral thermal tolerance have been demonstrated in laboratory conditions; however, it is unclear how long these heterologous relationships persist in nature. Here, we test the persistence of a novel symbiosis between Acropora palmata and Durusdinium spp. from Mote Marine Laboratory's ex situ nursery by outplanting clonal replicates (ramets) of five A. palmata host genotypes to natural reefs in the lower Florida Keys. Amplicon sequencing analysis of ITS2-type profiles revealed that the majority of surviving ramets remained dominated by Durusdinium spp. two years after transplantation. However, 15% of ramets, including representatives of all genotypes, exhibited some degree of symbiont shuffling or switching at six of eight sites, including complete takeover by site-specific strains of the native symbiont, Symbiodinium fitti. The predominant long-term stability of the novel symbiosis supports the potential effectiveness of symbiont modification as a management tool. Although, the finding that 6-7 year-old coral can alter symbiont community composition in the absence of bleaching indicates that Symbiodiniaceae communities are indeed capable of great flexibility under ambient conditions.
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Affiliation(s)
- Holland Elder
- University of Southern California, 3616 Trousdale Parkway, AHF 231, Los Angeles, CA, 90089, USA.
| | - Wyatt C Million
- University of Southern California, 3616 Trousdale Parkway, AHF 231, Los Angeles, CA, 90089, USA
| | - Erich Bartels
- Mote Marine Laboratory, 24244 Overseas Hwy, Summerland Key, FL, 33042, USA
| | - Cory J Krediet
- Eckerd College, 4200 54th Ave., St. Petersburg, FL, 33711, USA
| | - Erinn M Muller
- Mote Marine Laboratory, 1600 Ken Thompson Parkway, Sarasota, FL, 34236, USA
| | - Carly D Kenkel
- University of Southern California, 3616 Trousdale Parkway, AHF 231, Los Angeles, CA, 90089, USA
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6
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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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7
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LaJeunesse TC, Casado-Amezúa P, Hume BCC, Butler CC, Mordret S, Piredda R, De Luca P, Pannone R, Sarno D, Wiedenmann J, D’Ambra I. Mutualistic dinoflagellates with big disparities in ribosomal DNA variation may confound estimates of symbiont diversity and ecology in the jellyfish Cotylorhiza tuberculata. Symbiosis 2022. [DOI: 10.1007/s13199-022-00880-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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8
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Baker LJ, Reich HG, Kitchen SA, Grace Klinges J, Koch HR, Baums IB, Muller EM, Thurber RV. The coral symbiont Candidatus Aquarickettsia is variably abundant in threatened Caribbean acroporids and transmitted horizontally. THE ISME JOURNAL 2022; 16:400-411. [PMID: 34363004 PMCID: PMC8776821 DOI: 10.1038/s41396-021-01077-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 06/28/2021] [Accepted: 07/22/2021] [Indexed: 02/07/2023]
Abstract
The symbiont "Candidatus Aquarickettsia rohweri" infects a diversity of aquatic hosts. In the threatened Caribbean coral, Acropora cervicornis, Aquarickettsia proliferates in response to increased nutrient exposure, resulting in suppressed growth and increased disease susceptibility and mortality of coral. This study evaluated the extent, as well as the ecology and evolution of Aquarickettsia infecting threatened corals, Ac. cervicornis, and Ac. palmata and their hybrid ("Ac. prolifera"). Aquarickettsia was found in all acroporids, with coral host and geographic location impacting the infection magnitude. Phylogenomic and genome-wide single-nucleotide variant analysis of Aquarickettsia found phylogenetic clustering by geographic region, not by coral taxon. Analysis of Aquarickettsia fixation indices suggests multiple sequential infections of the same coral colony are unlikely. Furthermore, relative to other Rickettsiales species, Aquarickettsia is undergoing positive selection, with Florida populations experiencing greater positive selection relative to other Caribbean locations. This may be due in part to Aquarickettsia proliferating in response to greater nutrient stress in Florida, as indicated by greater in situ replication rates in these corals. Aquarickettsia was not found to significantly codiversify with either the coral animal or the coral's algal symbiont (Symbiodinium "fitti"). Quantitative PCR analysis showed that gametes, larvae, recruits, and juveniles from susceptible, captive-reared coral genets were not infected with Aquarickettsia. Thus, horizontal transmission of Aquarickettsia via coral mucocytes or an unidentified host is more likely. The prevalence of Aquarickettsia in Ac. cervicornis and its high abundance in the Florida coral population suggests that coral disease mitigation efforts focus on preventing early infection via horizontal transmission.
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Affiliation(s)
- Lydia J Baker
- Department of Microbiology, Oregon State University, Corvallis, OR, USA.
| | - Hannah G Reich
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | - Sheila A Kitchen
- Division of Biology and Biological Engineering, California Institute of Science and Technology, Pasadena, CA, USA
| | - J Grace Klinges
- Department of Microbiology, Oregon State University, Corvallis, OR, USA
| | - Hanna R Koch
- Coral Restoration Program, Mote Marine Laboratory, Summerland Key, FL, USA
| | - Iliana B Baums
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | - Erinn M Muller
- Coral Restoration Program, Mote Marine Laboratory, Summerland Key, FL, USA
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9
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Turnham KE, Wham DC, Sampayo E, LaJeunesse TC. Mutualistic microalgae co-diversify with reef corals that acquire symbionts during egg development. THE ISME JOURNAL 2021; 15:3271-3285. [PMID: 34012104 PMCID: PMC8528872 DOI: 10.1038/s41396-021-01007-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 04/23/2021] [Accepted: 05/04/2021] [Indexed: 02/04/2023]
Abstract
The application of molecular genetics has reinvigorated and improved how species are defined and investigated scientifically, especially for morphologically cryptic micro-organisms. Here we show how species recognition improves understanding of the ecology and evolution of mutualisms between reef-building corals and their mutualistic dinoflagellates (i.e. Symbiodiniaceae). A combination of genetic, ecological, and morphological evidence defines two sibling species of Cladocopium (formerly Symbiodinium Clade C), specific only to host corals in the common genus Pocillopora, which transmit their obligate symbionts during oogenesis. Cladocopium latusorum sp. nov. is symbiotic with P. grandis/meandrina while the smaller-celled C. pacificum sp. nov. associates with P. verrucosa. Both symbiont species form mutualisms with Pocillopora that brood their young. Populations of each species, like their hosts, are genetically well connected across the tropical and subtropical Pacific Ocean, indicating a capacity for long-range dispersal. A molecular clock approximates their speciation during the late Pliocene or early Pleistocene as Earth underwent cycles of precipitous cooling and warming; and corresponds to when their hosts were also diversifying. The long temporal and spatial maintenance of high host fidelity, as well as genetic connectivity across thousands of kilometers, indicates that distinct ecological attributes and close evolutionary histories will restrain the adaptive responses of corals and their specialized symbionts to rapid climate warming.
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Affiliation(s)
| | - Drew C Wham
- Penn State University, University Park, PA, USA
| | | | - Todd C LaJeunesse
- Penn State University, University Park, PA, USA.
- Penn State Institutes of Energy and the Environment, University Park, PA, USA.
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10
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Cunning R, Parker KE, Johnson-Sapp K, Karp RF, Wen AD, Williamson OM, Bartels E, D'Alessandro M, Gilliam DS, Hanson G, Levy J, Lirman D, Maxwell K, Million WC, Moulding AL, Moura A, Muller EM, Nedimyer K, Reckenbeil B, van Hooidonk R, Dahlgren C, Kenkel C, Parkinson JE, Baker AC. Census of heat tolerance among Florida's threatened staghorn corals finds resilient individuals throughout existing nursery populations. Proc Biol Sci 2021; 288:20211613. [PMID: 34666521 DOI: 10.1098/rspb.2021.1613] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The rapid loss of reef-building corals owing to ocean warming is driving the development of interventions such as coral propagation and restoration, selective breeding and assisted gene flow. Many of these interventions target naturally heat-tolerant individuals to boost climate resilience, but the challenges of quickly and reliably quantifying heat tolerance and identifying thermotolerant individuals have hampered implementation. Here, we used coral bleaching automated stress systems to perform rapid, standardized heat tolerance assays on 229 colonies of Acropora cervicornis across six coral nurseries spanning Florida's Coral Reef, USA. Analysis of heat stress dose-response curves for each colony revealed a broad range in thermal tolerance among individuals (approx. 2.5°C range in Fv/Fm ED50), with highly reproducible rankings across independent tests (r = 0.76). Most phenotypic variation occurred within nurseries rather than between them, pointing to a potentially dominant role of fixed genetic effects in setting thermal tolerance and widespread distribution of tolerant individuals throughout the population. The identification of tolerant individuals provides immediately actionable information to optimize nursery and restoration programmes for Florida's threatened staghorn corals. This work further provides a blueprint for future efforts to identify and source thermally tolerant corals for conservation interventions worldwide.
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Affiliation(s)
- Ross Cunning
- Daniel P. Haerther Center for Conservation and Research, John G. Shedd Aquarium, Chicago, IL, USA
| | - Katherine E Parker
- Daniel P. Haerther Center for Conservation and Research, John G. Shedd Aquarium, Chicago, IL, USA
| | - Kelsey Johnson-Sapp
- Department of Marine Biology and Ecology, University of Miami, Miami, FL, USA
| | - Richard F Karp
- Department of Marine Biology and Ecology, University of Miami, Miami, FL, USA
| | - Alexandra D Wen
- Department of Marine Biology and Ecology, University of Miami, Miami, FL, USA
| | - Olivia M Williamson
- Department of Marine Biology and Ecology, University of Miami, Miami, FL, USA
| | - Erich Bartels
- Elizabeth Moore International Center for Coral Reef Research and Restoration, Mote Marine Laboratory, Summerland Key, FL, USA
| | | | - David S Gilliam
- Halmos College of Arts and Sciences, Nova Southeastern University, Dania Beach, FL, USA
| | - Grace Hanson
- Halmos College of Arts and Sciences, Nova Southeastern University, Dania Beach, FL, USA
| | - Jessica Levy
- Coral Restoration Foundation, Key Largo, FL, USA
| | - Diego Lirman
- Department of Marine Biology and Ecology, University of Miami, Miami, FL, USA
| | - Kerry Maxwell
- Florida Fish and Wildlife Conservation, Marathon, FL, USA
| | - Wyatt C Million
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Alison L Moulding
- Protected Resources Division, NOAA Fisheries Southeast Regional Office, St Petersburg, FL, USA
| | - Amelia Moura
- Coral Restoration Foundation, Key Largo, FL, USA
| | - Erinn M Muller
- Coral Health and Disease Program, Mote Marine Laboratory, Sarasota, FL, USA
| | | | | | - Ruben van Hooidonk
- Cooperative Institute for Marine and Atmospheric Studies, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, USA.,Ocean Chemistry and Ecosystems Division, NOAA Atlantic Oceanographic and Meteorological Laboratory, Miami, FL, USA
| | | | - Carly Kenkel
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - John E Parkinson
- Department of Integrative Biology, University of South Florida, Tampa, FL, USA
| | - Andrew C Baker
- Department of Marine Biology and Ecology, University of Miami, Miami, FL, USA
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11
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Figueroa RI, Howe-Kerr LI, Correa AMS. Direct evidence of sex and a hypothesis about meiosis in Symbiodiniaceae. Sci Rep 2021; 11:18838. [PMID: 34552138 PMCID: PMC8458349 DOI: 10.1038/s41598-021-98148-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 08/30/2021] [Indexed: 02/08/2023] Open
Abstract
Dinoflagellates in the family Symbiodiniaceae are obligate endosymbionts of diverse marine invertebrates, including corals, and impact the capacity of their hosts to respond to climate change-driven ocean warming. Understanding the conditions under which increased genetic variation in Symbiodiniaceae arises via sexual recombination can support efforts to evolve thermal tolerance in these symbionts and ultimately mitigate coral bleaching, the breakdown of the coral-Symbiodiniaceae partnership under stress. However, direct observations of meiosis in Symbiodiniaceae have not been reported, despite various lines of indirect evidence that it occurs. We present the first cytological evidence of sex in Symbiodiniaceae based on nuclear DNA content and morphology using Image Flow Cytometry, Cell Sorting and Confocal Microscopy. We show the Symbiodiniaceae species, Cladocopium latusorum, undergoes gamete conjugation, zygote formation, and meiosis within a dominant reef-building coral in situ. On average, sex was detected in 1.5% of the cells analyzed (N = 10,000-40,000 cells observed per sample in a total of 20 samples obtained from 3 Pocillopora colonies). We hypothesize that meiosis follows a two-step process described in other dinoflagellates, in which diploid zygotes form dyads during meiosis I, and triads and tetrads as final products of meiosis II. This study sets the stage for investigating environmental triggers of Symbiodiniaceae sexuality and can accelerate the assisted evolution of a key coral symbiont in order to combat reef degradation.
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Affiliation(s)
- R. I. Figueroa
- Spanish Institute of Oceanography in Vigo (IEO-CSIC), Subida a Radio Faro, 50, 36390 Vigo, Spain
| | - L. I. Howe-Kerr
- grid.21940.3e0000 0004 1936 8278BioSciences Department, Rice University, Houston, TX USA
| | - A. M. S. Correa
- grid.21940.3e0000 0004 1936 8278BioSciences Department, Rice University, Houston, TX USA
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12
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Reich HG, Kitchen SA, Stankiewicz KH, Devlin-Durante M, Fogarty ND, Baums IB. Genomic variation of an endosymbiotic dinoflagellate (Symbiodinium 'fitti') among closely related coral hosts. Mol Ecol 2021; 30:3500-3514. [PMID: 33964051 DOI: 10.1111/mec.15952] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 05/01/2021] [Accepted: 05/04/2021] [Indexed: 12/20/2022]
Abstract
Mutualisms where hosts are coupled metabolically to their symbionts often exhibit high partner fidelity. Most reef-building coral species form obligate symbioses with a specific species of photosymbionts, dinoflagellates in the family Symbiodiniaceae, despite needing to acquire symbionts early in their development from environmental sources. Three Caribbean acroporids (Acropora palmata, A. cervicornis and their F1 hybrid) are sympatric across much of their range, but often occupy different depth and light habitats. Throughout this range, both species and their hybrid associate with the endosymbiotic dinoflagellate Symbiodinium 'fitti'. Because light (and therefore depth) influences the physiology of dinoflagellates, we investigated whether S. 'fitti' populations from each host taxon were differentiated genetically. Single nucleotide polymorphisms (SNPs) among S. 'fitti' strains were identified by aligning shallow metagenomic sequences of acroporid colonies sampled from across the Caribbean to a ~600-Mb draft assembly of the S. 'fitti' genome (from the CFL14120 A. cervicornis metagenome). Phylogenomic and multivariate analyses revealed that genomic variation among S. 'fitti' strains partitioned to each host taxon rather than by biogeographical origin. This is particularly noteworthy because the hybrid has a sparse fossil record and may be of relatively recent origin. A subset (37.6%) of the SNPs putatively under selection were nonsynonymous mutations predicted to alter protein efficiency. Differences in genomic variation of S. 'fitti' strains from each host taxon may reflect the unique selection pressures created by the microenvironments associated with each host. The nonrandom sorting among S. 'fitti' strains to different hosts could be the basis for lineage diversification via disruptive selection, leading to ecological specialization and ultimately speciation.
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Affiliation(s)
- Hannah G Reich
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | - Sheila A Kitchen
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | | | | | - Nicole D Fogarty
- Department of Biology and Marine Biology, Center for Marine Science, University of North Carolina Wilmington, Wilmington, NC, USA
| | - Iliana B Baums
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
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13
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Cornwell BH, Hernández L. Genetic structure in the endosymbiont Breviolum 'muscatinei' is correlated with geographical location, environment and host species. Proc Biol Sci 2021; 288:20202896. [PMID: 33715441 PMCID: PMC7944108 DOI: 10.1098/rspb.2020.2896] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Corals and cnidarians form symbioses with dinoflagellates across a wide range of habitats from the tropics to temperate zones. Notably, these partnerships create the foundation of coral reef ecosystems and are at risk of breaking down due to climate change. This symbiosis couples the fitness of the partners, where adaptations in one species can benefit the holobiont. However, the scales over which each partner can match their current-and future-environment are largely unknown. We investigated population genetic patterns of temperate anemones (Anthopleura spp.) and their endosymbiont Breviolum 'muscatinei', across an extensive geographical range to identify the spatial scales over which local adaptation is possible. Similar to previously published results, two solitary host species exhibited isolation by distance across hundreds of kilometres. However, symbionts exhibited genetic structure across multiple spatial scales, from geographical location to depth in the intertidal zone, and host species, suggesting that symbiont populations are more likely than their hosts to adaptively mitigate the impact of increasing temperatures.
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Affiliation(s)
- Brendan H Cornwell
- Center for Population Biology, University of California, Davis, CA 95616, USA
| | - Luis Hernández
- Departamento de Ciencias Marinas y Costeras, Universidad Autónoma de Baja California Sur, La Paz, Baja California Sur, Mexico
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14
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Abstract
Climate-driven reef decline has prompted the development of next-generation coral conservation strategies, many of which hinge on the movement of adaptive variation across genetic and environmental gradients. This process is limited by our understanding of how genetic and genotypic drivers of coral bleaching will manifest in different environmental conditions. We reciprocally transplanted 10 genotypes of Acropora cervicornis across eight sites along a 60 km span of the Florida Reef Tract and documented significant genotype × environment interactions in bleaching response during the severe 2015 bleaching event. Performance relative to site mean was significantly different between genotypes and can be mostly explained by ensemble models of correlations with genetic markers. The high explanatory power was driven by significant enrichment of loci associated DNA repair, cell signalling and apoptosis. No genotypes performed above (or below) bleaching average at all sites, so genomic predictors can provide practitioners with 'confidence intervals' about the chance of success in novel habitats. These data have important implications for assisted gene flow and managed relocation, and their integration with traditional active restoration.
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Affiliation(s)
- Crawford Drury
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL 33149, USA
| | - Diego Lirman
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL 33149, USA
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15
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Porro B, Zamoum T, Mallien C, Hume BCC, Voolstra CR, Röttinger E, Furla P, Forcioli D. Horizontal acquisition of Symbiodiniaceae in the Anemonia viridis (Cnidaria, Anthozoa) species complex. Mol Ecol 2020; 30:391-405. [PMID: 33249664 DOI: 10.1111/mec.15755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 10/29/2020] [Accepted: 11/13/2020] [Indexed: 12/01/2022]
Abstract
All metazoans are in fact holobionts, resulting from the association of several organisms, and organismal adaptation is then due to the composite response of this association to the environment. Deciphering the mechanisms of symbiont acquisition in a holobiont is therefore essential to understanding the extent of its adaptive capacities. In cnidarians, some species acquire their photosynthetic symbionts directly from their parents (vertical transmission) but may also acquire symbionts from the environment (horizontal acquisition) at the adult stage. The Mediterranean snakelocks sea anemone, Anemonia viridis (Forskål, 1775), passes down symbionts from one generation to the next by vertical transmission, but the capacity for such horizontal acquisition is still unexplored. To unravel the flexibility of the association between the different host lineages identified in A. viridis and its Symbiodiniaceae, we genotyped both the animal hosts and their symbiont communities in members of host clones in five different locations in the North Western Mediterranean Sea. The composition of within-host-symbiont populations was more dependent on the geographical origin of the hosts than their membership to a given lineage or even to a given clone. Additionally, similarities in host-symbiont communities were greater among genets (i.e. among different clones) than among ramets (i.e. among members of the same given clonal genotype). Taken together, our results demonstrate that A. viridis may form associations with a range of symbiotic dinoflagellates and suggest a capacity for horizontal acquisition. A mixed-mode transmission strategy in A. viridis, as we posit here, may help explain the large phenotypic plasticity that characterizes this anemone.
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Affiliation(s)
- Barbara Porro
- CNRS, INSERM, Institute for Research on Cancer and Aging (IRCAN), Université Côte d'Azur, Nice, France
| | - Thamilla Zamoum
- CNRS, INSERM, Institute for Research on Cancer and Aging (IRCAN), Université Côte d'Azur, Nice, France
| | - Cédric Mallien
- CNRS, INSERM, Institute for Research on Cancer and Aging (IRCAN), Université Côte d'Azur, Nice, France
| | - Benjamin C C Hume
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | | | - Eric Röttinger
- CNRS, INSERM, Institute for Research on Cancer and Aging (IRCAN), Université Côte d'Azur, Nice, France
| | - Paola Furla
- CNRS, INSERM, Institute for Research on Cancer and Aging (IRCAN), Université Côte d'Azur, Nice, France
| | - Didier Forcioli
- CNRS, INSERM, Institute for Research on Cancer and Aging (IRCAN), Université Côte d'Azur, Nice, France
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16
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Aichelman HE, Barshis DJ. Adaptive divergence, neutral panmixia, and algal symbiont population structure in the temperate coral Astrangia poculata along the Mid-Atlantic United States. PeerJ 2020; 8:e10201. [PMID: 33240603 PMCID: PMC7680023 DOI: 10.7717/peerj.10201] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 09/27/2020] [Indexed: 12/11/2022] Open
Abstract
Astrangia poculata is a temperate scleractinian coral that exists in facultative symbiosis with the dinoflagellate alga Breviolum psygmophilum across a range spanning the Gulf of Mexico to Cape Cod, Massachusetts. Our previous work on metabolic thermal performance of Virginia (VA) and Rhode Island (RI) populations of A. poculata revealed physiological signatures of cold (RI) and warm (VA) adaptation of these populations to their respective local thermal environments. Here, we used whole-transcriptome sequencing (mRNA-Seq) to evaluate genetic differences and identify potential loci involved in the adaptive signature of VA and RI populations. Sequencing data from 40 A. poculata individuals, including 10 colonies from each population and symbiotic state (VA-white, VA-brown, RI-white, and RI-brown), yielded a total of 1,808 host-associated and 59 algal symbiont-associated single nucleotide polymorphisms (SNPs) post filtration. Fst outlier analysis identified 66 putative high outlier SNPs in the coral host and 4 in the algal symbiont. Differentiation of VA and RI populations in the coral host was driven by putatively adaptive loci, not neutral divergence (Fst = 0.16, p = 0.001 and Fst = 0.002, p = 0.269 for outlier and neutral SNPs respectively). In contrast, we found evidence of neutral population differentiation in B. psygmophilum (Fst = 0.093, p = 0.001). Several putatively adaptive host loci occur on genes previously associated with the coral stress response. In the symbiont, three of four putatively adaptive loci are associated with photosystem proteins. The opposing pattern of neutral differentiation in B. psygmophilum, but not the A. poculata host, reflects the contrasting dynamics of coral host and algal symbiont population connectivity, dispersal, and gene by environment interactions.
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Affiliation(s)
- Hannah E Aichelman
- Department of Biology, Boston University, Boston, MA, USA.,Department of Biological Sciences, Old Dominion University, Norfolk, VA, USA
| | - Daniel J Barshis
- Department of Biological Sciences, Old Dominion University, Norfolk, VA, USA
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17
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Davies SW, Moreland KN, Wham DC, Kanke MR, Matz MV. Cladocopium community divergence in two Acropora coral hosts across multiple spatial scales. Mol Ecol 2020; 29:4559-4572. [PMID: 33002237 DOI: 10.1111/mec.15668] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 09/14/2020] [Accepted: 09/18/2020] [Indexed: 12/11/2022]
Abstract
Many broadly-dispersing corals acquire their algal symbionts (Symbiodiniaceae) "horizontally" from their environment upon recruitment. Horizontal transmission could promote coral fitness across diverse environments provided that corals can associate with divergent algae across their range and that these symbionts exhibit reduced dispersal potential. Here we quantified community divergence of Cladocopium algal symbionts in two coral host species (Acropora hyacinthus, Acropora digitifera) across two spatial scales (reefs on the same island, and between islands) across the Micronesian archipelago using microsatellites. We find that both hosts associated with a variety of multilocus genotypes (MLG) within two genetically distinct Cladocopium lineages (C40, C21), confirming that Acropora coral hosts associate with a range of Cladocopium symbionts across this region. Both C40 and C21 included multiple asexual lineages bearing identical MLGs, many of which spanned host species, reef sites within islands, and even different islands. Both C40 and C21 exhibited moderate host specialization and divergence across islands. In addition, within every island, algal symbiont communities were significantly clustered by both host species and reef site, highlighting that coral-associated Cladocopium communities are structured across small spatial scales and within hosts on the same reef. This is in stark contrast to their coral hosts, which never exhibited significant genetic divergence between reefs on the same island. These results support the view that horizontal transmission could improve local fitness for broadly dispersing Acropora coral species.
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Affiliation(s)
- Sarah W Davies
- Department of Biology, Boston University, Boston, MA, USA.,Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Kelsey N Moreland
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Drew C Wham
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Matt R Kanke
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Mikhail V Matz
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
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18
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van Oppen MJH, Medina M. Coral evolutionary responses to microbial symbioses. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190591. [PMID: 32772672 PMCID: PMC7435167 DOI: 10.1098/rstb.2019.0591] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/09/2020] [Indexed: 12/19/2022] Open
Abstract
This review explores how microbial symbioses may have influenced and continue to influence the evolution of reef-building corals (Cnidaria; Scleractinia). The coral holobiont comprises a diverse microbiome including dinoflagellate algae (Dinophyceae; Symbiodiniaceae), bacteria, archaea, fungi and viruses, but here we focus on the Symbiodiniaceae as knowledge of the impact of other microbial symbionts on coral evolution is scant. Symbiosis with Symbiodiniaceae has extended the coral's metabolic capacity through metabolic handoffs and horizontal gene transfer (HGT) and has contributed to the ecological success of these iconic organisms. It necessitated the prior existence or the evolution of a series of adaptations of the host to attract and select the right symbionts, to provide them with a suitable environment and to remove disfunctional symbionts. Signatures of microbial symbiosis in the coral genome include HGT from Symbiodiniaceae and bacteria, gene family expansions, and a broad repertoire of oxidative stress response and innate immunity genes. Symbiosis with Symbiodiniaceae has permitted corals to occupy oligotrophic waters as the algae provide most corals with the majority of their nutrition. However, the coral-Symbiodiniaceae symbiosis is sensitive to climate warming, which disrupts this intimate relationship, causing coral bleaching, mortality and a worldwide decline of coral reefs. This article is part of the theme issue 'The role of the microbiome in host evolution'.
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Affiliation(s)
- Madeleine J. H. van Oppen
- School of BioSciences, The University of Melbourne, Parkville, 3010 Victoria, Australia
- Australian Institute of Marine Science, PMB No. 3, Townsville MC, 4810 Queensland, Australia
| | - Mónica Medina
- Department of Biology, The Pennsylvania State University, 208 Mueller Lab, University Park, PA 16802, USA
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19
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Temperature transcends partner specificity in the symbiosis establishment of a cnidarian. ISME JOURNAL 2020; 15:141-153. [PMID: 32934356 PMCID: PMC7852570 DOI: 10.1038/s41396-020-00768-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 08/13/2020] [Accepted: 09/02/2020] [Indexed: 12/21/2022]
Abstract
Coral reef research has predominantly focused on the effect of temperature on the breakdown of coral-dinoflagellate symbioses. However, less is known about how increasing temperature affects the establishment of new coral-dinoflagellate associations. Inter-partner specificity and environment-dependent colonization are two constraints proposed to limit the acquisition of more heat tolerant symbionts. Here, we investigated the symbiotic dynamics of various photosymbionts in different host genotypes under “optimal” and elevated temperature conditions. To do this, we inoculated symbiont-free polyps of the sea anemone Exaiptasia pallida originating from Hawaii (H2), North Carolina (CC7), and the Red Sea (RS) with the same mixture of native symbiont strains (Breviolum minutum, Symbiodinium linucheae, S. microadriaticum, and a Breviolum type from the Red Sea) at 25 and 32 °C, and assessed their ITS2 composition, colonization rates, and PSII photochemical efficiency (Fv/Fm). Symbiont communities across thermal conditions differed significantly for all hosts, suggesting that temperature rather than partner specificity had a stronger effect on symbiosis establishment. Overall, we detected higher abundances of more heat resistant Symbiodiniaceae types in the 32 °C treatments. Our data further showed that PSII photophysiology under elevated temperature improved with thermal pre-exposure (i.e., higher Fv/Fm), yet, this effect depended on host genotype and was influenced by active feeding as photochemical efficiency dropped in response to food deprivation. These findings highlight the role of temperature and partner fidelity in the establishment and performance of symbiosis and demonstrate the importance of heterotrophy for symbiotic cnidarians to endure and recover from stress.
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20
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Kitchen SA, Von Kuster G, Kuntz KLV, Reich HG, Miller W, Griffin S, Fogarty ND, Baums IB. STAGdb: a 30K SNP genotyping array and Science Gateway for Acropora corals and their dinoflagellate symbionts. Sci Rep 2020; 10:12488. [PMID: 32719467 PMCID: PMC7385180 DOI: 10.1038/s41598-020-69101-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 06/22/2020] [Indexed: 11/26/2022] Open
Abstract
Standardized identification of genotypes is necessary in animals that reproduce asexually and form large clonal populations such as coral. We developed a high-resolution hybridization-based genotype array coupled with an analysis workflow and database for the most speciose genus of coral, Acropora, and their symbionts. We designed the array to co-analyze host and symbionts based on bi-allelic single nucleotide polymorphisms (SNP) markers identified from genomic data of the two Caribbean Acropora species as well as their dominant dinoflagellate symbiont, Symbiodinium ‘fitti’. SNPs were selected to resolve multi-locus genotypes of host (called genets) and symbionts (called strains), distinguish host populations and determine ancestry of coral hybrids between Caribbean acroporids. Pacific acroporids can also be genotyped using a subset of the SNP loci and additional markers enable the detection of symbionts belonging to the genera Breviolum, Cladocopium, and Durusdinium. Analytic tools to produce multi-locus genotypes of hosts based on these SNP markers were combined in a workflow called the Standard Tools for Acroporid Genotyping (STAG). The STAG workflow and database are contained within a customized Galaxy environment (https://coralsnp.science.psu.edu/galaxy/), which allows for consistent identification of host genet and symbiont strains and serves as a template for the development of arrays for additional coral genera. STAG data can be used to track temporal and spatial changes of sampled genets necessary for restoration planning and can be applied to downstream genomic analyses. Using STAG, we uncover bi-directional hybridization between and population structure within Caribbean acroporids and detect a cryptic Acroporid species in the Pacific.
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Affiliation(s)
- S A Kitchen
- Department of Biology, The Pennsylvania State University, 208 Mueller Laboratory, University Park, PA, 16802, USA
| | - G Von Kuster
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - K L Vasquez Kuntz
- Department of Biology, The Pennsylvania State University, 208 Mueller Laboratory, University Park, PA, 16802, USA
| | - H G Reich
- Department of Biology, The Pennsylvania State University, 208 Mueller Laboratory, University Park, PA, 16802, USA
| | - W Miller
- Centre for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, PA, 16802, USA
| | - S Griffin
- NOAA Restoration Center, 260 Guard Rd., Aguadilla, PR, 00603, USA
| | - Nicole D Fogarty
- Department of Biology and Marine Biology, Center for Marine Science, University of North Carolina Wilmington, Wilmington, NC, 28403, USA
| | - I B Baums
- Department of Biology, The Pennsylvania State University, 208 Mueller Laboratory, University Park, PA, 16802, USA.
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21
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Chen B, Yu K, Qin Z, Liang J, Wang G, Huang X, Wu Q, Jiang L. Dispersal, genetic variation, and symbiont interaction network of heat-tolerant endosymbiont Durusdinium trenchii: Insights into the adaptive potential of coral to climate change. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 723:138026. [PMID: 32213418 DOI: 10.1016/j.scitotenv.2020.138026] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 03/10/2020] [Accepted: 03/16/2020] [Indexed: 06/10/2023]
Abstract
Global warming has degraded coral reef ecosystems worldwide. Some corals develop thermal tolerance by associating with heat-tolerant Symbiodiniaceae. Here, we studied the mechanisms surrounding the dispersal, genetic variation and symbionts interaction of heat-tolerant Durusdinium trenchii across 13° latitudes in the South China Sea (SCS), to explore the possible mechanisms underlying these changes. Our results showed that Durusdinium trenchii are widely distributed in the seawater from the SCS. Our analyses of microsatellite loci revealed that D. trenchii has a high genetic diversity in the SCS; STRUCTURE analysis indicated that D. trenchii can be divided into four populations within the SCS; There exist positive correlations between genetic variation and geographic isolation, average sea surface temperature (SST) and variations in SST. Network modelling inferences showed that D. trenchii is a key species in the Symbiodiniaceae communities in the tropical SCS and contributes the greatest number of co-exclusion relationships. These results indicated that D. trenchii can affect the rare Symbiodiniaceae community. The long lifespan and the monsoon-driven ocean currents have shaped the wide distribution of D. trenchii. But low SST limits the ability of D. trenchii to establish stable symbioses with coral in the subtropical habitats. Geographical isolation and SST have shaped significant genetic variation of D.trenchii around the SCS. Our data reveals the biogeography and genetic population characteristics of D. trenchii in the Indo-Pacific region, and suggests that heat-tolerance and high genetic diversity of D. trenchii aid the corals with their adaptation to climate change.
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Affiliation(s)
- Biao Chen
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning, China; Coral Reef Research Center of China, Guangxi University, Nanning, China; School of Marine Sciences, Guangxi University, Nanning, China
| | - Kefu Yu
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning, China; Coral Reef Research Center of China, Guangxi University, Nanning, China; School of Marine Sciences, Guangxi University, Nanning, China.
| | - Zhenjun Qin
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning, China; Coral Reef Research Center of China, Guangxi University, Nanning, China; School of Marine Sciences, Guangxi University, Nanning, China
| | - Jiayuan Liang
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning, China; Coral Reef Research Center of China, Guangxi University, Nanning, China; School of Marine Sciences, Guangxi University, Nanning, China
| | - Guanghua Wang
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning, China; Coral Reef Research Center of China, Guangxi University, Nanning, China; School of Marine Sciences, Guangxi University, Nanning, China
| | - Xueyong Huang
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning, China; Coral Reef Research Center of China, Guangxi University, Nanning, China; School of Marine Sciences, Guangxi University, Nanning, China
| | - Qian Wu
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning, China; Coral Reef Research Center of China, Guangxi University, Nanning, China; School of Marine Sciences, Guangxi University, Nanning, China
| | - Leilei Jiang
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning, China; Coral Reef Research Center of China, Guangxi University, Nanning, China; School of Marine Sciences, Guangxi University, Nanning, China
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22
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Eckert RJ, Reaume AM, Sturm AB, Studivan MS, Voss JD. Depth Influences Symbiodiniaceae Associations Among Montastraea cavernosa Corals on the Belize Barrier Reef. Front Microbiol 2020; 11:518. [PMID: 32328040 PMCID: PMC7160519 DOI: 10.3389/fmicb.2020.00518] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 03/10/2020] [Indexed: 12/21/2022] Open
Abstract
In Belize, shallow populations (10 and 16 m) of the coral species Montastraea cavernosa from the back reef and reef crest are genetically differentiated from deeper populations on the fore reef and reef wall (25 and 35 m). Like many species of scleractinian corals, M. cavernosa has an obligate symbiosis with dinoflagellate microalgae from the family Symbiodiniaceae. Here, we describe the Symbiodiniaceae taxa found within previously sampled and genotyped M. cavernosa populations along a depth gradient on the Belize Barrier Reef by implementing high-throughput sequencing of the ITS2 region of Symbiodiniaceae ribosomal DNA and the SymPortal analysis framework. While Symbiodiniaceae ITS2 type profiles across all sampling depths were almost entirely (99.99%) from the genus Cladocopium (formerly Symbiodinium Clade C), shallow (10 and 16 m) populations had a greater diversity of ITS2 type profiles in comparison to deeper (25 and 35 m) populations. Permutational multivariate analysis of variance (PERMANOVA) confirmed significant differences in ITS2 type profiles between shallow and deep sample populations. Overall Symbiodiniaceae communities changed significantly with depth, following patterns similar to the coral host's population genetic structure. Though physiological differences among species in the cosmopolitan genus Cladocopium are not well-described, our results suggest that although some members of Cladocopium are depth-generalists, shallow M. cavernosa populations in Belize may harbor shallow-specialized Symbiodiniaceae not found in deeper populations.
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Affiliation(s)
- Ryan J. Eckert
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Boca Raton, FL, United States
| | | | | | | | - Joshua D. Voss
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Boca Raton, FL, United States
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23
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Claar DC, Tietjen KL, Cox KD, Gates RD, Baum JK. Chronic disturbance modulates symbiont (Symbiodiniaceae) beta diversity on a coral reef. Sci Rep 2020; 10:4492. [PMID: 32161299 PMCID: PMC7066189 DOI: 10.1038/s41598-020-60929-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 01/30/2020] [Indexed: 11/09/2022] Open
Abstract
Chronic disturbance can disrupt ecological interactions including the foundational symbiosis between reef-building corals and the dinoflagellate family Symbiodiniaceae. Symbiodiniaceae are photosynthetic endosymbionts necessary for coral survival, but many Symbiodiniaceae can also be found free-living in the environment. Since most coral species acquire new Symbiodiniaceae from the environment each generation, free-living Symbiodiniaceae represent important pools for coral symbiont acquisition. Yet, little is known about the diversity of, or impacts of disturbance on, free-living Symbiodiniaceae. To determine how chronic and pulse disturbances influence Symbiodiniaceae communities, we sampled three reef habitat compartments - sediment, water, and coral (Pocillopora grandis, Montipora aequituberculata, Porites lobata) - at sites exposed to different levels of chronic anthropogenic disturbance, before, during, and after a major storm. Almost no (4%) Symbiodiniaceae amplicon sequence variants (ASVs) were found in all three compartments, and over half were found uniquely in coral. Sites experiencing chronic disturbance were typically associated with higher symbiont beta diversity (i.e., variability and turnover) across reef habitat compartments. Pulse stress, from the storm, exhibited some influence on symbiont beta diversity but the effect was inconsistent. This suggests that in this ecosystem, the effects of chronic disturbance are more prominent than temporal variability during a pulse disturbance for shaping symbiont communities.
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Affiliation(s)
- Danielle C Claar
- Department of Biology, University of Victoria, Victoria, British Columbia, V8W 2Y2, Canada. .,University of Washington, School of Aquatic and Fisheries Science, 1122 NE Boat St, Seattle, WA, 98105, USA.
| | - Kristina L Tietjen
- Department of Biology, University of Victoria, Victoria, British Columbia, V8W 2Y2, Canada
| | - Kieran D Cox
- Department of Biology, University of Victoria, Victoria, British Columbia, V8W 2Y2, Canada.,Hakai Institute, Calvert Island, British Columbia, Canada
| | - Ruth D Gates
- Hawaii Institute of Marine Biology, Kaneohe, HI, 96744, USA
| | - Julia K Baum
- Department of Biology, University of Victoria, Victoria, British Columbia, V8W 2Y2, Canada. .,Hawaii Institute of Marine Biology, Kaneohe, HI, 96744, USA.
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24
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Krueger T, Horwitz N, Bodin J, Giovani ME, Escrig S, Fine M, Meibom A. Intracellular competition for nitrogen controls dinoflagellate population density in corals. Proc Biol Sci 2020; 287:20200049. [PMID: 32126963 PMCID: PMC7126079 DOI: 10.1098/rspb.2020.0049] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The density of dinoflagellate microalgae in the tissue of symbiotic corals is an important determinant for health and productivity of the coral animal. Yet, the specific mechanism for their regulation and the consequence for coral nutrition are insufficiently understood due to past methodological limitations to resolve the fine-scale metabolic consequences of fluctuating densities. Here, we characterized the physiological and nutritional consequences of symbiont density variations on the colony and tissue level in Stylophora pistillata from the Red Sea. Alterations in symbiont photophysiology maintained coral productivity and host nutrition across a broad range of symbiont densities. However, we demonstrate that density-dependent nutrient competition between individual symbiont cells, manifested as reduced nitrogen assimilation and cell biomass, probably creates the negative feedback mechanism for symbiont population growth that ultimately defines the steady-state density. Despite fundamental changes in symbiont nitrogen assimilation, we found no density-related metabolic optimum beyond which host nutrient assimilation or tissue biomass declined, indicating that host nutrient demand is sufficiently met across the typically observed range of symbiont densities under ambient conditions.
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Affiliation(s)
- Thomas Krueger
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Noa Horwitz
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel.,The Interuniversity Institute for Marine Sciences, Eilat 88103, Israel
| | - Julia Bodin
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Maria-Evangelia Giovani
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Stéphane Escrig
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Maoz Fine
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel.,The Interuniversity Institute for Marine Sciences, Eilat 88103, Israel
| | - Anders Meibom
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.,Center for Advanced Surface Analysis, Institute of Earth Sciences, University of Lausanne, 1015 Lausanne, Switzerland
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25
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Baums IB, Baker AC, Davies SW, Grottoli AG, Kenkel CD, Kitchen SA, Kuffner IB, LaJeunesse TC, Matz MV, Miller MW, Parkinson JE, Shantz AA. Considerations for maximizing the adaptive potential of restored coral populations in the western Atlantic. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2019; 29:e01978. [PMID: 31332879 PMCID: PMC6916196 DOI: 10.1002/eap.1978] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 06/13/2019] [Accepted: 06/21/2019] [Indexed: 05/06/2023]
Abstract
Active coral restoration typically involves two interventions: crossing gametes to facilitate sexual larval propagation; and fragmenting, growing, and outplanting adult colonies to enhance asexual propagation. From an evolutionary perspective, the goal of these efforts is to establish self-sustaining, sexually reproducing coral populations that have sufficient genetic and phenotypic variation to adapt to changing environments. Here, we provide concrete guidelines to help restoration practitioners meet this goal for most Caribbean species of interest. To enable the persistence of coral populations exposed to severe selection pressure from many stressors, a mixed provenance strategy is suggested: genetically unique colonies (genets) should be sourced both locally as well as from more distant, environmentally distinct sites. Sourcing three to four genets per reef along environmental gradients should be sufficient to capture a majority of intraspecies genetic diversity. It is best for practitioners to propagate genets with one or more phenotypic traits that are predicted to be valuable in the future, such as low partial mortality, high wound healing rate, high skeletal growth rate, bleaching resilience, infectious disease resilience, and high sexual reproductive output. Some effort should also be reserved for underperforming genets because colonies that grow poorly in nurseries sometimes thrive once returned to the reef and may harbor genetic variants with as yet unrecognized value. Outplants should be clustered in groups of four to six genets to enable successful fertilization upon maturation. Current evidence indicates that translocating genets among distant reefs is unlikely to be problematic from a population genetic perspective but will likely provide substantial adaptive benefits. Similarly, inbreeding depression is not a concern given that current practices only raise first-generation offspring. Thus, proceeding with the proposed management strategies even in the absence of a detailed population genetic analysis of the focal species at sites targeted for restoration is the best course of action. These basic guidelines should help maximize the adaptive potential of reef-building corals facing a rapidly changing environment.
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Affiliation(s)
- Iliana B. Baums
- Department of BiologyPennsylvania State UniversityUniversity ParkPennsylvania16803USA
| | - Andrew C. Baker
- Department of Marine Biology and EcologyRosenstiel School of Marine and Atmospheric ScienceUniversity of MiamiMiamiFlorida33149USA
| | - Sarah W. Davies
- Department of BiologyBoston UniversityBostonMassachusetts02215USA
| | | | - Carly D. Kenkel
- Department of Biological SciencesUniversity of Southern CaliforniaLos AngelesCalifornia90007USA
| | - Sheila A. Kitchen
- Department of BiologyPennsylvania State UniversityUniversity ParkPennsylvania16803USA
| | - Ilsa B. Kuffner
- U.S. Geological Survey600 4th Street S.St. PetersburgFlorida33701USA
| | - Todd C. LaJeunesse
- Department of BiologyPennsylvania State UniversityUniversity ParkPennsylvania16803USA
| | - Mikhail V. Matz
- Department of Integrative BiologyThe University of Texas at AustinAustinTexas78712USA
| | | | - John E. Parkinson
- SECORE InternationalMiamiFlorida33145USA
- Department of Integrative BiologyUniversity of South FloridaTampaFlorida33620USA
| | - Andrew A. Shantz
- Department of BiologyPennsylvania State UniversityUniversity ParkPennsylvania16803USA
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26
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Durante MK, Baums IB, Williams DE, Vohsen S, Kemp DW. What drives phenotypic divergence among coral clonemates of Acropora palmata? Mol Ecol 2019; 28:3208-3224. [PMID: 31282031 PMCID: PMC6852117 DOI: 10.1111/mec.15140] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 05/10/2019] [Accepted: 05/13/2019] [Indexed: 12/16/2022]
Abstract
Evolutionary rescue of populations depends on their ability to produce phenotypic variation that is heritable and adaptive. DNA mutations are the best understood mechanisms to create phenotypic variation, but other, less well-studied mechanisms exist. Marine benthic foundation species provide opportunities to study these mechanisms because many are dominated by isogenic stands produced through asexual reproduction. For example, Caribbean acroporid corals are long lived and reproduce asexually via breakage of branches. Fragmentation is often the dominant mode of local population maintenance. Thus, large genets with many ramets (colonies) are common. Here, we observed phenotypic variation in stress responses within genets following the coral bleaching events in 2014 and 2015 caused by high water temperatures. This was not due to genetic variation in their symbiotic dinoflagellates (Symbiodinium "fitti") because each genet of this coral species typically harbours a single strain of S. "fitti". Characterization of the microbiome via 16S tag sequencing correlated the abundance of only two microbiome members (Tepidiphilus, Endozoicomonas) with a bleaching response. Epigenetic changes were significantly correlated with the host's genetic background, the location of the sampled polyps within the colonies (e.g., branch vs. base of colony), and differences in the colonies' condition during the bleaching event. We conclude that long-term microenvironmental differences led to changes in the way the ramets methylated their genomes, contributing to the differential bleaching response. However, most of the variation in differential bleaching response among clonemates of Acropora palmata remains unexplained. This research provides novel data and hypotheses to help understand intragenet variability in stress phenotypes of sessile marine species.
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Affiliation(s)
| | | | - Dana E. Williams
- National Oceanic and Atmospheric AdministrationSoutheast Fisheries Science CenterMiamiFLUSA
| | - Sam Vohsen
- The Pennsylvania State UniversityUniversity ParkPAUSA
| | - Dustin W. Kemp
- The Pennsylvania State UniversityUniversity ParkPAUSA
- Present address:
University of Alabama at BirminghamBirminghamALUSA
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27
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Brian JI, Davy SK, Wilkinson SP. Multi-gene incongruence consistent with hybridisation in Cladocopium (Symbiodiniaceae), an ecologically important genus of coral reef symbionts. PeerJ 2019; 7:e7178. [PMID: 31289699 PMCID: PMC6598746 DOI: 10.7717/peerj.7178] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 05/22/2019] [Indexed: 12/23/2022] Open
Abstract
Coral reefs rely on their intracellular dinoflagellate symbionts (family Symbiodiniaceae) for nutritional provision in nutrient-poor waters, yet this association is threatened by thermally stressful conditions. Despite this, the evolutionary potential of these symbionts remains poorly characterised. In this study, we tested the potential for divergent Symbiodiniaceae types to sexually reproduce (i.e. hybridise) within Cladocopium, the most ecologically prevalent genus in this family. With sequence data from three organelles (cob gene, mitochondrion; psbAncr region, chloroplast; and ITS2 region, nucleus), we utilised the Incongruence Length Difference test, Approximately Unbiased test, tree hybridisation analyses and visual inspection of raw data in stepwise fashion to highlight incongruences between organelles, and thus provide evidence of reticulate evolution. Using this approach, we identified three putative hybrid Cladocopium samples among the 158 analysed, at two of the seven sites sampled. These samples were identified as the common Cladocopium types C40 or C1 with respect to the mitochondria and chloroplasts, but the rarer types C3z, C3u and C1# with respect to their nuclear identity. These five Cladocopium types have previously been confirmed as evolutionarily distinct and were also recovered in non-incongruent samples multiple times, which is strongly suggestive that they sexually reproduced to produce the incongruent samples. A concomitant inspection of next generation sequencing data for these samples suggests that other plausible explanations, such as incomplete lineage sorting or the presence of co-dominance, are much less likely. The approach taken in this study allows incongruences between gene regions to be identified with confidence, and brings new light to the evolutionary potential within Symbiodiniaceae.
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Affiliation(s)
- Joshua I Brian
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Simon K Davy
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Shaun P Wilkinson
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
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28
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Abstract
Genomic sequence data for non-model organisms are increasingly available requiring the development of efficient and reproducible workflows. Here, we develop the first genomic resources and reproducible workflows for two threatened members of the reef-building coral genus Acropora We generated genomic sequence data from multiple samples of the Caribbean A. cervicornis (staghorn coral) and A. palmata (elkhorn coral), and predicted millions of nucleotide variants among these two species and the Pacific A. digitifera A subset of predicted nucleotide variants were verified using restriction length polymorphism assays and proved useful in distinguishing the two Caribbean acroporids and the hybrid they form ("A. prolifera"). Nucleotide variants are freely available from the Galaxy server (usegalaxy.org), and can be analyzed there with computational tools and stored workflows that require only an internet browser. We describe these data and some of the analysis tools, concentrating on fixed differences between A. cervicornis and A. palmata In particular, we found that fixed amino acid differences between these two species were enriched in proteins associated with development, cellular stress response, and the host's interactions with associated microbes, for instance in the ABC transporters and superoxide dismutase. Identified candidate genes may underlie functional differences in how these threatened species respond to changing environments. Users can expand the presented analyses easily by adding genomic data from additional species, as they become available.
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29
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Hume BCC, Smith EG, Ziegler M, Warrington HJM, Burt JA, LaJeunesse TC, Wiedenmann J, Voolstra CR. SymPortal: A novel analytical framework and platform for coral algal symbiont next-generation sequencing ITS2 profiling. Mol Ecol Resour 2019; 19:1063-1080. [PMID: 30740899 PMCID: PMC6618109 DOI: 10.1111/1755-0998.13004] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 01/30/2019] [Accepted: 01/31/2019] [Indexed: 12/01/2022]
Abstract
We present SymPortal (SymPortal.org), a novel analytical framework and platform for genetically resolving the algal symbionts of reef corals using next‐generation sequencing (NGS) data of the ITS2 rDNA. Although the ITS2 marker is widely used to genetically characterize taxa within the family Symbiodiniaceae (formerly the genus Symbiodinium), the multicopy nature of the marker complicates its use. Commonly, the intragenomic diversity resultant from this multicopy nature is collapsed by analytical approaches, thereby focusing on only the most abundant sequences. In contrast, SymPortal employs logic to identify within‐sample informative intragenomic sequences, which we have termed ‘defining intragenomic variants' (DIVs), to identify ITS2‐type profiles representative of putative Symbiodiniaceae taxa. By making use of this intragenomic ITS2 diversity, SymPortal is able to resolve genetic delineations using the ITS2 marker at a level that was previously only possible by using additional genetic markers. We demonstrate this by comparing this novel approach to the most commonly used alternative approach for NGS ITS2 data, the 97% similarity clustering to operational taxonomic units (OTUs). The SymPortal platform accepts NGS raw sequencing data as input to provide an easy‐to‐use, standardization‐enforced, and community‐driven framework that integrates with a database to gain resolving power with increased use. We consider that SymPortal, in conjunction with ongoing large‐scale sampling and sequencing efforts, should play an instrumental role in making future sampling efforts more comparable and in maximizing their efficacy in working towards the classification of the global Symbiodiniaceae diversity.
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Affiliation(s)
- Benjamin C C Hume
- Division of Biological and Environmental Science and Engineering (BESE), Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Edward G Smith
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Maren Ziegler
- Division of Biological and Environmental Science and Engineering (BESE), Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | | | - John A Burt
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Todd C LaJeunesse
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania
| | - Joerg Wiedenmann
- Coral Reef Laboratory, Ocean and Earth Sciences, University of Southampton, Southampton, UK.,Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Christian R Voolstra
- Division of Biological and Environmental Science and Engineering (BESE), Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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Drury C, Greer JB, Baums I, Gintert B, Lirman D. Clonal diversity impacts coral cover in Acropora cervicornisthickets: Potential relationships between density, growth, and polymorphisms. Ecol Evol 2019; 9:4518-4531. [PMID: 31031924 PMCID: PMC6476746 DOI: 10.1002/ece3.5035] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 02/12/2019] [Accepted: 02/13/2019] [Indexed: 12/25/2022] Open
Abstract
As coral reefs decline, cryptic sources of resistance and resilience to stress may be increasingly important for the persistence of these communities. Among these sources, inter- and intraspecific diversity remain understudied on coral reefs but extensively impact a variety of traits in other ecosystems. We use a combination of field and sequencing data at two sites in Florida and two in the Dominican Republic to examine clonal diversity and genetic differentiation of high- and low-density aggregations of the threatened coral Acropora cervicornisin the Caribbean. We find that high-density aggregations called thickets are composed of up to 30 genotypes at a single site, but 47% of genotypes are also found as isolated, discrete colonies outside these aggregations. Genet-ramet ratios are comparable for thickets (0.636) and isolated colonies after rarefaction (0.569), suggesting the composition of each aggregation is not substantially different and highlighting interactions between colonies as a potential influence on structure. There are no differences in growth rate, but a significant positive correlation between genotypic diversity and coral cover, which may be due to the influence of interactions between colonies on survivorship or fragment retention during asexual reproduction. Many polymorphisms distinguish isolated colonies from thickets despite the shared genotypes found here, including putative nonsynonymous mutations that change amino acid sequence in 25 loci. These results highlight intraspecific diversity as a density-dependent factor that may impact traits important for the structure and function of coral reefs.
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Affiliation(s)
- Crawford Drury
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric ScienceUniversity of MiamiMiamiFlorida
| | - Justin B. Greer
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric ScienceUniversity of MiamiMiamiFlorida
| | - Iliana Baums
- Department of BiologyPennsylvania State UniversityUniversity ParkPennsylvania
| | - Brooke Gintert
- Department of Marine Geoscience, Rosenstiel School of Marine and Atmospheric ScienceUniversity of MiamiMiamiFlorida
| | - Diego Lirman
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric ScienceUniversity of MiamiMiamiFlorida
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31
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Manzello DP, Matz MV, Enochs IC, Valentino L, Carlton RD, Kolodziej G, Serrano X, Towle EK, Jankulak M. Role of host genetics and heat-tolerant algal symbionts in sustaining populations of the endangered coral Orbicella faveolata in the Florida Keys with ocean warming. GLOBAL CHANGE BIOLOGY 2019; 25:1016-1031. [PMID: 30552831 DOI: 10.1111/gcb.14545] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 09/28/2018] [Accepted: 11/30/2018] [Indexed: 05/28/2023]
Abstract
Identifying which factors lead to coral bleaching resistance is a priority given the global decline of coral reefs with ocean warming. During the second year of back-to-back bleaching events in the Florida Keys in 2014 and 2015, we characterized key environmental and biological factors associated with bleaching resilience in the threatened reef-building coral Orbicella faveolata. Ten reefs (five inshore, five offshore, 179 corals total) were sampled during bleaching (September 2015) and recovery (May 2016). Corals were genotyped with 2bRAD and profiled for algal symbiont abundance and type. O. faveolata at the inshore sites, despite higher temperatures, demonstrated significantly higher bleaching resistance and better recovery compared to offshore. The thermotolerant Durusdinium trenchii (formerly Symbiondinium trenchii) was the dominant endosymbiont type region-wide during initial (78.0% of corals sampled) and final (77.2%) sampling; >90% of the nonbleached corals were dominated by D. trenchii. 2bRAD host genotyping found no genetic structure among reefs, but inshore sites showed a high level of clonality. While none of the measured environmental parameters were correlated with bleaching, 71% of variation in bleaching resistance and 73% of variation in the proportion of D. trenchii was attributable to differences between genets, highlighting the leading role of genetics in shaping natural bleaching patterns. Notably, D. trenchii was rarely dominant in O. faveolata from the Florida Keys in previous studies, even during bleaching. The region-wide high abundance of D. trenchii was likely driven by repeated bleaching associated with the two warmest years on record for the Florida Keys (2014 and 2015). On inshore reefs in the Upper Florida Keys, O. faveolata was most abundant, had the highest bleaching resistance, and contained the most corals dominated by D. trenchii, illustrating a causal link between heat tolerance and ecosystem resilience with global change.
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Affiliation(s)
- Derek P Manzello
- Atlantic Oceanographic and Meteorological Laboratories (AOML), NOAA, Miami, Florida
| | - Mikhail V Matz
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas
| | - Ian C Enochs
- Atlantic Oceanographic and Meteorological Laboratories (AOML), NOAA, Miami, Florida
| | - Lauren Valentino
- Atlantic Oceanographic and Meteorological Laboratories (AOML), NOAA, Miami, Florida
- Cooperative Institute for Marine and Atmospheric Studies, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, Florida
| | - Renee D Carlton
- Khaled bin Sultan Living Oceans Foundation, Landover, Maryland
| | - Graham Kolodziej
- Atlantic Oceanographic and Meteorological Laboratories (AOML), NOAA, Miami, Florida
- Cooperative Institute for Marine and Atmospheric Studies, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, Florida
| | - Xaymara Serrano
- Atlantic Oceanographic and Meteorological Laboratories (AOML), NOAA, Miami, Florida
- Cooperative Institute for Marine and Atmospheric Studies, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, Florida
| | - Erica K Towle
- Office of the NOAA Administrator, Silver Spring, Maryland
| | - Mike Jankulak
- Atlantic Oceanographic and Meteorological Laboratories (AOML), NOAA, Miami, Florida
- Cooperative Institute for Marine and Atmospheric Studies, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, Florida
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32
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Petersen KL, Paytan A, Rahav E, Levy O, Silverman J, Barzel O, Potts D, Bar-Zeev E. Impact of brine and antiscalants on reef-building corals in the Gulf of Aqaba - Potential effects from desalination plants. WATER RESEARCH 2018; 144:183-191. [PMID: 30029077 DOI: 10.1016/j.watres.2018.07.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 07/03/2018] [Accepted: 07/04/2018] [Indexed: 06/08/2023]
Abstract
Seawater reverse osmosis (SWRO) is becoming an increasingly important source of potable water in arid and semi-arid regions worldwide. Discharge of brine-effluent from desalination facilities has been shown to significantly impact coastal marine ecosystems ranging from seagrass meadows to microbial communities. In this study, we examined the impacts of increased salinity (10% above ambient) and presence of antiscalants (0.2 mg L-1, polyphosphonate-based) on three reef-building coral species; Stylophora pistillata, Acropora tenuis and Pocillopora verrucosa, from the Gulf of Aqaba (northern Red-Sea). Our results indicate that the corals, as well as associated bacteria and algae, were significantly impaired by the elevated salinity and antiscalants, leading to partial bleaching. Specifically, the abundance of bacteria and symbiotic algae as well as calcification rates were typically lower (20-85%, 50-90% and 40-50%, respectively) following incubations with both amendments. However, the impact of desalination brine was often species-specific. Thus, we propose that the ecotoxicological criteria used for hard corals should be determined based on the sensitivity of key species in the community dominating the area affected by desalination discharge.
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Affiliation(s)
- Karen Lykkebo Petersen
- Department of Earth and Planetary Science, University of California Santa Cruz, CA, 95064, USA
| | - Adina Paytan
- Institute of Marine Science, University of California, Santa Cruz, CA, 95064, USA
| | - Eyal Rahav
- Israel Oceanographic and Limnological Research, Haifa, 31080, Israel
| | - Oren Levy
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 52900, Israel
| | - Jacob Silverman
- Israel Oceanographic and Limnological Research, Haifa, 31080, Israel
| | - Oriya Barzel
- Israel Oceanographic and Limnological Research, Haifa, 31080, Israel; Institute of Earth Sciences, Edmond Safra Campus of Natural Sciences, Givat-Ram, Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Donald Potts
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, CA, 95064, USA
| | - Edo Bar-Zeev
- Zuckerberg Institute for Water Research, Ben-Gurion University of the Negev, 84990, Israel.
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33
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Lewis AM, Chan AN, LaJeunesse TC. New Species of Closely Related Endosymbiotic Dinoflagellates in the Greater Caribbean have Niches Corresponding to Host Coral Phylogeny. J Eukaryot Microbiol 2018; 66:469-482. [DOI: 10.1111/jeu.12692] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 09/25/2018] [Accepted: 09/26/2018] [Indexed: 12/23/2022]
Affiliation(s)
- Allison M. Lewis
- Department of Biology Pennsylvania State University University Park Pennsylvania 16802
| | - Andrea N. Chan
- Department of Biology Pennsylvania State University University Park Pennsylvania 16802
| | - Todd C. LaJeunesse
- Department of Biology Pennsylvania State University University Park Pennsylvania 16802
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34
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Muller EM, Bartels E, Baums IB. Bleaching causes loss of disease resistance within the threatened coral species Acropora cervicornis. eLife 2018; 7:35066. [PMID: 30203745 PMCID: PMC6133546 DOI: 10.7554/elife.35066] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Accepted: 07/30/2018] [Indexed: 12/24/2022] Open
Abstract
Determining the adaptive potential of foundation species, such as reef-building corals, is urgent as the oceans warm and coral populations decline. Theory predicts that corals may adapt to climate change via selection on standing genetic variation. Yet, corals face not only rising temperatures but also novel diseases. We studied the interaction between two major stressors affecting colonies of the threatened coral, Acropora cervicornis: white-band disease and high water temperature. We determined that 27% of A. cervicornis were disease resistant prior to a thermal anomaly. However, disease resistance was largely lost during a bleaching event because of more compromised coral hosts or increased pathogenic dose/virulence. There was no tradeoff between disease resistance and temperature tolerance; disease susceptibility was independent of Symbiodinium strain. The present study shows that susceptibility to temperature stress creates an increased risk in disease-associated mortality, and only rare genets may maintain or gain infectious disease resistance under high temperature. We conclude that A. cervicornis populations in the lower Florida Keys harbor few existing genotypes that are resistant to both warming and disease. The staghorn coral was once prevalent throughout the Florida Reef Tract. However, the last few decades have seen a substantial reduction in the coral population because of disease outbreaks and increasing ocean temperatures. The staghorn coral shows no evidence of natural recovery, and so has been the focus of restoration efforts throughout much of the Florida region. Why put the time and effort into growing corals that are unlikely to survive within environmental conditions that continue to deteriorate? One reason is that the genetic make-up – the genotype – of some corals makes them more resilient to certain threats. However, there could be tradeoffs associated with these resilient traits. For example, a coral may be able to tolerate heat, but may easily succumb to disease. Previous studies have identified some staghorn coral genotypes that are resistant to an infection called white-band disease. The influence of high water temperatures on the ability of the coral to resist this disease was not known. There also remained the possibility that more varieties of coral might show similar disease resistance. To investigate Muller et al. conducted two experiments exposing staghorn coral genotypes to white-band diseased tissue before and during a coral bleaching event. Approximately 25% of the population of staghorn tested was resistant to white-band disease before the bleaching event. When the corals were exposed to white-band disease during bleaching, twice as much of the coral died. Two out of the 15, or 13%, of the coral genotypes tested were resistant to the disease even while bleached. Additionally, the level of bleaching within the coral genotypes was not related to how easily they developed white-band disease, suggesting that there are no direct tradeoffs between heat tolerance and disease resistance. These results suggest that there are very hardy corals, created by nature, already in existence. Incorporating these traits thoughtfully into coral restoration plans may increase the likelihood of population-based recovery. The Florida Reef Tract is estimated to be worth over six billion dollars to the state economy, providing over 70,000 jobs and attracting millions of tourists into Florida each year. However, much of these ecosystem services will be lost if living coral is not restored within the reef tract. The results presented by Muller et al. emphasize the need for maintaining high genetic diversity while increasing resiliency when restoring coral. They also emphasize that disease resistant corals, even when bleached, already exist and may be an integral part of the recovery of Florida’s reef tract.
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Affiliation(s)
- Erinn M Muller
- Coral Health and Disease Program, Mote Marine Laboratory, Sarasota, United States
| | - Erich Bartels
- Coral Reef Monitoring and Assessment Program, Mote Marine Laboratory, Florida, United States
| | - Iliana B Baums
- Department of Biology, Pennsylvania State University, Pennsylvania, United States
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35
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Barfield SJ, Aglyamova GV, Bay LK, Matz MV. Contrasting effects of
Symbiodinium
identity on coral host transcriptional profiles across latitudes. Mol Ecol 2018; 27:3103-3115. [DOI: 10.1111/mec.14774] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 05/29/2018] [Indexed: 01/08/2023]
Affiliation(s)
- Sarah J. Barfield
- Department of Integrative Biology University of Texas at Austin Austin Texas
| | - Galina V. Aglyamova
- Department of Integrative Biology University of Texas at Austin Austin Texas
| | - Line K. Bay
- Australian Institute of Marine Science Townsville QLD Australia
| | - Mikhail V. Matz
- Department of Integrative Biology University of Texas at Austin Austin Texas
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36
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Vančurová L, Muggia L, Peksa O, Řídká T, Škaloud P. The complexity of symbiotic interactions influences the ecological amplitude of the host: A case study in Stereocaulon (lichenized Ascomycota). Mol Ecol 2018; 27:3016-3033. [PMID: 29900606 DOI: 10.1111/mec.14764] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 06/03/2018] [Accepted: 06/05/2018] [Indexed: 01/21/2023]
Abstract
Symbiosis plays a fundamental role in nature. Lichens are among the best known, globally distributed symbiotic systems whose ecology is shaped by the requirements of all symbionts forming the holobiont. The widespread lichen-forming fungal genus Stereocaulon provides a suitable model to study the ecology of microscopic green algal symbionts (i.e., phycobionts) within the lichen symbiosis. We analysed 282 Stereocaulon specimens, collected in diverse habitats worldwide, using the algal ITS rDNA and actin gene sequences and fungal ITS rDNA sequences. Phylogenetic analyses revealed a great diversity among the predominant phycobionts. The algal genus Asterochloris (Trebouxiophyceae) was recovered in most sampled thalli, but two additional genera, Vulcanochloris and Chloroidium, were also found. We used variation-partitioning analyses to investigate the effects of climatic conditions, substrate/habitat characteristic, spatial distribution and mycobionts on phycobiont distribution. Based on an analogy, we examined the effects of climate, substrate/habitat, spatial distribution and phycobionts on mycobiont distribution. According to our analyses, the distribution of phycobionts is primarily driven by mycobionts and vice versa. Specificity and selectivity of both partners, as well as their ecological requirements and the width of their niches, vary significantly among the species-level lineages. We demonstrated that species-level lineages, which accept more symbiotic partners, have wider climatic niches, overlapping with the niches of their partners. Furthermore, the survival of lichens on substrates with high concentrations of heavy metals appears to be supported by their association with toxicity-tolerant phycobionts. In general, low specificity towards phycobionts allows the host to associate with ecologically diversified algae, thereby broadening its ecological amplitude.
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Affiliation(s)
- Lucie Vančurová
- Faculty of Science, Department of Botany, Charles University, Prague 2, Czech Republic
| | - Lucia Muggia
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Ondřej Peksa
- The West Bohemian Museum in Pilsen, Plzeň, Czech Republic
| | - Tereza Řídká
- Faculty of Science, Department of Botany, Charles University, Prague 2, Czech Republic
| | - Pavel Škaloud
- Faculty of Science, Department of Botany, Charles University, Prague 2, Czech Republic
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37
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How does an animal behave like a plant? Physiological and molecular adaptations of zooxanthellae and their hosts to symbiosis. C R Biol 2018; 341:276-280. [DOI: 10.1016/j.crvi.2018.03.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 03/13/2018] [Indexed: 12/26/2022]
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38
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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] [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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39
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40
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Devlin-Durante MK, Baums IB. Genome-wide survey of single-nucleotide polymorphisms reveals fine-scale population structure and signs of selection in the threatened Caribbean elkhorn coral, Acropora palmata. PeerJ 2017; 5:e4077. [PMID: 29181279 PMCID: PMC5701561 DOI: 10.7717/peerj.4077] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 10/31/2017] [Indexed: 12/18/2022] Open
Abstract
The advent of next-generation sequencing tools has made it possible to conduct fine-scale surveys of population differentiation and genome-wide scans for signatures of selection in non-model organisms. Such surveys are of particular importance in sharply declining coral species, since knowledge of population boundaries and signs of local adaptation can inform restoration and conservation efforts. Here, we use genome-wide surveys of single-nucleotide polymorphisms in the threatened Caribbean elkhorn coral, Acropora palmata, to reveal fine-scale population structure and infer the major barrier to gene flow that separates the eastern and western Caribbean populations between the Bahamas and Puerto Rico. The exact location of this break had been subject to discussion because two previous studies based on microsatellite data had come to differing conclusions. We investigate this contradiction by analyzing an extended set of 11 microsatellite markers including the five previously employed and discovered that one of the original microsatellite loci is apparently under selection. Exclusion of this locus reconciles the results from the SNP and the microsatellite datasets. Scans for outlier loci in the SNP data detected 13 candidate loci under positive selection, however there was no correlation between available environmental parameters and genetic distance. Together, these results suggest that reef restoration efforts should use local sources and utilize existing functional variation among geographic regions in ex situ crossing experiments to improve stress resistance of this species.
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Affiliation(s)
- Meghann K Devlin-Durante
- Department of Biology, Pennsylvania State University, University Park, PA, United States of America
| | - Iliana B Baums
- Department of Biology, Pennsylvania State University, University Park, PA, United States of America
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41
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Williams DE, Miller MW, Bright AJ, Pausch RE, Valdivia A. Thermal stress exposure, bleaching response, and mortality in the threatened coral Acropora palmata. MARINE POLLUTION BULLETIN 2017; 124:189-197. [PMID: 28751030 DOI: 10.1016/j.marpolbul.2017.07.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 07/01/2017] [Accepted: 07/01/2017] [Indexed: 06/07/2023]
Abstract
Demographic data for Elkhorn coral, Acropora palmata, and in situ water temperature data from seven upper Florida Keys (USA) reefs revealed three warm thermal stress events between 2010 and 2016. During a mild bleaching event in 2011, up to 59% of colonies bleached, but no mortality resulted. In both 2014 and 2015, severe and unprecedented bleaching was observed with up to 100% of colonies bleached. A. palmata live tissue cover declined by one-third following the 2014-2015 events. Colony mortality of mildly- and non-bleached colonies did not differ but increased significantly with more severe bleaching. Increased bleaching prevalence corresponded to maximum daily average water temperatures above 31.3°C. However, the cumulative days with daily average exceeding 31.0°C provided a better predictor of bleaching response. The bleaching response of surviving colonies in 2015 was not consistent with acclimatization as most individual colonies bleached at least as badly as in 2014.
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Affiliation(s)
- D E Williams
- University of Miami Rosenstiel School of Marine and Atmospheric Sciences, Cooperative Institute for Marine and Atmospheric Studies, 4600 Rickenbacker Cswy, Miami, FL 33149, USA; NOAA National Marine Fisheries Service, Southeast Fisheries Science Center, 75 Virginia Beach Drive, Miami, FL 33149, USA.
| | - M W Miller
- NOAA National Marine Fisheries Service, Southeast Fisheries Science Center, 75 Virginia Beach Drive, Miami, FL 33149, USA
| | - A J Bright
- University of Miami Rosenstiel School of Marine and Atmospheric Sciences, Cooperative Institute for Marine and Atmospheric Studies, 4600 Rickenbacker Cswy, Miami, FL 33149, USA; NOAA National Marine Fisheries Service, Southeast Fisheries Science Center, 75 Virginia Beach Drive, Miami, FL 33149, USA
| | - R E Pausch
- University of Miami Rosenstiel School of Marine and Atmospheric Sciences, Cooperative Institute for Marine and Atmospheric Studies, 4600 Rickenbacker Cswy, Miami, FL 33149, USA; NOAA National Marine Fisheries Service, Southeast Fisheries Science Center, 75 Virginia Beach Drive, Miami, FL 33149, USA
| | - A Valdivia
- University of Miami Rosenstiel School of Marine and Atmospheric Sciences, Cooperative Institute for Marine and Atmospheric Studies, 4600 Rickenbacker Cswy, Miami, FL 33149, USA
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42
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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] [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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43
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Drury C, Schopmeyer S, Goergen E, Bartels E, Nedimyer K, Johnson M, Maxwell K, Galvan V, Manfrino C, Lirman D. Genomic patterns in Acropora cervicornis show extensive population structure and variable genetic diversity. Ecol Evol 2017; 7:6188-6200. [PMID: 28861224 PMCID: PMC5574808 DOI: 10.1002/ece3.3184] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 05/08/2017] [Accepted: 05/21/2017] [Indexed: 12/21/2022] Open
Abstract
Threatened Caribbean coral communities can benefit from high‐resolution genetic data used to inform management and conservation action. We use Genotyping by Sequencing (GBS) to investigate genetic patterns in the threatened coral, Acropora cervicornis, across the Florida Reef Tract (FRT) and the western Caribbean. Results show extensive population structure at regional scales and resolve previously unknown structure within the FRT. Different regions also exhibit up to threefold differences in genetic diversity (He), suggesting targeted management based on the goals and resources of each population is needed. Patterns of genetic diversity have a strong spatial component, and our results show Broward and the Lower Keys are among the most diverse populations in Florida. The genetic diversity of Caribbean staghorn coral is concentrated within populations and within individual reefs (AMOVA), highlighting the complex mosaic of population structure. This variance structure is similar over regional and local scales, which suggests that in situ nurseries are adequately capturing natural patterns of diversity, representing a resource that can replicate the average diversity of wild assemblages, serving to increase intraspecific diversity and potentially leading to improved biodiversity and ecosystem function. Results presented here can be translated into specific goals for the recovery of A. cervicornis, including active focus on low diversity areas, protection of high diversity and connectivity, and practical thresholds for responsible restoration.
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Affiliation(s)
- Crawford Drury
- Department of Marine Biology and Ecology Rosenstiel School of Marine and Atmospheric Science University of Miami Miami FL USA
| | - Stephanie Schopmeyer
- Department of Marine Biology and Ecology Rosenstiel School of Marine and Atmospheric Science University of Miami Miami FL USA
| | - Elizabeth Goergen
- Department of Marine and Environmental Sciences Nova Southeastern University Dania Beach FL USA
| | - Erich Bartels
- Mote Marine Tropical Research Laboratory Summerland Key FL USA
| | | | | | - Kerry Maxwell
- Federal Fish and Wildlife Conservation Commission Marathon FL USA
| | - Victor Galvan
- Punta Cana Ecological Foundation Punta Cana Dominican Republic
| | - Carrie Manfrino
- Central Caribbean Marine Institute Princeton NJ USA.,Little Cayman Research Centre Little Cayman Cayman Islands
| | - Diego Lirman
- Department of Marine Biology and Ecology Rosenstiel School of Marine and Atmospheric Science University of Miami Miami FL USA
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44
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Cunning R, Gates RD, Edmunds PJ. Using high-throughput sequencing of ITS2 to describe Symbiodinium metacommunities in St. John, US Virgin Islands. PeerJ 2017. [PMID: 28649474 PMCID: PMC5482262 DOI: 10.7717/peerj.3472] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Symbiotic microalgae (Symbiodinium spp.) strongly influence the performance and stress-tolerance of their coral hosts, making the analysis of Symbiodinium communities in corals (and metacommunities on reefs) advantageous for many aspects of coral reef research. High-throughput sequencing of ITS2 nrDNA offers unprecedented scale in describing these communities, yet high intragenomic variability at this locus complicates the resolution of biologically meaningful diversity. Here, we demonstrate that generating operational taxonomic units by clustering ITS2 sequences at 97% similarity within, but not across, samples collapses sequence diversity that is more likely to be intragenomic, while preserving diversity that is more likely interspecific. We utilize this ‘within-sample clustering’ to analyze Symbiodinium from ten host taxa on shallow reefs on the north and south shores of St. John, US Virgin Islands. While Symbiodinium communities did not differ between shores, metacommunity network analysis of host-symbiont associations revealed Symbiodinium lineages occupying ‘dominant’ and ‘background’ niches, and coral hosts that are more ‘flexible’ or ‘specific’ in their associations with Symbiodinium. These methods shed new light on important questions in coral symbiosis ecology, and demonstrate how application-specific bioinformatic pipelines can improve the analysis of metabarcoding data in microbial metacommunity studies.
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Affiliation(s)
- Ross Cunning
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, United States of America
| | - Ruth D Gates
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, United States of America
| | - Peter J Edmunds
- Department of Biology, California State University, Northridge, CA, United States of America
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45
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Molecular characterization reveals the complexity of previously overlooked coral-exosymbiont interactions and the implications for coral-guild ecology. Sci Rep 2017; 7:44923. [PMID: 28358026 PMCID: PMC5372162 DOI: 10.1038/srep44923] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 02/06/2017] [Indexed: 11/16/2022] Open
Abstract
Several obligate associate crabs and shrimps species may co-occur and interact within a single coral host, leading to patterns of associations that can provide essential ecological services. However, knowledge of the dynamics of interactions in this system is limited, partly because identifying species involved in the network remains challenging. In this study, we assessed the diversity of the decapods involved in exosymbiotic assemblages for juvenile and adult Pocillopora damicornis types α and β on reefs of New Caledonia and Reunion Island. This approach revealed complex patterns of association at regional and local scales with a prevalence of assemblages involving crab-shrimp partnerships. Furthermore, the distinction of two lineages in the snapping shrimp Alpheus lottini complex, rarely recognized in ecological studies, reveals a key role for cryptic diversity in structuring communities of mutualists. The existence of partnerships between species that occurred more commonly than expected by chance suggests an increased advantage for the host or a better adaptation of associated species to local environmental conditions. The consideration of cryptic diversity helps to accurately describe the complexity of interaction webs for diverse systems such as coral reefs, as well as the functional roles of dominant associated species for the persistence of coral populations.
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46
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Thornhill DJ, Howells EJ, Wham DC, Steury TD, Santos SR. Population genetics of reef coral endosymbionts (Symbiodinium
, Dinophyceae). Mol Ecol 2017; 26:2640-2659. [DOI: 10.1111/mec.14055] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 01/20/2017] [Accepted: 01/23/2017] [Indexed: 01/02/2023]
Affiliation(s)
- D. J. Thornhill
- Department of Biological Sciences and Molette Biology Laboratory for Environmental and Climate Change Studies; Auburn University; 101 Rouse Life Sciences Building Auburn AL 36849 USA
| | - E. J. Howells
- Center for Genomics and Systems Biology; New York University Abu Dhabi; PO Box 129188 Abu Dhabi United Arab Emirates
| | - D. C. Wham
- Department of Biology; Pennsylvania State University; 208 Mueller Laboratory University Park PA 16802 USA
| | - T. D. Steury
- School of Forestry and Wildlife Sciences; Auburn University; 3301 Forestry and Wildlife Building Auburn AL 36849 USA
| | - S. R. Santos
- Department of Biological Sciences and Molette Biology Laboratory for Environmental and Climate Change Studies; Auburn University; 101 Rouse Life Sciences Building Auburn AL 36849 USA
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47
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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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48
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Grillo MA, De Mita S, Burke PV, Solórzano-Lowell KLS, Heath KD. Intrapopulation genomics in a model mutualist: Population structure and candidate symbiosis genes under selection in Medicago truncatula. Evolution 2016; 70:2704-2717. [PMID: 27757965 DOI: 10.1111/evo.13095] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 10/05/2016] [Accepted: 10/10/2016] [Indexed: 01/15/2023]
Abstract
Bottom-up evolutionary approaches, including geographically explicit population genomic analyses, have the power to reveal the mechanistic basis of adaptation. Here, we conduct a population genomic analysis in the model legume, Medicago truncatula, to characterize population genetic structure and identify symbiosis-related genes showing evidence of spatially variable selection. Using RAD-seq, we generated over 26,000 SNPs from 191 accessions from within three regions of the native range in Europe. Results from STRUCTURE analysis identify five distinct genetic clusters with divisions that separate east and west regions in the Mediterranean basin. Much of the genetic variation is maintained within sampling sites, and there is evidence for isolation by distance. Extensive linkage disequilibrium was identified, particularly within populations. We conducted genetic outlier analysis with FST -based genome scans and a Bayesian modeling approach (PCAdapt). There were 70 core outlier loci shared between these distinct methods with one clear candidate symbiosis related gene, DMI1. This work sets that stage for functional experiments to determine the important phenotypes that selection has acted upon and complementary efforts in rhizobium populations.
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Affiliation(s)
- Michael A Grillo
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801
| | - Stephane De Mita
- INRA Nancy-Lorraine, UMR 1136 Interactions Arbres Microorganismes, Route d'Amance, 54280, Champenoux, France
| | - Patricia V Burke
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801
| | | | - Katy D Heath
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801
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49
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Coral symbioses under prolonged environmental change: living near tolerance range limits. Sci Rep 2016; 6:36271. [PMID: 27805069 PMCID: PMC5090243 DOI: 10.1038/srep36271] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 10/13/2016] [Indexed: 02/08/2023] Open
Abstract
As climate change progresses, understanding the long-term response of corals and their endosymbionts (Symbiodinium) to prolonged environmental change is of immediate importance. Here, a total of 1152 fragments from 72 colonies of three common coral species (Stylophora pistillata, Pocillopora damicornis, Seriatopora hystrix) underwent a 32-month reciprocal depth transplantation. Genetic analysis showed that while S. hystrix maintained its generalist symbiont, some S. pistillata and P. damicornis underwent temporary changes in resident symbionts immediately after stress (transplantation; natural bleaching). These temporary changes were phylogenetically constrained to ‘host-compatible’ symbionts only and reversion to original symbionts occurred within 7 to 12 months, indicating long-term fidelity and stability of adult symbioses. Measurements of symbiont photo-physiology (dark adapted yield, pressure over photosystem II) and coral health (host protein, bleaching status, mortality) indicated a broad acclimatory capacity. However, this came at an apparent energetic expense as disproportionate mortality amongst symbioses that persisted outside their distribution range was observed following a natural bleaching event. As environmental changes due to climate change become more continuous in nature, sub-lethal effects linked to the existence near tolerance range limits coupled with the inability of adult coral colonies to change resident symbionts makes corals particularly susceptible to additional environmental fluctuations or stress events and reduces the resilience of coral populations.
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50
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Devlin‐Durante MK, Miller MW, Precht WF, Baums IB, Carne L, Smith TB, Banaszak AT, Greer L, Irwin A, Fogarty ND, Williams DE. How old are you? Genet age estimates in a clonal animal. Mol Ecol 2016; 25:5628-5646. [DOI: 10.1111/mec.13865] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 09/12/2016] [Accepted: 09/19/2016] [Indexed: 01/10/2023]
Affiliation(s)
- M. K. Devlin‐Durante
- Department of Biology The Pennsylvania State University 208 Mueller Lab University Park PA 16802 USA
| | - M. W. Miller
- Southeast Fisheries Science Center National Marine Fisheries Service 75 Virginia Beach Dr. Miami FL 33149 USA
| | - W. F. Precht
- Marine & Coastal Programs Dial Cordy & Associates 90 Osceola Ave Jacksonville Beach FL 32250 USA
| | - I. B. Baums
- Department of Biology The Pennsylvania State University 208 Mueller Lab University Park PA 16802 USA
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