1
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Ashey J, McKelvie H, Freeman J, Shpilker P, Zane LH, Becker DM, Cowen L, Richmond RH, Paul VJ, Seneca FO, Putnam HM. Characterizing transcriptomic responses to sediment stress across location and morphology in reef-building corals. PeerJ 2024; 12:e16654. [PMID: 38313033 PMCID: PMC10836209 DOI: 10.7717/peerj.16654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 11/20/2023] [Indexed: 02/06/2024] Open
Abstract
Anthropogenic activities increase sediment suspended in the water column and deposition on reefs can be largely dependent on colony morphology. Massive and plating corals have a high capacity to trap sediments, and active removal mechanisms can be energetically costly. Branching corals trap less sediment but are more susceptible to light limitation caused by suspended sediment. Despite deleterious effects of sediments on corals, few studies have examined the molecular response of corals with different morphological characteristics to sediment stress. To address this knowledge gap, this study assessed the transcriptomic responses of branching and massive corals in Florida and Hawai'i to varying levels of sediment exposure. Gene expression analysis revealed a molecular responsiveness to sediments across species and sites. Differential Gene Expression followed by Gene Ontology (GO) enrichment analysis identified that branching corals had the largest transcriptomic response to sediments, in developmental processes and metabolism, while significantly enriched GO terms were highly variable between massive corals, despite similar morphologies. Comparison of DEGs within orthogroups revealed that while all corals had DEGs in response to sediment, there was not a concerted gene set response by morphology or location. These findings illuminate the species specificity and genetic basis underlying coral susceptibility to sediments.
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Affiliation(s)
- Jill Ashey
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, United States
| | - Hailey McKelvie
- Department of Computer Science, Tufts University, Medford, Massachusetts, United States
| | - John Freeman
- Department of Computer Science, Tufts University, Medford, Massachusetts, United States
| | - Polina Shpilker
- Department of Computer Science, Tufts University, Medford, Massachusetts, United States
| | - Lauren H. Zane
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, United States
| | - Danielle M. Becker
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, United States
| | - Lenore Cowen
- Department of Computer Science, Tufts University, Medford, Massachusetts, United States
| | - Robert H. Richmond
- Kewalo Marine Lab, University of Hawaii at Manoa, Honolulu, Hawaii, United States
| | - Valerie J. Paul
- Smithsonian Marine Station, Smithsonian, Fort Pierce, Florida, United States
| | | | - Hollie M. Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, United States
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2
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Brown KT, Lenz EA, Glass BH, Kruse E, McClintock R, Drury C, Nelson CE, Putnam HM, Barott KL. Divergent bleaching and recovery trajectories in reef-building corals following a decade of successive marine heatwaves. Proc Natl Acad Sci U S A 2023; 120:e2312104120. [PMID: 38113265 PMCID: PMC10756270 DOI: 10.1073/pnas.2312104120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 11/17/2023] [Indexed: 12/21/2023] Open
Abstract
Increasingly frequent marine heatwaves are devastating coral reefs. Corals that survive these extreme events must rapidly recover if they are to withstand subsequent events, and long-term survival in the face of rising ocean temperatures may hinge on recovery capacity and acclimatory gains in heat tolerance over an individual's lifespan. To better understand coral recovery trajectories in the face of successive marine heatwaves, we monitored the responses of bleaching-susceptible and bleaching-resistant individuals of two dominant coral species in Hawai'i, Montipora capitata and Porites compressa, over a decade that included three marine heatwaves. Bleaching-susceptible colonies of P. compressa exhibited beneficial acclimatization to heat stress (i.e., less bleaching) following repeat heatwaves, becoming indistinguishable from bleaching-resistant conspecifics during the third heatwave. In contrast, bleaching-susceptible M. capitata repeatedly bleached during all successive heatwaves and exhibited seasonal bleaching and substantial mortality for up to 3 y following the third heatwave. Encouragingly, bleaching-resistant individuals of both species remained pigmented across the entire time series; however, pigmentation did not necessarily indicate physiological resilience. Specifically, M. capitata displayed incremental yet only partial recovery of symbiont density and tissue biomass across both bleaching phenotypes up to 35 mo following the third heatwave as well as considerable partial mortality. Conversely, P. compressa appeared to recover across most physiological metrics within 2 y and experienced little to no mortality. Ultimately, these results indicate that even some visually robust, bleaching-resistant corals can carry the cost of recurring heatwaves over multiple years, leading to divergent recovery trajectories that may erode coral reef resilience in the Anthropocene.
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Affiliation(s)
- Kristen T. Brown
- Department of Biology, University of Pennsylvania, Philadelphia, PA19104
| | - Elizabeth A. Lenz
- University of Hawai’i Sea Grant College Program, University of Hawai’i at Mānoa, Honolulu, HI96822
| | - Benjamin H. Glass
- Department of Biology, University of Pennsylvania, Philadelphia, PA19104
| | - Elisa Kruse
- Department of Biology, University of Pennsylvania, Philadelphia, PA19104
| | - Rayna McClintock
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, Department of Oceanography, University of Hawai’i at Mānoa, Honolulu, HI96822
| | - Crawford Drury
- Hawai’i Institute of Marine Biology, University of Hawai’i at Mānoa, Kāne‘ohe, HI96744
| | - Craig E. Nelson
- University of Hawai’i Sea Grant College Program, University of Hawai’i at Mānoa, Honolulu, HI96822
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, Department of Oceanography, University of Hawai’i at Mānoa, Honolulu, HI96822
| | - Hollie M. Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, RI02881
| | - Katie L. Barott
- Department of Biology, University of Pennsylvania, Philadelphia, PA19104
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3
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Scucchia F, Wong K, Zaslansky P, Putnam HM, Goodbody-Gringley G, Mass T. Morphological and genetic mechanisms underlying the plasticity of the coral Porites astreoides across depths in Bermuda. J Struct Biol 2023; 215:108036. [PMID: 37832837 DOI: 10.1016/j.jsb.2023.108036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 10/08/2023] [Accepted: 10/10/2023] [Indexed: 10/15/2023]
Abstract
The widespread decline of shallow-water coral reefs has fueled interest in assessing whether mesophotic reefs can act as refugia replenishing deteriorated shallower reefs through larval exchange. Here we explore the morphological and molecular basis facilitating survival of planulae and adults of the coral Porites astreoides (Lamarck, 1816; Hexacorallia: Poritidae) along the vertical depth gradient in Bermuda. We found differences in micro-skeletal features such as bigger calyxes and coarser surface of the skeletal spines in shallow corals. Yet, tomographic reconstructions reveal an analogous mineral distribution between shallow and mesophotic adults, pointing to similar skeleton growth dynamics. Our study reveals patterns of host genetic connectivity and minimal symbiont depth-zonation across a broader depth range than previously known for this species in Bermuda. Transcriptional variations across life stages showed different regulation of metabolism and stress response functions, unraveling molecular responses to environmental conditions at different depths. Overall, these findings increase our understanding of coral acclimatory capability across broad vertical gradients, ultimately allowing better evaluation of the refugia potential of mesophotic reefs.
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Affiliation(s)
- Federica Scucchia
- Department of Marine Biology, Leon H. Charney School of Marine Sciences University of Haifa, Israel; The Interuniversity Institute of Marine Sciences, Eilat, Israel.
| | - Kevin Wong
- Department of Biological Sciences, University of Rhode Island, Kingston, United States
| | - Paul Zaslansky
- Department for Operative, Preventive and Pediatric Dentistry, Charité-Universitätsmedizin, Berlin, Germany
| | - Hollie M Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, United States
| | - Gretchen Goodbody-Gringley
- Central Caribbean Marine Institute, Little Cayman, Cayman Islands; Bermuda Institute of Ocean Sciences, St. George's, Bermuda
| | - Tali Mass
- Department of Marine Biology, Leon H. Charney School of Marine Sciences University of Haifa, Israel.
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4
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Abstract
As climate change increases the rate of environmental change and the frequency and intensity of disturbance events, selective forces intensify. However, given the complicated interplay between plasticity and selection for ecological - and thus evolutionary - outcomes, understanding the proximate signals, molecular mechanisms and the role of environmental history becomes increasingly critical for eco-evolutionary forecasting. To enhance the accuracy of our forecasting, we must characterize environmental signals at a level of resolution that is relevant to the organism, such as the microhabitat it inhabits and its intracellular conditions, while also quantifying the biological responses to these signals in the appropriate cells and tissues. In this Commentary, we provide historical context to some of the long-standing challenges in global change biology that constrain our capacity for eco-evolutionary forecasting using reef-building corals as a focal model. We then describe examples of mismatches between the scales of external signals relative to the sensors and signal transduction cascades that initiate and maintain cellular responses. Studying cellular responses at this scale is crucial because these responses are the basis of acclimation to changing environmental conditions and the potential for environmental 'memory' of prior or historical conditions through molecular mechanisms. To challenge the field, we outline some unresolved questions and suggest approaches to align experimental work with an organism's perception of the environment; these aspects are discussed with respect to human interventions.
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Affiliation(s)
- Zoe Dellaert
- Department of Biological Sciences, University of Rhode Island, 120 Flagg Rd, Kingston, RI 02881, USA
| | - Hollie M Putnam
- Department of Biological Sciences, University of Rhode Island, 120 Flagg Rd, Kingston, RI 02881, USA
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5
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Glass BH, Ashey J, Okongwu AR, Putnam HM, Barott KL. Characterization of a sperm motility signalling pathway in a gonochoric coral suggests conservation across cnidarian sexual systems. Proc Biol Sci 2023; 290:20230085. [PMID: 37528706 PMCID: PMC10394420 DOI: 10.1098/rspb.2023.0085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 07/10/2023] [Indexed: 08/03/2023] Open
Abstract
Most stony corals liberate their gametes into the water column via broadcast spawning, where fertilization hinges upon the activation of directional sperm motility. Sperm from gonochoric and hermaphroditic corals display distinct morphological and molecular phenotypes, yet it is unknown whether the signalling pathways controlling sperm motility are also distinct between these sexual systems. Here, we addressed this knowledge gap using the gonochoric, broadcast spawning coral Astrangia poculata. We found that cytosolic alkalinization of sperm activates the pH-sensing enzyme soluble adenylyl cyclase (sAC), which is required for motility. Additionally, we demonstrate for the first time in any cnidarian that sAC activity leads to protein kinase A (PKA) activation, and that PKA activity contributes to sperm motility activation. Ultrastructures of A. poculata sperm displayed morphological homology with other gonochoric cnidarians, and sAC exhibited broad structural and functional conservation across this phylum. These results indicate a conserved role for pH-dependent sAC-cAMP-PKA signalling in sperm motility across coral sexual systems, and suggest that the role of this pathway in sperm motility may be ancestral in metazoans. Finally, the dynamics of this pH-sensitive pathway may play a critical role in determining the sensitivity of marine invertebrate reproduction to anthropogenic ocean acidification.
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Affiliation(s)
- Benjamin H. Glass
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jill Ashey
- Department of Biological Sciences, University of Rhode Island, Kingston, RI 02881, USA
| | | | - Hollie M. Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, RI 02881, USA
| | - Katie L. Barott
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
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6
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Stephens TG, Strand EL, Putnam HM, Bhattacharya D. Ploidy Variation and Its Implications for Reproduction and Population Dynamics in Two Sympatric Hawaiian Coral Species. Genome Biol Evol 2023; 15:evad149. [PMID: 37566739 PMCID: PMC10445776 DOI: 10.1093/gbe/evad149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/24/2023] [Accepted: 08/04/2023] [Indexed: 08/13/2023] Open
Abstract
Standing genetic variation is a major driver of fitness and resilience and therefore of fundamental importance for threatened species such as stony corals. We analyzed RNA-seq data generated from 132 Montipora capitata and 119 Pocillopora acuta coral colonies collected from Kāne'ohe Bay, O'ahu, Hawai'i. Our goals were to determine the extent of colony genetic variation and to study reproductive strategies in these two sympatric species. Surprisingly, we found that 63% of the P. acuta colonies were triploid, with putative independent origins of the different triploid clades. These corals have spread primarily via asexual reproduction and are descended from a small number of genotypes, whose diploid ancestor invaded the bay. In contrast, all M. capitata colonies are diploid and outbreeding, with almost all colonies genetically distinct. Only two cases of asexual reproduction, likely via fragmentation, were identified in this species. We report two distinct strategies in sympatric coral species that inhabit the largest sheltered body of water in the main Hawaiian Islands. These data highlight divergence in reproductive behavior and genome biology, both of which contribute to coral resilience and persistence.
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Affiliation(s)
- Timothy G Stephens
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
| | - Emma L Strand
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Hollie M Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
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7
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Reich HG, Camp EF, Roger LM, Putnam HM. The trace metal economy of the coral holobiont: supplies, demands and exchanges. Biol Rev Camb Philos Soc 2023; 98:623-642. [PMID: 36897260 DOI: 10.1111/brv.12922] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/23/2022]
Abstract
The juxtaposition of highly productive coral reef ecosystems in oligotrophic waters has spurred substantial interest and progress in our understanding of macronutrient uptake, exchange, and recycling among coral holobiont partners (host coral, dinoflagellate endosymbiont, endolithic algae, fungi, viruses, bacterial communities). By contrast, the contribution of trace metals to the physiological performance of the coral holobiont and, in turn, the functional ecology of reef-building corals remains unclear. The coral holobiont's trace metal economy is a network of supply, demand, and exchanges upheld by cross-kingdom symbiotic partnerships. Each partner has unique trace metal requirements that are central to their biochemical functions and the metabolic stability of the holobiont. Organismal homeostasis and the exchanges among partners determine the ability of the coral holobiont to adjust to fluctuating trace metal supplies in heterogeneous reef environments. This review details the requirements for trace metals in core biological processes and describes how metal exchanges among holobiont partners are key to sustaining complex nutritional symbioses in oligotrophic environments. Specifically, we discuss how trace metals contribute to partner compatibility, ability to cope with stress, and thereby to organismal fitness and distribution. Beyond holobiont trace metal cycling, we outline how the dynamic nature of the availability of environmental trace metal supplies can be influenced by a variability of abiotic factors (e.g. temperature, light, pH, etc.). Climate change will have profound consequences on the availability of trace metals and further intensify the myriad stressors that influence coral survival. Lastly, we suggest future research directions necessary for understanding the impacts of trace metals on the coral holobiont symbioses spanning subcellular to organismal levels, which will inform nutrient cycling in coral ecosystems more broadly. Collectively, this cross-scale elucidation of the role of trace metals for the coral holobiont will allow us to improve forecasts of future coral reef function.
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Affiliation(s)
- Hannah G Reich
- Department of Biological Sciences, University of Rhode Island, 120 Flagg Road, Kingston, RI, 02881, USA
| | - Emma F Camp
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Liza M Roger
- Chemical & Life Science Engineering, Virginia Commonwealth University, 601 W. Main Street, Richmond, VA, 23284, USA
| | - Hollie M Putnam
- Department of Biological Sciences, University of Rhode Island, 120 Flagg Road, Kingston, RI, 02881, USA
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8
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Li S, Roger LM, Kumar L, Lewinski NA, Klein-Seetharaman J, Putnam HM, Yang J. High-frequency imagery to capture coral tissue (Montipora capricornis) response to environmental stress, a pilot study. PLoS One 2023; 18:e0283042. [PMID: 36943854 PMCID: PMC10030036 DOI: 10.1371/journal.pone.0283042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 02/28/2023] [Indexed: 03/23/2023] Open
Abstract
Environment stress is a major threat to the existence of coral reefs and has generated a lot of interest in the coral research community. Under the environmental stress, corals can experience tissue loss and/or the breakdown of symbiosis between the cnidarian host and its symbiotic algae causing the coral tissue to appear white as the skeleton can be seen by transparency. Image analysis is a common method used to assess tissue response under the environmental stress. However, the traditional approach is limited by the dynamic nature of the coral-algae symbiosis. Here, we observed coral tissue response in the scleractinian coral, Montipora capricornis, using high frequency image analysis throughout the experiment, as opposed to the typical start/end point assessment method. Color analysis reveals that the process can be divided into five stages with two critical stages according to coral tissue morphology and color ratio. We further explore changes to the morphology of individual polyps by means of the Pearson correlation coefficient and recurrence plots, where the quasi-periodic and nonstationary dynamics can be identified. The recurrence quantification analysis also allows the comparison between the different polyps. Our research provides a detailed visual and mathematical analysis of coral tissue response to environmental stress, which potentially shows universal applicability. Moreover, our approach provides a robust quantitative advancement for improving our insight into a suite of biotic responses in the perspective of coral health evaluation and fate prediction.
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Affiliation(s)
- Shuaifeng Li
- Department of Aeronautics and Astronautics, University of Washington, Seattle, WA, United States of America
| | - Liza M Roger
- Department of Chemical and Life Science and Engineering, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Lokender Kumar
- Department of Physics, Colorado School of Mines, Golden, CO, United States of America
| | - Nastassja A Lewinski
- Department of Chemical and Life Science and Engineering, Virginia Commonwealth University, Richmond, VA, United States of America
| | | | - Hollie M Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, United States of America
| | - Jinkyu Yang
- Department of Aeronautics and Astronautics, University of Washington, Seattle, WA, United States of America
- Department of Mechanical Engineering, Seoul National University, Seoul, Republic of Korea
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9
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Davies SW, Gamache MH, Howe-Kerr LI, Kriefall NG, Baker AC, Banaszak AT, Bay LK, Bellantuono AJ, Bhattacharya D, Chan CX, Claar DC, Coffroth MA, Cunning R, Davy SK, del Campo J, Díaz-Almeyda EM, Frommlet JC, Fuess LE, González-Pech RA, Goulet TL, Hoadley KD, Howells EJ, Hume BCC, Kemp DW, Kenkel CD, Kitchen SA, LaJeunesse TC, Lin S, McIlroy SE, McMinds R, Nitschke MR, Oakley CA, Peixoto RS, Prada C, Putnam HM, Quigley K, Reich HG, Reimer JD, Rodriguez-Lanetty M, Rosales SM, Saad OS, Sampayo EM, Santos SR, Shoguchi E, Smith EG, Stat M, Stephens TG, Strader ME, Suggett DJ, Swain TD, Tran C, Traylor-Knowles N, Voolstra CR, Warner ME, Weis VM, Wright RM, Xiang T, Yamashita H, Ziegler M, Correa AMS, Parkinson JE. Building consensus around the assessment and interpretation of Symbiodiniaceae diversity. PeerJ 2023; 11:e15023. [PMID: 37151292 PMCID: PMC10162043 DOI: 10.7717/peerj.15023] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 02/17/2023] [Indexed: 05/09/2023] Open
Abstract
Within microeukaryotes, genetic variation and functional variation sometimes accumulate more quickly than morphological differences. To understand the evolutionary history and ecology of such lineages, it is key to examine diversity at multiple levels of organization. In the dinoflagellate family Symbiodiniaceae, which can form endosymbioses with cnidarians (e.g., corals, octocorals, sea anemones, jellyfish), other marine invertebrates (e.g., sponges, molluscs, flatworms), and protists (e.g., foraminifera), molecular data have been used extensively over the past three decades to describe phenotypes and to make evolutionary and ecological inferences. Despite advances in Symbiodiniaceae genomics, a lack of consensus among researchers with respect to interpreting genetic data has slowed progress in the field and acted as a barrier to reconciling observations. Here, we identify key challenges regarding the assessment and interpretation of Symbiodiniaceae genetic diversity across three levels: species, populations, and communities. We summarize areas of agreement and highlight techniques and approaches that are broadly accepted. In areas where debate remains, we identify unresolved issues and discuss technologies and approaches that can help to fill knowledge gaps related to genetic and phenotypic diversity. We also discuss ways to stimulate progress, in particular by fostering a more inclusive and collaborative research community. We hope that this perspective will inspire and accelerate coral reef science by serving as a resource to those designing experiments, publishing research, and applying for funding related to Symbiodiniaceae and their symbiotic partnerships.
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Affiliation(s)
- Sarah W. Davies
- Department of Biology, Boston University, Boston, MA, United States
| | - Matthew H. Gamache
- Department of Integrative Biology, University of South Florida, Tampa, FL, United States
| | | | | | - Andrew C. Baker
- Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL, United States
| | - Anastazia T. Banaszak
- Unidad Académica de Sistemas Arrecifales, Universidad Nacional Autónoma de México, Puerto Morelos, Mexico
| | - Line Kolind Bay
- Australian Institute of Marine Science, Townsville, Australia
| | - Anthony J. Bellantuono
- Department of Biological Sciences, Florida International University, Miami, FL, United States
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, United States
| | - Cheong Xin Chan
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Danielle C. Claar
- Nearshore Habitat Program, Washington State Department of Natural Resources, Olympia, WA, USA
| | | | - Ross Cunning
- Daniel P. Haerther Center for Conservation and Research, John G. Shedd Aquarium, Chicago, IL, United States
| | - Simon K. Davy
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Javier del Campo
- Institut de Biologia Evolutiva (CSIC - Universitat Pompeu Fabra), Barcelona, Catalonia, Spain
| | | | - Jörg C. Frommlet
- Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
| | - Lauren E. Fuess
- Department of Biology, Texas State University, San Marcos, TX, United States
| | - Raúl A. González-Pech
- Department of Integrative Biology, University of South Florida, Tampa, FL, United States
- Department of Biology, Pennsylvania State University, State College, PA, United States
| | - Tamar L. Goulet
- Department of Biology, University of Mississippi, University, MS, United States
| | - Kenneth D. Hoadley
- Department of Biological Sciences, University of Alabama—Tuscaloosa, Tuscaloosa, AL, United States
| | - Emily J. Howells
- National Marine Science Centre, Faculty of Science and Engineering, Southern Cross University, Coffs Harbour, NSW, Australia
| | | | - Dustin W. Kemp
- Department of Biology, University of Alabama—Birmingham, Birmingham, Al, United States
| | - Carly D. Kenkel
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Sheila A. Kitchen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
| | - Todd C. LaJeunesse
- Department of Biology, Pennsylvania State University, University Park, PA, United States
| | - Senjie Lin
- Department of Marine Sciences, University of Connecticut, Mansfield, CT, United States
| | - Shelby E. McIlroy
- Swire Institute of Marine Science, School of Biological Sciences, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Ryan McMinds
- Center for Global Health and Infectious Disease Research, University of South Florida, Tampa, FL, United States
| | | | - Clinton A. Oakley
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Raquel S. Peixoto
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Carlos Prada
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, United States
| | - Hollie M. Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, United States
| | | | - Hannah G. Reich
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, United States
| | - James Davis Reimer
- Department of Biology, Chemistry and Marine Sciences, Faculty of Science, University of the Ryukyus, Nishihara, Okinawa, Japan
| | | | - Stephanie M. Rosales
- The Cooperative Institute For Marine and Atmospheric Studies, Miami, FL, United States
| | - Osama S. Saad
- Department of Biological Oceanography, Red Sea University, Port-Sudan, Sudan
| | - Eugenia M. Sampayo
- School of Biological Sciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Scott R. Santos
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, United States
| | - Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Edward G. Smith
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Michael Stat
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, Australia
| | - Timothy G. Stephens
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, United States
| | - Marie E. Strader
- Department of Biology, Texas A&M University, College Station, TX, United States
| | - David J. Suggett
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Timothy D. Swain
- Department of Marine and Environmental Science, Nova Southeastern University, Dania Beach, FL, United States
| | - Cawa Tran
- Department of Biology, University of San Diego, San Diego, CA, United States
| | - Nikki Traylor-Knowles
- Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL, United States
| | | | - Mark E. Warner
- School of Marine Science and Policy, University of Delaware, Lewes, DE, United States
| | - Virginia M. Weis
- Department of Integrative Biology, Oregon State University, Corvallis, OR, United States
| | - Rachel M. Wright
- Department of Biological Sciences, Southern Methodist University, Dallas, TX, United States
| | - Tingting Xiang
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Hiroshi Yamashita
- Fisheries Technology Institute, Japan Fisheries Research and Education Agency, Ishigaki, Okinawa, Japan
| | - Maren Ziegler
- Department of Animal Ecology & Systematics, Justus Liebig University Giessen (Germany), Giessen, Germany
| | | | - John Everett Parkinson
- Department of Integrative Biology, University of South Florida, Tampa, FL, United States
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10
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Stephens TG, Lee J, Jeong Y, Yoon HS, Putnam HM, Majerová E, Bhattacharya D. High-quality genome assembles from key Hawaiian coral species. Gigascience 2022; 11:6815755. [PMID: 36352542 PMCID: PMC9646523 DOI: 10.1093/gigascience/giac098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 08/11/2022] [Accepted: 09/22/2022] [Indexed: 11/11/2022] Open
Abstract
Background Coral reefs house about 25% of marine biodiversity and are critical for the livelihood of many communities by providing food, tourism revenue, and protection from wave surge. These magnificent ecosystems are under existential threat from anthropogenic climate change. Whereas extensive ecological and physiological studies have addressed coral response to environmental stress, high-quality reference genome data are lacking for many of these species. The latter issue hinders efforts to understand the genetic basis of stress resistance and to design informed coral conservation strategies. Results We report genome assemblies from 4 key Hawaiian coral species, Montipora capitata, Pocillopora acuta, Pocillopora meandrina, and Porites compressa. These species, or members of these genera, are distributed worldwide and therefore of broad scientific and ecological importance. For M. capitata, an initial assembly was generated from short-read Illumina and long-read PacBio data, which was then scaffolded into 14 putative chromosomes using Omni-C sequencing. For P. acuta, P. meandrina, and P. compressa, high-quality assemblies were generated using short-read Illumina and long-read PacBio data. The P. acuta assembly is from a triploid individual, making it the first reference genome of a nondiploid coral animal. Conclusions These assemblies are significant improvements over available data and provide invaluable resources for supporting multiomics studies into coral biology, not just in Hawaiʻi but also in other regions, where related species exist. The P. acuta assembly provides a platform for studying polyploidy in corals and its role in genome evolution and stress adaptation in these organisms.
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Affiliation(s)
- Timothy G Stephens
- Department of Biochemistry and Microbiology, Rutgers University , New Brunswick, NJ 08901, USA
| | - JunMo Lee
- Department of Oceanography, Kyungpook National University , Daegu, Buk-gu 41566, Korea
| | - YuJin Jeong
- Department of Oceanography, Kyungpook National University , Daegu, Buk-gu 41566, Korea
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University , Suwon 16419, Korea
| | - Hollie M Putnam
- Department of Biological Sciences, University of Rhode Island , Kingston, RI 02881, USA
| | - Eva Majerová
- Hawaiʻi Institute of Marine Biology , Kāneʻohe, HI 96744, USA
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University , New Brunswick, NJ 08901, USA
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11
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Vega Thurber R, Schmeltzer ER, Grottoli AG, van Woesik R, Toonen RJ, Warner M, Dobson KL, McLachlan RH, Barott K, Barshis DJ, Baumann J, Chapron L, Combosch DJ, Correa AMS, DeCarlo TM, Hagedorn M, Hédouin L, Hoadley K, Felis T, Ferrier-Pagès C, Kenkel C, Kuffner IB, Matthews J, Medina M, Meyer C, Oster C, Price J, Putnam HM, Sawall Y. Unified methods in collecting, preserving, and archiving coral bleaching and restoration specimens to increase sample utility and interdisciplinary collaboration. PeerJ 2022; 10:e14176. [PMID: 36345483 PMCID: PMC9636870 DOI: 10.7717/peerj.14176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 09/13/2022] [Indexed: 12/15/2022] Open
Abstract
Coral reefs are declining worldwide primarily because of bleaching and subsequent mortality resulting from thermal stress. Currently, extensive efforts to engage in more holistic research and restoration endeavors have considerably expanded the techniques applied to examine coral samples. Despite such advances, coral bleaching and restoration studies are often conducted within a specific disciplinary focus, where specimens are collected, preserved, and archived in ways that are not always conducive to further downstream analyses by specialists in other disciplines. This approach may prevent the full utilization of unexpended specimens, leading to siloed research, duplicative efforts, unnecessary loss of additional corals to research endeavors, and overall increased costs. A recent US National Science Foundation-sponsored workshop set out to consolidate our collective knowledge across the disciplines of Omics, Physiology, and Microscopy and Imaging regarding the methods used for coral sample collection, preservation, and archiving. Here, we highlight knowledge gaps and propose some simple steps for collecting, preserving, and archiving coral-bleaching specimens that can increase the impact of individual coral bleaching and restoration studies, as well as foster additional analyses and future discoveries through collaboration. Rapid freezing of samples in liquid nitrogen or placing at -80 °C to -20 °C is optimal for most Omics and Physiology studies with a few exceptions; however, freezing samples removes the potential for many Microscopy and Imaging-based analyses due to the alteration of tissue integrity during freezing. For Microscopy and Imaging, samples are best stored in aldehydes. The use of sterile gloves and receptacles during collection supports the downstream analysis of host-associated bacterial and viral communities which are particularly germane to disease and restoration efforts. Across all disciplines, the use of aseptic techniques during collection, preservation, and archiving maximizes the research potential of coral specimens and allows for the greatest number of possible downstream analyses.
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Affiliation(s)
- Rebecca Vega Thurber
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Emily R. Schmeltzer
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Andréa G. Grottoli
- School of Earth Sciences, Ohio State University, Columbus, OH, United States
| | - Robert van Woesik
- Institute for Global Ecology, Florida Institute of Technology, Melbourne, Fl, United States
| | - Robert J. Toonen
- Hawai’i Institute of Marine Biology, University of Hawai’i at Mānoa, Kāne’ohe, HI, United States
| | - Mark Warner
- School of Marine Science and Policy, University of Delaware, Lewes, DE, United States
| | - Kerri L. Dobson
- School of Earth Sciences, Ohio State University, Columbus, OH, United States
| | - Rowan H. McLachlan
- Department of Microbiology, Oregon State University, Corvallis, OR, United States,School of Earth Sciences, Ohio State University, Columbus, OH, United States
| | - Katie Barott
- Department of Biology, University of Pennsylvania, Philadelphia, PA, United States
| | - Daniel J. Barshis
- Department of Biological Sciences, Old Dominion University, Norfolk, VA, United States
| | - Justin Baumann
- Biology Department, Bowdoin College, Brunswick, ME, United States
| | - Leila Chapron
- School of Earth Sciences, Ohio State University, Columbus, OH, United States
| | | | | | - Thomas M. DeCarlo
- College of Natural and Computational Sciences, Hawai’i Pacific University, Honolulu, HI, United States
| | - Mary Hagedorn
- Hawai’i Institute of Marine Biology, University of Hawai’i at Mānoa, Kāne’ohe, HI, United States,Conservation Biology Institute, Smithsonian, Kāne’ohe, HI, United States
| | - Laetitia Hédouin
- Centre de Recherches Insulaires et Observatoire de l’Environnement, Chargée de Recherches CNRS, Papetō’ai, Moorea, French Polynesia
| | - Kenneth Hoadley
- Department of Biological Sciences, University of Alabama – Tuscaloosa, Tuscaloosa, AL, United States
| | - Thomas Felis
- MARUM – Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | | | - Carly Kenkel
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | | | - Jennifer Matthews
- Climate Change Cluster, University of Technology Sydney, Sydney, Australia
| | - Mónica Medina
- Department of Biology, Pennsylvania State University, University Park, PA, United States
| | - Christopher Meyer
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian, Washington DC, United States
| | - Corinna Oster
- MARUM – Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - James Price
- School of Earth Sciences, Ohio State University, Columbus, OH, United States
| | - Hollie M. Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, United States
| | - Yvonne Sawall
- Bermuda Institute of Ocean Sciences, St. George’s, St. George’s, Bermuda
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12
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Gurr SJ, Trigg SA, Vadopalas B, Roberts SB, Putnam HM. Acclimatory gene expression of primed clams enhances robustness to elevated pCO 2. Mol Ecol 2022; 31:5005-5023. [PMID: 35947503 DOI: 10.1111/mec.16644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 08/02/2022] [Accepted: 08/02/2022] [Indexed: 11/30/2022]
Abstract
Sub-lethal exposure to environmental challenges may enhance ability to cope with chronic or repeated change, a process known as priming. In a previous study, pre-exposure to seawater enriched with pCO2 improved growth and reduced antioxidant capacity of juvenile Pacific geoduck Panopea generosa, suggesting that transcriptional shifts may drive phenotypic modifications post-priming. To this end, juvenile clams were sampled and TagSeq gene expression data analyzed after 1) a 110-day acclimation under ambient (921 μatm, naïve) and moderately-elevated pCO2 (2870 μatm, pre-exposed); then following 2) a second 7-day exposure to three pCO2 treatments (ambient: 754 μatm; moderately-elevated: 2750 μatm; severely-elevated: 4940 μatm), a 7-day return to ambient pCO2 , and a third 7-day exposure to two pCO2 treatments (ambient: 967 μatm; moderately-elevated: 3030 μatm). Pre-exposed geoducks frontloaded genes for stress and apoptosis/innate immune response, homeostatic processes, protein degradation, and transcriptional modifiers. Pre-exposed geoducks were also responsive to subsequent encounters, with gene sets enriched for mitochondrial recycling and immune defense under elevated pCO2 and energy metabolism and biosynthesis under ambient recovery. In contrast, gene sets with higher expression in naïve clams were enriched for fatty-acid degradation and glutathione components, suggesting naïve clams could be depleting endogenous fuels, with unsustainable energetic requirements if changes in carbonate chemistry persist. Collectively, our transcriptomic data indicates pCO2 priming during post-larval periods could, via gene expression regulation, enhance robustness in bivalves to environmental change. Such priming approaches may be beneficial for aquaculture, as seafood demand intensifies concurrent with increasing climate change in marine systems.
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Affiliation(s)
- Samuel J Gurr
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, USA
| | - Shelly A Trigg
- University of Washington, School of Aquatic and Fishery Sciences, Seattle, WA, USA
| | | | - Steven B Roberts
- University of Washington, School of Aquatic and Fishery Sciences, Seattle, WA, USA
| | - Hollie M Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, USA
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13
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Chille EE, Strand EL, Scucchia F, Neder M, Schmidt V, Sherman MO, Mass T, Putnam HM. Energetics, but not development, is impacted in coral embryos exposed to ocean acidification. J Exp Biol 2022; 225:277171. [PMID: 35938380 DOI: 10.1242/jeb.243187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 08/03/2022] [Indexed: 11/20/2022]
Abstract
In light of the chronic stress and mass mortality reef-building corals face under climate change, it is critical to understand the processes driving reef persistence and replenishment, including coral reproduction and development. Here we quantify gene expression and sensitivity to ocean acidification across a set of developmental stages in the rice coral, Montipora capitata. Embryos and swimming larvae were exposed to pH treatments 7.8 (Ambient), 7.6 (Low) and 7.3 (Xlow) from fertilization to 9 days post-fertilization. Embryo and larval volume, and stage-specific gene expression were compared between treatments to determine the effects of acidified seawater on early development. While there was no measurable size differentiation between pH treatments at the fertilized egg and prawn chip (9 hours post-fertilization) stages, early gastrulae and larvae raised in reduced pH treatments were significantly smaller than those raised in ambient seawater, suggesting an energetic cost to developing under low pH. However, no differentially expressed genes were found until the swimming larval stage. Notably, gene expression patterns of larvae developing at pH 7.8 and pH 7.3 were more similar than those developing at pH 7.6. Larvae from pH 7.6 showed upregulation of genes involved in cell division, regulation of transcription, lipid metabolism, and response to oxidative stress in comparison to the other two treatments. While low pH appears to increase energetic demands and trigger oxidative stress in larvae, the developmental process is robust to this at a molecular level, with the swimming larval stage reached in all pH treatments.
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Affiliation(s)
- E E Chille
- Department of Biological Sciences, University of Rhode Island, Rhode Island, USA
| | - E L Strand
- Department of Biological Sciences, University of Rhode Island, Rhode Island, USA
| | - F Scucchia
- Department of Marine Biology, The Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel.,The Interuniversity Institute of Marine Sciences, Eilat, Israel
| | - M Neder
- Department of Marine Biology, The Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel.,The Interuniversity Institute of Marine Sciences, Eilat, Israel
| | - V Schmidt
- Yale School of Medicine, Yale University, Connecticut, USA
| | - M O Sherman
- Department of Biological Sciences, University of Rhode Island, Rhode Island, USA
| | - T Mass
- Department of Marine Biology, The Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel.,Morris Kahn Marine Research Station, The Leon H. Charney School of Marine Sciences, University of Haifa, Sdot Yam, Israel
| | - H M Putnam
- Department of Biological Sciences, University of Rhode Island, Rhode Island, USA
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14
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Abstract
Anthropogenic effects have contributed to substantial declines in coral reefs worldwide. However, some corals are more resilient to environmental changes and have increased in relative abundance, thus these species may shape future reef communities. Here, we provide the first draft reference genome for the mustard hill coral, Porites astreoides, collected in Bermuda. DNA was sequenced via Pacific Biosciences (PacBio) HiFi long-read technology. PacBio read assembly with FALCON UnZip resulted in a 678-Mbp assembly with 3051 contigs with an N50 of 412,256 and the BUSCO completeness analysis resulted in 90.9% of the metazoan gene set. An ab initio transcriptome was also produced with 64,636 gene models with a transcriptome BUSCO completeness analysis of 77.5% versus the metazoan gene set. Functional annotation was completed for 86.6% of proteins. These data are valuable resources for improving biological knowledge of P. astreoides, facilitating comparative genomics for corals, and supporting evidence-based restoration and human-assisted evolution of corals.
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Affiliation(s)
- Kevin H. Wong
- University of Rhode Island, Department of Biological Sciences, USA, Corresponding authors. E-mail: ;
| | - Hollie M. Putnam
- University of Rhode Island, Department of Biological Sciences, USA, Corresponding authors. E-mail: ;
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15
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Cowen LJ, Putnam HM. Bioinformatics of Corals: Investigating Heterogeneous Omics Data from Coral Holobionts for Insight into Reef Health and Resilience. Annu Rev Biomed Data Sci 2022; 5:205-231. [PMID: 35537462 DOI: 10.1146/annurev-biodatasci-122120-030732] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Coral reefs are home to over two million species and provide habitat for roughly 25% of all marine animals, but they are being severely threatened by pollution and climate change. A large amount of genomic, transcriptomic, and other omics data is becoming increasingly available from different species of reef-building corals, the unicellular dinoflagellates, and the coral microbiome (bacteria, archaea, viruses, fungi, etc.). Such new data present an opportunity for bioinformatics researchers and computational biologists to contribute to a timely, compelling, and urgent investigation of critical factors that influence reef health and resilience. Expected final online publication date for the Annual Review of Biomedical Data Science, Volume 5 is August 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Lenore J Cowen
- Department of Computer Science, Tufts University, Medford, Massachusetts, USA;
| | - Hollie M Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, USA;
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16
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Williams A, Pathmanathan JS, Stephens TG, Su X, Chiles EN, Conetta D, Putnam HM, Bhattacharya D. Multi-omic characterization of the thermal stress phenome in the stony coral Montipora capitata. PeerJ 2021; 9:e12335. [PMID: 34824906 PMCID: PMC8590396 DOI: 10.7717/peerj.12335] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 09/28/2021] [Indexed: 11/22/2022] Open
Abstract
Background Corals, which form the foundation of biodiverse reef ecosystems, are under threat from warming oceans. Reefs provide essential ecological services, including food, income from tourism, nutrient cycling, waste removal, and the absorption of wave energy to mitigate erosion. Here, we studied the coral thermal stress response using network methods to analyze transcriptomic and polar metabolomic data generated from the Hawaiian rice coral Montipora capitata. Coral nubbins were exposed to ambient or thermal stress conditions over a 5-week period, coinciding with a mass spawning event of this species. The major goal of our study was to expand the inventory of thermal stress-related genes and metabolites present in M. capitata and to study gene-metabolite interactions. These interactions provide the foundation for functional or genetic analysis of key coral genes as well as provide potentially diagnostic markers of pre-bleaching stress. A secondary goal of our study was to analyze the accumulation of sex hormones prior to and during mass spawning to understand how thermal stress may impact reproductive success in M. capitata. Methods M. capitata was exposed to thermal stress during its spawning cycle over the course of 5 weeks, during which time transcriptomic and polar metabolomic data were collected. We analyzed these data streams individually, and then integrated both data sets using MAGI (Metabolite Annotation and Gene Integration) to investigate molecular transitions and biochemical reactions. Results Our results reveal the complexity of the thermal stress phenome in M. capitata, which includes many genes involved in redox regulation, biomineralization, and reproduction. The size and number of modules in the gene co-expression networks expanded from the initial stress response to the onset of bleaching. The later stages involved the suppression of metabolite transport by the coral host, including a variety of sodium-coupled transporters and a putative ammonium transporter, possibly as a response to reduction in algal productivity. The gene-metabolite integration data suggest that thermal treatment results in the activation of animal redox stress pathways involved in quenching molecular oxygen to prevent an overabundance of reactive oxygen species. Lastly, evidence that thermal stress affects reproductive activity was provided by the downregulation of CYP-like genes and the irregular production of sex hormones during the mass spawning cycle. Overall, redox regulation and metabolite transport are key components of the coral animal thermal stress phenome. Mass spawning was highly attenuated under thermal stress, suggesting that global climate change may negatively impact reproductive behavior in this species.
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Affiliation(s)
- Amanda Williams
- Microbial Biology Graduate Program, Rutgers University, New Brunswick, United States
| | - Jananan S Pathmanathan
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, United States
| | - Timothy G Stephens
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, United States
| | - Xiaoyang Su
- Department of Medicine, Division of Endocrinology, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, United States.,Metabolomics Shared Resource, Rutgers Cancer Institute of New Jersey, Rutgers University,New Brunswick, United States
| | - Eric N Chiles
- Metabolomics Shared Resource, Rutgers Cancer Institute of New Jersey, Rutgers University,New Brunswick, United States
| | - Dennis Conetta
- Department of Biological Sciences, University of Rhode Island, Kingston, United States
| | - Hollie M Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, United States
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, United States
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17
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Trigg SA, Venkataraman YR, Gavery MR, Roberts SB, Bhattacharya D, Downey-Wall A, Eirin-Lopez JM, Johnson KM, Lotterhos KE, Puritz JB, Putnam HM. Invertebrate methylomes provide insight into mechanisms of environmental tolerance and reveal methodological biases. Mol Ecol Resour 2021; 22:1247-1261. [PMID: 34709728 DOI: 10.1111/1755-0998.13542] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 10/08/2021] [Accepted: 10/11/2021] [Indexed: 12/12/2022]
Abstract
There is a growing focus on the role of DNA methylation in the ability of marine invertebrates to rapidly respond to changing environmental factors and anthropogenic impacts. However, genome-wide DNA methylation studies in nonmodel organisms are currently hampered by a limited understanding of methodological biases. Here, we compare three methods for quantifying DNA methylation at single base-pair resolution-whole genome bisulfite sequencing (WGBS), reduced representation bisulfite sequencing (RRBS), and methyl-CpG binding domain bisulfite sequencing (MBDBS)-using multiple individuals from two reef-building coral species with contrasting environmental sensitivity. All methods reveal substantially greater methylation in Montipora capitata (11.4%) than the more sensitive Pocillopora acuta (2.9%). The majority of CpG methylation in both species occurs in gene bodies and flanking regions. In both species, MBDBS has the greatest capacity for detecting CpGs in coding regions at our sequencing depth, but MBDBS may be influenced by intrasample methylation heterogeneity. RRBS yields robust information for specific loci albeit without enrichment of any particular genome feature and with significantly reduced genome coverage. Relative genome size strongly influences the number and location of CpGs detected by each method when sequencing depth is limited, illuminating nuances in cross-species comparisons. As genome-wide methylation differences, supported by data across bisulfite sequencing methods, may contribute to environmental sensitivity phenotypes in critical marine invertebrate taxa, these data provide a genomic resource for investigating the functional role of DNA methylation in environmental tolerance.
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Affiliation(s)
- Shelly A Trigg
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, USA
| | - Yaamini R Venkataraman
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, USA.,Biology Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Mackenzie R Gavery
- Environmental and Fisheries Sciences Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, USA
| | - Steven B Roberts
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, USA
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, USA
| | - Alan Downey-Wall
- Department of Marine and Environmental Sciences, Northeastern University, Nahant, Massachusetts, USA
| | - Jose M Eirin-Lopez
- Environmental Epigenetics Laboratory, Institute of Environment, Florida International University, North Miami, Florida, USA
| | - Kevin M Johnson
- Center for Coastal Marine Sciences, California Polytechnic State University, San Luis Obispo, California, USA.,California Sea Grant, University of California San Diego, La Jolla, California, USA
| | - Katie E Lotterhos
- Department of Marine and Environmental Sciences, Northeastern University, Nahant, Massachusetts, USA
| | - Jonathan B Puritz
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Hollie M Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, USA
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18
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Scucchia F, Malik A, Putnam HM, Mass T. Genetic and physiological traits conferring tolerance to ocean acidification in mesophotic corals. Glob Chang Biol 2021; 27:5276-5294. [PMID: 34310005 DOI: 10.1111/gcb.15812] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 07/15/2021] [Accepted: 07/20/2021] [Indexed: 06/13/2023]
Abstract
The integrity of coral reefs worldwide is jeopardized by ocean acidification (OA). Most studies conducted so far have focused on the vulnerability to OA of corals inhabiting shallow reefs while nothing is currently known about the response of mesophotic scleractinian corals. In this study, we assessed the susceptibility to OA of corals, together with their algal partners, inhabiting a wide depth range. We exposed fragments of the depth generalist coral Stylophora pistillata collected from either 5 or 45 m to simulated future OA conditions, and assessed key molecular, physiological and photosynthetic processes influenced by the lowered pH. Our comparative analysis reveals that mesophotic and shallow S. pistillata corals are genetically distinct and possess different symbiont types. Under the exposure to acidification conditions, we observed a 50% drop of metabolic rate in shallow corals, whereas mesophotic corals were able to maintain unaltered metabolic rates. Overall, our gene expression and physiological analyses show that mesophotic corals possess a greater capacity to cope with the effects of OA compared to their shallow counterparts. Such capability stems from physiological characteristics (i.e., biomass and lipids energetics), a greater capacity to regulate cellular acid-base parameters, and a higher baseline expression of cell adhesion and extracellular matrix genes. Moreover, our gene expression analysis suggests that the enhanced symbiont photochemical efficiency under high pCO2 levels could prevent acidosis of the host cells and it could support a greater translocation of photosynthates, increasing the energy pool available to the host. With this work, we provide new insights on the response to OA of corals living at mesophotic depths. Our investigation discloses key genetic and physiological traits underlying the potential for corals to cope with future OA conditions.
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Affiliation(s)
- Federica Scucchia
- Department of Marine Biology, Leon H. Charney school of Marine Sciences, University of Haifa, Haifa, Israel
- The Interuniversity Institute of Marine Sciences, Eilat, Israel
| | - Assaf Malik
- Department of Marine Biology, Leon H. Charney school of Marine Sciences, University of Haifa, Haifa, Israel
| | - Hollie M Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Tali Mass
- Department of Marine Biology, Leon H. Charney school of Marine Sciences, University of Haifa, Haifa, Israel
- Morris Kahn Marine Research Station, The Leon H. Charney School of Marine Sciences, University of Haifa, Sdot Yam, Israel
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19
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Gurr SJ, Wanamaker SA, Vadopalas B, Roberts SB, Putnam HM. Repeat exposure to hypercapnic seawater modifies growth and oxidative status in a tolerant burrowing clam. J Exp Biol 2021; 224:269329. [PMID: 34027545 DOI: 10.1242/jeb.233932] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 05/18/2021] [Indexed: 01/06/2023]
Abstract
Although low levels of thermal stress, irradiance and dietary restriction can have beneficial effects for many taxa, stress acclimation remains little studied in marine invertebrates, even though they are threatened by climate change stressors such as ocean acidification. To test the role of life-stage and stress-intensity dependence in eliciting enhanced tolerance under subsequent stress encounters, we initially conditioned pediveliger Pacific geoduck (Panopea generosa) larvae to ambient and moderately elevated PCO2 (920 µatm and 2800 µatm, respectively) for 110 days. Then, clams were exposed to ambient, moderate or severely elevated PCO2 (750, 2800 or 4900 µatm, respectively) for 7 days and, following 7 days in ambient conditions, a 7-day third exposure to ambient (970 µatm) or moderate PCO2 (3000 µatm). Initial conditioning to moderate PCO2 stress followed by second and third exposure to severe and moderate PCO2 stress increased respiration rate, organic biomass and shell size, suggesting a stress-intensity-dependent effect on energetics. Additionally, stress-acclimated clams had lower antioxidant capacity compared with clams under ambient conditions, supporting the hypothesis that stress over postlarval-to-juvenile development affects oxidative status later in life. Time series and stress intensity-specific approaches can reveal life-stages and magnitudes of exposure, respectively, that may elicit beneficial phenotypic variation.
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Affiliation(s)
- Samuel J Gurr
- University of Rhode Island, College of the Environment and Life Sciences, 120 Flagg Rd, Kingston, RI 02881, USA
| | - Shelly A Wanamaker
- University of Washington, School of Aquatic and Fishery Sciences, 1122 NE Boat St, Seattle, WA 98105, USA
| | - Brent Vadopalas
- University of Washington, Washington Sea Grant, 3716 Brooklyn Ave NE, Seattle, WA 98105, USA
| | - Steven B Roberts
- University of Washington, School of Aquatic and Fishery Sciences, 1122 NE Boat St, Seattle, WA 98105, USA
| | - Hollie M Putnam
- University of Rhode Island, College of the Environment and Life Sciences, 120 Flagg Rd, Kingston, RI 02881, USA
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Wong KH, Goodbody-Gringley G, de Putron SJ, Becker DM, Chequer A, Putnam HM. Brooded coral offspring physiology depends on the combined effects of parental press and pulse thermal history. Glob Chang Biol 2021; 27:3179-3195. [PMID: 33914388 DOI: 10.1111/gcb.15629] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 03/22/2021] [Accepted: 03/22/2021] [Indexed: 06/12/2023]
Abstract
Reef-building corals respond to the temporal integration of both pulse events (i.e., heat waves) and press thermal history (i.e., local environment) via physiological changes, with ecological consequences. We used a "press-pulse-press" experimental framework to expose the brooding coral Porites astreoides to various thermal histories to understand the physiological response of temporal dynamics within and across generations. We collected adult colonies from two reefs (outer Rim reef and inner Patch reef) in Bermuda with naturally contrasting thermal regimes as our initial "press" scenario, followed by a 21-day ex situ "pulse" thermal stress of 30.4°C during larval brooding, and a "press" year-long adult reciprocal transplant between the original sites. Higher endosymbiont density and holobiont protein was found in corals originating from the lower thermal variability site (Rim) compared to the higher thermal variability site (Patch). The thermal pulse event drove significant declines in photosynthesis, endosymbiont density, and chlorophyll a, with bleaching phenotype convergence for adults from both histories. Following the reciprocal transplant, photosynthesis was higher in previously heated corals, indicating recovery from the thermal pulse. The effect of origin (initial press) modulated the response to transplant site for endosymbiont density and chlorophyll a, suggesting contrasting acclimation strategies. Higher respiration and photosynthetic rates were found in corals originating from the Rim site, indicating greater energy available for reproduction, supported by larger larvae released from Rim corals post-transplantation. Notably, parental exposure to the pulse thermal event resulted in increased offspring plasticity when parents were transplanted to foreign sites, highlighting the legacy of the pulse event and the importance of the environment during recovery in contributing to cross-generational or developmental plasticity. Together, these findings provide novel insight into the role of historical disturbance events in driving differential outcomes within and across generations, which is of critical importance in forecasting reef futures.
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Affiliation(s)
- Kevin H Wong
- Department of Biology, University of Rhode Island, Kingston, RI, USA
| | - Gretchen Goodbody-Gringley
- Bermuda Institute of Ocean Sciences, St. George's, Bermuda
- Central Caribbean Marine Institute, Little Cayman Island, Cayman Islands
| | | | - Danielle M Becker
- Department of Biology, University of Rhode Island, Kingston, RI, USA
| | - Alex Chequer
- Bermuda Institute of Ocean Sciences, St. George's, Bermuda
| | - Hollie M Putnam
- Department of Biology, University of Rhode Island, Kingston, RI, USA
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21
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Scucchia F, Malik A, Zaslansky P, Putnam HM, Mass T. Combined responses of primary coral polyps and their algal endosymbionts to decreasing seawater pH. Proc Biol Sci 2021; 288:20210328. [PMID: 34157872 PMCID: PMC8220278 DOI: 10.1098/rspb.2021.0328] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
With coral reefs declining globally, resilience of these ecosystems hinges on successful coral recruitment. However, knowledge of the acclimatory and/or adaptive potential in response to environmental challenges such as ocean acidification (OA) in earliest life stages is limited. Our combination of physiological measurements, microscopy, computed tomography techniques and gene expression analysis allowed us to thoroughly elucidate the mechanisms underlying the response of early-life stages of corals, together with their algal partners, to the projected decline in oceanic pH. We observed extensive physiological, morphological and transcriptional changes in surviving recruits, and the transition to a less-skeleton/more-tissue phenotype. We found that decreased pH conditions stimulate photosynthesis and endosymbiont growth, and gene expression potentially linked to photosynthates translocation. Our unique holistic study discloses the previously unseen intricate net of interacting mechanisms that regulate the performance of these organisms in response to OA.
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Affiliation(s)
- Federica Scucchia
- Department of Marine Biology, The Leon H. Charney School of Marine Sciences, University of Haifa, Haifa 3498838, Israel.,The Interuniversity Institute of Marine Sciences, Eilat 88103, Israel
| | - Assaf Malik
- Department of Marine Biology, The Leon H. Charney School of Marine Sciences, University of Haifa, Haifa 3498838, Israel
| | - Paul Zaslansky
- Department for Operative and Preventive Dentistry, Charité-Center for Dental and Craniofacial Sciences, Universitätsmedizin Berlin, Berlin 14197, Germany
| | - Hollie M Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, RI 02881, USA
| | - Tali Mass
- Department of Marine Biology, The Leon H. Charney School of Marine Sciences, University of Haifa, Haifa 3498838, Israel.,Morris Kahn Marine Research Station, The Leon H. Charney School of Marine Sciences, University of Haifa, Sdot Yam, Israel
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22
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Davies SW, Putnam HM, Ainsworth T, Baum JK, Bove CB, Crosby SC, Côté IM, Duplouy A, Fulweiler RW, Griffin AJ, Hanley TC, Hill T, Humanes A, Mangubhai S, Metaxas A, Parker LM, Rivera HE, Silbiger NJ, Smith NS, Spalding AK, Traylor-Knowles N, Weigel BL, Wright RM, Bates AE. Promoting inclusive metrics of success and impact to dismantle a discriminatory reward system in science. PLoS Biol 2021; 19:e3001282. [PMID: 34129646 PMCID: PMC8205123 DOI: 10.1371/journal.pbio.3001282] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Success and impact metrics in science are based on a system that perpetuates sexist and racist “rewards” by prioritizing citations and impact factors. These metrics are flawed and biased against already marginalized groups and fail to accurately capture the breadth of individuals’ meaningful scientific impacts. We advocate shifting this outdated value system to advance science through principles of justice, equity, diversity, and inclusion. We outline pathways for a paradigm shift in scientific values based on multidimensional mentorship and promoting mentee well-being. These actions will require collective efforts supported by academic leaders and administrators to drive essential systemic change. This Essay argues that success and impact metrics in science are based on a system that perpetuates sexist and racist ‘rewards’ by prioritizing citations and impact factors; the authors advocate shifting this outdated value system to advance science through principles of justice, equity, diversity, and inclusion.
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Affiliation(s)
- Sarah W. Davies
- Department of Biology, Boston University, Boston, Massachusetts, United States of America
- * E-mail: (SWD); (HMP); (AEB)
| | - Hollie M. Putnam
- Department of Biological Sciences, University of Rhode Island, Rhode Island, United States of America
- * E-mail: (SWD); (HMP); (AEB)
| | - Tracy Ainsworth
- School of Biological Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Julia K. Baum
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Colleen B. Bove
- Department of Biology, Boston University, Boston, Massachusetts, United States of America
| | - Sarah C. Crosby
- Harbor Watch, Earthplace, Inc., Westport, Connecticut, United States of America
| | - Isabelle M. Côté
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Anne Duplouy
- The University of Helsinki, Organismal and Evolutionary Biology Research Program, Helsinki, Finland
| | - Robinson W. Fulweiler
- Department of Earth and Environment & Department of Biology, Boston University, Boston, Massachusetts, United States of America
| | - Alyssa J. Griffin
- Department of Earth & Planetary Sciences & Bodega Marine Laboratory, University of California, Davis, California, United States of America
| | - Torrance C. Hanley
- Marine Science Center, Northeastern University, Nahant, Massachusetts, United States of America
| | - Tessa Hill
- Department of Earth & Planetary Sciences & Bodega Marine Laboratory, University of California, Davis, California, United States of America
| | - Adriana Humanes
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | | | - Anna Metaxas
- Department of Oceanography, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Laura M. Parker
- School of Biological Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Hanny E. Rivera
- Department of Biology, Boston University, Boston, Massachusetts, United States of America
| | - Nyssa J. Silbiger
- Department of Biology, California State University, Northridge, Northridge, California, United States of America
| | - Nicola S. Smith
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Ana K. Spalding
- School of Public Policy, College of Liberal Arts, Oregon State University, Corvallis, Oregon, United States of America
- Smithsonian Tropical Research Institute, Panama City, Panama
| | - Nikki Traylor-Knowles
- University of Miami, Rosenstiel School of Marine and Atmospheric Sciences, Miami, Florida, United States of America
| | - Brooke L. Weigel
- Committee on Evolutionary Biology, University of Chicago, Chicago, Illinois, United States of America
| | - Rachel M. Wright
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, United States of America
| | - Amanda E. Bates
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, New Foundland, Canada
- * E-mail: (SWD); (HMP); (AEB)
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23
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Innis T, Allen-Waller L, Brown KT, Sparagon W, Carlson C, Kruse E, Huffmyer AS, Nelson CE, Putnam HM, Barott KL. Marine heatwaves depress metabolic activity and impair cellular acid-base homeostasis in reef-building corals regardless of bleaching susceptibility. Glob Chang Biol 2021; 27:2728-2743. [PMID: 33784420 DOI: 10.1111/gcb.15622] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/18/2021] [Accepted: 03/21/2021] [Indexed: 06/12/2023]
Abstract
Ocean warming is causing global coral bleaching events to increase in frequency, resulting in widespread coral mortality and disrupting the function of coral reef ecosystems. However, even during mass bleaching events, many corals resist bleaching despite exposure to abnormally high temperatures. While the physiological effects of bleaching have been well documented, the consequences of heat stress for bleaching-resistant individuals are not well understood. In addition, much remains to be learned about how heat stress affects cellular-level processes that may be overlooked at the organismal level, yet are crucial for coral performance in the short term and ecological success over the long term. Here we compared the physiological and cellular responses of bleaching-resistant and bleaching-susceptible corals throughout the 2019 marine heatwave in Hawai'i, a repeat bleaching event that occurred 4 years after the previous regional event. Relative bleaching susceptibility within species was consistent between the two bleaching events, yet corals of both resistant and susceptible phenotypes exhibited pronounced metabolic depression during the heatwave. At the cellular level, bleaching-susceptible corals had lower intracellular pH than bleaching-resistant corals at the peak of bleaching for both symbiont-hosting and symbiont-free cells, indicating greater disruption of acid-base homeostasis in bleaching-susceptible individuals. Notably, cells from both phenotypes were unable to compensate for experimentally induced cellular acidosis, indicating that acid-base regulation was significantly impaired at the cellular level even in bleaching-resistant corals and in cells containing symbionts. Thermal disturbances may thus have substantial ecological consequences, as even small reallocations in energy budgets to maintain homeostasis during stress can negatively affect fitness. These results suggest concern is warranted for corals coping with ocean acidification alongside ocean warming, as the feedback between temperature stress and acid-base regulation may further exacerbate the physiological effects of climate change.
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Affiliation(s)
- Teegan Innis
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Kristen T Brown
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
- ARC Centre of Excellence for Coral Reef Studies and School of Biological Sciences, University of Queensland, St. Lucia, Qld, Australia
| | - Wesley Sparagon
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, Department of Oceanography and Sea Grant College Program, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | | | - Elisa Kruse
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Ariana S Huffmyer
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, USA
| | - Craig E Nelson
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, Department of Oceanography and Sea Grant College Program, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - Hollie M Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, USA
| | - Katie L Barott
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
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Wall CB, Ricci CA, Wen AD, Ledbetter BE, Klinger DE, Mydlarz LD, Gates RD, Putnam HM. Shifting baselines: Physiological legacies contribute to the response of reef corals to frequent heatwaves. Funct Ecol 2021. [DOI: 10.1111/1365-2435.13795] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Christopher B. Wall
- Hawai'i Institute of Marine Biology University of Hawai'i at Mānoa Kāne'ohe HI USA
- Pacific Biosciences Research Center University of Hawai'i at Mānoa Honolulu HI USA
| | - Contessa A. Ricci
- Department of Biology University of Texas at Arlington Arlington TX USA
| | - Alexandra D. Wen
- Hawai'i Institute of Marine Biology University of Hawai'i at Mānoa Kāne'ohe HI USA
- Rosenstiel School of Marine and Atmospheric Science University of Miami Miami FL USA
| | - Bren E. Ledbetter
- Department of Biology University of Texas at Arlington Arlington TX USA
| | | | - Laura D. Mydlarz
- Department of Biology University of Texas at Arlington Arlington TX USA
| | - Ruth D. Gates
- Hawai'i Institute of Marine Biology University of Hawai'i at Mānoa Kāne'ohe HI USA
| | - Hollie M. Putnam
- Department of Biological Sciences University of Rhode Island Kingston RI USA
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25
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Li S, Roger LM, Kumar L, Lewinski NA, Klein-Seetharaman J, Gagnon A, Putnam HM, Yang J. Digital image processing to detect subtle motion in stony coral. Sci Rep 2021; 11:7722. [PMID: 33833260 PMCID: PMC8032694 DOI: 10.1038/s41598-021-85800-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/24/2021] [Indexed: 02/01/2023] Open
Abstract
Coral reef ecosystems support significant biological activities and harbor huge diversity, but they are facing a severe crisis driven by anthropogenic activities and climate change. An important behavioral trait of the coral holobiont is coral motion, which may play an essential role in feeding, competition, reproduction, and thus survival and fitness. Therefore, characterizing coral behavior through motion analysis will aid our understanding of basic biological and physical coral functions. However, tissue motion in the stony scleractinian corals that contribute most to coral reef construction are subtle and may be imperceptible to both the human eye and commonly used imaging techniques. Here we propose and apply a systematic approach to quantify and visualize subtle coral motion across a series of light and dark cycles in the scleractinian coral Montipora capricornis. We use digital image correlation and optical flow techniques to quantify and characterize minute coral motions under different light conditions. In addition, as a visualization tool, motion magnification algorithm magnifies coral motions in different frequencies, which explicitly displays the distinctive dynamic modes of coral movement. Specifically, our assessment of displacement, strain, optical flow, and mode shape quantify coral motion under different light conditions, and they all show that M. capricornis exhibits more active motions at night compared to day. Our approach provides an unprecedented insight into micro-scale coral movement and behavior through macro-scale digital imaging, thus offering a useful empirical toolset for the coral research community.
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Affiliation(s)
- Shuaifeng Li
- grid.34477.330000000122986657Department of Aeronautics and Astronautics, University of Washington, Seattle, WA 98195-2400 USA
| | - Liza M. Roger
- grid.224260.00000 0004 0458 8737Department of Chemical and Life Science and Engineering, Virginia Commonwealth University, Richmond, VA USA
| | - Lokender Kumar
- grid.254549.b0000 0004 1936 8155Department of Physics, Colorado School of Mines, Golden, CO USA
| | - Nastassja A. Lewinski
- grid.224260.00000 0004 0458 8737Department of Chemical and Life Science and Engineering, Virginia Commonwealth University, Richmond, VA USA
| | - Judith Klein-Seetharaman
- grid.254549.b0000 0004 1936 8155Department of Chemistry, Colorado School of Mines, Golden, CO USA
| | - Alex Gagnon
- grid.34477.330000000122986657School of Oceanography, University of Washington, Seattle, WA USA
| | - Hollie M. Putnam
- grid.20431.340000 0004 0416 2242Department of Biological Sciences, University of Rhode Island, Kingston, RI 02881 USA
| | - Jinkyu Yang
- grid.34477.330000000122986657Department of Aeronautics and Astronautics, University of Washington, Seattle, WA 98195-2400 USA
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26
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Roger LM, Reich HG, Lawrence E, Li S, Vizgaudis W, Brenner N, Kumar L, Klein-Seetharaman J, Yang J, Putnam HM, Lewinski NA. Applying model approaches in non-model systems: A review and case study on coral cell culture. PLoS One 2021; 16:e0248953. [PMID: 33831033 PMCID: PMC8031391 DOI: 10.1371/journal.pone.0248953] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 03/09/2021] [Indexed: 12/19/2022] Open
Abstract
Model systems approaches search for commonality in patterns underlying biological diversity and complexity led by common evolutionary paths. The success of the approach does not rest on the species chosen but on the scalability of the model and methods used to develop the model and engage research. Fine-tuning approaches to improve coral cell cultures will provide a robust platform for studying symbiosis breakdown, the calcification mechanism and its disruption, protein interactions, micronutrient transport/exchange, and the toxicity of nanoparticles, among other key biological aspects, with the added advantage of minimizing the ethical conundrum of repeated testing on ecologically threatened organisms. The work presented here aimed to lay the foundation towards development of effective methods to sort and culture reef-building coral cells with the ultimate goal of obtaining immortal cell lines for the study of bleaching, disease and toxicity at the cellular and polyp levels. To achieve this objective, the team conducted a thorough review and tested the available methods (i.e. cell dissociation, isolation, sorting, attachment and proliferation). The most effective and reproducible techniques were combined to consolidate culture methods and generate uncontaminated coral cell cultures for ~7 days (10 days maximum). The tests were conducted on scleractinian corals Pocillopora acuta of the same genotype to harmonize results and reduce variation linked to genetic diversity. The development of cell separation and identification methods in conjunction with further investigations into coral cell-type specific metabolic requirements will allow us to tailor growth media for optimized monocultures as a tool for studying essential reef-building coral traits such as symbiosis, wound healing and calcification at multiple scales.
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Affiliation(s)
- Liza M. Roger
- Life Science and Engineering, Virginia Commonwealth University, Richmond, Virginia, United States of America
- * E-mail: ,
| | - Hannah G. Reich
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, United States of America
| | - Evan Lawrence
- Life Science and Engineering, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Shuaifeng Li
- Aeronautics and Astronautics, University of Washington, Seattle, Washington, United States of America
| | - Whitney Vizgaudis
- Department of Chemistry, Colorado School of Mines, Golden, Colorado, United States of America
| | - Nathan Brenner
- Department of Chemistry, Colorado School of Mines, Golden, Colorado, United States of America
| | - Lokender Kumar
- Department of Chemistry, Colorado School of Mines, Golden, Colorado, United States of America
| | | | - Jinkyu Yang
- Aeronautics and Astronautics, University of Washington, Seattle, Washington, United States of America
| | - Hollie M. Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, United States of America
| | - Nastassja A. Lewinski
- Life Science and Engineering, Virginia Commonwealth University, Richmond, Virginia, United States of America
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27
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Fox MD, Nelson CE, Oliver TA, Quinlan ZA, Remple K, Glanz J, Smith JE, Putnam HM. Differential resistance and acclimation of two coral species to chronic nutrient enrichment reflect life‐history traits. Funct Ecol 2021. [DOI: 10.1111/1365-2435.13780] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Michael D. Fox
- Center for Marine Biodiversity and Conservation Scripps Institution of Oceanography University of California San Diego San Diego CA USA
| | - Craig E. Nelson
- Department of Oceanography and Sea Grant College Program Center for Microbial Oceanography: Research and Education University of Hawai‘i at Mānoa Honolulu HI USA
| | - Thomas A. Oliver
- Pacific Islands Fisheries Science Center NOAA Inouye Regional Center Honolulu HI USA
| | - Zachary A. Quinlan
- Department of Oceanography and Sea Grant College Program Center for Microbial Oceanography: Research and Education University of Hawai‘i at Mānoa Honolulu HI USA
- Department of Biology San Diego State University San Diego CA USA
| | - Kristina Remple
- Department of Oceanography and Sea Grant College Program Center for Microbial Oceanography: Research and Education University of Hawai‘i at Mānoa Honolulu HI USA
| | - Jess Glanz
- Department of Biology California State University Northridge Northridge CA USA
| | - Jennifer E. Smith
- Center for Marine Biodiversity and Conservation Scripps Institution of Oceanography University of California San Diego San Diego CA USA
| | - Hollie M. Putnam
- Department of Biological Sciences University of Rhode Island Kingston RI USA
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Abstract
ABSTRACT
The swiftly changing climate presents a challenge to organismal fitness by creating a mismatch between the current environment and phenotypes adapted to historic conditions. Acclimatory mechanisms may be especially crucial for sessile benthic marine taxa, such as reef-building corals, where climate change factors including ocean acidification and increasing temperature elicit strong negative physiological responses such as bleaching, disease and mortality. Here, within the context of multiple stressors threatening marine organisms, I describe the wealth of metaorganism response mechanisms to rapid ocean change and the ontogenetic shifts in organism interactions with the environment that can generate plasticity. I then highlight the need to consider the interactions of rapid and evolutionary responses in an adaptive (epi)genetic continuum. Building on the definitions of these mechanisms and continuum, I also present how the interplay of the microbiome, epigenetics and parental effects creates additional avenues for rapid acclimatization. To consider under what conditions epigenetic inheritance has a more substantial role, I propose investigation into the offset of timing of gametogenesis leading to different environmental integration times between eggs and sperm and the consequences of this for gamete epigenetic compatibility. Collectively, non-genetic, yet heritable phenotypic plasticity will have significant ecological and evolutionary implications for sessile marine organism persistence under rapid climate change. As such, reef-building corals present ideal and time-sensitive models for further development of our understanding of adaptive feedback loops in a multi-player (epi)genetic continuum.
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Affiliation(s)
- Hollie M. Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, RI 02881, USA
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29
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Zaquin T, Malik A, Drake JL, Putnam HM, Mass T. Evolution of Protein-Mediated Biomineralization in Scleractinian Corals. Front Genet 2021; 12:618517. [PMID: 33633782 PMCID: PMC7902050 DOI: 10.3389/fgene.2021.618517] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 01/08/2021] [Indexed: 12/19/2022] Open
Abstract
While recent strides have been made in understanding the biological process by which stony corals calcify, much remains to be revealed, including the ubiquity across taxa of specific biomolecules involved. Several proteins associated with this process have been identified through proteomic profiling of the skeletal organic matrix (SOM) extracted from three scleractinian species. However, the evolutionary history of this putative “biomineralization toolkit,” including the appearance of these proteins’ throughout metazoan evolution, remains to be resolved. Here we used a phylogenetic approach to examine the evolution of the known scleractinians’ SOM proteins across the Metazoa. Our analysis reveals an evolutionary process dominated by the co-option of genes that originated before the cnidarian diversification. Each one of the three species appears to express a unique set of the more ancient genes, representing the independent co-option of SOM proteins, as well as a substantial proportion of proteins that evolved independently. In addition, in some instances, the different species expressed multiple orthologous proteins sharing the same evolutionary history. Furthermore, the non-random clustering of multiple SOM proteins within scleractinian-specific branches suggests the conservation of protein function between distinct species for what we posit is part of the scleractinian “core biomineralization toolkit.” This “core set” contains proteins that are likely fundamental to the scleractinian biomineralization mechanism. From this analysis, we infer that the scleractinians’ ability to calcify was achieved primarily through multiple lineage-specific protein expansions, which resulted in a new functional role that was not present in the parent gene.
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Affiliation(s)
- Tal Zaquin
- Department of Marine Biology, The Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Assaf Malik
- Department of Marine Biology, The Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Jeana L Drake
- Department of Marine Biology, The Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Hollie M Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, United States
| | - Tali Mass
- Department of Marine Biology, The Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
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30
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Williams A, Chiles EN, Conetta D, Pathmanathan JS, Cleves PA, Putnam HM, Su X, Bhattacharya D. Metabolomic shifts associated with heat stress in coral holobionts. Sci Adv 2021; 7:eabd4210. [PMID: 33523848 PMCID: PMC7775768 DOI: 10.1126/sciadv.abd4210] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 11/06/2020] [Indexed: 05/26/2023]
Abstract
Understanding the response of the coral holobiont to environmental change is crucial to inform conservation efforts. The most pressing problem is "coral bleaching," usually precipitated by prolonged thermal stress. We used untargeted, polar metabolite profiling to investigate the physiological response of the coral species Montipora capitata and Pocillopora acuta to heat stress. Our goal was to identify diagnostic markers present early in the bleaching response. From the untargeted UHPLC-MS data, a variety of co-regulated dipeptides were found that have the highest differential accumulation in both species. The structures of four dipeptides were determined and showed differential accumulation in symbiotic and aposymbiotic (alga-free) populations of the sea anemone Aiptasia (Exaiptasia pallida), suggesting the deep evolutionary origins of these dipeptides and their involvement in symbiosis. These and other metabolites may be used as diagnostic markers for thermal stress in wild coral.
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Affiliation(s)
- Amanda Williams
- Microbial Biology Graduate Program, Rutgers University, New Brunswick, NJ 08901, USA
| | - Eric N Chiles
- Metabolomics Shared Resource, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ 08901, USA
| | - Dennis Conetta
- Department of Biological Sciences, University of Rhode Island, Kingston, RI 02881, USA
| | - Jananan S Pathmanathan
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
| | - Phillip A Cleves
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Hollie M Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, RI 02881, USA
| | - Xiaoyang Su
- Metabolomics Shared Resource, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ 08901, USA.
- Division of Endocrinology, Department of Medicine, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ 08901, USA
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA.
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Van Etten J, Shumaker A, Mass T, Putnam HM, Bhattacharya D. Transcriptome analysis provides a blueprint of coral egg and sperm functions. PeerJ 2020; 8:e9739. [PMID: 32874783 PMCID: PMC7441918 DOI: 10.7717/peerj.9739] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 07/26/2020] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Reproductive biology and the evolutionary constraints acting on dispersal stages are poorly understood in many stony coral species. A key piece of missing information is egg and sperm gene expression. This is critical for broadcast spawning corals, such as our model, the Hawaiian species Montipora capitata, because eggs and sperm are exposed to environmental stressors during dispersal. Furthermore, parental effects such as transcriptome investment may provide a means for cross- or trans-generational plasticity and be apparent in egg and sperm transcriptome data. METHODS Here, we analyzed M. capitata egg and sperm transcriptomic data to address three questions: (1) Which pathways and functions are actively transcribed in these gametes? (2) How does sperm and egg gene expression differ from adult tissues? (3) Does gene expression differ between these gametes? RESULTS We show that egg and sperm display surprisingly similar levels of gene expression and overlapping functional enrichment patterns. These results may reflect similar environmental constraints faced by these motile gametes. We find significant differences in differential expression of egg vs. adult and sperm vs. adult RNA-seq data, in contrast to very few examples of differential expression when comparing egg vs. sperm transcriptomes. Lastly, using gene ontology and KEGG orthology data we show that both egg and sperm have markedly repressed transcription and translation machinery compared to the adult, suggesting a dependence on parental transcripts. We speculate that cell motility and calcium ion binding genes may be involved in gamete to gamete recognition in the water column and thus, fertilization.
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Affiliation(s)
- Julia Van Etten
- Graduate Program in Ecology and Evolution, Rutgers, The State University of New Jersey, New Brunswick, NJ, United States of America
| | - Alexander Shumaker
- Microbial Biology Graduate Program, Rutgers, The State University of New Jersey, New Brunswick, NJ, United States of America
| | - Tali Mass
- Department of Marine Biology, University of Haifa, Haifa, Israel
| | - Hollie M. Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, United States of America
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, NJ, United States of America
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Putnam HM, Ritson-Williams R, Cruz JA, Davidson JM, Gates RD. Environmentally-induced parental or developmental conditioning influences coral offspring ecological performance. Sci Rep 2020; 10:13664. [PMID: 32788607 PMCID: PMC7423898 DOI: 10.1038/s41598-020-70605-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 06/23/2020] [Indexed: 01/22/2023] Open
Abstract
The persistence of reef building corals is threatened by human-induced environmental change. Maintaining coral reefs into the future requires not only the survival of adults, but also the influx of recruits to promote genetic diversity and retain cover following adult mortality. Few studies examine the linkages among multiple life stages of corals, despite a growing knowledge of carryover effects in other systems. We provide a novel test of coral parental conditioning to ocean acidification (OA) and tracking of offspring for 6 months post-release to better understand parental or developmental priming impacts on the processes of offspring recruitment and growth. Coral planulation was tracked for 3 months following adult exposure to high pCO2 and offspring from the second month were reciprocally exposed to ambient and high pCO2 for an additional 6 months. Offspring of parents exposed to high pCO2 had greater settlement and survivorship immediately following release, retained survivorship benefits during 1 and 6 months of continued exposure, and further displayed growth benefits to at least 1 month post release. Enhanced performance of offspring from parents exposed to high conditions was maintained despite the survivorship in both treatments declining in continued exposure to OA. Conditioning of the adults while they brood their larvae, or developmental acclimation of the larvae inside the adult polyps, may provide a form of hormetic conditioning, or environmental priming that elicits stimulatory effects. Defining mechanisms of positive acclimatization, with potential implications for carry over effects, cross-generational plasticity, and multi-generational plasticity, is critical to better understanding ecological and evolutionary dynamics of corals under regimes of increasing environmental disturbance. Considering environmentally-induced parental or developmental legacies in ecological and evolutionary projections may better account for coral reef response to the chronic stress regimes characteristic of climate change.
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Affiliation(s)
- Hollie M Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, USA.
| | | | - Jolly Ann Cruz
- Micronesia Islands Nature Alliance, Garapan, Saipan, CNMI, 96950, USA
| | - Jennifer M Davidson
- Hawai'i Institute of Marine Biology, University of Hawai'i, Mānoa, Honolulu, HI, USA
| | - Ruth D Gates
- Hawai'i Institute of Marine Biology, University of Hawai'i, Mānoa, Honolulu, HI, USA
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Abstract
One response to the coral reef crisis has been human intervention to enhance selection on the fittest corals through cultivation. This requires genotypes to be identified for intervention, with a primary basis for this choice being growth: corals that quickly grow on contemporary reefs might be future winners. To test for temporal stability of growth as a predictor of future performance, genotypes of the coral Porites spp. were grown in common gardens in Mo'orea, French Polynesia. Growth was measured every two to four months throughout 2018, and each period was used as a predictor of growth over the subsequent period. Area-normalized growth explained less than 29% of the variance in subsequent growth, but for biomass-normalized growth this increased to 45-60%, and was highest when summer growth was used to predict autumn growth. The capacity of initial growth to predict future performance is dependent on the units of measurement and the time of year in which it is measured. The final choice of traits to quantify performance must be informed through consideration of the species and the normalization that best capture the information inherent in the biological processes mediating variation in traits values.
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Affiliation(s)
- Peter J Edmunds
- Department of Biology, California State University, 18111 Nordhoff Street, Northridge, CA 91330-8303, USA
| | - Hollie M Putnam
- Department of Biological Science, University of Rhode Island, 120 Flagg Road, Kingston, RI 02881, USA
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Gurr SJ, Vadopalas B, Roberts SB, Putnam HM. Metabolic recovery and compensatory shell growth of juvenile Pacific geoduck Panopea generosa following short-term exposure to acidified seawater. Conserv Physiol 2020; 8:coaa024. [PMID: 32274068 PMCID: PMC7125045 DOI: 10.1093/conphys/coaa024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 12/12/2019] [Accepted: 02/27/2020] [Indexed: 06/11/2023]
Abstract
While acute stressors can be detrimental, environmental stress conditioning can improve performance. To test the hypothesis that physiological status is altered by stress conditioning, we subjected juvenile Pacific geoduck, Panopea generosa, to repeated exposures of elevated pCO2 in a commercial hatchery setting followed by a period in ambient common garden. Respiration rate and shell length were measured for juvenile geoduck periodically throughout short-term repeated reciprocal exposure periods in ambient (~550 μatm) or elevated (~2400 μatm) pCO2 treatments and in common, ambient conditions, 5 months after exposure. Short-term exposure periods comprised an initial 10-day exposure followed by 14 days in ambient before a secondary 6-day reciprocal exposure. The initial exposure to elevated pCO2 significantly reduced respiration rate by 25% relative to ambient conditions, but no effect on shell growth was detected. Following 14 days in common garden, ambient conditions, reciprocal exposure to elevated or ambient pCO2 did not alter juvenile respiration rates, indicating ability for metabolic recovery under subsequent conditions. Shell growth was negatively affected during the reciprocal treatment in both exposure histories; however, clams exposed to the initial elevated pCO2 showed compensatory growth with 5.8% greater shell length (on average between the two secondary exposures) after 5 months in ambient conditions. Additionally, clams exposed to the secondary elevated pCO2 showed 52.4% increase in respiration rate after 5 months in ambient conditions. Early exposure to low pH appears to trigger carryover effects suggesting bioenergetic re-allocation facilitates growth compensation. Life stage-specific exposures to stress can determine when it may be especially detrimental, or advantageous, to apply stress conditioning for commercial production of this long-lived burrowing clam.
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Affiliation(s)
- Samuel J Gurr
- College of the Environment and Life Sciences, University of Rhode Island, 120 Flagg Rd, Kingston, RI 02881, USA
| | - Brent Vadopalas
- Washington Sea Grant, University of Washington, 3716 Brooklyn Ave NE, Seattle, WA 98105, USA
| | - Steven B Roberts
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat St, Seattle, WA 98105, USA
| | - Hollie M Putnam
- College of the Environment and Life Sciences, University of Rhode Island, 120 Flagg Rd, Kingston, RI 02881, USA
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Byrne M, Foo SA, Ross PM, Putnam HM. Limitations of cross- and multigenerational plasticity for marine invertebrates faced with global climate change. Glob Chang Biol 2020; 26:80-102. [PMID: 31670444 DOI: 10.1111/gcb.14882] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 09/12/2019] [Indexed: 05/18/2023]
Abstract
Although cross generation (CGP) and multigenerational (MGP) plasticity have been identified as mechanisms of acclimation to global change, the weight of evidence indicates that parental conditioning over generations is not a panacea to rescue stress sensitivity in offspring. For many species, there were no benefits of parental conditioning. Even when improved performance was observed, this waned over time within a generation or across generations and fitness declined. CGP and MGP studies identified resilient species with stress tolerant genotypes in wild populations and selected family lines. Several bivalves possess favourable stress tolerance and phenotypically plastic traits potentially associated with genetic adaptation to life in habitats where they routinely experience temperature and/or acidification stress. These traits will be important to help 'climate proof' shellfish ventures. Species that are naturally stress tolerant and those that naturally experience a broad range of environmental conditions are good candidates to provide insights into the physiological and molecular mechanisms involved in CGP and MGP. It is challenging to conduct ecologically relevant global change experiments over the long times commensurate with the pace of changing climate. As a result, many studies present stressors in a shock-type exposure at rates much faster than projected scenarios. With more gradual stressor introduction over longer experimental durations and in context with conditions species are currently acclimatized and/or adapted to, the outcomes for sensitive species might differ. We highlight the importance to understand primordial germ cell development and the timing of gametogenesis with respect to stressor exposure. Although multigenerational exposure to global change stressors currently appears limited as a universal tool to rescue species in the face of changing climate, natural proxies of future conditions (upwelling zones, CO2 vents, naturally warm habitats) show that phenotypic adjustment and/or beneficial genetic selection is possible for some species, indicating complex plasticity-adaptation interactions.
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Affiliation(s)
- Maria Byrne
- School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Shawna A Foo
- Center for Global Discovery and Conservation Science, Arizona State University, Tempe, AZ, USA
| | - Pauline M Ross
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Hollie M Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, USA
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Cleves PA, Shumaker A, Lee J, Putnam HM, Bhattacharya D. Unknown to Known: Advancing Knowledge of Coral Gene Function. Trends Genet 2019; 36:93-104. [PMID: 31882190 DOI: 10.1016/j.tig.2019.11.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/31/2019] [Accepted: 11/06/2019] [Indexed: 12/18/2022]
Abstract
Given the catastrophic changes befalling coral reefs, understanding coral gene function is essential to advance reef conservation. This has proved challenging due to the paucity of genomic data and genetic tools available for corals. Recently, CRISPR/Cas9 gene editing was applied to these species; however, a major bottleneck is the identification and prioritization of candidate genes for manipulation. This issue is exacerbated by the many unknown ('dark') coral genes that may play key roles in the stress response. We review the use of gene coexpression networks that incorporate both known and unknown genes to identify targets for reverse genetic analysis. This approach also provides a framework for the annotation of dark genes in established interaction networks to improve our fundamental knowledge of coral gene function.
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Affiliation(s)
- Phillip A Cleves
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Alexander Shumaker
- Microbial Biology Graduate Program, Rutgers University, New Brunswick, NJ 08901, USA
| | - JunMo Lee
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA; Current address: Department of Oceanography, Kyungpook National University, Daegu 41566, Korea
| | - Hollie M Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, RI 02881, USA
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA.
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Silbiger NJ, Nelson CE, Remple K, Sevilla JK, Quinlan ZA, Putnam HM, Fox MD, Donahue MJ. Nutrient pollution disrupts key ecosystem functions on coral reefs. Proc Biol Sci 2019; 285:rspb.2017.2718. [PMID: 29875294 DOI: 10.1098/rspb.2017.2718] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 05/14/2018] [Indexed: 11/12/2022] Open
Abstract
There is a long history of examining the impacts of nutrient pollution and pH on coral reefs. However, little is known about how these two stressors interact and influence coral reef ecosystem functioning. Using a six-week nutrient addition experiment, we measured the impact of elevated nitrate (NO-3) and phosphate (PO3-4) on net community calcification (NCC) and net community production (NCP) rates of individual taxa and combined reef communities. Our study had four major outcomes: (i) NCC rates declined in response to nutrient addition in all substrate types, (ii) the mixed community switched from net calcification to net dissolution under medium and high nutrient conditions, (iii) nutrients augmented pH variability through modified photosynthesis and respiration rates, and (iv) nutrients disrupted the relationship between NCC and aragonite saturation state documented in ambient conditions. These results indicate that the negative effect of NO-3 and PO3-4 addition on reef calcification is likely both a direct physiological response to nutrients and also an indirect response to a shifting pH environment from altered NCP rates. Here, we show that nutrient pollution could make reefs more vulnerable to global changes associated with ocean acidification and accelerate the predicted shift from net accretion to net erosion.
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Affiliation(s)
- Nyssa J Silbiger
- Department of Biology, California State University, Northridge, CA 91330, USA
| | - Craig E Nelson
- Center for Microbial Oceanography: Research and Education, Department of Oceanography and Sea Grant College Program, University of Hawai'i at Mānoa, Honolulu, HI 96822, USA
| | - Kristina Remple
- Center for Microbial Oceanography: Research and Education, Department of Oceanography and Sea Grant College Program, University of Hawai'i at Mānoa, Honolulu, HI 96822, USA
| | - Jessica K Sevilla
- Department of Biology, University of Hawai'i at Mānoa, Honolulu, HI 96822, USA
| | - Zachary A Quinlan
- Center for Microbial Oceanography: Research and Education, Department of Oceanography and Sea Grant College Program, University of Hawai'i at Mānoa, Honolulu, HI 96822, USA.,Department of Biology, University of Hawai'i at Mānoa, Honolulu, HI 96822, USA
| | - Hollie M Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, RI 02881, USA
| | - Michael D Fox
- Scripps Institution of Oceanography, University of California, San Diego, CA 92093, USA
| | - Megan J Donahue
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI 96744, USA
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Calosi P, Putnam HM, Twitchett RJ, Vermandele F. Marine Metazoan Modern Mass Extinction: Improving Predictions by Integrating Fossil, Modern, and Physiological Data. Ann Rev Mar Sci 2019; 11:369-390. [PMID: 30216738 DOI: 10.1146/annurev-marine-010318-095106] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Evolution, extinction, and dispersion are fundamental processes affecting marine biodiversity. Until recently, studies of extant marine systems focused mainly on evolution and dispersion, with extinction receiving less attention. Past extinction events have, however, helped shape the evolutionary history of marine ecosystems, with ecological and evolutionary legacies still evident in modern seas. Current anthropogenic global changes increase extinction risk and pose a significant threat to marine ecosystems, which are critical for human use and sustenance. The evaluation of these threats and the likely responses of marine ecosystems requires a better understanding of evolutionary processes that affect marine ecosystems under global change. Here, we discuss how knowledge of ( a) changes in biodiversity of ancient marine ecosystems to past extinctions events, ( b) the patterns of sensitivity and biodiversity loss in modern marine taxa, and ( c) the physiological mechanisms underpinning species' sensitivity to global change can be exploited and integrated to advance our critical thinking in this area.
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Affiliation(s)
- Piero Calosi
- Département de Biologie, Chimie et Géographie, Université du Québec à Rimouski, Rimouski, Quebec G5L 3A1, Canada; ,
| | - Hollie M Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island 02881, USA;
| | - Richard J Twitchett
- Department of Earth Sciences, Natural History Museum, London SW7 5BD, United Kingdom;
| | - Fanny Vermandele
- Département de Biologie, Chimie et Géographie, Université du Québec à Rimouski, Rimouski, Quebec G5L 3A1, Canada; ,
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Abstract
Marine organisms' persistence hinges on the capacity for acclimatization and adaptation to the myriad of interacting environmental stressors associated with global climate change. In this context, epigenetics-mechanisms that facilitate phenotypic variation through genotype-environment interactions-are of great interest ecologically and evolutionarily. Our comprehensive review of marine environmental epigenetics guides our recommendations of four key areas for future research: the dynamics of wash-in and wash-out of epigenetic effects, the mechanistic understanding of the interplay of different epigenetic marks and the interaction with the microbiome, the capacity for and mechanisms of transgenerational epigenetic inheritance, and the evolutionary implications of the interaction of genetic and epigenetic features. Emerging insights in marine environmental epigenetics can be applied to critical issues such as aquaculture, biomonitoring, and biological invasions, thereby improving our ability to explain and predict the responses of marine taxa to global climate change.
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Affiliation(s)
- Jose M Eirin-Lopez
- Environmental Epigenetics Laboratory, Center for Coastal Oceans Research, Institute for Water and Environment, Florida International University, North Miami, Florida 33181, USA;
| | - Hollie M Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island 02881, USA;
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Abstract
Reef-building corals provide the foundation for the structural and biological diversity of coral-reef ecosystems. These massive biological structures, which can be seen from space, are the culmination of complex interactions between the tiny polyps of the coral animal in concert with its unicellular symbiotic algae and a wide diversity of closely associated microorganisms (bacteria, archaea, fungi, and viruses). While reef-building corals have persisted in various forms for over 200 million years, human-induced conditions threaten their function and persistence. The scope for loss associated with the destruction of coral reef systems is economically, biologically, physically and culturally immense. Here, we provide a micro-to-macro perspective on the biology of scleractinian corals and discuss how cellular processes of the host and symbionts potentially affect the response of these reef builders to the wide variety of both natural and anthropogenic stressors encountered by corals in the Anthropocene. We argue that the internal physicochemical settings matter to both the performance of the host and microbiome, as bio-physical feedbacks may enhance stress tolerance through environmentally mediated host priming and effects on microbiome ecological and evolutionary dynamics.
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Affiliation(s)
- Hollie M Putnam
- University of Rhode Island, Department of Biological Sciences, Kingston, RI, USA.
| | - Katie L Barott
- University of Pennsylvania, Department of Biology, Philadelphia, PA, USA; Hawaii Institute for Marine Biology, University of Hawai'i, Manoa, HI, USA
| | - Tracy D Ainsworth
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Australia
| | - Ruth D Gates
- Hawaii Institute for Marine Biology, University of Hawai'i, Manoa, HI, USA
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Guest JR, Edmunds PJ, Gates RD, Kuffner IB, Andersson AJ, Barnes BB, Chollett I, Courtney TA, Elahi R, Gross K, Lenz EA, Mitarai S, Mumby PJ, Nelson HR, Parker BA, Putnam HM, Rogers CS, Toth LT. A framework for identifying and characterising coral reef “oases” against a backdrop of degradation. J Appl Ecol 2018. [DOI: 10.1111/1365-2664.13179] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- James R. Guest
- Hawai'i Institute of Marine BiologyUniversity of Hawai'i Kāneʻohe Hawaii
| | - Peter J. Edmunds
- Department of BiologyCalifornia State University Northridge California
| | - Ruth D. Gates
- Hawai'i Institute of Marine BiologyUniversity of Hawai'i Kāneʻohe Hawaii
| | - Ilsa B. Kuffner
- U.S. Geological SurveySt. Petersburg Coastal & Marine Science Center St. Petersburg Florida
| | - Andreas J. Andersson
- Scripps Institution of OceanographyUniversity of California, San Diego La Jolla California
| | - Brian B. Barnes
- College of Marine ScienceUniversity of South Florida St Petersburg Florida
| | - Iliana Chollett
- Smithsonian Marine StationSmithsonian Institution Fort Pierce Florida
| | - Travis A. Courtney
- Scripps Institution of OceanographyUniversity of California, San Diego La Jolla California
| | - Robin Elahi
- Hopkins Marine StationStanford University Pacific Grove California
| | - Kevin Gross
- Biomathematics Graduate ProgramNorth Carolina State University Raleigh North Carolina
| | - Elizabeth A. Lenz
- Hawai'i Institute of Marine BiologyUniversity of Hawai'i Kāneʻohe Hawaii
| | - Satoshi Mitarai
- Okinawa Institute of Science and Technology Graduate University Okinawa Japan
| | - Peter J. Mumby
- Marine Spatial Ecology LabSchool of Biological Sciences and ARC Centre of Excellence for Reef StudiesUniversity of Queensland St Lucia Qld Australia
| | - Hannah R. Nelson
- Department of BiologyCalifornia State University Northridge California
| | - Britt A. Parker
- The Baldwin Group, Inc. on Contract at the NOAA Coral Reef Conservation Program Silver Spring Maryland
| | - Hollie M. Putnam
- Department of Biological SciencesUniversity of Rhode Island Kingston Rhode Island
| | - Caroline S. Rogers
- U.S. Geological Survey, Wetland and Aquatic Research Center St John Virgin Islands
| | - Lauren T. Toth
- U.S. Geological SurveySt. Petersburg Coastal & Marine Science Center St. Petersburg Florida
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van Oppen MJH, Gates RD, Blackall LL, Cantin N, Chakravarti LJ, Chan WY, Cormick C, Crean A, Damjanovic K, Epstein H, Harrison PL, Jones TA, Miller M, Pears RJ, Peplow LM, Raftos DA, Schaffelke B, Stewart K, Torda G, Wachenfeld D, Weeks AR, Putnam HM. Shifting paradigms in restoration of the world's coral reefs. Glob Chang Biol 2017; 23:3437-3448. [PMID: 28247459 DOI: 10.1111/gcb.13647] [Citation(s) in RCA: 161] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 01/19/2017] [Accepted: 01/23/2017] [Indexed: 05/18/2023]
Abstract
Many ecosystems around the world are rapidly deteriorating due to both local and global pressures, and perhaps none so precipitously as coral reefs. Management of coral reefs through maintenance (e.g., marine-protected areas, catchment management to improve water quality), restoration, as well as global and national governmental agreements to reduce greenhouse gas emissions (e.g., the 2015 Paris Agreement) is critical for the persistence of coral reefs. Despite these initiatives, the health and abundance of corals reefs are rapidly declining and other solutions will soon be required. We have recently discussed options for using assisted evolution (i.e., selective breeding, assisted gene flow, conditioning or epigenetic programming, and the manipulation of the coral microbiome) as a means to enhance environmental stress tolerance of corals and the success of coral reef restoration efforts. The 2014-2016 global coral bleaching event has sharpened the focus on such interventionist approaches. We highlight the necessity for consideration of alternative (e.g., hybrid) ecosystem states, discuss traits of resilient corals and coral reef ecosystems, and propose a decision tree for incorporating assisted evolution into restoration initiatives to enhance climate resilience of coral reefs.
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Affiliation(s)
- Madeleine J H van Oppen
- Australian Institute of Marine Science, PMB No. 3, Townsville MC, QLD, 4810, Australia
- School of BioSciences, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Ruth D Gates
- Hawaii Institute of Marine Biology, Kaneohe, HI, 96744, USA
| | - Linda L Blackall
- School of BioSciences, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Neal Cantin
- Australian Institute of Marine Science, PMB No. 3, Townsville MC, QLD, 4810, Australia
| | - Leela J Chakravarti
- Australian Institute of Marine Science, PMB No. 3, Townsville MC, QLD, 4810, Australia
- AIMS@JCU, James Cook University, Townsville, QLD, 4811, Australia
- College of Marine and Environmental Sciences, James Cook University, Townsville, QLD, 4811, Australia
| | - Wing Y Chan
- Australian Institute of Marine Science, PMB No. 3, Townsville MC, QLD, 4810, Australia
- School of BioSciences, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Craig Cormick
- ThinkOutsideThe, 12 Giffen Close, Holt, ACT, 2615, Australia
| | - Angela Crean
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Katarina Damjanovic
- Australian Institute of Marine Science, PMB No. 3, Townsville MC, QLD, 4810, Australia
- School of BioSciences, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Hannah Epstein
- Australian Institute of Marine Science, PMB No. 3, Townsville MC, QLD, 4810, Australia
- AIMS@JCU, James Cook University, Townsville, QLD, 4811, Australia
- College of Marine and Environmental Sciences, James Cook University, Townsville, QLD, 4811, Australia
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia
| | - Peter L Harrison
- Marine Ecology Research Centre, School of Environment, Science and Engineering, Southern Cross University, Lismore, NSW, Australia
| | - Thomas A Jones
- USDA-Agricultural Research Service, Forage and Range Research Laboratory, Logan, UT, 84322-6300, USA
| | - Margaret Miller
- National Oceanic and Atmospheric Administration-National Marine Fisheries Service, Miami, FL, USA
| | - Rachel J Pears
- Great Barrier Reef Marine Park Authority, PO Box 1379, Townsville, QLD, 4810, Australia
| | - Lesa M Peplow
- Australian Institute of Marine Science, PMB No. 3, Townsville MC, QLD, 4810, Australia
| | - David A Raftos
- Department of Biological Sciences, Macquarie University, North Ryde, NSW, 2109, Australia
| | - Britta Schaffelke
- Australian Institute of Marine Science, PMB No. 3, Townsville MC, QLD, 4810, Australia
| | - Kristen Stewart
- SUNY College of Environmental Science and Forestry, Syracuse, NY, 13210-2788, USA
| | - Gergely Torda
- Australian Institute of Marine Science, PMB No. 3, Townsville MC, QLD, 4810, Australia
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia
| | - David Wachenfeld
- Great Barrier Reef Marine Park Authority, PO Box 1379, Townsville, QLD, 4810, Australia
| | - Andrew R Weeks
- School of BioSciences, University of Melbourne, Parkville, VIC, 3010, Australia
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Qiu H, Zelzion E, Putnam HM, Gates RD, Wagner NE, Adams DK, Bhattacharya D. Discovery of SCORs: Anciently derived, highly conserved gene-associated repeats in stony corals. Genomics 2017. [PMID: 28634029 DOI: 10.1016/j.ygeno.2017.06.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Stony coral (Scleractinia) genomes are still poorly explored and many questions remain about their evolution and contribution to the success and longevity of reefs. We analyzed transcriptome and genome data from Montipora capitata, Acropora digitifera, and transcriptome data from 20 other coral species. To our surprise, we found highly conserved, anciently derived, Scleractinia COral-specific Repeat families (SCORs) that are abundant in all the studied lineages. SCORs form complex secondary structures and are located in untranslated regions and introns, but most abundant in intergenic DNA. These repeat families have undergone frequent duplication and degradation, suggesting a 'boom and bust' cycle of invasion and loss. We speculate that due to their surprisingly high sequence identities across deeply diverged corals, physical association with genes, and dynamic evolution, SCORs might have adaptive functions in corals that need to be explored using population genomic and function-based approaches.
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Affiliation(s)
- Huan Qiu
- Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, NJ 08901, USA
| | - Ehud Zelzion
- Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, NJ 08901, USA
| | | | - Ruth D Gates
- Hawai'i Institute of Marine Biology, Kaneohe, HI 96744, USA
| | - Nicole E Wagner
- Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, NJ 08901, USA
| | - Diane K Adams
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ 08901, USA
| | - Debashish Bhattacharya
- Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, NJ 08901, USA.
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Sogin EM, Putnam HM, Nelson CE, Anderson P, Gates RD. Correspondence of coral holobiont metabolome with symbiotic bacteria, archaea and Symbiodinium communities. Environ Microbiol Rep 2017; 9:310-315. [PMID: 28464532 DOI: 10.1111/1758-2229.12541] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 01/25/2017] [Accepted: 03/12/2017] [Indexed: 06/07/2023]
Abstract
Microbial symbiotic partners, such as those associated with Scleractinian corals, mediate biochemical transformations that influence host performance and survival. While evidence suggests microbial community composition partly accounts for differences in coral physiology, how these symbionts affect metabolic pathways remains underexplored. We aimed to assess functional implications of variation among coral-associated microbial partners in hospite. To this end, we characterized and compared metabolomic profiles and microbial community composition from nine reef-building coral species. These data demonstrate metabolite profiles and microbial communities are species-specific and are correlated to one another. Using Porites spp. as a case study, we present evidence that the relative abundance of different sub-clades of Symbiodinium and bacterial/archaeal families are linked to positive and negative metabolomic signatures. Our data suggest that while some microbial partners benefit the union, others are more opportunistic with potential detriment to the host. Consequently, coral partner choice likely influences cellular metabolic activities and, therefore, holobiont nutrition.
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Affiliation(s)
- Emilia M Sogin
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, USA
| | - Hollie M Putnam
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, USA
| | - Craig E Nelson
- Department of Oceanography and Sea Grant College Program, Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - Paul Anderson
- Department of Computer Science, College of Charleston, Charleston, NC, USA
| | - Ruth D Gates
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, USA
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Putnam HM, Adams DK, Zelzion E, Wagner NE, Qiu H, Mass T, Falkowski PG, Gates RD, Bhattacharya D. Divergent evolutionary histories of DNA markers in a Hawaiian population of the coral Montipora capitata. PeerJ 2017; 5:e3319. [PMID: 28533967 PMCID: PMC5438590 DOI: 10.7717/peerj.3319] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Accepted: 04/15/2017] [Indexed: 11/20/2022] Open
Abstract
We investigated intra- and inter-colony sequence variation in a population of the dominant Hawaiian coral Montipora capitata by analyzing marker gene and genomic data. Ribosomal ITS1 regions showed evidence of a reticulate history among the colonies, suggesting incomplete rDNA repeat homogenization. Analysis of the mitochondrial genome identified a major (M. capitata) and a minor (M. flabellata) haplotype in single polyp-derived sperm bundle DNA with some colonies containing 2–3 different mtDNA haplotypes. In contrast, Pax-C and newly identified single-copy nuclear genes showed either no sequence differences or minor variations in SNP frequencies segregating among the colonies. Our data suggest past mitochondrial introgression in M. capitata, whereas nuclear single-copy loci show limited variation, highlighting the divergent evolutionary histories of these coral DNA markers.
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Affiliation(s)
- Hollie M Putnam
- Hawai'i Institute of Marine Biology, Kaneohe, HI, United States of America.,Department of Biological Sciences, University of Rhode Island, Kingston, RI, United States of America
| | - Diane K Adams
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, United States of America
| | - Ehud Zelzion
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, NJ, United States of America
| | - Nicole E Wagner
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, NJ, United States of America
| | - Huan Qiu
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, NJ, United States of America
| | - Tali Mass
- Marine Biology Department, University of Haifa, Haifa, Israel
| | - Paul G Falkowski
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, United States of America.,Department of Earth and Planetary Sciences, Rutgers University, Piscataway, NJ, United States of America
| | - Ruth D Gates
- Hawai'i Institute of Marine Biology, Kaneohe, HI, United States of America
| | - Debashish Bhattacharya
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, NJ, United States of America
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Mass T, Putnam HM, Drake JL, Zelzion E, Gates RD, Bhattacharya D, Falkowski PG. Temporal and spatial expression patterns of biomineralization proteins during early development in the stony coral Pocillopora damicornis. Proc Biol Sci 2017; 283:rspb.2016.0322. [PMID: 27122561 DOI: 10.1098/rspb.2016.0322] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 04/01/2016] [Indexed: 11/12/2022] Open
Abstract
Reef-building corals begin as non-calcifying larvae that, upon settling, rapidly begin to accrete skeleton and a protein-rich skeletal organic matrix that attach them to the reef. Here, we characterized the temporal and spatial expression pattern of a suite of biomineralization genes during three stages of larval development in the reef-building coral Pocillopora damicornis: stage I, newly released; stage II, oral-aborally compressed and stage III, settled and calcifying spat. Transcriptome analysis revealed 3882 differentially expressed genes that clustered into four distinctly different patterns of expression change across the three developmental stages. Immunolocalization analysis further reveals the spatial arrangement of coral acid-rich proteins (CARPs) in the overall architecture of the emerging skeleton. These results provide the first analysis of the timing of the biomineralization 'toolkit' in the early life history of a stony coral.
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Affiliation(s)
- Tali Mass
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences, Kaneohe, HI 96744, USA
| | | | - Jeana L Drake
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences, Kaneohe, HI 96744, USA
| | - Ehud Zelzion
- Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, NJ 08901, USA
| | - Ruth D Gates
- Hawaii Institute of Marine Biology, Kaneohe, HI 96744, USA
| | - Debashish Bhattacharya
- Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, NJ 08901, USA Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ 08901, USA
| | - Paul G Falkowski
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences, Kaneohe, HI 96744, USA Department of Earth and Planetary Sciences, Rutgers University, Piscataway, NJ 08854, USA
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Putnam HM, Davidson JM, Gates RD. Ocean acidification influences host DNA methylation and phenotypic plasticity in environmentally susceptible corals. Evol Appl 2016; 9:1165-1178. [PMID: 27695524 PMCID: PMC5039329 DOI: 10.1111/eva.12408] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 06/27/2016] [Indexed: 12/13/2022] Open
Abstract
As climate change challenges organismal fitness by creating a phenotype-environment mismatch, phenotypic plasticity generated by epigenetic mechanisms (e.g., DNA methylation) can provide a temporal buffer for genetic adaptation. Epigenetic mechanisms may be crucial for sessile benthic marine organisms, such as reef-building corals, where ocean acidification (OA) and warming reflect in strong negative responses. We tested the potential for scleractinian corals to exhibit phenotypic plasticity associated with a change in DNA methylation in response to OA. Clonal coral fragments of the environmentally sensitive Pocillopora damicornis and more environmentally robust Montipora capitata were exposed to fluctuating ambient pH (7.9-7.65) and low pH (7.6-7.35) conditions in common garden tanks for ~6 weeks. M. capitata responded weakly, or acclimated more quickly, to OA, with no difference in calcification, minimal separation of metabolomic profiles, and no change in DNA methylation between treatments. Conversely, P. damicornis exhibited diminished calcification at low pH, stronger separation in metabolomic profiles, and responsiveness of DNA methylation to treatment. Our data suggest corals differ in their temporal dynamics and sensitivity for environmentally triggered real-time epigenetic reprogramming. The generation of potentially heritable plasticity via environmental induction of DNA methylation provides an avenue for assisted evolution applications in corals under rapid climate change.
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Affiliation(s)
- Hollie M. Putnam
- Hawaii Institute of Marine BiologyUniversity of HawaiiKaneoheHIUSA
| | | | - Ruth D. Gates
- Hawaii Institute of Marine BiologyUniversity of HawaiiKaneoheHIUSA
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48
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Madin JS, Hoogenboom MO, Connolly SR, Darling ES, Falster DS, Huang D, Keith SA, Mizerek T, Pandolfi JM, Putnam HM, Baird AH. A Trait-Based Approach to Advance Coral Reef Science. Trends Ecol Evol 2016; 31:419-428. [DOI: 10.1016/j.tree.2016.02.012] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 02/09/2016] [Accepted: 02/11/2016] [Indexed: 11/29/2022]
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Bhattacharya D, Agrawal S, Aranda M, Baumgarten S, Belcaid M, Drake JL, Erwin D, Foret S, Gates RD, Gruber DF, Kamel B, Lesser MP, Levy O, Liew YJ, MacManes M, Mass T, Medina M, Mehr S, Meyer E, Price DC, Putnam HM, Qiu H, Shinzato C, Shoguchi E, Stokes AJ, Tambutté S, Tchernov D, Voolstra CR, Wagner N, Walker CW, Weber AP, Weis V, Zelzion E, Zoccola D, Falkowski PG. Comparative genomics explains the evolutionary success of reef-forming corals. eLife 2016; 5. [PMID: 27218454 PMCID: PMC4878875 DOI: 10.7554/elife.13288] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 04/20/2016] [Indexed: 12/30/2022] Open
Abstract
Transcriptome and genome data from twenty stony coral species and a selection of reference bilaterians were studied to elucidate coral evolutionary history. We identified genes that encode the proteins responsible for the precipitation and aggregation of the aragonite skeleton on which the organisms live, and revealed a network of environmental sensors that coordinate responses of the host animals to temperature, light, and pH. Furthermore, we describe a variety of stress-related pathways, including apoptotic pathways that allow the host animals to detoxify reactive oxygen and nitrogen species that are generated by their intracellular photosynthetic symbionts, and determine the fate of corals under environmental stress. Some of these genes arose through horizontal gene transfer and comprise at least 0.2% of the animal gene inventory. Our analysis elucidates the evolutionary strategies that have allowed symbiotic corals to adapt and thrive for hundreds of millions of years. DOI:http://dx.doi.org/10.7554/eLife.13288.001 For millions of years, reef-building stony corals have created extensive habitats for numerous marine plants and animals in shallow tropical seas. Stony corals consist of many small, tentacled animals called polyps. These polyps secrete a mineral called aragonite to create the reef – an external ‘skeleton’ that supports and protects the corals. Photosynthesizing algae live inside the cells of stony corals, and each species depends on the other to survive. The algae produce the coral’s main source of food, although they also produce some waste products that can harm the coral if they build up inside cells. If the oceans become warmer and more acidic, the coral are more likely to become stressed and expel the algae from their cells in a process known as coral bleaching. This makes the coral more likely to die or become diseased. Corals have survived previous periods of ocean warming, although it is not known how they evolved to do so. The evolutionary history of an organism can be traced by studying its genome – its complete set of DNA – and the RNA molecules encoded by these genes. Bhattacharya et al. performed this analysis for twenty stony coral species, and compared the resulting genome and RNA sequences with the genomes of other related marine organisms, such as sea anemones and sponges. In particular, Bhattacharya et al. examined “ortholog” groups of genes, which are present in different species and evolved from a common ancestral gene. This analysis identified the genes in the corals that encode the proteins responsible for constructing the aragonite skeleton. The coral genome also encodes a network of environmental sensors that coordinate how the polyps respond to temperature, light and acidity. Bhattacharya et al. also uncovered a variety of stress-related pathways, including those that detoxify the polyps of the damaging molecules generated by algae, and the pathways that enable the polyps to adapt to environmental stress. Many of these genes were recruited from other species in a process known as horizontal gene transfer. The oceans are expected to become warmer and more acidic in the coming centuries. Provided that humans do not physically destroy the corals’ habitats, the evidence found by Bhattacharya et al. suggests that the genome of the corals contains the diversity that will allow them to adapt to these new conditions. DOI:http://dx.doi.org/10.7554/eLife.13288.002
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Affiliation(s)
- Debashish Bhattacharya
- Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, United States.,Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, United States
| | - Shobhit Agrawal
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Manuel Aranda
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Sebastian Baumgarten
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Mahdi Belcaid
- Hawaii Institute of Marine Biology, Kaneohe, United States
| | - Jeana L Drake
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, United States
| | - Douglas Erwin
- Smithsonian Institution, National Museum of Natural History, Washington, United States
| | - Sylvian Foret
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Australia.,Research School of Biology, Australian National University, Canberra, Australia
| | - Ruth D Gates
- Hawaii Institute of Marine Biology, Kaneohe, United States
| | - David F Gruber
- American Museum of Natural History, Sackler Institute for Comparative Genomics, New York, United States.,Department of Natural Sciences, City University of New York, Baruch College and The Graduate Center, New York, United States
| | - Bishoy Kamel
- Department of Biology, Mueller Lab, Penn State University, University Park, United States
| | - Michael P Lesser
- School of Marine Science and Ocean Engineering, University of New Hampshire, Durham, United States
| | - Oren Levy
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gam, Israel
| | - Yi Jin Liew
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Matthew MacManes
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, United States
| | - Tali Mass
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, United States.,Marine Biology Department, The Leon H. Charney School of Marine Sciences, University of Haifa, Mt. Carmel, Israel
| | - Monica Medina
- Department of Biology, Mueller Lab, Penn State University, University Park, United States
| | - Shaadi Mehr
- American Museum of Natural History, Sackler Institute for Comparative Genomics, New York, United States.,Biological Science Department, State University of New York, College at Old Westbury, New York, United States
| | - Eli Meyer
- Department of Integrative Biology, Oregon State University, Corvallis, United States
| | - Dana C Price
- Department of Plant Biology and Pathology, Rutgers University, New Brunswick, United States
| | | | - Huan Qiu
- Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, United States
| | - Chuya Shinzato
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Alexander J Stokes
- Laboratory of Experimental Medicine and Department of Cell and Molecular Biology, John A. Burns School of Medicine, Honolulu, United States.,Chaminade University, Honolulu, United States
| | | | - Dan Tchernov
- Marine Biology Department, The Leon H. Charney School of Marine Sciences, University of Haifa, Mt. Carmel, Israel
| | - Christian R Voolstra
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Nicole Wagner
- Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, United States
| | - Charles W Walker
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, United States
| | - Andreas Pm Weber
- Institute of Plant Biochemistry, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Virginia Weis
- Department of Integrative Biology, Oregon State University, Corvallis, United States
| | - Ehud Zelzion
- Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, United States
| | | | - Paul G Falkowski
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, United States.,Department of Earth and Planetary Sciences, Rutgers University, New Jersey, United States
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Boulotte NM, Dalton SJ, Carroll AG, Harrison PL, Putnam HM, Peplow LM, van Oppen MJ. Exploring the Symbiodinium rare biosphere provides evidence for symbiont switching in reef-building corals. ISME J 2016; 10:2693-2701. [PMID: 27093048 PMCID: PMC5113844 DOI: 10.1038/ismej.2016.54] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Revised: 02/12/2016] [Accepted: 02/25/2016] [Indexed: 01/18/2023]
Abstract
Reef-building corals possess a range of acclimatisation and adaptation mechanisms to respond to seawater temperature increases. In some corals, thermal tolerance increases through community composition changes of their dinoflagellate endosymbionts (Symbiodinium spp.), but this mechanism is believed to be limited to the Symbiodinium types already present in the coral tissue acquired during early life stages. Compelling evidence for symbiont switching, that is, the acquisition of novel Symbiodinium types from the environment, by adult coral colonies, is currently lacking. Using deep sequencing analysis of Symbiodinium rDNA internal transcribed spacer 2 (ITS2) PCR amplicons from two pocilloporid coral species, we show evidence consistent with de novo acquisition of Symbiodinium types from the environment by adult corals following two consecutive bleaching events. Most of these newly detected symbionts remained in the rare biosphere (background types occurring below 1% relative abundance), but one novel type reached a relative abundance of ~33%. Two de novo acquired Symbiodinium types belong to the thermally resistant clade D, suggesting that this switching may have been driven by consecutive thermal bleaching events. Our results are particularly important given the maternal mode of Symbiodinium transmission in the study species, which generally results in high symbiont specificity. These findings will cause a paradigm shift in our understanding of coral-Symbiodinium symbiosis flexibility and mechanisms of environmental acclimatisation in corals.
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Affiliation(s)
- Nadine M Boulotte
- National Marine Science Centre, School of Environment, Science and Engineering, Southern Cross University, Coffs Harbour, New South Wales, Australia.,Marine Ecology Research Centre, School of Environment, Science and Engineering, Southern Cross University, Lismore, New South Wales, Australia
| | - Steven J Dalton
- National Marine Science Centre, School of Environment, Science and Engineering, Southern Cross University, Coffs Harbour, New South Wales, Australia.,Marine Ecology Research Centre, School of Environment, Science and Engineering, Southern Cross University, Lismore, New South Wales, Australia
| | - Andrew G Carroll
- Marine Ecology Research Centre, School of Environment, Science and Engineering, Southern Cross University, Lismore, New South Wales, Australia
| | - Peter L Harrison
- Marine Ecology Research Centre, School of Environment, Science and Engineering, Southern Cross University, Lismore, New South Wales, Australia
| | - Hollie M Putnam
- Hawaii Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i, Kaneohe, HI, USA
| | - Lesa M Peplow
- Australian Institute of Marine Science, Townsville MC, Queensland, Australia
| | - Madeleine Jh van Oppen
- Australian Institute of Marine Science, Townsville MC, Queensland, Australia.,School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
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