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Strader ME, Wright RM, Pezner AK, Nuttall MF, Aichelman HE, Davies SW. Intersection of coral molecular responses to a localized mortality event and ex situ deoxygenation. Ecol Evol 2024; 14:e11275. [PMID: 38654712 PMCID: PMC11036075 DOI: 10.1002/ece3.11275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 03/22/2024] [Accepted: 04/01/2024] [Indexed: 04/26/2024] Open
Abstract
In July 2016, East Bank of Flower Garden Banks (FGB) National Marine Sanctuary experienced a localized mortality event (LME) of multiple invertebrate species that ultimately led to reductions in coral cover. Abiotic data taken directly after the event suggested that acute deoxygenation contributed to the mortality. Despite the large impact of this event on the coral community, there was no direct evidence that this LME was driven by acute deoxygenation, and thus we explored whether gene expression responses of corals to the LME would indicate what abiotic factors may have contributed to the LME. Gene expression of affected and unaffected corals sampled during the mortality event revealed evidence of the physiological consequences of the LME on coral hosts and their algal symbionts from two congeneric species (Orbicella franksi and Orbicella faveolata). Affected colonies of both species differentially regulated genes involved in mitochondrial regulation and oxidative stress. To further test the hypothesis that deoxygenation led to the LME, we measured coral host and algal symbiont gene expression in response to ex situ experimental deoxygenation (control = 6.9 ± 0.08 mg L-1, anoxic = 0.083 ± 0.017 mg L-1) in healthy O. faveolata colonies from the FGB. However, this deoxygenation experiment revealed divergent gene expression patterns compared to the corals sampled during the LME and was more similar to a generalized coral environmental stress response. It is therefore likely that while the LME was connected to low oxygen, it was a series of interconnected stressors that elicited the unique gene expression responses observed here. These in situ and ex situ data highlight how field responses to stressors are unique from those in controlled laboratory conditions, and that the complexities of deoxygenation events in the field likely arise from interactions between multiple environmental factors simultaneously.
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Affiliation(s)
- Marie E. Strader
- Department of BiologyTexas A&M UniversityCollege StationTexasUSA
| | - Rachel M. Wright
- Department of Biological SciencesSouthern Methodist UniversityDallasTexasUSA
| | | | | | | | - Sarah W. Davies
- Department of BiologyBoston UniversityBostonMassachusettsUSA
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2
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Matthews JL, Ueland M, Bartels N, Lawson CA, Lockwood TE, Wu Y, Camp EF. Multi-Chemical Omics Analysis of the Symbiodiniaceae Durusdinium trenchii under Heat Stress. Microorganisms 2024; 12:317. [PMID: 38399721 PMCID: PMC10893086 DOI: 10.3390/microorganisms12020317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 01/22/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
The urgency of responding to climate change for corals necessitates the exploration of innovative methods to swiftly enhance our understanding of crucial processes. In this study, we employ an integrated chemical omics approach, combining elementomics, metabolomics, and volatilomics methodologies to unravel the biochemical pathways associated with the thermal response of the coral symbiont, Symbiodiniaceae Durusdinium trenchii. We outline the complimentary sampling approaches and discuss the standardised data corrections used to allow data integration and comparability. Our findings highlight the efficacy of individual methods in discerning differences in the biochemical response of D. trenchii under both control and stress-inducing temperatures. However, a deeper insight emerges when these methods are integrated, offering a more comprehensive understanding, particularly regarding oxidative stress pathways. Employing correlation network analysis enhanced the interpretation of volatile data, shedding light on the potential metabolic origins of volatiles with undescribed functions and presenting promising candidates for further exploration. Elementomics proves to be less straightforward to integrate, likely due to no net change in elements but rather elements being repurposed across compounds. The independent and integrated data from this study informs future omic profiling studies and recommends candidates for targeted research beyond Symbiodiniaceae biology. This study highlights the pivotal role of omic integration in advancing our knowledge, addressing critical gaps, and guiding future research directions in the context of climate change and coral reef preservation.
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Affiliation(s)
- Jennifer L. Matthews
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Maiken Ueland
- Centre for Forensic Sciences, School of Mathematical and Physical Sciences, University of Technology Sydney, Ultimo, NSW 2007, Australia
- Hyphenated Mass Spectrometry Laboratory, School of Mathematical and Physical Sciences, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Natasha Bartels
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Caitlin A. Lawson
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007, Australia
- School of Environmental and Life Sciences, University of Newcastle, Ourimbah, NSW 2258, Australia
| | - Thomas E. Lockwood
- Hyphenated Mass Spectrometry Laboratory, School of Mathematical and Physical Sciences, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Yida Wu
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Emma F. Camp
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007, Australia
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Beavers KM, Van Buren EW, Rossin AM, Emery MA, Veglia AJ, Karrick CE, MacKnight NJ, Dimos BA, Meiling SS, Smith TB, Apprill A, Muller EM, Holstein DM, Correa AMS, Brandt ME, Mydlarz LD. Stony coral tissue loss disease induces transcriptional signatures of in situ degradation of dysfunctional Symbiodiniaceae. Nat Commun 2023; 14:2915. [PMID: 37217477 DOI: 10.1038/s41467-023-38612-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 05/10/2023] [Indexed: 05/24/2023] Open
Abstract
Stony coral tissue loss disease (SCTLD), one of the most pervasive and virulent coral diseases on record, affects over 22 species of reef-building coral and is decimating reefs throughout the Caribbean. To understand how different coral species and their algal symbionts (family Symbiodiniaceae) respond to this disease, we examine the gene expression profiles of colonies of five species of coral from a SCTLD transmission experiment. The included species vary in their purported susceptibilities to SCTLD, and we use this to inform gene expression analyses of both the coral animal and their Symbiodiniaceae. We identify orthologous coral genes exhibiting lineage-specific differences in expression that correlate to disease susceptibility, as well as genes that are differentially expressed in all coral species in response to SCTLD infection. We find that SCTLD infection induces increased expression of rab7, an established marker of in situ degradation of dysfunctional Symbiodiniaceae, in all coral species accompanied by genus-level shifts in Symbiodiniaceae photosystem and metabolism gene expression. Overall, our results indicate that SCTLD infection induces symbiophagy across coral species and that the severity of disease is influenced by Symbiodiniaceae identity.
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Affiliation(s)
- Kelsey M Beavers
- Biology Department, University of Texas at Arlington, Arlington, TX, USA
| | - Emily W Van Buren
- Biology Department, University of Texas at Arlington, Arlington, TX, USA
| | - Ashley M Rossin
- Department of Oceanography and Coastal Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Madison A Emery
- Biology Department, University of Texas at Arlington, Arlington, TX, USA
| | - Alex J Veglia
- Department of BioSciences, Rice University, Houston, TX, USA
| | - Carly E Karrick
- Department of BioSciences, Rice University, Houston, TX, USA
| | | | - Bradford A Dimos
- Biology Department, University of Texas at Arlington, Arlington, TX, USA
| | - Sonora S Meiling
- Center for Marine and Environmental Studies, University of the Virgin Islands, St. Thomas, USVI, USA
| | - Tyler B Smith
- Center for Marine and Environmental Studies, University of the Virgin Islands, St. Thomas, USVI, USA
| | - Amy Apprill
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | | | - Daniel M Holstein
- Department of Oceanography and Coastal Sciences, Louisiana State University, Baton Rouge, LA, USA
| | | | - Marilyn E Brandt
- Center for Marine and Environmental Studies, University of the Virgin Islands, St. Thomas, USVI, USA
| | - Laura D Mydlarz
- Biology Department, University of Texas at Arlington, Arlington, TX, USA.
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4
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Ashley IA, Kitchen SA, Gorman LM, Grossman AR, Oakley CA, Suggett DJ, Weis VM, Rosset SL, Davy SK. Genomic conservation and putative downstream functionality of the phosphatidylinositol signalling pathway in the cnidarian-dinoflagellate symbiosis. Front Microbiol 2023; 13:1094255. [PMID: 36777026 PMCID: PMC9909359 DOI: 10.3389/fmicb.2022.1094255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 12/28/2022] [Indexed: 01/28/2023] Open
Abstract
The mutualistic cnidarian-dinoflagellate symbiosis underpins the evolutionary success of stony corals and the persistence of coral reefs. However, a molecular understanding of the signalling events that lead to the successful establishment and maintenance of this symbiosis remains unresolved. For example, the phosphatidylinositol (PI) signalling pathway has been implicated during the establishment of multiple mutualistic and parasitic interactions across the kingdoms of life, yet its role within the cnidarian-dinoflagellate symbiosis remains unexplored. Here, we aimed to confirm the presence and assess the specific enzymatic composition of the PI signalling pathway across cnidaria and dinoflagellates by compiling 21 symbiotic anthozoan (corals and sea anemones) and 28 symbiotic dinoflagellate (Symbiodiniaceae) transcriptomic and genomic datasets and querying genes related to this pathway. Presence or absence of PI-kinase and PI-phosphatase orthologs were also compared between a broad sampling of taxonomically related symbiotic and non-symbiotic species. Across the symbiotic anthozoans analysed, there was a complete and highly conserved PI pathway, analogous to the pathway found in model eukaryotes. The Symbiodiniaceae pathway showed similarities to its sister taxon, the Apicomplexa, with the absence of PI 4-phosphatases. However, conversely to Apicomplexa, there was also an expansion of homologs present in the PI5-phosphatase and PI5-kinase groups, with unique Symbiodiniaceae proteins identified that are unknown from non-symbiotic unicellular organisms. Additionally, we aimed to unravel the putative functionalities of the PI signalling pathway in this symbiosis by analysing phosphoinositide (PIP)-binding proteins. Analysis of phosphoinositide (PIP)-binding proteins showed that, on average, 2.23 and 1.29% of the total assemblies of anthozoan and Symbiodiniaceae, respectively, have the potential to bind to PIPs. Enrichment of Gene Ontology (GO) terms associated with predicted PIP-binding proteins within each taxon revealed a broad range of functions, including compelling links to processes putatively involved in symbiosis regulation. This analysis establishes a baseline for current understanding of the PI pathway across anthozoans and Symbiodiniaceae, and thus a framework to target future research.
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Affiliation(s)
- Immy A. Ashley
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Sheila A. Kitchen
- Department of Marine Biology, Texas A&M University at Galveston, Galveston, TX, United States
| | - Lucy M. Gorman
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Arthur R. Grossman
- Department of Plant Biology, The Carnegie Institution, Stanford, CA, United States
| | - Clinton A. Oakley
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - David J. Suggett
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Broadway, NSW, Australia
| | - Virginia M. Weis
- Department of Integrative Biology, Oregon State University, Corvallis, OR, United States
| | - Sabrina L. Rosset
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Simon K. Davy
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand,*Correspondence: Simon K. Davy,
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Mashini AG, Oakley CA, Beepat SS, Peng L, Grossman AR, Weis VM, Davy SK. The Influence of Symbiosis on the Proteome of the Exaiptasia Endosymbiont Breviolum minutum. Microorganisms 2023; 11:292. [PMID: 36838257 PMCID: PMC9967746 DOI: 10.3390/microorganisms11020292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/13/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023] Open
Abstract
The cellular mechanisms responsible for the regulation of nutrient exchange, immune response, and symbiont population growth in the cnidarian-dinoflagellate symbiosis are poorly resolved. Here, we employed liquid chromatography-mass spectrometry to elucidate proteomic changes associated with symbiosis in Breviolum minutum, a native symbiont of the sea anemone Exaiptasia diaphana ('Aiptasia'). We manipulated nutrients available to the algae in culture and to the holobiont in hospite (i.e., in symbiosis) and then monitored the impacts of our treatments on host-endosymbiont interactions. Both the symbiotic and nutritional states had significant impacts on the B. minutum proteome. B. minutum in hospite showed an increased abundance of proteins involved in phosphoinositol metabolism (e.g., glycerophosphoinositol permease 1 and phosphatidylinositol phosphatase) relative to the free-living alga, potentially reflecting inter-partner signalling that promotes the stability of the symbiosis. Proteins potentially involved in concentrating and fixing inorganic carbon (e.g., carbonic anhydrase, V-type ATPase) and in the assimilation of nitrogen (e.g., glutamine synthase) were more abundant in free-living B. minutum than in hospite, possibly due to host-facilitated access to inorganic carbon and nitrogen limitation by the host when in hospite. Photosystem proteins increased in abundance at high nutrient levels irrespective of the symbiotic state, as did proteins involved in antioxidant defences (e.g., superoxide dismutase, glutathione s-transferase). Proteins involved in iron metabolism were also affected by the nutritional state, with an increased iron demand and uptake under low nutrient treatments. These results detail the changes in symbiont physiology in response to the host microenvironment and nutrient availability and indicate potential symbiont-driven mechanisms that regulate the cnidarian-dinoflagellate symbiosis.
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Affiliation(s)
| | - Clinton A. Oakley
- School of Biological Sciences, Victoria University of Wellington, Wellington 6140, New Zealand
| | - Sandeep S. Beepat
- School of Biological Sciences, Victoria University of Wellington, Wellington 6140, New Zealand
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Lifeng Peng
- School of Biological Sciences, Victoria University of Wellington, Wellington 6140, New Zealand
- Centre for Biodiscovery, Victoria University of Wellington, Wellington 6140, New Zealand
| | - Arthur R. Grossman
- Department of Plant Biology, The Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Virginia M. Weis
- Department of Integrative Biology, Oregon State University, Corvallis, OR 97331, USA
| | - Simon K. Davy
- School of Biological Sciences, Victoria University of Wellington, Wellington 6140, New Zealand
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6
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Davies SW, Gamache MH, Howe-Kerr LI, Kriefall NG, Baker AC, Banaszak AT, Bay LK, Bellantuono AJ, Bhattacharya D, Chan CX, Claar DC, Coffroth MA, Cunning R, Davy SK, del Campo J, Díaz-Almeyda EM, Frommlet JC, Fuess LE, González-Pech RA, Goulet TL, Hoadley KD, Howells EJ, Hume BCC, Kemp DW, Kenkel CD, Kitchen SA, LaJeunesse TC, Lin S, McIlroy SE, McMinds R, Nitschke MR, Oakley CA, Peixoto RS, Prada C, Putnam HM, Quigley K, Reich HG, Reimer JD, Rodriguez-Lanetty M, Rosales SM, Saad OS, Sampayo EM, Santos SR, Shoguchi E, Smith EG, Stat M, Stephens TG, Strader ME, Suggett DJ, Swain TD, Tran C, Traylor-Knowles N, Voolstra CR, Warner ME, Weis VM, Wright RM, Xiang T, Yamashita H, Ziegler M, Correa AMS, Parkinson JE. Building consensus around the assessment and interpretation of Symbiodiniaceae diversity. PeerJ 2023; 11:e15023. [PMID: 37151292 PMCID: PMC10162043 DOI: 10.7717/peerj.15023] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 02/17/2023] [Indexed: 05/09/2023] Open
Abstract
Within microeukaryotes, genetic variation and functional variation sometimes accumulate more quickly than morphological differences. To understand the evolutionary history and ecology of such lineages, it is key to examine diversity at multiple levels of organization. In the dinoflagellate family Symbiodiniaceae, which can form endosymbioses with cnidarians (e.g., corals, octocorals, sea anemones, jellyfish), other marine invertebrates (e.g., sponges, molluscs, flatworms), and protists (e.g., foraminifera), molecular data have been used extensively over the past three decades to describe phenotypes and to make evolutionary and ecological inferences. Despite advances in Symbiodiniaceae genomics, a lack of consensus among researchers with respect to interpreting genetic data has slowed progress in the field and acted as a barrier to reconciling observations. Here, we identify key challenges regarding the assessment and interpretation of Symbiodiniaceae genetic diversity across three levels: species, populations, and communities. We summarize areas of agreement and highlight techniques and approaches that are broadly accepted. In areas where debate remains, we identify unresolved issues and discuss technologies and approaches that can help to fill knowledge gaps related to genetic and phenotypic diversity. We also discuss ways to stimulate progress, in particular by fostering a more inclusive and collaborative research community. We hope that this perspective will inspire and accelerate coral reef science by serving as a resource to those designing experiments, publishing research, and applying for funding related to Symbiodiniaceae and their symbiotic partnerships.
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Affiliation(s)
- Sarah W. Davies
- Department of Biology, Boston University, Boston, MA, United States
| | - Matthew H. Gamache
- Department of Integrative Biology, University of South Florida, Tampa, FL, United States
| | | | | | - Andrew C. Baker
- Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL, United States
| | - Anastazia T. Banaszak
- Unidad Académica de Sistemas Arrecifales, Universidad Nacional Autónoma de México, Puerto Morelos, Mexico
| | - Line Kolind Bay
- Australian Institute of Marine Science, Townsville, Australia
| | - Anthony J. Bellantuono
- Department of Biological Sciences, Florida International University, Miami, FL, United States
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, United States
| | - Cheong Xin Chan
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Danielle C. Claar
- Nearshore Habitat Program, Washington State Department of Natural Resources, Olympia, WA, USA
| | | | - Ross Cunning
- Daniel P. Haerther Center for Conservation and Research, John G. Shedd Aquarium, Chicago, IL, United States
| | - Simon K. Davy
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Javier del Campo
- Institut de Biologia Evolutiva (CSIC - Universitat Pompeu Fabra), Barcelona, Catalonia, Spain
| | | | - Jörg C. Frommlet
- Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
| | - Lauren E. Fuess
- Department of Biology, Texas State University, San Marcos, TX, United States
| | - Raúl A. González-Pech
- Department of Integrative Biology, University of South Florida, Tampa, FL, United States
- Department of Biology, Pennsylvania State University, State College, PA, United States
| | - Tamar L. Goulet
- Department of Biology, University of Mississippi, University, MS, United States
| | - Kenneth D. Hoadley
- Department of Biological Sciences, University of Alabama—Tuscaloosa, Tuscaloosa, AL, United States
| | - Emily J. Howells
- National Marine Science Centre, Faculty of Science and Engineering, Southern Cross University, Coffs Harbour, NSW, Australia
| | | | - Dustin W. Kemp
- Department of Biology, University of Alabama—Birmingham, Birmingham, Al, United States
| | - Carly D. Kenkel
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Sheila A. Kitchen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
| | - Todd C. LaJeunesse
- Department of Biology, Pennsylvania State University, University Park, PA, United States
| | - Senjie Lin
- Department of Marine Sciences, University of Connecticut, Mansfield, CT, United States
| | - Shelby E. McIlroy
- Swire Institute of Marine Science, School of Biological Sciences, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Ryan McMinds
- Center for Global Health and Infectious Disease Research, University of South Florida, Tampa, FL, United States
| | | | - Clinton A. Oakley
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Raquel S. Peixoto
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Carlos Prada
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, United States
| | - Hollie M. Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, United States
| | | | - Hannah G. Reich
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, United States
| | - James Davis Reimer
- Department of Biology, Chemistry and Marine Sciences, Faculty of Science, University of the Ryukyus, Nishihara, Okinawa, Japan
| | | | - Stephanie M. Rosales
- The Cooperative Institute For Marine and Atmospheric Studies, Miami, FL, United States
| | - Osama S. Saad
- Department of Biological Oceanography, Red Sea University, Port-Sudan, Sudan
| | - Eugenia M. Sampayo
- School of Biological Sciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Scott R. Santos
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, United States
| | - Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Edward G. Smith
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Michael Stat
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, Australia
| | - Timothy G. Stephens
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, United States
| | - Marie E. Strader
- Department of Biology, Texas A&M University, College Station, TX, United States
| | - David J. Suggett
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Timothy D. Swain
- Department of Marine and Environmental Science, Nova Southeastern University, Dania Beach, FL, United States
| | - Cawa Tran
- Department of Biology, University of San Diego, San Diego, CA, United States
| | - Nikki Traylor-Knowles
- Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL, United States
| | | | - Mark E. Warner
- School of Marine Science and Policy, University of Delaware, Lewes, DE, United States
| | - Virginia M. Weis
- Department of Integrative Biology, Oregon State University, Corvallis, OR, United States
| | - Rachel M. Wright
- Department of Biological Sciences, Southern Methodist University, Dallas, TX, United States
| | - Tingting Xiang
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Hiroshi Yamashita
- Fisheries Technology Institute, Japan Fisheries Research and Education Agency, Ishigaki, Okinawa, Japan
| | - Maren Ziegler
- Department of Animal Ecology & Systematics, Justus Liebig University Giessen (Germany), Giessen, Germany
| | | | - John Everett Parkinson
- Department of Integrative Biology, University of South Florida, Tampa, FL, United States
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7
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Immunolocalization of Metabolite Transporter Proteins in a Model Cnidarian-Dinoflagellate Symbiosis. Appl Environ Microbiol 2022; 88:e0041222. [PMID: 35678605 DOI: 10.1128/aem.00412-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bidirectional nutrient flow between partners is integral to the cnidarian-dinoflagellate endosymbiosis. However, our current knowledge of the transporter proteins that regulate nutrient and metabolite trafficking is nascent. Four transmembrane transporters that likely play an important role in interpartner nitrogen and carbon exchange were investigated with immunocytochemistry in the model sea anemone Exaiptasia diaphana ("Aiptasia"; strain NZ1): ammonium transporter 1 (AMT1), V-type proton ATPase (VHA), facilitated glucose transporter member 8 (GLUT8), and aquaporin-3 (AQP3). Anemones lacking symbionts were compared with those in symbiosis with either their typical, homologous dinoflagellate symbiont, Breviolum minutum, or the heterologous species, Durusdinium trenchii and Symbiodinium microadriaticum. AMT1 and VHA were only detected in symbiotic Aiptasia, irrespective of symbiont type. However, GLUT8 and AQP3 were detected in both symbiotic and aposymbiotic states. All transporters were localized to both the epidermis and gastrodermis, though localization patterns in host tissues were heavily influenced by symbiont identity, with S. microadriaticum-colonized anemones showing the most distinct patterns. These patterns suggested disruption of fixed carbon and inorganic nitrogen fluxes when in symbiosis with heterologous versus homologous symbionts. This study enhances our understanding of nutrient transport and host-symbiont integration, while providing a platform for further investigation of nutrient transporters and the host-symbiont interface in the cnidarian-dinoflagellate symbiosis. IMPORTANCE Coral reefs are in serious decline, in particular due to the thermally induced dysfunction of the cnidarian-dinoflagellate symbiosis that underlies their success. Yet our ability to react to this crisis is hindered by limited knowledge of how this symbiosis functions. Indeed, we still have much to learn about the cellular integration that determines whether a particular host-symbiont combination can persist, and hence whether corals might be able to adapt by acquiring new, more thermally resistant symbionts. Here, we employed immunocytochemistry to localize and quantify key nutrient transporters in tissues of the sea anemone Aiptasia, a globally adopted model system for this symbiosis, and compared the expression of these transporters when the host is colonized by native versus nonnative symbionts. We showed a clear link between transporter expression and symbiont identity, elucidating the cellular events that dictate symbiosis success, and we provide a methodological platform for further examination of cellular integration in this ecologically important symbiosis.
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Dimos B, Emery M, Beavers K, MacKnight N, Brandt M, Demuth J, Mydlarz L. Adaptive Variation in Homolog Number Within Transcript Families Promotes Expression Divergence in Reef-Building Coral. Mol Ecol 2022; 31:2594-2610. [PMID: 35229964 DOI: 10.1111/mec.16414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 02/10/2022] [Accepted: 02/22/2022] [Indexed: 11/30/2022]
Abstract
Gene expression, especially in multi-species experiments, is used to gain insight into the genetic basis of how organisms adapt and respond to changing environments. However, evolutionary processes which can influence gene expression patterns between species such as the presence of paralogs which arise from gene duplication events are rarely accounted for. Paralogous transcripts can alter the transcriptional output of a gene and thus exclusion of these transcripts can obscure important biological differences between species. To address this issue, we investigated how differences in transcript family size is associated with divergent gene expression patterns in five species of Caribbean reef-building corals. We demonstrate that transcript families that are rapidly evolving in terms of size have increased levels of expression divergence. Additionally, these rapidly evolving transcript families are enriched for multiple biological processes, with genes involved in the coral innate immune system demonstrating pronounced variation in homolog number between species. Overall, this investigation demonstrates the importance of incorporating paralogous transcripts when comparing gene expression across species by influencing both transcriptional output and the number of transcripts within biological processes. As this investigation was based on transcriptome assemblies, additional insights into the relationship between gene duplications and expression patterns will likely emergence once more genome assemblies are available for study.
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Affiliation(s)
- Bradford Dimos
- Department of Biology, University of Texas at Arlington, Arlington, TX, 76019, USA
| | - Madison Emery
- Department of Biology, University of Texas at Arlington, Arlington, TX, 76019, USA
| | - Kelsey Beavers
- Department of Biology, University of Texas at Arlington, Arlington, TX, 76019, USA
| | - Nicholas MacKnight
- Department of Biology, University of Texas at Arlington, Arlington, TX, 76019, USA
| | - Marilyn Brandt
- Center for Marine and Environmental Studies, University of the Virgin Islands, St. Thomas, US Virgin Islands, 00802, USA
| | - Jeffery Demuth
- Department of Biology, University of Texas at Arlington, Arlington, TX, 76019, USA
| | - Laura Mydlarz
- Department of Biology, University of Texas at Arlington, Arlington, TX, 76019, USA
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9
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Alphaflexivirus Genomes in Stony Coral Tissue Loss Disease-Affected, Disease-Exposed, and Disease-Unexposed Coral Colonies in the U.S. Virgin Islands. Microbiol Resour Announc 2022; 11:e0119921. [PMID: 35175123 PMCID: PMC8852308 DOI: 10.1128/mra.01199-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Stony coral tissue loss disease (SCTLD) is decimating Caribbean corals. Here, through the metatranscriptomic assembly and annotation of two alphaflexivirus-like strains, we provide genomic evidence of filamentous viruses in SCTLD-affected, -exposed, and -unexposed coral colonies. These data will assist in clarifying the roles of viruses in SCTLD.
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10
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Avila-Magaña V, Kamel B, DeSalvo M, Gómez-Campo K, Enríquez S, Kitano H, Rohlfs RV, Iglesias-Prieto R, Medina M. Elucidating gene expression adaptation of phylogenetically divergent coral holobionts under heat stress. Nat Commun 2021; 12:5731. [PMID: 34593802 PMCID: PMC8484447 DOI: 10.1038/s41467-021-25950-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 09/01/2021] [Indexed: 02/08/2023] Open
Abstract
As coral reefs struggle to survive under climate change, it is crucial to know whether they have the capacity to withstand changing conditions, particularly increasing seawater temperatures. Thermal tolerance requires the integrative response of the different components of the coral holobiont (coral host, algal photosymbiont, and associated microbiome). Here, using a controlled thermal stress experiment across three divergent Caribbean coral species, we attempt to dissect holobiont member metatranscriptome responses from coral taxa with different sensitivities to heat stress and use phylogenetic ANOVA to study the evolution of gene expression adaptation. We show that coral response to heat stress is a complex trait derived from multiple interactions among holobiont members. We identify host and photosymbiont genes that exhibit lineage-specific expression level adaptation and uncover potential roles for bacterial associates in supplementing the metabolic needs of the coral-photosymbiont duo during heat stress. Our results stress the importance of integrative and comparative approaches across a wide range of species to better understand coral survival under the predicted rise in sea surface temperatures.
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Affiliation(s)
- Viridiana Avila-Magaña
- grid.29857.310000 0001 2097 4281Biology Department, The Pennsylvania State University, University Park, PA USA ,grid.266190.a0000000096214564Ecology and Evolutionary Biology Department, University of Colorado Boulder, Boulder, CO USA
| | - Bishoy Kamel
- grid.266832.b0000 0001 2188 8502Center for Evolutionary and Theoretical Immunology, University of New Mexico, Albuquerque, NM USA ,grid.184769.50000 0001 2231 4551Present Address: US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Michael DeSalvo
- grid.266096.d0000 0001 0049 1282School of Natural Sciences, University of California, Merced, CA USA ,grid.418190.50000 0001 2187 0556Thermo Fisher Scientific, Carlsbad, CA USA
| | - Kelly Gómez-Campo
- grid.29857.310000 0001 2097 4281Biology Department, The Pennsylvania State University, University Park, PA USA
| | - Susana Enríquez
- grid.9486.30000 0001 2159 0001Unidad Académica de Sistemas Arrecifales Puerto Morelos, ICMyL, Universidad Nacional Autónoma de México, Cancún, Mexico
| | - Hiroaki Kitano
- grid.452864.9The Systems Biology Institute, Tokyo, Japan ,grid.250464.10000 0000 9805 2626Okinawa Institute of Science and Technology, Okinawa, Japan
| | - Rori V. Rohlfs
- grid.263091.f0000000106792318Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Roberto Iglesias-Prieto
- grid.29857.310000 0001 2097 4281Biology Department, The Pennsylvania State University, University Park, PA USA
| | - Mónica Medina
- grid.29857.310000 0001 2097 4281Biology Department, The Pennsylvania State University, University Park, PA USA
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11
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Voolstra CR, Valenzuela JJ, Turkarslan S, Cárdenas A, Hume BCC, Perna G, Buitrago-López C, Rowe K, Orellana MV, Baliga NS, Paranjape S, Banc-Prandi G, Bellworthy J, Fine M, Frias-Torres S, Barshis DJ. Contrasting heat stress response patterns of coral holobionts across the Red Sea suggest distinct mechanisms of thermal tolerance. Mol Ecol 2021; 30:4466-4480. [PMID: 34342082 DOI: 10.1111/mec.16064] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 06/04/2021] [Accepted: 06/30/2021] [Indexed: 12/18/2022]
Abstract
Corals from the northern Red Sea, in particular the Gulf of Aqaba (GoA), have exceptionally high bleaching thresholds approaching >5℃ above their maximum monthly mean (MMM) temperatures. These elevated thresholds are thought to be due to historical selection, as corals passed through the warmer Southern Red Sea during recolonization from the Arabian Sea. To test this hypothesis, we determined thermal tolerance thresholds of GoA versus central Red Sea (CRS) Stylophora pistillata corals using multi-temperature acute thermal stress assays to determine thermal thresholds. Relative thermal thresholds of GoA and CRS corals were indeed similar and exceptionally high (~7℃ above MMM). However, absolute thermal thresholds of CRS corals were on average 3℃ above those of GoA corals. To explore the molecular underpinnings, we determined gene expression and microbiome response of the coral holobiont. Transcriptomic responses differed markedly, with a strong response to the thermal stress in GoA corals and their symbiotic algae versus a remarkably muted response in CRS colonies. Concomitant to this, coral and algal genes showed temperature-induced expression in GoA corals, while exhibiting fixed high expression (front-loading) in CRS corals. Bacterial community composition of GoA corals changed dramatically under heat stress, whereas CRS corals displayed stable assemblages. We interpret the response of GoA corals as that of a resilient population approaching a tipping point in contrast to a pattern of consistently elevated thermal resistance in CRS corals that cannot further attune. Such response differences suggest distinct thermal tolerance mechanisms that may affect the response of coral populations to ocean warming.
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Affiliation(s)
| | | | | | - Anny Cárdenas
- Department of Biology, University of Konstanz, Konstanz, Germany
| | | | - Gabriela Perna
- Department of Biology, University of Konstanz, Konstanz, Germany
| | | | - Katherine Rowe
- School of Science, The University of Waikato, Hamilton, New Zealand
| | - Monica V Orellana
- Institute for Systems Biology, Seattle, USA.,Polar Science Center, University of Washington, Seattle, USA
| | - Nitin S Baliga
- Institute for Systems Biology, Seattle, USA.,Departments of Biology and Microbiology, University of Washington, Seattle, USA.,Molecular and Cellular Biology Program, University of Washington, Seattle, USA.,Lawrence Berkeley National Laboratory, Berkeley, USA
| | | | - Guilhem Banc-Prandi
- The Interuniversity Institute for Marine Sciences (IUI), Eilat, Israel.,The Goodman Faculty of Life Sciences, Bar Ilan University, Ramat-Gan, Israel
| | - Jessica Bellworthy
- The Interuniversity Institute for Marine Sciences (IUI), Eilat, Israel.,The Goodman Faculty of Life Sciences, Bar Ilan University, Ramat-Gan, Israel
| | - Maoz Fine
- The Interuniversity Institute for Marine Sciences (IUI), Eilat, Israel.,The Goodman Faculty of Life Sciences, Bar Ilan University, Ramat-Gan, Israel
| | | | - Daniel J Barshis
- Department of Biological Sciences, Old Dominion University, Norfolk, USA
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12
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Levy S, Elek A, Grau-Bové X, Menéndez-Bravo S, Iglesias M, Tanay A, Mass T, Sebé-Pedrós A. A stony coral cell atlas illuminates the molecular and cellular basis of coral symbiosis, calcification, and immunity. Cell 2021; 184:2973-2987.e18. [PMID: 33945788 PMCID: PMC8162421 DOI: 10.1016/j.cell.2021.04.005] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/24/2021] [Accepted: 04/05/2021] [Indexed: 02/06/2023]
Abstract
Stony corals are colonial cnidarians that sustain the most biodiverse marine ecosystems on Earth: coral reefs. Despite their ecological importance, little is known about the cell types and molecular pathways that underpin the biology of reef-building corals. Using single-cell RNA sequencing, we define over 40 cell types across the life cycle of Stylophora pistillata. We discover specialized immune cells, and we uncover the developmental gene expression dynamics of calcium-carbonate skeleton formation. By simultaneously measuring the transcriptomes of coral cells and the algae within them, we characterize the metabolic programs involved in symbiosis in both partners. We also trace the evolution of these coral cell specializations by phylogenetic integration of multiple cnidarian cell type atlases. Overall, this study reveals the molecular and cellular basis of stony coral biology.
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Affiliation(s)
- Shani Levy
- Department of Marine Biology, The Leon H. Charney School of Marine Sciences, University of Haifa, Mt. Carmel, Haifa 3498838, Israel; Morris Kahn Marine Research Station, The Leon H. Charney School of Marine Sciences, University of Haifa, Sdot Yam, Israel
| | - Anamaria Elek
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Xavier Grau-Bové
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Simón Menéndez-Bravo
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Marta Iglesias
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Amos Tanay
- Department of Computer Science and Applied Mathematics and Department of Biological Regulation, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Tali Mass
- Department of Marine Biology, The Leon H. Charney School of Marine Sciences, University of Haifa, Mt. Carmel, Haifa 3498838, Israel; Morris Kahn Marine Research Station, The Leon H. Charney School of Marine Sciences, University of Haifa, Sdot Yam, Israel.
| | - Arnau Sebé-Pedrós
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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13
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Iha C, Dougan KE, Varela JA, Avila V, Jackson CJ, Bogaert KA, Chen Y, Judd LM, Wick R, Holt KE, Pasella MM, Ricci F, Repetti SI, Medina M, Marcelino VR, Chan CX, Verbruggen H. Genomic adaptations to an endolithic lifestyle in the coral-associated alga Ostreobium. Curr Biol 2021; 31:1393-1402.e5. [PMID: 33548192 DOI: 10.1016/j.cub.2021.01.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 11/21/2020] [Accepted: 01/07/2021] [Indexed: 02/06/2023]
Abstract
The green alga Ostreobium is an important coral holobiont member, playing key roles in skeletal decalcification and providing photosynthate to bleached corals that have lost their dinoflagellate endosymbionts. Ostreobium lives in the coral's skeleton, a low-light environment with variable pH and O2 availability. We present the Ostreobium nuclear genome and a metatranscriptomic analysis of healthy and bleached corals to improve our understanding of Ostreobium's adaptations to its extreme environment and its roles as a coral holobiont member. The Ostreobium genome has 10,663 predicted protein-coding genes and shows adaptations for life in low and variable light conditions and other stressors in the endolithic environment. This alga presents a rich repertoire of light-harvesting complex proteins but lacks many genes for photoprotection and photoreceptors. It also has a large arsenal of genes for oxidative stress response. An expansion of extracellular peptidases suggests that Ostreobium may supplement its energy needs by feeding on the organic skeletal matrix, and a diverse set of fermentation pathways allows it to live in the anoxic skeleton at night. Ostreobium depends on other holobiont members for vitamin B12, and our metatranscriptomes identify potential bacterial sources. Metatranscriptomes showed Ostreobium becoming a dominant agent of photosynthesis in bleached corals and provided evidence for variable responses among coral samples and different Ostreobium genotypes. Our work provides a comprehensive understanding of the adaptations of Ostreobium to its extreme environment and an important genomic resource to improve our comprehension of coral holobiont resilience, bleaching, and recovery.
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Affiliation(s)
- Cintia Iha
- School of BioSciences, University of Melbourne, Melbourne, VIC 3010, Australia.
| | - Katherine E Dougan
- School of Chemistry and Molecular Biosciences and Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Javier A Varela
- School of Microbiology, Centre for Synthetic Biology and Biotechnology, Environmental Research Institute, and APC Microbiome Institute, University College Cork, Cork T12 YN60, Ireland
| | - Viridiana Avila
- Pennsylvania State University, University Park, PA 16802, USA
| | | | - Kenny A Bogaert
- Phycology Research Group, Ghent University, Krijgslaan 281 S8, 9000 Gent, Belgium
| | - Yibi Chen
- School of Chemistry and Molecular Biosciences and Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Louise M Judd
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia
| | - Ryan Wick
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia
| | - Kathryn E Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia; London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK
| | - Marisa M Pasella
- School of BioSciences, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Francesco Ricci
- School of BioSciences, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Sonja I Repetti
- School of BioSciences, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Mónica Medina
- Pennsylvania State University, University Park, PA 16802, USA
| | - Vanessa R Marcelino
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia
| | - Cheong Xin Chan
- School of Chemistry and Molecular Biosciences and Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Melbourne, VIC 3010, Australia.
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14
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Metcalfe KS, Murali R, Mullin SW, Connon SA, Orphan VJ. Experimentally-validated correlation analysis reveals new anaerobic methane oxidation partnerships with consortium-level heterogeneity in diazotrophy. THE ISME JOURNAL 2021; 15:377-396. [PMID: 33060828 PMCID: PMC8027057 DOI: 10.1038/s41396-020-00757-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 07/28/2020] [Accepted: 08/21/2020] [Indexed: 02/08/2023]
Abstract
Archaeal anaerobic methanotrophs ("ANME") and sulfate-reducing Deltaproteobacteria ("SRB") form symbiotic multicellular consortia capable of anaerobic methane oxidation (AOM), and in so doing modulate methane flux from marine sediments. The specificity with which ANME associate with particular SRB partners in situ, however, is poorly understood. To characterize partnership specificity in ANME-SRB consortia, we applied the correlation inference technique SparCC to 310 16S rRNA amplicon libraries prepared from Costa Rica seep sediment samples, uncovering a strong positive correlation between ANME-2b and members of a clade of Deltaproteobacteria we termed SEEP-SRB1g. We confirmed this association by examining 16S rRNA diversity in individual ANME-SRB consortia sorted using flow cytometry and by imaging ANME-SRB consortia with fluorescence in situ hybridization (FISH) microscopy using newly-designed probes targeting the SEEP-SRB1g clade. Analysis of genome bins belonging to SEEP-SRB1g revealed the presence of a complete nifHDK operon required for diazotrophy, unusual in published genomes of ANME-associated SRB. Active expression of nifH in SEEP-SRB1g within ANME-2b-SEEP-SRB1g consortia was then demonstrated by microscopy using hybridization chain reaction (HCR-) FISH targeting nifH transcripts and diazotrophic activity was documented by FISH-nanoSIMS experiments. NanoSIMS analysis of ANME-2b-SEEP-SRB1g consortia incubated with a headspace containing CH4 and 15N2 revealed differences in cellular 15N-enrichment between the two partners that varied between individual consortia, with SEEP-SRB1g cells enriched in 15N relative to ANME-2b in one consortium and the opposite pattern observed in others, indicating both ANME-2b and SEEP-SRB1g are capable of nitrogen fixation, but with consortium-specific variation in whether the archaea or bacterial partner is the dominant diazotroph.
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Affiliation(s)
- Kyle S Metcalfe
- Division of Geological and Planetary Sciences, California Institute of Technology, 1200 E California Blvd, Mail Code 170-25, Pasadena, CA, 91125, USA.
| | - Ranjani Murali
- Division of Geological and Planetary Sciences, California Institute of Technology, 1200 E California Blvd, Mail Code 170-25, Pasadena, CA, 91125, USA
| | - Sean W Mullin
- Division of Geological and Planetary Sciences, California Institute of Technology, 1200 E California Blvd, Mail Code 170-25, Pasadena, CA, 91125, USA
| | - Stephanie A Connon
- Division of Geological and Planetary Sciences, California Institute of Technology, 1200 E California Blvd, Mail Code 170-25, Pasadena, CA, 91125, USA
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, 1200 E California Blvd, Mail Code 170-25, Pasadena, CA, 91125, USA.
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15
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Kirk AL, Clowez S, Lin F, Grossman AR, Xiang T. Transcriptome Reprogramming of Symbiodiniaceae Breviolum minutum in Response to Casein Amino Acids Supplementation. Front Physiol 2020; 11:574654. [PMID: 33329024 PMCID: PMC7710908 DOI: 10.3389/fphys.2020.574654] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 09/18/2020] [Indexed: 01/08/2023] Open
Abstract
Dinoflagellates in the family Symbiodiniaceae can live freely in ocean waters or form a symbiosis with a variety of cnidarians including corals, sea anemones, and jellyfish. Trophic plasticity of Symbiodiniaceae is critical to its ecological success as it moves between environments. However, the molecular mechanisms underlying these trophic shifts in Symbiodiniaceae are still largely unknown. Using Breviolum minutum strain SSB01 (designated SSB01) as a model, we showed that Symbiodiniaceae go through a physiological and transcriptome reprogramming when the alga is grown with the organic nitrogen containing nutrients in hydrolyzed casein, but not with inorganic nutrients. SSB01 grows at a much faster rate and maintains stable photosynthetic efficiency when supplemented with casein amino acids compared to only inorganic nutrients or seawater. These physiological changes are driven by massive transcriptome changes in SSB01 supplemented with casein amino acids. The levels of transcripts encoding proteins involved in altering DNA conformation such as DNA topoisomerases, histones, and chromosome structural components were all significantly changed. Functional enrichment analysis also revealed processes involved in translation, ion transport, generation of second messengers, and phosphorylation. The physiological and molecular changes that underlie in vitro trophic transitions in Symbiodiniaceae can serve as an orthogonal platform to further understand the factors that impact the Symbiodiniaceae lifestyle.
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Affiliation(s)
- Andrea L. Kirk
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, NC, United States
| | - Sophie Clowez
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, United States
| | - Fan Lin
- Brightseed Inc., San Francisco, CA, United States
| | - Arthur R. Grossman
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, United States
| | - Tingting Xiang
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, NC, United States
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16
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Davies SW, Moreland KN, Wham DC, Kanke MR, Matz MV. Cladocopium community divergence in two Acropora coral hosts across multiple spatial scales. Mol Ecol 2020; 29:4559-4572. [PMID: 33002237 DOI: 10.1111/mec.15668] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 09/14/2020] [Accepted: 09/18/2020] [Indexed: 12/11/2022]
Abstract
Many broadly-dispersing corals acquire their algal symbionts (Symbiodiniaceae) "horizontally" from their environment upon recruitment. Horizontal transmission could promote coral fitness across diverse environments provided that corals can associate with divergent algae across their range and that these symbionts exhibit reduced dispersal potential. Here we quantified community divergence of Cladocopium algal symbionts in two coral host species (Acropora hyacinthus, Acropora digitifera) across two spatial scales (reefs on the same island, and between islands) across the Micronesian archipelago using microsatellites. We find that both hosts associated with a variety of multilocus genotypes (MLG) within two genetically distinct Cladocopium lineages (C40, C21), confirming that Acropora coral hosts associate with a range of Cladocopium symbionts across this region. Both C40 and C21 included multiple asexual lineages bearing identical MLGs, many of which spanned host species, reef sites within islands, and even different islands. Both C40 and C21 exhibited moderate host specialization and divergence across islands. In addition, within every island, algal symbiont communities were significantly clustered by both host species and reef site, highlighting that coral-associated Cladocopium communities are structured across small spatial scales and within hosts on the same reef. This is in stark contrast to their coral hosts, which never exhibited significant genetic divergence between reefs on the same island. These results support the view that horizontal transmission could improve local fitness for broadly dispersing Acropora coral species.
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Affiliation(s)
- Sarah W Davies
- Department of Biology, Boston University, Boston, MA, USA.,Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Kelsey N Moreland
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Drew C Wham
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Matt R Kanke
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Mikhail V Matz
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
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17
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Sex in Symbiodiniaceae dinoflagellates: genomic evidence for independent loss of the canonical synaptonemal complex. Sci Rep 2020; 10:9792. [PMID: 32555361 PMCID: PMC7299967 DOI: 10.1038/s41598-020-66429-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 05/19/2020] [Indexed: 01/07/2023] Open
Abstract
Dinoflagellates of the Symbiodiniaceae family encompass diverse symbionts that are critical to corals and other species living in coral reefs. It is well known that sexual reproduction enhances adaptive evolution in changing environments. Although genes related to meiotic functions were reported in Symbiodiniaceae, cytological evidence of meiosis and fertilisation are however yet to be observed in these taxa. Using transcriptome and genome data from 21 Symbiodiniaceae isolates, we studied genes that encode proteins associated with distinct stages of meiosis and syngamy. We report the absence of genes that encode main components of the synaptonemal complex (SC), a protein structure that mediates homologous chromosomal pairing and class I crossovers. This result suggests an independent loss of canonical SCs in the alveolates, that also includes the SC-lacking ciliates. We hypothesise that this loss was due in part to permanently condensed chromosomes and repeat-rich sequences in Symbiodiniaceae (and other dinoflagellates) which favoured the SC-independent class II crossover pathway. Our results reveal novel insights into evolution of the meiotic molecular machinery in the ecologically important Symbiodiniaceae and in other eukaryotes.
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18
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Swain TD, Lax S, Backman V, Marcelino LA. Uncovering the role of Symbiodiniaceae assemblage composition and abundance in coral bleaching response by minimizing sampling and evolutionary biases. BMC Microbiol 2020; 20:124. [PMID: 32429833 PMCID: PMC7236918 DOI: 10.1186/s12866-020-01765-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 03/26/2020] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Biodiversity and productivity of coral-reef ecosystems depend upon reef-building corals and their associations with endosymbiotic Symbiodiniaceae, which offer diverse functional capabilities to their hosts. The number of unique symbiotic partners (richness) and relative abundances (evenness) have been hypothesized to affect host response to climate change induced thermal stress. Symbiodiniaceae assemblages with many unique phylotypes may provide greater physiological flexibility or form less stable symbioses; assemblages with low abundance phylotypes may allow corals to retain thermotolerant symbionts or represent associations with less-suitable symbionts. RESULTS Here we demonstrate that true richness of Symbiodiniaceae phylotype assemblages is generally not discoverable from direct enumeration of unique phylotypes in association records and that cross host-species comparisons are biased by sampling and evolutionary patterns among species. These biases can be minimized through rarefaction of richness (rarefied-richness) and evenness (Probability of Interspecific Encounter, PIE), and analyses that account for phylogenetic patterns. These standardized metrics were calculated for individual Symbiodiniaceae assemblages composed of 377 unique ITS2 phylotypes associated with 123 coral species. Rarefied-richness minimized correlations with sampling effort, while maintaining important underlying characteristics across host bathymetry and geography. Phylogenetic comparative methods reveal significant increases in coral bleaching and mortality associated with increasing Symbiodiniaceae assemblage richness and evenness at the level of host species. CONCLUSIONS These results indicate that the potential flexibility afforded by assemblages characterized by many phylotypes present at similar relative abundances does not result in decreased bleaching risk and point to the need to characterize the overall functional and genetic diversity of Symbiodiniaceae assemblages to quantify their effect on host fitness under climate change.
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Affiliation(s)
- Timothy D Swain
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, 60208, USA
- Integrative Research Center, Field Museum of Natural History, Chicago, IL, 60605, USA
- Department of Marine and Environmental Science, Nova Southeastern University, Dania Beach, FL, 33004, USA
| | - Simon Lax
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, 60637, USA
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Vadim Backman
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Luisa A Marcelino
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, 60208, USA.
- Integrative Research Center, Field Museum of Natural History, Chicago, IL, 60605, USA.
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19
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Chakravarti LJ, Buerger P, Levin RA, van Oppen MJH. Gene regulation underpinning increased thermal tolerance in a laboratory-evolved coral photosymbiont. Mol Ecol 2020; 29:1684-1703. [PMID: 32268445 DOI: 10.1111/mec.15432] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 03/07/2020] [Accepted: 03/16/2020] [Indexed: 12/12/2022]
Abstract
Small increases in ocean temperature can disrupt the obligate symbiosis between corals and dinoflagellate microalgae, resulting in coral bleaching. Little is known about the genes that drive the physiological and bleaching response of algal symbionts to elevated temperature. Moreover, many studies to-date have compared highly divergent strains, making it challenging to accredit specific genes to contrasting traits. Here, we compare transcriptional responses at ambient (27°C) and bleaching-relevant (31°C) temperatures in a monoclonal, wild-type (WT) strain of Symbiodiniaceae to those of a selected-strain (SS), derived from the same monoclonal culture and experimentally evolved to elevated temperature over 80 generations (2.5 years). Thousands of genes were differentially expressed at a log fold-change of >8 between the WT and SS over a 35 days temperature treatment period. At 31°C, WT cells exhibited a temporally unstable transcriptomic response upregulating genes involved in the universal stress response such as molecular chaperoning, protein repair, protein degradation and DNA repair. Comparatively, SS cells exhibited a temporally stable transcriptomic response and downregulated many stress response genes that were upregulated by the WT. Among the most highly upregulated genes in the SS at 31°C were algal transcription factors and a gene probably of bacterial origin that encodes a type II secretion system protein, suggesting interactions with bacteria may contribute to the increased thermal tolerance of the SS. Genes and functional pathways conferring thermal tolerance in the SS could be targeted in future genetic engineering experiments designed to develop thermally resilient algal symbionts for use in coral restoration and conservation.
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Affiliation(s)
- Leela J Chakravarti
- Australian Institute of Marine Science, Townsville MC, Qld, Australia.,AIMS@JCU, Australian Institute of Marine Science, College of Marine and Environmental Sciences, James Cook University, Townsville, Qld, Australia.,College of Marine and Environmental Sciences, James Cook University, Townsville, Qld, Australia.,Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, Australia
| | - Patrick Buerger
- CSIRO, Land & Water, Canberra, ACT, Australia.,School of BioSciences, University of Melbourne, Parkville, Vic, Australia
| | | | - Madeleine J H van Oppen
- Australian Institute of Marine Science, Townsville MC, Qld, Australia.,School of BioSciences, University of Melbourne, Parkville, Vic, Australia
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20
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Ren F, Yan DH, Wu G, Sun X, Song X, Li R. Distinctive Gene Expression Profiles and Effectors Consistent With Host Specificity in Two Formae Speciales of Marssonina brunnea. Front Microbiol 2020; 11:276. [PMID: 32210930 PMCID: PMC7076119 DOI: 10.3389/fmicb.2020.00276] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 02/06/2020] [Indexed: 11/13/2022] Open
Abstract
The knowledge on the host specificity of a pathogen underlying an interaction is becoming an urgent necessity for global warming. In this study, the gene expression profiles and the roles of effectors in host specificity were integrally characterized with two formae speciales, multigermtubi and monogermtubi, of a hemibiotrophic pathogen Marssonina brunnea when they were infecting respective susceptible poplar hosts. With a functional genome comparison referring to a de novo transcriptome of M. brunnea and Pathogen-Host Interaction database functional annotations, the multigermtubi strain showed abundant and significant differentially expressed unigenes (DEGs) (more than 40%) in colonizing the initial invasion stage and in the necrotrophic stage. The monogermtubi strain induced less than 10% of DEGs in the initial invasion stage but which abruptly increased to more than 80% DEGs in the necrotrophic stage. Both strains induced the least DEGs in the biotrophic stage compared to the initial invasion and necrotrophic stages. The orthologs of the effector genes Ecp6, PemG1, XEG1, ACE1, and Mg3LysM were exclusively induced by one of the two formae speciales depending on the infection stages. Some unigenes homologous to carbohydrate lytic enzyme genes, especially pectate lyases, were notably induced with multigermtubi forma specialis infection but not expressed in the monogermtubi forma specialis at an earlier infection stage. The extraordinary differences in the functional genome level between the two formae speciales of M. brunnea could be fundamental to exploring their host specificity determinant and evolution. This study also firstly provided the fungal transcriptome of the monogermtubi forma specialis for M. brunnea.
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Affiliation(s)
- Fei Ren
- Research Institute of Forest Ecology, Environment and Protection, Key Laboratory of Forest Protection Affiliated to State Forestry and Grassland Administration of China, Chinese Academy of Forestry, Beijing, China
- Institute of Cereal & Oil Science and Technology, Academy of National Food and Strategic Reserves Administration, Beijing, China
| | - Dong-Hui Yan
- Research Institute of Forest Ecology, Environment and Protection, Key Laboratory of Forest Protection Affiliated to State Forestry and Grassland Administration of China, Chinese Academy of Forestry, Beijing, China
| | - Guanghua Wu
- Research Institute of Forest Ecology, Environment and Protection, Key Laboratory of Forest Protection Affiliated to State Forestry and Grassland Administration of China, Chinese Academy of Forestry, Beijing, China
| | - Xiaoming Sun
- Research Institute of Forest Ecology, Environment and Protection, Key Laboratory of Forest Protection Affiliated to State Forestry and Grassland Administration of China, Chinese Academy of Forestry, Beijing, China
| | - Xiaoyu Song
- Research Institute of Forest Ecology, Environment and Protection, Key Laboratory of Forest Protection Affiliated to State Forestry and Grassland Administration of China, Chinese Academy of Forestry, Beijing, China
| | - Ruhua Li
- Research Institute of Forest Ecology, Environment and Protection, Key Laboratory of Forest Protection Affiliated to State Forestry and Grassland Administration of China, Chinese Academy of Forestry, Beijing, China
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21
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Li T, Lin X, Yu L, Lin S, Rodriguez IB, Ho TY. RNA-seq profiling of Fugacium kawagutii reveals strong responses in metabolic processes and symbiosis potential to deficiencies of iron and other trace metals. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 705:135767. [PMID: 31972930 DOI: 10.1016/j.scitotenv.2019.135767] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 10/09/2019] [Accepted: 11/24/2019] [Indexed: 06/10/2023]
Abstract
A healthy symbiotic relationship between corals and Symbiodiniaceae relies on suitable temperature and adequate nutrients including trace metals. Besides global warming, trace metal deficiency has been shown to cause coral bleaching, a phenomenon responsible for extensive coral reef degradation around the world. How trace metal deficiency impacts Symbiodiniaceae and coral symbiosis is poorly understood, however. In this study, we applied RNA-seq to investigate how Fugacium kawagutii responds to the deficiency of five trace metals (Fe2+, Zn2+, Cu2+, Mn2+, Ni2+). We identified 685 to 2805 differentially expressed genes (DEGs) from these trace metal deficiency conditions, among which 372 were commonly regulated by all the five trace metals and were significantly enriched in energy metabolism (e.g. fatty acid synthesis). Furthermore, genes associated with extracellular matrix (ECM), cell surface structure and cell adhesion were impacted, suggesting that the ability of recognition and adhesion of F. kawagutii may be altered by trace metal deficiencies. In addition, among the five metals, Fe2+ deficiency exhibited the strongest influence, with Fe-rich redox elements and many antioxidant synthesis genes being markedly down-regulated, indicative of adaptive reduction of Fe demand but a compromised ability to combat oxidative stress. Overall, deficiency of trace metals (especially Fe) seems to repress growth and ability of ROS scavenging, elevate energy metabolism and innate immunity, and alter cell adhesion capability, with implications in symbiosis disruption and coral bleaching.
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Affiliation(s)
- Tangcheng Li
- State Key Laboratory of Marine Environmental Science, Xiamen Key Laboratory of Urban Sea Ecological Conservation and Restoration (USER), Xiamen University, Xiamen 361000, Fujian,China
| | - Xin Lin
- State Key Laboratory of Marine Environmental Science, Xiamen Key Laboratory of Urban Sea Ecological Conservation and Restoration (USER), Xiamen University, Xiamen 361000, Fujian,China
| | - Liying Yu
- State Key Laboratory of Marine Environmental Science, Xiamen Key Laboratory of Urban Sea Ecological Conservation and Restoration (USER), Xiamen University, Xiamen 361000, Fujian,China
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science, Xiamen Key Laboratory of Urban Sea Ecological Conservation and Restoration (USER), Xiamen University, Xiamen 361000, Fujian,China; Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA.
| | - Irene B Rodriguez
- Research Center for Environmental Changes, Academia Sinica, Taipei, Taiwan; Institute of Oceanography, National Taiwan University, Taipei, Taiwan
| | - Tung-Yuan Ho
- Research Center for Environmental Changes, Academia Sinica, Taipei, Taiwan; Institute of Oceanography, National Taiwan University, Taipei, Taiwan
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22
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Insights on the genetic repertoire of the coral Mussismilia braziliensis endosymbiont Symbiodinium. Symbiosis 2020. [DOI: 10.1007/s13199-020-00664-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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23
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Yu L, Li T, Li L, Lin X, Li H, Liu C, Guo C, Lin S. SAGER: a database of Symbiodiniaceae and Algal Genomic Resource. Database (Oxford) 2020; 2020:baaa051. [PMID: 32621601 PMCID: PMC7334889 DOI: 10.1093/database/baaa051] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 06/05/2020] [Accepted: 06/05/2020] [Indexed: 11/19/2022]
Abstract
Symbiodiniaceae dinoflagellates are essential endosymbionts of reef building corals and some other invertebrates. Information of their genome structure and function is critical for understanding coral symbiosis and bleaching. With the rapid development of sequencing technology, genome draft assemblies of several Symbiodiniaceae species and diverse marine algal genomes have become publicly available but spread in multiple separate locations. Here, we present a Symbiodiniaceae and Algal Genomic Resource Database (SAGER), a user-friendly online repository for integrating existing genomic data of Symbiodiniaceae species and diverse marine algal gene sets from MMETSP and PhyloDB databases. Relevant algal data are included to facilitate comparative analyses. The database is freely accessible at http://sampgr.org.cn. It provides comprehensive tools for studying gene function, expression and comparative genomics, including search tools to identify gene information from Symbiodiniaceae species, and BLAST tool to find orthologs from marine algae and protists. Moreover, SAGER integrates transcriptome datasets derived from diverse culture conditions of corresponding Symbiodiniaceae species. SAGER was developed with the capacity to incorporate future Symbiodiniaceae and algal genome and transcriptome data, and will serve as an open-access and sustained platform providing genomic and molecular tools that can be conveniently used to study Symbiodiniaceae and other marine algae. Database URL: http://sampgr.org.cn.
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Affiliation(s)
- Liying Yu
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Tangcheng Li
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Ling Li
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Xin Lin
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Hongfei Li
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Chichi Liu
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Chentao Guo
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
- Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA
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24
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Cryptic ecological and geographic diversification in coral-associated nudibranchs. Mol Phylogenet Evol 2019; 144:106698. [PMID: 31812568 DOI: 10.1016/j.ympev.2019.106698] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 11/03/2019] [Accepted: 11/30/2019] [Indexed: 12/18/2022]
Abstract
Coral reefs are among the most biologically diverse ecosystems of the world, yet little is known about the processes creating and maintaining their diversity. Ecologically, corallivory in nudibranchs resembles phytophagy in insects- a process that for decades has served as a model for ecological speciation via host shifting. This study uses extensive field collections, DNA sequencing, and phylogenetic analyses to reconstruct the evolutionary history of coral-associated nudibranchs and assess the relative roles that host shifting and geography may have played in their diversification. We find that the number of species is three times higher than the number previously known to science, with evidence for both allopatric and ecological divergence through host shifting and host specialization. Results contribute to growing support for the importance of ecological diversification in marine environments and provide evidence for new species in the genus Tenellia.
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25
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Genome-Wide Analysis of Cell Cycle-Regulating Genes in the Symbiotic Dinoflagellate Breviolum minutum. G3-GENES GENOMES GENETICS 2019; 9:3843-3853. [PMID: 31551286 PMCID: PMC6829154 DOI: 10.1534/g3.119.400363] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
A delicate relationship exists between reef-building corals and their photosynthetic endosymbionts. Unfortunately, this relationship can be disrupted, with corals expelling these algae when temperatures rise even marginally above the average summer maximum. Interestingly, several studies indicate that failure of corals to regulate symbiont cell divisions at high temperatures may underlie this disruption; increased proliferation of symbionts may stress host cells by over-production of reactive oxygen species or by disrupting the flow of nutrients. This needs to be further investigated, so to begin deciphering the molecular mechanisms controlling the cell cycle in these organisms, we used a computational approach to identify putative cell cycle-regulating genes in the genome of the dinoflagellate Breviolum minutum. This species is important as an endosymbiont of Aiptasia pallida—an anemone that is used as a model for studying coral biology. We then correlated expression of these putative cell cycle genes with cell cycle phase in diurnally growing B. minutum in culture. This approach allowed us to identify a cyclin/cyclin-dependent kinase pair that may function in the G1/S transition—a likely point for coral cells to exert control over algal cell divisions.
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26
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Unique quantitative Symbiodiniaceae signature of coral colonies revealed through spatio-temporal survey in Moorea. Sci Rep 2019; 9:7921. [PMID: 31138834 PMCID: PMC6538640 DOI: 10.1038/s41598-019-44017-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 04/25/2019] [Indexed: 12/20/2022] Open
Abstract
One of the mechanisms of rapid adaptation or acclimatization to environmental changes in corals is through the dynamics of the composition of their associated endosymbiotic Symbiodiniaceae community. The various species of these dinoflagellates are characterized by different biological properties, some of which can confer stress tolerance to the coral host. Compelling evidence indicates that the corals’ Symbiodiniaceae community can change via shuffling and/or switching but the ecological relevance and the governance of these processes remain elusive. Using a qPCR approach to follow the dynamics of Symbiodiniaceae genera in tagged colonies of three coral species over a 10–18 month period, we detected putative genus-level switching of algal symbionts, with coral species-specific rates of occurrence. However, the dynamics of the corals’ Symbiodiniaceae community composition was not driven by environmental parameters. On the contrary, putative shuffling event were observed in two coral species during anomalous seawater temperatures and nutrient concentrations. Most notably, our results reveal that a suit of permanent Symbiodiniaceae genera is maintained in each colony in a specific range of quantities, giving a unique ‘Symbiodiniaceae signature’ to the host. This individual signature, together with sporadic symbiont switching may account for the intra-specific differences in resistance and resilience observed during environmental anomalies.
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27
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Chakravarti LJ, Negri AP, van Oppen MJH. Thermal and Herbicide Tolerances of Chromerid Algae and Their Ability to Form a Symbiosis With Corals. Front Microbiol 2019; 10:173. [PMID: 30809207 PMCID: PMC6379472 DOI: 10.3389/fmicb.2019.00173] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 01/22/2019] [Indexed: 11/13/2022] Open
Abstract
Reef-building corals form an obligate symbiosis with photosynthetic microalgae in the family Symbiodiniaceae that meet most of their energy requirements. This symbiosis is under threat from the unprecedented rate of ocean warming as well as the simultaneous pressure of local stressors such as poor water quality. Only 1°C above mean summer sea surface temperatures (SSTs) on the Great Barrier Reef (GBR) can trigger the loss of Symbiodiniaceae from the host, and very low concentrations of the most common herbicide, diuron, can disrupt the photosynthetic activity of microalgae. In an era of rapid environmental change, investigation into the assisted evolution of the coral holobiont is underway in an effort to enhance the resilience of corals. Apicomplexan-like microalgae were discovered in 2008 and the Phylum Chromerida (chromerids) was created. Chromerids have been isolated from corals and contain a functional photosynthetic plastid. Their discovery therefore opens a new avenue of research into the use of alternative/additional photosymbionts of corals. However, only two studies to-date have investigated the symbiotic nature of Chromera velia with corals and thus little is known about the coral-chromerid relationship. Furthermore, the response of chromerids to environmental stressors has not been examined. Here we tested the performance of four chromerid strains and the common dinoflagellate symbiont Cladocopium goreaui (formerly Symbiodinium goreaui, ITS2 type C1) in response to elevated temperature, diuron and their combined exposure. Three of the four chromerid strains exhibited high thermal tolerances and two strains showed exceptional herbicide tolerances, greater than observed for any photosynthetic microalgae, including C. goreaui. We also investigated the onset of symbiosis between the chromerids and larvae of two common GBR coral species under ambient and stress conditions. Levels of colonization of coral larvae with the chromerid strains were low compared to colonization with C. goreaui. We did not observe any overall negative or positive larval fitness effects of the inoculation with chromerid algae vs. C. goreaui. However, we cannot exclude the possibility that chromerid algae may have more important roles in later coral life stages and recommend this be the focus of future studies.
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Affiliation(s)
- Leela J. Chakravarti
- Australian Institute of Marine Science, Townsville MC, QLD, Australia
- AIMS@JCU, Australian Institute of Marine Science, College of Marine and Environmental Sciences, James Cook University, Townsville, QLD, Australia
- College of Marine and Environmental Sciences, James Cook University, Townsville, QLD, Australia
| | - Andrew P. Negri
- Australian Institute of Marine Science, Townsville MC, QLD, Australia
| | - Madeleine J. H. van Oppen
- Australian Institute of Marine Science, Townsville MC, QLD, Australia
- School of BioSciences University of Melbourne, Parkville, VIC, Australia
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28
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Revisiting “Genetic Diversity of Symbiotic Dinoflagellates in the Genus Symbiodinium”. Protist 2018; 169:784-787. [DOI: 10.1016/j.protis.2018.06.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 06/28/2018] [Indexed: 11/23/2022]
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29
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LaJeunesse TC, Parkinson JE, Gabrielson PW, Jeong HJ, Reimer JD, Voolstra CR, Santos SR. Systematic Revision of Symbiodiniaceae Highlights the Antiquity and Diversity of Coral Endosymbionts. Curr Biol 2018; 28:2570-2580.e6. [PMID: 30100341 DOI: 10.1016/j.cub.2018.07.008] [Citation(s) in RCA: 650] [Impact Index Per Article: 108.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 06/08/2018] [Accepted: 07/03/2018] [Indexed: 11/18/2022]
Abstract
The advent of molecular data has transformed the science of organizing and studying life on Earth. Genetics-based evidence provides fundamental insights into the diversity, ecology, and origins of many biological systems, including the mutualisms between metazoan hosts and their micro-algal partners. A well-known example is the dinoflagellate endosymbionts ("zooxanthellae") that power the growth of stony corals and coral reef ecosystems. Once assumed to encompass a single panmictic species, genetic evidence has revealed a divergent and rich diversity within the zooxanthella genus Symbiodinium. Despite decades of reporting on the significance of this diversity, the formal systematics of these eukaryotic microbes have not kept pace, and a major revision is long overdue. With the consideration of molecular, morphological, physiological, and ecological data, we propose that evolutionarily divergent Symbiodinium "clades" are equivalent to genera in the family Symbiodiniaceae, and we provide formal descriptions for seven of them. Additionally, we recalibrate the molecular clock for the group and amend the date for the earliest diversification of this family to the middle of the Mesozoic Era (∼160 mya). This timing corresponds with the adaptive radiation of analogs to modern shallow-water stony corals during the Jurassic Period and connects the rise of these symbiotic dinoflagellates with the emergence and evolutionary success of reef-building corals. This improved framework acknowledges the Symbiodiniaceae's long evolutionary history while filling a pronounced taxonomic gap. Its adoption will facilitate scientific dialog and future research on the physiology, ecology, and evolution of these important micro-algae.
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Affiliation(s)
- Todd C LaJeunesse
- Department of Biology, The Pennsylvania State University, 208 Mueller Laboratory, University Park, PA 16802, USA.
| | - John Everett Parkinson
- Department of Integrative Biology, Oregon State University, 3029 Cordley Hall, Corvallis, OR 97331, USA.
| | - Paul W Gabrielson
- Herbarium and Biology Department, University of North Carolina-Chapel Hill, Coker Hall, CB 3280, Chapel Hill, NC 27599, USA
| | - Hae Jin Jeong
- School of Earth and Environmental Sciences, College of Natural Sciences, Seoul National University, Seoul 151-747, Republic of Korea; Advanced Institutes of Convergence Technology, Suwon, Gyeonggi-do 16229, Republic of Korea
| | - James Davis Reimer
- Molecular Invertebrate Systematics and Ecology Laboratory, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213, Japan
| | - Christian R Voolstra
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Scott R Santos
- Department of Biological Sciences and Molette Laboratory for Climate Change and Environmental Studies, Auburn University, 101 Rouse Life Sciences Building, Auburn, AL 36849, USA
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30
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Parkinson JE, Tivey TR, Mandelare PE, Adpressa DA, Loesgen S, Weis VM. Subtle Differences in Symbiont Cell Surface Glycan Profiles Do Not Explain Species-Specific Colonization Rates in a Model Cnidarian-Algal Symbiosis. Front Microbiol 2018; 9:842. [PMID: 29765363 PMCID: PMC5938612 DOI: 10.3389/fmicb.2018.00842] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 04/12/2018] [Indexed: 11/13/2022] Open
Abstract
Mutualisms between cnidarian hosts and dinoflagellate endosymbionts are foundational to coral reef ecosystems. These symbioses are often re-established every generation with high specificity, but gaps remain in our understanding of the cellular mechanisms that control symbiont recognition and uptake dynamics. Here, we tested whether differences in glycan profiles among different symbiont species account for the different rates at which they initially colonize aposymbiotic polyps of the model sea anemone Aiptasia (Exaiptasia pallida). First, we used a lectin array to characterize the glycan profiles of colonizing Symbiodinium minutum (ITS2 type B1) and noncolonizing Symbiodinium pilosum (ITS2 type A2), finding subtle differences in the binding of lectins Euonymus europaeus lectin (EEL) and Urtica dioica agglutinin lectin (UDA) that distinguish between high-mannoside and hybrid-type protein linked glycans. Next, we enzymatically cleaved glycans from the surfaces of S. minutum cultures and followed their recovery using flow cytometry, establishing a 48-72 h glycan turnover rate for this species. Finally, we exposed aposymbiotic host polyps to cultured S. minutum cells masked by EEL or UDA lectins for 48 h, then measured cell densities the following day. We found no effect of glycan masking on symbiont density, providing further support to the hypothesis that glycan-lectin interactions are more important for post-phagocytic persistence of specific symbionts than they are for initial uptake. We also identified several methodological and biological factors that may limit the utility of studying glycan masking in the Aiptasia system.
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Affiliation(s)
- John E. Parkinson
- Department of Integrative Biology, Oregon State University, Corvallis, OR, United States
| | - Trevor R. Tivey
- Department of Integrative Biology, Oregon State University, Corvallis, OR, United States
| | - Paige E. Mandelare
- Department of Chemistry, Oregon State University, Corvallis, OR, United States
| | - Donovon A. Adpressa
- Department of Chemistry, Oregon State University, Corvallis, OR, United States
| | - Sandra Loesgen
- Department of Chemistry, Oregon State University, Corvallis, OR, United States
| | - Virginia M. Weis
- Department of Integrative Biology, Oregon State University, Corvallis, OR, United States
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31
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Parkinson JE, Bartels E, Devlin‐Durante MK, Lustic C, Nedimyer K, Schopmeyer S, Lirman D, LaJeunesse TC, Baums IB. Extensive transcriptional variation poses a challenge to thermal stress biomarker development for endangered corals. Mol Ecol 2018; 27:1103-1119. [DOI: 10.1111/mec.14517] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Revised: 12/29/2017] [Accepted: 01/16/2018] [Indexed: 12/11/2022]
Affiliation(s)
- John Everett Parkinson
- Department of Biology Pennsylvania State University State College PA USA
- Department of Integrative Biology Oregon State University Corvallis OR USA
| | - Erich Bartels
- Center for Coral Reef Research Mote Marine Laboratory Summerland Key FL USA
| | | | - Caitlin Lustic
- The Nature Conservancy Florida Keys Office Summerland Key FL USA
| | | | - Stephanie Schopmeyer
- Rosenstiel School of Marine and Atmospheric Science University of Miami Miami FL USA
| | - Diego Lirman
- Rosenstiel School of Marine and Atmospheric Science University of Miami Miami FL USA
| | - Todd C. LaJeunesse
- Department of Biology Pennsylvania State University State College PA USA
| | - Iliana B. Baums
- Department of Biology Pennsylvania State University State College PA USA
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32
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Isolation of uracil auxotroph mutants of coral symbiont alga for symbiosis studies. Sci Rep 2018; 8:3237. [PMID: 29459692 PMCID: PMC5818653 DOI: 10.1038/s41598-018-21499-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 02/01/2018] [Indexed: 11/26/2022] Open
Abstract
Coral reef ecosystems rely on stable symbiotic relationship between the dinoflagellate Symbiodinium spp. and host cnidarian animals. The collapse of such symbiosis could cause coral ‘bleaching’ and subsequent host death. Despite huge interest on Symbiodinium, lack of mutant strains and readily available genetic tools have hampered molecular research. A major issue was the tolerance to marker antibiotics. Here, we isolated Symbiodinium mutants requiring uracil for growth, and hence, useful in transformation screening. We cultured Symbiodinium spp. cells in the presence of 5-fluoroorotic acid (5FOA), which inhibits the growth of cells expressing URA3 encoding orotidine-5′-monophosphate decarboxylase, and isolated cells that require uracil for growth. Sequence analyses and genetic complementation tests using yeast demonstrated that one of the mutant cell lines had a point mutation in URA3, resulting in a splicing error at an unusual exon–intron junction, and consequently, loss of enzyme activity. This mutant could maintain a symbiotic relationship with the model sea anemone Exaiptasia pallida only in sea water containing uracil. Results show that the URA3 mutant will be a useful tool for screening Symbiodinium transformants, both ex and in hospite, as survival in the absence of uracil is possible only upon successful introduction of URA3.
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Deng J, Auchtung JM, Konstantinidis KT, Caro-Quintero A, Brettar I, Höfle M, Tiedje JM. Divergence in Gene Regulation Contributes to Sympatric Speciation of Shewanella baltica Strains. Appl Environ Microbiol 2018; 84:e02015-17. [PMID: 29222101 PMCID: PMC5795076 DOI: 10.1128/aem.02015-17] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Accepted: 11/30/2017] [Indexed: 12/19/2022] Open
Abstract
Niche partitioning and sequence evolution drive genomic and phenotypic divergence, which ultimately leads to bacterial diversification. This study investigated the genomic composition of two Shewanella baltica clades previously identified through multilocus sequencing typing and recovered from the redox transition zone in the central Baltic Sea. Comparative genomic analysis revealed significantly higher interclade than intraclade genomic dissimilarity and that a subset of genes present in clade A were associated with potential adaptation to respiration of sulfur compounds present in the redox transition zone. The transcriptomic divergence between two representative strains of clades A and D, OS185 and OS195, was also characterized and revealed marked regulatory differences. We found that both the transcriptional divergence of shared genes and expression of strain-specific genes led to differences in regulatory patterns between strains that correlate with environmental redox niches. For instance, under anoxic conditions of respiratory nitrate ammonification, OS185-the strain isolated from a nitrate-rich environment-upregulated nearly twice the number of shared genes upregulated by OS195-the strain isolated from an H2S-containing anoxic environment. Conversely, OS195 showed stronger induction of strain-specific genes, especially those associated with sulfur compound respiration, under thiosulfate-reducing conditions. A positive association between the level of transcriptional divergence and the level of sequence divergence for shared genes was also noted. Our results provide further support for the hypothesis that genomic changes impacting transcriptional regulation play an important role in the diversification of ecologically distinct populations.IMPORTANCE This study examined potential mechanisms through which co-occurring Shewanella baltica strains diversified to form ecologically distinct populations. At the time of isolation, the strains studied composed the major fraction of culturable nitrate-reducing communities in the Baltica Sea. Analysis of genomic content of 13 S. baltica strains from two clades representing different ecotypes demonstrated that one clade specifically possesses a number of genes that could favor successful adaptation to respire sulfur compounds in the portion of the water column from which these strains were isolated. In addition, transcriptional profiling of fully sequenced strains representative of these two clades, OS185 and OS195, under oxygen-, nitrate-, and thiosulfate-respiring conditions demonstrated that the strains exhibit relatively similar transcriptional responses during aerobic growth but more-distinct transcriptional responses under nitrate- and thiosulfate-respiring conditions. Results from this study provide insights into how genomic and gene regulatory diversification together impacted the redox specialization of the S. baltica strains.
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Affiliation(s)
- Jie Deng
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restorations, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
- Shanghai Institute of Eco-Chongming, Shanghai, China
- Center for Microbial Ecology, Michigan State University, East Lansing, Michigan, USA
| | - Jennifer M Auchtung
- Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA
| | | | - Ingrid Brettar
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Manfred Höfle
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - James M Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, Michigan, USA
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González AM, Prada CA, Ávila V, Medina M. Ecological Speciation in Corals. POPULATION GENOMICS 2018. [DOI: 10.1007/13836_2018_35] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Deng Y, Hu Z, Shang L, Peng Q, Tang YZ. Transcriptomic Analyses of Scrippsiella trochoidea Reveals Processes Regulating Encystment and Dormancy in the Life Cycle of a Dinoflagellate, with a Particular Attention to the Role of Abscisic Acid. Front Microbiol 2017; 8:2450. [PMID: 29312167 PMCID: PMC5732363 DOI: 10.3389/fmicb.2017.02450] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 11/27/2017] [Indexed: 12/26/2022] Open
Abstract
Due to the vital importance of resting cysts in the biology and ecology of many dinoflagellates, a transcriptomic investigation on Scrippsiella trochoidea was conducted with the aim to reveal the molecular processes and relevant functional genes regulating encystment and dormancy in dinoflagellates. We identified via RNA-seq 3,874 (out of 166,575) differentially expressed genes (DEGs) between resting cysts and vegetative cells; a pause of photosynthesis (confirmed via direct measurement of photosynthetic efficiency); an active catabolism including β-oxidation, glycolysis, glyoxylate pathway, and TCA in resting cysts (tested via measurements of respiration rate); 12 DEGs encoding meiotic recombination proteins and members of MEI2-like family potentially involved in sexual reproduction and encystment; elevated expressions in genes encoding enzymes responding to pathogens (chitin deacetylase) and ROS stress in cysts; and 134 unigenes specifically expressed in cysts. We paid particular attention to genes pertaining to phytohormone signaling and identified 4 key genes regulating abscisic acid (ABA) biosynthesis and catabolism, with further characterization based on their full-length cDNA obtained via RACE-PCR. The qPCR results demonstrated elevated biosynthesis and repressed catabolism of ABA during the courses of encystment and cyst dormancy, which was significantly enhanced by lower temperature (4 ± 1°C) and darkness. Direct measurements of ABA using UHPLC-MS/MS and ELISA in vegetative cells and cysts both fully supported qPCR results. These results collectively suggest a vital role of ABA in regulating encystment and maintenance of dormancy, akin to its function in seed dormancy of higher plants. Our results provided a critical advancement in understanding molecular processes in resting cysts of dinoflagellates.
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Affiliation(s)
- Yunyan Deng
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Zhangxi Hu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Lixia Shang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Quancai Peng
- Research Center of Analysis and Measurement, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Ying Zhong Tang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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Rare symbionts may contribute to the resilience of coral-algal assemblages. ISME JOURNAL 2017; 12:161-172. [PMID: 29192903 PMCID: PMC5739009 DOI: 10.1038/ismej.2017.151] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Revised: 08/02/2017] [Accepted: 08/14/2017] [Indexed: 01/31/2023]
Abstract
The association between corals and photosynthetic dinoflagellates (Symbiodinium spp.) is the key to the success of reef ecosystems in highly oligotrophic environments, but it is also their Achilles‘ heel due to its vulnerability to local stressors and the effects of climate change. Research during the last two decades has shaped a view that coral host–Symbiodinium pairings are diverse, but largely exclusive. Deep sequencing has now revealed the existence of a rare diversity of cryptic Symbiodinium assemblages within the coral holobiont, in addition to one or a few abundant algal members. While the contribution of the most abundant resident Symbiodinium species to coral physiology is widely recognized, the significance of the rare and low abundant background Symbiodinium remains a matter of debate. In this study, we assessed how coral–Symbiodinium communities assemble and how rare and abundant components together constitute the Symbiodinium community by analyzing 892 coral samples comprising >110 000 unique Symbiodinium ITS2 marker gene sequences. Using network modeling, we show that host–Symbiodinium communities assemble in non-random ‘clusters‘ of abundant and rare symbionts. Symbiodinium community structure follows the same principles as bacterial communities, for which the functional significance of rare members (the ‘rare bacterial biosphere’) has long been recognized. Importantly, the inclusion of rare Symbiodinium taxa in robustness analyses revealed a significant contribution to the stability of the host–symbiont community overall. As such, it highlights the potential functions rare symbionts may provide to environmental resilience of the coral holobiont.
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González-Pech RA, Ragan MA, Chan CX. Signatures of adaptation and symbiosis in genomes and transcriptomes of Symbiodinium. Sci Rep 2017; 7:15021. [PMID: 29101370 PMCID: PMC5670126 DOI: 10.1038/s41598-017-15029-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 10/19/2017] [Indexed: 12/02/2022] Open
Abstract
Symbiodinium is best-known as the photosynthetic symbiont of corals, but some clades are symbiotic in other organisms or include free-living forms. Identifying similarities and differences among these clades can help us understand their relationship with corals, and thereby inform on measures to manage coral reefs in a changing environment. Here, using sequences from 24 publicly available transcriptomes and genomes of Symbiodinium, we assessed 78,389 gene families in Symbiodinium clades and the immediate outgroup Polarella glacialis, and identified putative overrepresented functions in gene families that (1) distinguish Symbiodinium from other members of Order Suessiales, (2) are shared by all of the Symbiodinium clades for which we have data, and (3) based on available information, are specific to each clade. Our findings indicate that transmembrane transport, mechanisms of response to reactive oxygen species, and protection against UV radiation are functions enriched in all Symbiodinium clades but not in P. glacialis. Enrichment of these functions indicates the capability of Symbiodinium to establish and maintain symbiosis, and to respond and adapt to its environment. The observed differences in lineage-specific gene families imply extensive genetic divergence among clades. Our results provide a platform for future investigation of lineage- or clade-specific adaptation of Symbiodinium to their environment.
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Affiliation(s)
- Raúl A González-Pech
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Mark A Ragan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Cheong Xin Chan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia. .,School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia.
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Wang JT, Keshavmurthy S, Chu TY, Chen CA. Diverse responses of Symbiodinium types to menthol and DCMU treatment. PeerJ 2017; 5:e3843. [PMID: 29018600 PMCID: PMC5628609 DOI: 10.7717/peerj.3843] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 09/02/2017] [Indexed: 12/13/2022] Open
Abstract
To understand the mechanism of photosynthetic inhibition and generation of reactive oxygen species (ROS) in Symbiodinium types under stress, chemicals such as dichlorophenyl dimethylurea (DCMU) are widely used. Moreover, DCMU and recently menthol were used to generate aposymbiotic cnidarian hosts. While the effects of DCMU on Symbiodinium cells have been extensively studied, no studies have shown the mechanism behind menthol-induced coral bleaching. Moreover, no study has compared the effects of DCMU and menthol treatments on photosystem II (PSII) activity and generation of ROS in different Symbiodinium types. In this study, we utilized five freshly isolated Symbiodinium types (S. minutum (B1), S. goreaui (C1), C3, C15, and S. trenchii (D1a)) to compare the effects of DCMU and menthol treatments. Symbiodinium cells were exposed to DCMU and menthol at different concentrations for 4 h. Results showed that values of the 50% inhibitory concentration (IC50) for PSII inhibition were 0.72∼1.96 mM for menthol-treated cells compared to 29∼74 pM for DCMU-treated cells. Diverse responses of Symbiodinium types were displayed in terms of PSII tolerance to menthol (S. minutum > S. trenchii = C15 > C3 = S. goreaui), and also in the response curves. In contrast, responses were not so diverse when the different types were treated with DCMU. Three of five menthol-treated Symbiodinium types showed instant and significant ROS generation when PSII activity was inhibited, compared to no ROS being generated in DCMU-treated Symbiodinium types. Both results indicated that menthol inhibited Symbiodinium PSII activity through Symbiodinium type-dependent mechanisms, which were also distinct from those with DCMU treatment. This study further confirmed that photosynthetic functions Symbiodinium have diverse responses to stress even within the same clade.
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Affiliation(s)
- Jih-Terng Wang
- Graduate Institute of Biotechnology, Tajen University, Pingtung, Taiwan
| | | | - Tzu-Ying Chu
- Graduate Institute of Biotechnology, Tajen University, Pingtung, Taiwan
| | - Chaolun Allen Chen
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.,Institute of Oceanography, National Taiwan University, Taipei, Taiwan
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Macrander JC, Dimond JL, Bingham BL, Reitzel AM. Transcriptome sequencing and characterization of Symbiodinium muscatinei and Elliptochloris marina, symbionts found within the aggregating sea anemone Anthopleura elegantissima. Mar Genomics 2017; 37:82-91. [PMID: 28888836 DOI: 10.1016/j.margen.2017.08.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 08/26/2017] [Accepted: 08/27/2017] [Indexed: 12/20/2022]
Abstract
There is a growing body of literature using transcriptomic data to study how tropical cnidarians and their photosynthetic endosymbionts respond to environmental stressors and participate in metabolic exchange. Despite these efforts, our understanding of how essential genes function to facilitate symbiosis establishment and maintenance remains limited. The inclusion of taxonomically and ecologically diverse endosymbionts will enhance our understanding of these interactions. Here we characterize the transcriptomes of two very different symbionts found within the temperate sea anemone Anthopleura elegantissima: the chlorophyte Elliptochloris marina and the dinoflagellate Symbiodinium muscatinei. We use a multi-level approach to assess the diversity of genes found across S. muscatinei and E. marina transcriptomes, and compare their overall protein domains with other dinoflagellates and chlorophytes. Our analysis identified several genes that are potentially involved in mitigating stress response (e.g., heat shock proteins pathways for mediating reactive oxygen species) and metabolic exchange (e.g., ion transporters). Finally, we show that S. muscatinei and other Symbiodinium strains are equipped with a high salt peridinin-chl-protein (HSPCP) gene previously identified only in free-living dinoflagellates. The addition of these transcriptomes to the cnidarian-symbiont molecular toolkit will aid in understanding how these vitally important symbiotic relationships are established and maintained across a variety of environmental conditions.
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Affiliation(s)
- Jason C Macrander
- Department of Biological Sciences, University of North Carolina, Charlotte, 9201 University City Blvd, Charlotte, NC 28223, USA.
| | - James L Dimond
- Shannon Point Marine Center, Western Washington University, 1900 Shannon Point Road, Anacortes, WA 98221, USA
| | - Brian L Bingham
- Shannon Point Marine Center, Western Washington University, 1900 Shannon Point Road, Anacortes, WA 98221, USA; Department of Environmental Sciences, Western Washington University, 516 High Street, Bellingham, WA 98225, USA
| | - Adam M Reitzel
- Department of Biological Sciences, University of North Carolina, Charlotte, 9201 University City Blvd, Charlotte, NC 28223, USA
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Ochsenkühn MA, Röthig T, D’Angelo C, Wiedenmann J, Voolstra CR. The role of floridoside in osmoadaptation of coral-associated algal endosymbionts to high-salinity conditions. SCIENCE ADVANCES 2017; 3:e1602047. [PMID: 28835914 PMCID: PMC5559212 DOI: 10.1126/sciadv.1602047] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 07/19/2017] [Indexed: 05/12/2023]
Abstract
The endosymbiosis between Symbiodinium dinoflagellates and stony corals provides the foundation of coral reef ecosystems. The survival of these ecosystems is under threat at a global scale, and better knowledge is needed to conceive strategies for mitigating future reef loss. Environmental disturbance imposing temperature, salinity, and nutrient stress can lead to the loss of the Symbiodinium partner, causing so-called coral bleaching. Some of the most thermotolerant coral-Symbiodinium associations occur in the Persian/Arabian Gulf and the Red Sea, which also represent the most saline coral habitats. We studied whether Symbiodinium alter their metabolite content in response to high-salinity environments. We found that Symbiodinium cells exposed to high salinity produced high levels of the osmolyte 2-O-glycerol-α-d-galactopyranoside (floridoside), both in vitro and in their coral host animals, thereby increasing their capacity and, putatively, the capacity of the holobiont to cope with the effects of osmotic stress in extreme environments. Given that floridoside has been previously shown to also act as an antioxidant, this osmolyte may serve a dual function: first, to serve as a compatible organic osmolyte accumulated by Symbiodinium in response to elevated salinities and, second, to counter reactive oxygen species produced as a consequence of potential salinity and heat stress.
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Affiliation(s)
- Michael A. Ochsenkühn
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Division of Science and Engineering, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Till Röthig
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Cecilia D’Angelo
- Coral Reef Laboratory/Institute for Life Sciences, Ocean and Earth Science, University of Southampton, Southampton, UK
| | - Jörg Wiedenmann
- Coral Reef Laboratory/Institute for Life Sciences, Ocean and Earth Science, University of Southampton, Southampton, UK
| | - Christian R. Voolstra
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Corresponding author.
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Transcriptomes and expression profiling of deep-sea corals from the Red Sea provide insight into the biology of azooxanthellate corals. Sci Rep 2017; 7:6442. [PMID: 28743941 PMCID: PMC5526985 DOI: 10.1038/s41598-017-05572-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 05/31/2017] [Indexed: 12/15/2022] Open
Abstract
Despite the importance of deep-sea corals, our current understanding of their ecology and evolution is limited due to difficulties in sampling and studying deep-sea environments. Moreover, a recent re-evaluation of habitat limitations has been suggested after characterization of deep-sea corals in the Red Sea, where they live at temperatures of above 20 °C at low oxygen concentrations. To gain further insight into the biology of deep-sea corals, we produced reference transcriptomes and studied gene expression of three deep-sea coral species from the Red Sea, i.e. Dendrophyllia sp., Eguchipsammia fistula, and Rhizotrochus typus. Our analyses suggest that deep-sea coral employ mitochondrial hypometabolism and anaerobic glycolysis to manage low oxygen conditions present in the Red Sea. Notably, we found expression of genes related to surface cilia motion that presumably enhance small particle transport rates in the oligotrophic deep-sea environment. This is the first study to characterize transcriptomes and in situ gene expression for deep-sea corals. Our work offers several mechanisms by which deep-sea corals might cope with the distinct environmental conditions present in the Red Sea As such, our data provide direction for future research and further insight to organismal response of deep-sea coral to environmental change and ocean warming.
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Levin RA, Voolstra CR, Agrawal S, Steinberg PD, Suggett DJ, van Oppen MJH. Engineering Strategies to Decode and Enhance the Genomes of Coral Symbionts. Front Microbiol 2017; 8:1220. [PMID: 28713348 PMCID: PMC5492045 DOI: 10.3389/fmicb.2017.01220] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 06/16/2017] [Indexed: 11/13/2022] Open
Abstract
Elevated sea surface temperatures from a severe and prolonged El Niño event (2014–2016) fueled by climate change have resulted in mass coral bleaching (loss of dinoflagellate photosymbionts, Symbiodinium spp., from coral tissues) and subsequent coral mortality, devastating reefs worldwide. Genetic variation within and between Symbiodinium species strongly influences the bleaching tolerance of corals, thus recent papers have called for genetic engineering of Symbiodinium to elucidate the genetic basis of bleaching-relevant Symbiodinium traits. However, while Symbiodinium has been intensively studied for over 50 years, genetic transformation of Symbiodinium has seen little success likely due to the large evolutionary divergence between Symbiodinium and other model eukaryotes rendering standard transformation systems incompatible. Here, we integrate the growing wealth of Symbiodinium next-generation sequencing data to design tailored genetic engineering strategies. Specifically, we develop a testable expression construct model that incorporates endogenous Symbiodinium promoters, terminators, and genes of interest, as well as an internal ribosomal entry site from a Symbiodinium virus. Furthermore, we assess the potential for CRISPR/Cas9 genome editing through new analyses of the three currently available Symbiodinium genomes. Finally, we discuss how genetic engineering could be applied to enhance the stress tolerance of Symbiodinium, and in turn, coral reefs.
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Affiliation(s)
- Rachel A Levin
- Centre for Marine Bio-Innovation, The University of New South Wales, SydneyNSW, Australia.,School of Biological, Earth and Environmental Sciences, The University of New South Wales, SydneyNSW, Australia.,Climate Change Cluster, University of Technology Sydney, UltimoNSW, Australia
| | - Christian R Voolstra
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST),Thuwal, Saudi Arabia
| | - Shobhit Agrawal
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST),Thuwal, Saudi Arabia
| | - Peter D Steinberg
- Centre for Marine Bio-Innovation, The University of New South Wales, SydneyNSW, Australia.,School of Biological, Earth and Environmental Sciences, The University of New South Wales, SydneyNSW, Australia.,Sydney Institute of Marine Science, MosmanNSW, Australia
| | - David J Suggett
- Climate Change Cluster, University of Technology Sydney, UltimoNSW, Australia
| | - Madeleine J H van Oppen
- Australian Institute of Marine Science, TownsvilleQLD, Australia.,School of BioSciences, The University of Melbourne, ParkvilleVIC, Australia
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Tonk L, Sampayo EM, Chai A, Schrameyer V, Hoegh-Guldberg O. Symbiodinium (Dinophyceae) community patterns in invertebrate hosts from inshore marginal reefs of the southern Great Barrier Reef, Australia. JOURNAL OF PHYCOLOGY 2017; 53:589-600. [PMID: 28196275 DOI: 10.1111/jpy.12523] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 01/03/2017] [Indexed: 06/06/2023]
Abstract
The broad range in physiological variation displayed by Symbiodinium spp. has proven imperative during periods of environmental change and contribute to the survival of their coral host. Characterizing how host and Symbiodinium community assemblages differ across environmentally distinct habitats provides useful information to predict how corals will respond to major environmental change. Despite the extensive characterizations of Symbiodinium diversity found amongst reef cnidarians on the Great Barrier Reef (GBR) substantial biogeographic gaps exist, especially across inshore habitats. Here, we investigate Symbiodinium community patterns in invertebrates from inshore and mid-shelf reefs on the southern GBR, Australia. Dominant Symbiodinium types were characterized using denaturing gradient gel electrophoresis fingerprinting and sequencing of the ITS2 region of the ribosomal DNA. Twenty one genetically distinct Symbiodinium types including four novel types were identified from 321 reef-invertebrate samples comprising three sub-generic clades (A, C, and D). A range of host genera harbored C22a, which is normally rare or absent from inshore or low latitude reefs in the GBR. Multivariate analysis showed that host identity and sea surface temperature best explained the variation in symbiont communities across sites. Patterns of changes in Symbiodinium community assemblage over small geographic distances (100s of kilometers or less) indicate the likelihood that shifts in Symbiodinium distributions and associated host populations, may occur in response to future climate change impacting the GBR.
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Affiliation(s)
- Linda Tonk
- ARC Centre of Excellence for Coral Reef Studies and School of Biological Sciences, The University of Queensland, St. Lucia, Queensland, 4072, Australia
| | - Eugenia M Sampayo
- ARC Centre of Excellence for Coral Reef Studies and School of Biological Sciences, The University of Queensland, St. Lucia, Queensland, 4072, Australia
| | - Aaron Chai
- ARC Centre of Excellence for Coral Reef Studies and School of Biological Sciences, The University of Queensland, St. Lucia, Queensland, 4072, Australia
| | - Verena Schrameyer
- Plant Functional Biology & Climate Change Cluster, University of Technology Sydney, Broadway, New South Wales, 2007, Australia
| | - Ove Hoegh-Guldberg
- ARC Centre of Excellence for Coral Reef Studies and School of Biological Sciences, The University of Queensland, St. Lucia, Queensland, 4072, Australia
- Global Change Institute, The University of Queensland, St. Lucia, Queensland, 4072, Australia
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Sogin EM, Putnam HM, Nelson CE, Anderson P, Gates RD. Correspondence of coral holobiont metabolome with symbiotic bacteria, archaea and Symbiodinium communities. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:310-315. [PMID: 28464532 DOI: 10.1111/1758-2229.12541] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 01/25/2017] [Accepted: 03/12/2017] [Indexed: 06/07/2023]
Abstract
Microbial symbiotic partners, such as those associated with Scleractinian corals, mediate biochemical transformations that influence host performance and survival. While evidence suggests microbial community composition partly accounts for differences in coral physiology, how these symbionts affect metabolic pathways remains underexplored. We aimed to assess functional implications of variation among coral-associated microbial partners in hospite. To this end, we characterized and compared metabolomic profiles and microbial community composition from nine reef-building coral species. These data demonstrate metabolite profiles and microbial communities are species-specific and are correlated to one another. Using Porites spp. as a case study, we present evidence that the relative abundance of different sub-clades of Symbiodinium and bacterial/archaeal families are linked to positive and negative metabolomic signatures. Our data suggest that while some microbial partners benefit the union, others are more opportunistic with potential detriment to the host. Consequently, coral partner choice likely influences cellular metabolic activities and, therefore, holobiont nutrition.
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Affiliation(s)
- Emilia M Sogin
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, USA
| | - Hollie M Putnam
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, USA
| | - Craig E Nelson
- Department of Oceanography and Sea Grant College Program, Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - Paul Anderson
- Department of Computer Science, College of Charleston, Charleston, NC, USA
| | - Ruth D Gates
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, USA
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Mies M, Sumida PYG, Rädecker N, Voolstra CR. Marine Invertebrate Larvae Associated with Symbiodinium: A Mutualism from the Start? Front Ecol Evol 2017. [DOI: 10.3389/fevo.2017.00056] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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47
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Genotype and local environment dynamically influence growth, disturbance response and survivorship in the threatened coral, Acropora cervicornis. PLoS One 2017; 12:e0174000. [PMID: 28319134 PMCID: PMC5358778 DOI: 10.1371/journal.pone.0174000] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 03/01/2017] [Indexed: 01/17/2023] Open
Abstract
The relationship between the coral genotype and the environment is an important area of research in degraded coral reef ecosystems. We used a reciprocal outplanting experiment with 930 corals representing ten genotypes on each of eight reefs to investigate the influence of genotype and the environment on growth and survivorship in the threatened Caribbean staghorn coral, Acropora cervicornis. Coral genotype and site were strong drivers of coral growth and individual genotypes exhibited flexible, non-conserved reaction norms, complemented by ten-fold differences in growth between specific G-E combinations. Growth plasticity may diminish the influence of local adaptation, where foreign corals grew faster than native corals at their home sites. Novel combinations of environment and genotype also significantly affected disturbance response during and after the 2015 bleaching event, where these factors acted synergistically to drive variation in bleaching and recovery. Importantly, small differences in temperature stress elicit variable patterns of survivorship based on genotype and illustrate the importance of novel combinations of coral genetics and small differences between sites representing habitat refugia. In this context, acclimatization and flexibility is especially important given the long lifespan of corals coping with complex environmental change. The combined influence of site and genotype creates short-term differences in growth and survivorship, contributing to the standing genetic variation needed for adaptation to occur over longer timescales and the recovery of degraded reefs through natural mechanisms.
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48
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Gierz SL, Forêt S, Leggat W. Transcriptomic Analysis of Thermally Stressed Symbiodinium Reveals Differential Expression of Stress and Metabolism Genes. FRONTIERS IN PLANT SCIENCE 2017; 8:271. [PMID: 28293249 PMCID: PMC5328969 DOI: 10.3389/fpls.2017.00271] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 02/14/2017] [Indexed: 05/29/2023]
Abstract
Endosymbioses between dinoflagellate algae (Symbiodinium sp.) and scleractinian coral species form the foundation of coral reef ecosystems. The coral symbiosis is highly susceptible to elevated temperatures, resulting in coral bleaching, where the algal symbiont is released from host cells. This experiment aimed to determine the transcriptional changes in cultured Symbiodinium, to better understand the response of cellular mechanisms under future temperature conditions. Cultures were exposed to elevated temperatures (average 31°C) or control conditions (24.5°C) for a period of 28 days. Whole transcriptome sequencing of Symbiodinium cells on days 4, 19, and 28 were used to identify differentially expressed genes under thermal stress. A large number of genes representing 37.01% of the transcriptome (∼23,654 unique genes, FDR < 0.05) with differential expression were detected at no less than one of the time points. Consistent with previous studies of Symbiodinium gene expression, fold changes across the transcriptome were low, with 92.49% differentially expressed genes at ≤2-fold change. The transcriptional response included differential expression of genes encoding stress response components such as the antioxidant network and molecular chaperones, cellular components such as core photosynthesis machinery, integral light-harvesting protein complexes and enzymes such as fatty acid desaturases. Differential expression of genes encoding glyoxylate cycle enzymes were also found, representing the first report of this in Symbiodinium. As photosynthate transfer from Symbiodinium to coral hosts provides up to 90% of a coral's daily energy requirements, the implications of altered metabolic processes from exposure to thermal stress found in this study on coral-Symbiodinium associations are unknown and should be considered when assessing the stability of the symbiotic relationship under future climate conditions.
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Affiliation(s)
- Sarah L. Gierz
- College of Public Health, Medical and Veterinary Sciences, James Cook University, TownsvilleQLD, Australia
- Comparative Genomics Centre, James Cook University, TownsvilleQLD, Australia
| | - Sylvain Forêt
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, TownsvilleQLD, Australia
- Evolution, Ecology and Genetics, Research School of Biology, Australian National University, CanberraACT, Australia
| | - William Leggat
- College of Public Health, Medical and Veterinary Sciences, James Cook University, TownsvilleQLD, Australia
- Comparative Genomics Centre, James Cook University, TownsvilleQLD, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, TownsvilleQLD, Australia
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49
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Levin RA, Suggett DJ, Nitschke MR, van Oppen MJH, Steinberg PD. Expanding the Symbiodinium (Dinophyceae, Suessiales) Toolkit Through Protoplast Technology. J Eukaryot Microbiol 2017; 64:588-597. [PMID: 28120360 DOI: 10.1111/jeu.12393] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 01/11/2017] [Accepted: 01/13/2017] [Indexed: 11/27/2022]
Abstract
Dinoflagellates within the genus Symbiodinium are photosymbionts of many tropical reef invertebrates, including corals, making them central to the health of coral reefs. Symbiodinium have therefore gained significant research attention, though studies have been constrained by technical limitations. In particular, the generation of viable cells with their cell walls removed (termed protoplasts) has enabled a wide range of experimental techniques for bacteria, fungi, plants, and algae such as ultrastructure studies, virus infection studies, patch clamping, genetic transformation, and protoplast fusion. However, previous studies have struggled to remove the cell walls from armored dinoflagellates, potentially due to the internal placement of their cell walls. Here, we produce the first Symbiodinium protoplasts from three genetically and physiologically distinct strains via incubation with cellulase and osmotic agents. Digestion of the cell walls was verified by a lack of Calcofluor White fluorescence signal and by cell swelling in hypotonic culture medium. Fused protoplasts were also observed, motivating future investigation into intra- and inter-specific somatic hybridization of Symbiodinium. Following digestion and transfer to regeneration medium, protoplasts remained photosynthetically active, regrew cell walls, regained motility, and entered exponential growth. Generation of Symbiodinium protoplasts opens exciting, new avenues for researching these crucial symbiotic dinoflagellates, including genetic modification.
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Affiliation(s)
- Rachel A Levin
- Centre for Marine Bio-Innovation, The University of New South Wales, Sydney, NSW, 2052, Australia.,School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW, 2052, Australia.,Climate Change Cluster, University of Technology Sydney, Sydney, NSW, 2007, Australia
| | - David J Suggett
- Climate Change Cluster, University of Technology Sydney, Sydney, NSW, 2007, Australia
| | - Matthew R Nitschke
- Climate Change Cluster, University of Technology Sydney, Sydney, NSW, 2007, Australia
| | - Madeleine J H van Oppen
- Australian Institute of Marine Science, Townsville MC, Qld, 4810, Australia.,School of BioSciences, The University of Melbourne, Parkville, Vic., 3010, Australia
| | - Peter D Steinberg
- Centre for Marine Bio-Innovation, The University of New South Wales, Sydney, NSW, 2052, Australia.,School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW, 2052, Australia.,Sydney Institute of Marine Science, Chowder Bay Road, Mosman, NSW, 2088, Australia
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50
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Liew YJ, Li Y, Baumgarten S, Voolstra CR, Aranda M. Condition-specific RNA editing in the coral symbiont Symbiodinium microadriaticum. PLoS Genet 2017; 13:e1006619. [PMID: 28245292 PMCID: PMC5357065 DOI: 10.1371/journal.pgen.1006619] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 03/17/2017] [Accepted: 02/07/2017] [Indexed: 11/19/2022] Open
Abstract
RNA editing is a rare post-transcriptional event that provides cells with an additional level of gene expression regulation. It has been implicated in various processes including adaptation, viral defence and RNA interference; however, its potential role as a mechanism in acclimatization has just recently been recognised. Here, we show that RNA editing occurs in 1.6% of all nuclear-encoded genes of Symbiodinium microadriaticum, a dinoflagellate symbiont of reef-building corals. All base-substitution edit types were present, and statistically significant motifs were associated with three edit types. Strikingly, a subset of genes exhibited condition-specific editing patterns in response to different stressors that resulted in significant increases of non-synonymous changes. We posit that this previously unrecognised mechanism extends this organism's capability to respond to stress beyond what is encoded by the genome. This in turn may provide further acclimatization capacity to these organisms, and by extension, their coral hosts.
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Affiliation(s)
- Yi Jin Liew
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC), Biological and Environmental Sciences & Engineering Division (BESE), Thuwal, Saudi Arabia
| | - Yong Li
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC), Biological and Environmental Sciences & Engineering Division (BESE), Thuwal, Saudi Arabia
| | - Sebastian Baumgarten
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC), Biological and Environmental Sciences & Engineering Division (BESE), Thuwal, Saudi Arabia
| | - Christian R. Voolstra
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC), Biological and Environmental Sciences & Engineering Division (BESE), Thuwal, Saudi Arabia
| | - Manuel Aranda
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC), Biological and Environmental Sciences & Engineering Division (BESE), Thuwal, Saudi Arabia
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