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Bennett GM, Kwak Y, Maynard R. Endosymbioses Have Shaped the Evolution of Biological Diversity and Complexity Time and Time Again. Genome Biol Evol 2024; 16:evae112. [PMID: 38813885 PMCID: PMC11154151 DOI: 10.1093/gbe/evae112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 05/17/2024] [Accepted: 05/17/2024] [Indexed: 05/31/2024] Open
Abstract
Life on Earth comprises prokaryotes and a broad assemblage of endosymbioses. The pages of Molecular Biology and Evolution and Genome Biology and Evolution have provided an essential window into how these endosymbiotic interactions have evolved and shaped biological diversity. Here, we provide a current perspective on this knowledge by drawing on decades of revelatory research published in Molecular Biology and Evolution and Genome Biology and Evolution, and insights from the field at large. The accumulated work illustrates how endosymbioses provide hosts with novel phenotypes that allow them to transition between adaptive landscapes to access environmental resources. Such endosymbiotic relationships have shaped and reshaped life on Earth. The early serial establishment of mitochondria and chloroplasts through endosymbioses permitted massive upscaling of cellular energetics, multicellularity, and terrestrial planetary greening. These endosymbioses are also the foundation upon which all later ones are built, including everything from land-plant endosymbioses with fungi and bacteria to nutritional endosymbioses found in invertebrate animals. Common evolutionary mechanisms have shaped this broad range of interactions. Endosymbionts generally experience adaptive and stochastic genome streamlining, the extent of which depends on several key factors (e.g. mode of transmission). Hosts, in contrast, adapt complex mechanisms of resource exchange, cellular integration and regulation, and genetic support mechanisms to prop up degraded symbionts. However, there are significant differences between endosymbiotic interactions not only in how partners have evolved with each other but also in the scope of their influence on biological diversity. These differences are important considerations for predicting how endosymbioses will persist and adapt to a changing planet.
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Affiliation(s)
- Gordon M Bennett
- Department of Life and Environmental Sciences, University of California, Merced, CA, USA
- National Science Foundation Biological Integration Institute—INSITE, University of California, Merced, CA, USA
| | - Younghwan Kwak
- Department of Life and Environmental Sciences, University of California, Merced, CA, USA
- National Science Foundation Biological Integration Institute—INSITE, University of California, Merced, CA, USA
| | - Reo Maynard
- Department of Life and Environmental Sciences, University of California, Merced, CA, USA
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Xiao Y, Gao L, Li Z. Unique high-temperature tolerance mechanisms of zoochlorellae Symbiochlorum hainanensis derived from scleractinian coral Porites lutea. mBio 2024; 15:e0278023. [PMID: 38385710 DOI: 10.1128/mbio.02780-23] [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: 10/17/2023] [Accepted: 01/22/2024] [Indexed: 02/23/2024] Open
Abstract
Global warming is a key issue that causes coral bleaching mainly because of the thermosensitivity of zooxanthellae. Compared with the well-studied zooxanthellae Symbiodiniaceae in coral holobionts, we rarely know about other coral symbiotic algae, let alone their thermal tolerance. In this study, a zoochlorellae, Symbiochlorum hainanensis, isolated from the coral Porites lutea, was proven to have a threshold temperature of 38°C. Meanwhile, unique high-temperature tolerance mechanisms were suggested by integrated transcriptomics and real-time quantitative PCR, physiological and biochemical analyses, and electron microscopy observation. Under heat stress, S. hainanensis shared some similar response strategies with zooxanthellae Effrenium sp., such as increased ascorbate peroxidase, glutathione peroxidase, superoxide dismutase activities and chlorophyll a, thiamine, and thiamine phosphate contents. In particular, more chloroplast internal layered structure, increased CAT activity, enhanced selenate reduction, and thylakoid assembly pathways were highlighted for S. hainanensis's high-temperature tolerance. Notably, it is the first time to reveal a whole selenate reduction pathway from SeO42- to Se2- and its contribution to the high-temperature tolerance of S. hainanensis. These unique mechanisms, including antioxidation and maintaining photosynthesis homeostasis, efficiently ensure the high-temperature tolerance of S. hainanensis than Effrenium sp. Compared with the thermosensitivity of coral symbiotic zooxanthellae Symbiodiniaceae, this study provides novel insights into the high-temperature tolerance mechanisms of coral symbiotic zoochlorellae S. hainanensis, which will contribute to corals' survival in the warming oceans caused by global climate change. IMPORTANCE The increasing ocean temperature above 31°C-32°C might trigger a breakdown of the coral-Symbiodiniaceae symbioses or coral bleaching because of the thermosensitivity of Symbiodiniaceae; therefore, the exploration of alternative coral symbiotic algae with high-temperature tolerance is important for the corals' protection under warming oceans. This study proves that zoochlorellae Symbiochlorum hainanensis can tolerate 38°C, which is the highest temperature tolerance known for coral symbiotic algae to date, with unique high-temperature tolerance mechanisms. Particularly, for the first time, an internal selenium antioxidant mechanism of coral symbiotic S. hainanensis to high temperature was suggested.
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Affiliation(s)
- Yilin Xiao
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Luyao Gao
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhiyong Li
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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Hoepner CM, Stewart ZK, Qiao R, Fobert EK, Prentis PJ, Colella A, Chataway T, Burke da Silva K, Abbott CA. Proteotransciptomics of the Most Popular Host Sea Anemone Entacmaea quadricolor Reveals Not All Toxin Genes Expressed by Tentacles Are Recruited into Its Venom Arsenal. Toxins (Basel) 2024; 16:85. [PMID: 38393163 PMCID: PMC10893224 DOI: 10.3390/toxins16020085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/30/2024] [Accepted: 01/30/2024] [Indexed: 02/25/2024] Open
Abstract
While the unique symbiotic relationship between anemonefishes and sea anemones is iconic, it is still not fully understood how anemonefishes can withstand and thrive within the venomous environment of their host sea anemone. In this study, we used a proteotranscriptomics approach to elucidate the proteinaceous toxin repertoire from the most common host sea anemone, Entacmaea quadricolor. Although 1251 different toxin or toxin-like RNA transcripts were expressed in E. quadricolor tentacles (0.05% of gene clusters, 1.8% of expression) and 5375 proteins were detected in milked venom, only 4% of proteins detected in venom were putative toxins (230), and they only represent on average 14% of the normalised protein expression in the milked venom samples. Thus, most proteins in milked venom do not appear to have a toxin function. This work raises the perils of defining a dominant venom phenotype based on transcriptomics data alone in sea anemones, as we found that the dominant venom phenotype differs between the transcriptome and proteome abundance data. E. quadricolor venom contains a mixture of toxin-like proteins of unknown and known function. A newly identified toxin protein family, Z3, rich in conserved cysteines of unknown function, was the most abundant at the RNA transcript and protein levels. The venom was also rich in toxins from the Protease S1, Kunitz-type and PLA2 toxin protein families and contains toxins from eight venom categories. Exploring the intricate venom toxin components in other host sea anemones will be crucial for improving our understanding of how anemonefish adapt to the venomous environment.
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Affiliation(s)
- Cassie M. Hoepner
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia
| | - Zachary K. Stewart
- Centre for Agriculture and Bioeconomy, Queensland University of Technology, Brisbane, QLD 4001, Australia
| | - Robert Qiao
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia
| | - Emily K. Fobert
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia
- School of BioSciences, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Peter J. Prentis
- Centre for Agriculture and Bioeconomy, Queensland University of Technology, Brisbane, QLD 4001, Australia
| | - Alex Colella
- Flinders Proteomics Facility, College of Medicine and Public Health, Flinders University, Bedford Park, SA 5042, Australia
| | - Tim Chataway
- Flinders Proteomics Facility, College of Medicine and Public Health, Flinders University, Bedford Park, SA 5042, Australia
| | - Karen Burke da Silva
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia
| | - Catherine A. Abbott
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia
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Murthy MHS, Jasbi P, Lowe W, Kumar L, Olaosebikan M, Roger L, Yang J, Lewinski N, Daniels N, Cowen L, Klein-Seetharaman J. Insulin signaling and pharmacology in humans and in corals. PeerJ 2024; 12:e16804. [PMID: 38313028 PMCID: PMC10838073 DOI: 10.7717/peerj.16804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 12/27/2023] [Indexed: 02/06/2024] Open
Abstract
Once thought to be a unique capability of the Langerhans islets in the pancreas of mammals, insulin (INS) signaling is now recognized as an evolutionarily ancient function going back to prokaryotes. INS is ubiquitously present not only in humans but also in unicellular eukaryotes, fungi, worms, and Drosophila. Remote homologue identification also supports the presence of INS and INS receptor in corals where the availability of glucose is largely dependent on the photosynthetic activity of the symbiotic algae. The cnidarian animal host of corals operates together with a 20,000-sized microbiome, in direct analogy to the human gut microbiome. In humans, aberrant INS signaling is the hallmark of metabolic disease, and is thought to play a major role in aging, and age-related diseases, such as Alzheimer's disease. We here would like to argue that a broader view of INS beyond its human homeostasis function may help us understand other organisms, and in turn, studying those non-model organisms may enable a novel view of the human INS signaling system. To this end, we here review INS signaling from a new angle, by drawing analogies between humans and corals at the molecular level.
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Affiliation(s)
| | - Paniz Jasbi
- School of Molecular Sciences, Arizona State University, Phoenix, AZ, USA
| | - Whitney Lowe
- Departments of Chemistry & Physics, Colorado School of Mines, Golden, CO, United States
| | - Lokender Kumar
- Departments of Chemistry & Physics, Colorado School of Mines, Golden, CO, United States
| | | | - Liza Roger
- School of Molecular Sciences, Arizona State University, Phoenix, AZ, USA
- School of Ocean Futures, Arizona State University, Tempe, AZ, United States of America
| | - Jinkyu Yang
- Department of Aeronautics & Astronautics, University of Washington, Seattle, WA, USA
| | - Nastassja Lewinski
- Department of Chemical and Life Science Engineering, Virginia Commonwealth University, Richmond, VA, USA
| | - Noah Daniels
- Department of Computer Science, University of Rhode Island, Kingston, RI, USA
| | - Lenore Cowen
- Department of Computer Science, Tufts University, Medford, MA, USA
| | - Judith Klein-Seetharaman
- School of Molecular Sciences, Arizona State University, Phoenix, AZ, USA
- Departments of Chemistry & Physics, Colorado School of Mines, Golden, CO, United States
- College of Health Solutions, Arizona State University, Phoenix, AZ, United States
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Dougan KE, Deng ZL, Wöhlbrand L, Reuse C, Bunk B, Chen Y, Hartlich J, Hiller K, John U, Kalvelage J, Mansky J, Neumann-Schaal M, Overmann J, Petersen J, Sanchez-Garcia S, Schmidt-Hohagen K, Shah S, Spröer C, Sztajer H, Wang H, Bhattacharya D, Rabus R, Jahn D, Chan CX, Wagner-Döbler I. Multi-omics analysis reveals the molecular response to heat stress in a "red tide" dinoflagellate. Genome Biol 2023; 24:265. [PMID: 37996937 PMCID: PMC10666404 DOI: 10.1186/s13059-023-03107-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 11/10/2023] [Indexed: 11/25/2023] Open
Abstract
BACKGROUND "Red tides" are harmful algal blooms caused by dinoflagellate microalgae that accumulate toxins lethal to other organisms, including humans via consumption of contaminated seafood. These algal blooms are driven by a combination of environmental factors including nutrient enrichment, particularly in warm waters, and are increasingly frequent. The molecular, regulatory, and evolutionary mechanisms that underlie the heat stress response in these harmful bloom-forming algal species remain little understood, due in part to the limited genomic resources from dinoflagellates, complicated by the large sizes of genomes, exhibiting features atypical of eukaryotes. RESULTS We present the de novo assembled genome (~ 4.75 Gbp with 85,849 protein-coding genes), transcriptome, proteome, and metabolome from Prorocentrum cordatum, a globally abundant, bloom-forming dinoflagellate. Using axenic algal cultures, we study the molecular mechanisms that underpin the algal response to heat stress, which is relevant to current ocean warming trends. We present the first evidence of a complementary interplay between RNA editing and exon usage that regulates the expression and functional diversity of biomolecules, reflected by reduction in photosynthesis, central metabolism, and protein synthesis. These results reveal genomic signatures and post-transcriptional regulation for the first time in a pelagic dinoflagellate. CONCLUSIONS Our multi-omics analyses uncover the molecular response to heat stress in an important bloom-forming algal species, which is driven by complex gene structures in a large, high-G+C genome, combined with multi-level transcriptional regulation. The dynamics and interplay of molecular regulatory mechanisms may explain in part how dinoflagellates diversified to become some of the most ecologically successful organisms on Earth.
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Affiliation(s)
- Katherine E Dougan
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Zhi-Luo Deng
- Helmholtz-Center for Infection Research (HZI), Inhoffenstraße 7, Braunschweig, 38124, Germany
| | - Lars Wöhlbrand
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, 26129, Oldenburg, Germany
| | - Carsten Reuse
- Braunschweig Center for Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106, Brunswick, Germany
| | - Boyke Bunk
- German Culture Collection for Microorganisms and Cell Cultures (DSMZ), Inhoffenstraße 7B, 38124, Braunschweig, Germany
| | - Yibi Chen
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Juliane Hartlich
- Braunschweig Center for Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106, Brunswick, Germany
| | - Karsten Hiller
- Braunschweig Center for Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106, Brunswick, Germany
| | - Uwe John
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570, Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Ammerländer Heerstraße 231, 26129, Oldenburg, Germany
| | - Jana Kalvelage
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, 26129, Oldenburg, Germany
| | - Johannes Mansky
- Braunschweig Center for Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106, Brunswick, Germany
| | - Meina Neumann-Schaal
- German Culture Collection for Microorganisms and Cell Cultures (DSMZ), Inhoffenstraße 7B, 38124, Braunschweig, Germany
| | - Jörg Overmann
- German Culture Collection for Microorganisms and Cell Cultures (DSMZ), Inhoffenstraße 7B, 38124, Braunschweig, Germany
| | - Jörn Petersen
- German Culture Collection for Microorganisms and Cell Cultures (DSMZ), Inhoffenstraße 7B, 38124, Braunschweig, Germany
| | - Selene Sanchez-Garcia
- Braunschweig Center for Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106, Brunswick, Germany
| | - Kerstin Schmidt-Hohagen
- Braunschweig Center for Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106, Brunswick, Germany
| | - Sarah Shah
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Cathrin Spröer
- German Culture Collection for Microorganisms and Cell Cultures (DSMZ), Inhoffenstraße 7B, 38124, Braunschweig, Germany
| | - Helena Sztajer
- Braunschweig Center for Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106, Brunswick, Germany
| | - Hui Wang
- Braunschweig Center for Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106, Brunswick, Germany
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Ralf Rabus
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, 26129, Oldenburg, Germany
| | - Dieter Jahn
- Braunschweig Center for Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106, Brunswick, Germany
| | - Cheong Xin Chan
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia.
| | - Irene Wagner-Döbler
- Braunschweig Center for Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106, Brunswick, Germany.
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Zhang J, Li X, Wang X, Guan W. Transcriptome analysis of two bloom-forming Prorocentrum species reveals physiological changes related to light and temperature. HARMFUL ALGAE 2023; 125:102421. [PMID: 37220974 DOI: 10.1016/j.hal.2023.102421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 02/25/2023] [Accepted: 03/05/2023] [Indexed: 05/25/2023]
Abstract
Temperature and light substantially influence red tide succession. However, it remains unclear whether the molecular mechanisms differ among species. In this study, we measured the variation in the physiological parameters of growth and pigments and transcriptional levels of two bloom-forming dinoflagellates, namely Prorocentrum micans and P. cordatum. This was undertaken in four treatments that represented two factorial temperature combinations (LT: 20 °C, HT: 28 °C) and light conditions (LL: 50 µmol photons m-2 s-1, HL: 400 µmol photons m-2 s-1) for 7-day batch culture. Growth under high temperature and high light (HTHL) was the fastest, while growth under high temperature and low light (HTLL) was the slowest. The pigments (chlorophyll a and carotenoids) decreased significantly in all high light (HL) treatments, but not in high temperature (HT) treatments. HL alleviated the low light-caused photolimitation and enhanced the growth of both species at low temperatures. However, HT inhibited the growth of both species by inducing oxidative stress under low light conditions. HL mitigated the HT-induced stress on growth in both species by upregulating photosynthesis, antioxidase activity, protein folding, and degradation. The cells of P. micans were more sensitive to HT and HL than those of P. cordatum. This study deepens our understanding of the species-specific mechanism of dinoflagellates at the transcriptomic level, adapting to the future ocean changes including higher solar radiation and higher temperatures in the upper mixed layer.
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Affiliation(s)
- Jiazhu Zhang
- Wenzhou Key Laboratory of Sanitary Microbiology, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Xuanwen Li
- Wenzhou Key Laboratory of Sanitary Microbiology, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Xinjie Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, China), School of Environmental Science and Technology, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Wanchun Guan
- Wenzhou Key Laboratory of Sanitary Microbiology, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China.
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Reich HG, Camp EF, Roger LM, Putnam HM. The trace metal economy of the coral holobiont: supplies, demands and exchanges. Biol Rev Camb Philos Soc 2023; 98:623-642. [PMID: 36897260 DOI: 10.1111/brv.12922] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/23/2022]
Abstract
The juxtaposition of highly productive coral reef ecosystems in oligotrophic waters has spurred substantial interest and progress in our understanding of macronutrient uptake, exchange, and recycling among coral holobiont partners (host coral, dinoflagellate endosymbiont, endolithic algae, fungi, viruses, bacterial communities). By contrast, the contribution of trace metals to the physiological performance of the coral holobiont and, in turn, the functional ecology of reef-building corals remains unclear. The coral holobiont's trace metal economy is a network of supply, demand, and exchanges upheld by cross-kingdom symbiotic partnerships. Each partner has unique trace metal requirements that are central to their biochemical functions and the metabolic stability of the holobiont. Organismal homeostasis and the exchanges among partners determine the ability of the coral holobiont to adjust to fluctuating trace metal supplies in heterogeneous reef environments. This review details the requirements for trace metals in core biological processes and describes how metal exchanges among holobiont partners are key to sustaining complex nutritional symbioses in oligotrophic environments. Specifically, we discuss how trace metals contribute to partner compatibility, ability to cope with stress, and thereby to organismal fitness and distribution. Beyond holobiont trace metal cycling, we outline how the dynamic nature of the availability of environmental trace metal supplies can be influenced by a variability of abiotic factors (e.g. temperature, light, pH, etc.). Climate change will have profound consequences on the availability of trace metals and further intensify the myriad stressors that influence coral survival. Lastly, we suggest future research directions necessary for understanding the impacts of trace metals on the coral holobiont symbioses spanning subcellular to organismal levels, which will inform nutrient cycling in coral ecosystems more broadly. Collectively, this cross-scale elucidation of the role of trace metals for the coral holobiont will allow us to improve forecasts of future coral reef function.
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Affiliation(s)
- Hannah G Reich
- Department of Biological Sciences, University of Rhode Island, 120 Flagg Road, Kingston, RI, 02881, USA
| | - Emma F Camp
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Liza M Roger
- Chemical & Life Science Engineering, Virginia Commonwealth University, 601 W. Main Street, Richmond, VA, 23284, USA
| | - Hollie M Putnam
- Department of Biological Sciences, University of Rhode Island, 120 Flagg Road, Kingston, RI, 02881, USA
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Thirukanthan CS, Azra MN, Lananan F, Sara’ G, Grinfelde I, Rudovica V, Vincevica-Gaile Z, Burlakovs J. The Evolution of Coral Reef under Changing Climate: A Scientometric Review. Animals (Basel) 2023; 13:ani13050949. [PMID: 36899805 PMCID: PMC10000160 DOI: 10.3390/ani13050949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/19/2023] [Accepted: 03/03/2023] [Indexed: 03/09/2023] Open
Abstract
In this scientometric review, we employ the Web of Science Core Collection to assess current publications and research trends regarding coral reefs in relation to climate change. Thirty-seven keywords for climate change and seven keywords for coral reefs were used in the analysis of 7743 articles on coral reefs and climate change. The field entered an accelerated uptrend phase in 2016, and it is anticipated that this phase will last for the next 5 to 10 years of research publication and citation. The United States and Australia have produced the greatest number of publications in this field. A cluster (i.e., focused issue) analysis showed that coral bleaching dominated the literature from 2000 to 2010, ocean acidification from 2010 to 2020, and sea-level rise, as well as the central Red Sea (Africa/Asia), in 2021. Three different types of keywords appear in the analysis based on which are the (i) most recent (2021), (ii) most influential (highly cited), and (iii) mostly used (frequently used keywords in the article) in the field. The Great Barrier Reef, which is found in the waters of Australia, is thought to be the subject of current coral reef and climate change research. Interestingly, climate-induced temperature changes in "ocean warming" and "sea surface temperature" are the most recent significant and dominant keywords in the coral reef and climate change area.
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Affiliation(s)
- Chandra Segaran Thirukanthan
- Institute of Marine Biotechnology (IMB), Universiti Malaysia Terengganu (UMT), Kuala Nerus 21030, Terengganu, Malaysia
| | - Mohamad Nor Azra
- Institute of Marine Biotechnology (IMB), Universiti Malaysia Terengganu (UMT), Kuala Nerus 21030, Terengganu, Malaysia
- Research Center for Marine and Land Bioindustry, Earth Sciences and Maritime Organization, National Research and Innovation Agency (BRIN), Pemenang 83352, Indonesia
- Correspondence: (M.N.A.); (J.B.); Tel.: +609-6683785 (M.N.A.)
| | - Fathurrahman Lananan
- East Coast Environmental Research Institute, Universiti Sultan Zainal Abidin (UniSZA), Gong Badak Campus, Kuala Nerus 21300, Terengganu, Malaysia
| | - Gianluca Sara’
- Laboratory of Ecology, Earth and Marine Sciences Department, University of Palermo, 90133 Palermo, Italy
| | - Inga Grinfelde
- Laboratory of Forest and Water Resources, Latvia University of Life Sciences and Technologies, LV-3001 Jelgava, Latvia
| | - Vite Rudovica
- Department of Analytical Chemistry, University of Latvia, LV-1004 Riga, Latvia
| | | | - Juris Burlakovs
- Mineral and Energy Economy Research Institute of the Polish Academy of Sciences, 31-261 Krakow, Poland
- Correspondence: (M.N.A.); (J.B.); Tel.: +609-6683785 (M.N.A.)
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9
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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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10
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Ip JCH, Zhang Y, Xie JY, Yeung YH, Qiu JW. Comparative transcriptomics of two coral holobionts collected during the 2017 El Niño heat wave reveal differential stress response mechanisms. MARINE POLLUTION BULLETIN 2022; 182:114017. [PMID: 35963227 DOI: 10.1016/j.marpolbul.2022.114017] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/28/2022] [Accepted: 07/31/2022] [Indexed: 06/15/2023]
Abstract
Although coral species exhibit differential susceptibility to stressors, little is known about the underlying molecular mechanisms. Here we compared scleractinian corals Montipora peltiformis and Platygyra carnosa collected during the 2017 El Niño heat wave. Zooxanthellae density and chlorophyll a content declined and increased substantially during and after heat stress event, respective. However, the magnitude of change was larger in M. peltiformis. Transcriptome analysis showed that heat-stressed corals corresponded to metabolic depression and catabolism of amino acids in both hosts which might promote their survival. However, only M. peltiformis has developed the bleached coral phenotype with corresponding strong stress- and immune-related responses in the host and symbiont, and strong suppression of photosynthesis-related genes in the symbiont. Overall, our study reveals differences among species in the homeostatic capacity to prevent the development of the bleached phenotype under environmental stressors, eventually determining their likelihood of survival in the warming ocean.
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Affiliation(s)
- Jack Chi-Ho Ip
- Department of Biology, Hong Kong Baptist University, Hong Kong, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; HKBU Institute of Research and Continuing Education, Virtual University Park, Shenzhen, China
| | - Yanjie Zhang
- School of Life Sciences, Hainan University, Haikou, China.
| | - James Y Xie
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Yip Hung Yeung
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, Hong Kong, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; HKBU Institute of Research and Continuing Education, Virtual University Park, Shenzhen, China.
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11
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Nitschke MR, Rosset SL, Oakley CA, Gardner SG, Camp EF, Suggett DJ, Davy SK. The diversity and ecology of Symbiodiniaceae: A traits-based review. ADVANCES IN MARINE BIOLOGY 2022; 92:55-127. [PMID: 36208879 DOI: 10.1016/bs.amb.2022.07.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Among the most successful microeukaryotes to form mutualisms with animals are dinoflagellates in the family Symbiodiniaceae. These photosynthetic symbioses drive significant primary production and are responsible for the formation of coral reef ecosystems but are particularly sensitive when environmental conditions become extreme. Annual episodes of widespread coral bleaching (disassociation of the mutualistic partnership) and mortality are forecasted from the year 2060 under current trends of ocean warming. However, host cnidarians and dinoflagellate symbionts display exceptional genetic and functional diversity, and meaningful predictions of the future that embrace this biological complexity are difficult to make. A recent move to trait-based biology (and an understanding of how traits are shaped by the environment) has been adopted to move past this problem. The aim of this review is to: (1) provide an overview of the major cnidarian lineages that are symbiotic with Symbiodiniaceae; (2) summarise the symbiodiniacean genera associated with cnidarians with reference to recent changes in taxonomy and systematics; (3) examine the knowledge gaps in Symbiodiniaceae life history from a trait-based perspective; (4) review Symbiodiniaceae trait variation along three abiotic gradients (light, nutrients, and temperature); and (5) provide recommendations for future research of Symbiodiniaceae traits. We anticipate that a detailed understanding of traits will further reveal basic knowledge of the evolution and functional diversity of these mutualisms, as well as enhance future efforts to model stability and change in ecosystems dependent on cnidarian-dinoflagellate organisms.
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Affiliation(s)
- Matthew R Nitschke
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand; Climate Change Cluster, University of Technology Sydney, Broadway, NSW, Australia.
| | - Sabrina L Rosset
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Clinton A Oakley
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Stephanie G Gardner
- Center for Marine Science and Innovation, University of New South Wales Sydney, Kensington, NSW, Australia
| | - Emma F Camp
- Climate Change Cluster, University of Technology Sydney, Broadway, NSW, Australia
| | - David J Suggett
- Climate Change Cluster, University of Technology Sydney, Broadway, NSW, Australia
| | - Simon K Davy
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
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12
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Chen Y, Shah S, Dougan KE, van Oppen MJH, Bhattacharya D, Chan CX. Improved Cladocopium goreaui Genome Assembly Reveals Features of a Facultative Coral Symbiont and the Complex Evolutionary History of Dinoflagellate Genes. Microorganisms 2022; 10:microorganisms10081662. [PMID: 36014080 PMCID: PMC9412976 DOI: 10.3390/microorganisms10081662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/10/2022] [Accepted: 08/15/2022] [Indexed: 11/16/2022] Open
Abstract
Dinoflagellates of the family Symbiodiniaceae are crucial photosymbionts in corals and other marine organisms. Of these, Cladocopium goreaui is one of the most dominant symbiont species in the Indo-Pacific. Here, we present an improved genome assembly of C. goreaui combining new long-read sequence data with previously generated short-read data. Incorporating new full-length transcripts to guide gene prediction, the C. goreaui genome (1.2 Gb) exhibits a high extent of completeness (82.4% based on BUSCO protein recovery) and better resolution of repetitive sequence regions; 45,322 gene models were predicted, and 327 putative, topologically associated domains of the chromosomes were identified. Comparison with other Symbiodiniaceae genomes revealed a prevalence of repeats and duplicated genes in C. goreaui, and lineage-specific genes indicating functional innovation. Incorporating 2,841,408 protein sequences from 96 taxonomically diverse eukaryotes and representative prokaryotes in a phylogenomic approach, we assessed the evolutionary history of C. goreaui genes. Of the 5246 phylogenetic trees inferred from homologous protein sets containing two or more phyla, 35–36% have putatively originated via horizontal gene transfer (HGT), predominantly (19–23%) via an ancestral Archaeplastida lineage implicated in the endosymbiotic origin of plastids: 10–11% are of green algal origin, including genes encoding photosynthetic functions. Our results demonstrate the utility of long-read sequence data in resolving structural features of a dinoflagellate genome, and highlight how genetic transfer has shaped genome evolution of a facultative symbiont, and more broadly of dinoflagellates.
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Affiliation(s)
- Yibi Chen
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Sarah Shah
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Katherine E. Dougan
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Madeleine J. H. van Oppen
- School of Bioscience, The University of Melbourne, Parkville, VIC 3010, Australia
- Australian Institute of Marine Science, Townsville, QLD 4810, Australia
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
| | - Cheong Xin Chan
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Correspondence:
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13
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Bashir F, Kovács S, Ábrahám Á, Nagy K, Ayaydin F, Valkony-Kelemen I, Ferenc G, Galajda P, Tóth SZ, Sass L, Kós PB, Vass I, Szabó M. Viable protoplast formation of the coral endosymbiont alga Symbiodinium spp. in a microfluidics platform. LAB ON A CHIP 2022; 22:2986-2999. [PMID: 35588270 DOI: 10.1039/d2lc00130f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Symbiodiniaceae is an important dinoflagellate family which lives in endosymbiosis with reef invertebrates, including coral polyps, making them central to the holobiont. With coral reefs currently under extreme threat from climate change, there is a pressing need to improve our understanding on the stress tolerance and stress avoidance mechanisms of Symbiodinium spp. Reactive oxygen species (ROS) such as singlet oxygen are central players in mediating various stress responses; however, the detection of ROS using specific dyes is still far from definitive in intact Symbiodinium cells due to the hindrance of uptake of certain fluorescent dyes because of the presence of the cell wall. Protoplast technology provides a promising platform for studying oxidative stress with the main advantage of removed cell wall, however the preparation of viable protoplasts remains a significant challenge. Previous studies have successfully applied cellulose-based protoplast preparation in Symbiodiniaceae; however, the protoplast formation and regeneration process was found to be suboptimal. Here, we present a microfluidics-based platform which allowed protoplast isolation from individually trapped Symbiodinium cells, by using a precisely adjusted flow of cell wall digestion enzymes (cellulase and macerozyme). Trapped single cells exhibited characteristic changes in their morphology, cessation of cell division and a slight decrease in photosynthetic activity during protoplast formation. Following digestion and transfer to regeneration medium, protoplasts remained photosynthetically active, regrew cell walls, regained motility, and entered exponential growth. Elevated flow rates in the microfluidic chambers resulted in somewhat faster protoplast formation; however, cell wall digestion at higher flow rates partially compromised photosynthetic activity. Physiologically competent protoplasts prepared from trapped cells in microfluidic chambers allowed for the first time the visualization of the intracellular localization of singlet oxygen (using Singlet Oxygen Sensor Green dye) in Symbiodiniaceae, potentially opening new avenues for studying oxidative stress.
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Affiliation(s)
- Faiza Bashir
- Institute of Plant Biology, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary.
- Doctoral School of Biology, University of Szeged, Szeged, Hungary
| | - Sándor Kovács
- Institute of Plant Biology, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary.
| | - Ágnes Ábrahám
- Institute of Biophysics, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
- Doctoral School of Multidisciplinary Medical Sciences, University of Szeged, Szeged, Hungary
| | - Krisztina Nagy
- Institute of Biophysics, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
| | - Ferhan Ayaydin
- Cellular Imaging Laboratory, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
| | - Ildikó Valkony-Kelemen
- Cellular Imaging Laboratory, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
| | - Györgyi Ferenc
- Institute of Plant Biology, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary.
| | - Péter Galajda
- Institute of Biophysics, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
| | - Szilvia Z Tóth
- Institute of Plant Biology, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary.
| | - László Sass
- Institute of Plant Biology, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary.
| | - Péter B Kós
- Institute of Plant Biology, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary.
- Department of Biotechnology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Imre Vass
- Institute of Plant Biology, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary.
| | - Milán Szabó
- Institute of Plant Biology, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary.
- Climate Change Cluster, University of Technology Sydney, Australia
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14
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Teng GC, Boo MV, Lam SH, Pang CZ, Chew SF, Ip YK. Molecular characterization and light-dependent expression of glycerol facilitator (GlpF) in coccoid Symbiodiniaceae dinoflagellates of the giant clam Tridacna squamosa. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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15
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Bleaching physiology: who's the 'weakest link' - host vs. symbiont? Emerg Top Life Sci 2022; 6:17-32. [PMID: 35179208 DOI: 10.1042/etls20210228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 01/20/2022] [Accepted: 02/01/2022] [Indexed: 11/17/2022]
Abstract
Environmental stress, such as an increase in the sea surface temperature, triggers coral bleaching, a profound dysfunction of the mutualist symbiosis between the host cnidarians and their photosynthetic dinoflagellates of the Family Symbiodiniaceae. Because of climate change, mass coral bleaching events will increase in frequency and severity in the future, threatening the persistence of this iconic marine ecosystem at global scale. Strategies adapted to coral reefs preservation and restoration may stem from the identification of the succession of events and of the different molecular and cellular contributors to the bleaching phenomenon. To date, studies aiming to decipher the cellular cascade leading to temperature-related bleaching, emphasized the involvement of reactive species originating from compromised bioenergetic pathways (e.g. cellular respiration and photosynthesis). These molecules are responsible for damage to various cellular components causing the dysregulation of cellular homeostasis and the breakdown of symbiosis. In this review, we synthesize the current knowledge available in the literature on the cellular mechanisms caused by thermal stress, which can initiate or participate in the cell cascade leading to the loss of symbionts, with a particular emphasis on the role of each partner in the initiating processes.
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16
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Dungan AM, Hartman LM, Blackall LL, van Oppen MJH. Exploring microbiome engineering as a strategy for improved thermal tolerance in Exaiptasia diaphana. J Appl Microbiol 2022; 132:2940-2956. [PMID: 35104027 PMCID: PMC9303619 DOI: 10.1111/jam.15465] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 12/08/2021] [Accepted: 01/24/2022] [Indexed: 11/28/2022]
Abstract
Aims Fourteen percent of all living coral, equivalent to more than all the coral on the Great Barrier Reef, has died in the past decade as a result of climate change‐driven bleaching. Inspired by the ‘oxidative stress theory of coral bleaching’, we investigated whether a bacterial consortium designed to scavenge free radicals could integrate into the host microbiome and improve thermal tolerance of the coral model, Exaiptasia diaphana. Methods and Results E. diaphana anemones were inoculated with a consortium of high free radical scavenging (FRS) bacteria, a consortium of congeneric low FRS bacteria, or sterile seawater as a control, then exposed to elevated temperature. Increases in the relative abundance of Labrenzia during the first 2 weeks following the last inoculation provided evidence for temporary inoculum integration into the E. diaphana microbiome. Initial uptake of other consortium members was inconsistent, and these bacteria did not persist either in E. diaphana’s microbiome over time. Given their non‐integration into the host microbiome, the ability of the FRS consortium to mitigate thermal stress could not be assessed. Importantly, there were no physiological impacts (negative or positive) of the bacterial inoculations on the holobiont. Conclusions The introduced bacteria were not maintained in the anemone microbiome over time, thus, their protective effect is unknown. Achieving long‐term integration of bacteria into cnidarian microbiomes remains a research priority. Significance and Impact of the Study Microbiome engineering strategies to mitigate coral bleaching may assist coral reefs in their persistence until climate change has been curbed. This study provides insights that will inform microbiome manipulation approaches in coral bleaching mitigation research.
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Affiliation(s)
- Ashley M Dungan
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Leon M Hartman
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia.,Swinburne University of Technology, Hawthorn, VIC, Australia
| | - Linda L Blackall
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Madeleine J H van Oppen
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia.,Australian Institute of Marine Science, Townsville, Australia
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17
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The Implication Inferred from the Expression of Small Heat-Shock Protein Genes in Dinoflagellate Resting Cysts Buried in Marine Sediment. DIVERSITY 2021. [DOI: 10.3390/d13100471] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Dinoflagellates are unicellular eukaryotic microalgae, occupying pivotal niches in aquatic ecosystems with great ecological, biological, and economic significance. Small heat shock proteins (sHsps) are the most omnipresent, but the least conserved, family of molecular chaperones found in all domains of life. Although their common name (small Hsp) implies to exclusively stress their heat shock-responsive function, many sHsps in fact engage in a variety of physiological processes, from cell growth and proliferation to embryogenesis, development, differentiation, apoptosis, and even to human disease prevention. Recent years have greatly expanded our understanding of sHsps in higher plants; however, comprehensive study aiming to delineate the composition and expression pattern of dinoflagellate sHsp gene family has not yet been performed. In this study, we constructed dinoflagellate-specific environmental cDNA library from marine sediment and sequenced using the third-generation sequencing technique. Screening of sHsp genes from the library returned 13 entries with complete coding regions, which were considered to be transcriptionally activated in the natural community of dinoflagellate resting cysts. All the 13 dinoflagellate sHsps consisted of a solely characteristic α-crystallin domain, covering 88–123 amino acid residues with the typical A-X-X-X-N-G-V-L motif, flanked by variable N- and C-terminal extensions. Multiple alignment revealed considerable amino acid divergence (~26.7% average similarity) among them. An unexpected close relationship was revealed between dinoflagellate and green algal sHsps in the phylogenetic tree, seemingly reflecting a close evolutionary relationship of these sHsps themselves. We confirmed that sHsp mRNAs are expressed during dormancy of the resting cyst assemblages of dinoflagellates that were buried in marine sediment, which raised the possibility that the sHsp expression is part of the machinery of maintaining the dormancy or/and the adaptation to ambient conditions of dinoflagellate resting cysts. Our results, although preliminary, gained an important glance on the universal presence of sHsps in dinoflagellates and their active expressions in the assemblage of resting cysts that were buried in the marine sediment. The essentiality of sHsps functioning in resting cysts necessitate more intensive and extensive investigations on all possible functions of Hsps in dinoflagellates, a group of protists with vital ecological and biological importance.
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18
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Figueroa RI, Howe-Kerr LI, Correa AMS. Direct evidence of sex and a hypothesis about meiosis in Symbiodiniaceae. Sci Rep 2021; 11:18838. [PMID: 34552138 PMCID: PMC8458349 DOI: 10.1038/s41598-021-98148-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 08/30/2021] [Indexed: 02/08/2023] Open
Abstract
Dinoflagellates in the family Symbiodiniaceae are obligate endosymbionts of diverse marine invertebrates, including corals, and impact the capacity of their hosts to respond to climate change-driven ocean warming. Understanding the conditions under which increased genetic variation in Symbiodiniaceae arises via sexual recombination can support efforts to evolve thermal tolerance in these symbionts and ultimately mitigate coral bleaching, the breakdown of the coral-Symbiodiniaceae partnership under stress. However, direct observations of meiosis in Symbiodiniaceae have not been reported, despite various lines of indirect evidence that it occurs. We present the first cytological evidence of sex in Symbiodiniaceae based on nuclear DNA content and morphology using Image Flow Cytometry, Cell Sorting and Confocal Microscopy. We show the Symbiodiniaceae species, Cladocopium latusorum, undergoes gamete conjugation, zygote formation, and meiosis within a dominant reef-building coral in situ. On average, sex was detected in 1.5% of the cells analyzed (N = 10,000-40,000 cells observed per sample in a total of 20 samples obtained from 3 Pocillopora colonies). We hypothesize that meiosis follows a two-step process described in other dinoflagellates, in which diploid zygotes form dyads during meiosis I, and triads and tetrads as final products of meiosis II. This study sets the stage for investigating environmental triggers of Symbiodiniaceae sexuality and can accelerate the assisted evolution of a key coral symbiont in order to combat reef degradation.
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Affiliation(s)
- R. I. Figueroa
- Spanish Institute of Oceanography in Vigo (IEO-CSIC), Subida a Radio Faro, 50, 36390 Vigo, Spain
| | - L. I. Howe-Kerr
- grid.21940.3e0000 0004 1936 8278BioSciences Department, Rice University, Houston, TX USA
| | - A. M. S. Correa
- grid.21940.3e0000 0004 1936 8278BioSciences Department, Rice University, Houston, TX USA
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19
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Insights into the Structure of Rubisco from Dinoflagellates-In Silico Studies. Int J Mol Sci 2021; 22:ijms22168524. [PMID: 34445230 PMCID: PMC8395205 DOI: 10.3390/ijms22168524] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/30/2021] [Accepted: 08/04/2021] [Indexed: 02/06/2023] Open
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is one of the best studied enzymes. It is crucial for photosynthesis, and thus for all of biosphere’s productivity. There are four isoforms of this enzyme, differing by amino acid sequence composition and quaternary structure. However, there is still a group of organisms, dinoflagellates, single-cell eukaryotes, that are confirmed to possess Rubisco, but no successful purification of the enzyme of such origin, and hence a generation of a crystal structure was reported to date. Here, we are using in silico tools to generate the possible structure of Rubisco from a dinoflagellate representative, Symbiodinium sp. We selected two templates: Rubisco from Rhodospirillum rubrum and Rhodopseudomonas palustris. Both enzymes are the so-called form II Rubiscos, but the first is exclusively a homodimer, while the second one forms homo-hexamers. Obtained models show no differences in amino acids crucial for Rubisco activity. The variation was found at two closely located inserts in the C-terminal domain, of which one extends a helix and the other forms a loop. These inserts most probably do not play a direct role in the enzyme’s activity, but may be responsible for interaction with an unknown protein partner, possibly a regulator or a chaperone. Analysis of the possible oligomerization interface indicated that Symbiodinium sp. Rubisco most likely forms a trimer of homodimers, not just a homodimer. This hypothesis was empowered by calculation of binding energies. Additionally, we found that the protein of study is significantly richer in cysteine residues, which may be the cause for its activity loss shortly after cell lysis. Furthermore, we evaluated the influence of the loop insert, identified exclusively in the Symbiodinium sp. protein, on the functionality of the recombinantly expressed R. rubrum Rubisco. All these findings shed new light onto dinoflagellate Rubisco and may help in future obtainment of a native, active enzyme.
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20
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Curran A, Barnard S. What is the role of zooxanthellae during coral bleaching? Review of zooxanthellae and their response to environmental stress. S AFR J SCI 2021. [DOI: 10.17159/sajs.2021/8369] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Coral reefs are diverse and productive but sensitive ecosystems. Due to the impact of climate change, these organisms are in danger of dying out, mainly through the process of coral bleaching, which is the process by which zooxanthellae (algal endosymbionts) are expelled from their respective coral hosts, causing the coral to lose colour and become white. Coral bleaching has been linked to increases in sea surface temperatures as well as an increase in light intensity. We reviewed the different zooxanthellae taxa and their ecological traits, as well as the information available on the protective mechanisms present in zooxanthellae cells when they experience environmental stress conditions, such as temperature fluctuations, specifically concentrating on heat shock proteins and their response to antioxidant stress. The eight clades (A–H) previously recognised were reorganised into seven existing genera. Different zooxanthellae taxa exhibit different ecological traits such as their photosynthetic stress responses to light and temperature. Zooxanthellae have the ability to regulate the number and type of heat shock proteins (Hsps) they produce during a heat response. They can also regulate the host’s respective Hsps. Antioxidant responses that can prevent coral hosts from expelling the zooxanthellae, can be found both within exposed coral tissue and the zooxanthellae cells. Despite the lower likelihood of bleaching in South African coral reefs, genetic engineering presents a useful tool to understand and adapt traits within zooxanthellae genotypes to help mitigate coral bleaching in the future.
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Affiliation(s)
- Anuschka Curran
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | - Sandra Barnard
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
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21
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Chan WY, Oakeshott JG, Buerger P, Edwards OR, van Oppen MJH. Adaptive responses of free-living and symbiotic microalgae to simulated future ocean conditions. GLOBAL CHANGE BIOLOGY 2021; 27:1737-1754. [PMID: 33547698 DOI: 10.1111/gcb.15546] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 01/21/2021] [Accepted: 01/24/2021] [Indexed: 06/12/2023]
Abstract
Marine microalgae are a diverse group of microscopic eukaryotic and prokaryotic organisms capable of photosynthesis. They are important primary producers and carbon sinks but their physiology and persistence are severely affected by global climate change. Powerful experimental evolution technologies are being used to examine the potential of microalgae to respond adaptively to current and predicted future conditions, as well as to develop resources to facilitate species conservation and restoration of ecosystem functions. This review synthesizes findings and insights from experimental evolution studies of marine microalgae in response to elevated temperature and/or pCO2 . Adaptation to these environmental conditions has been observed in many studies of marine dinoflagellates, diatoms and coccolithophores. An enhancement in traits such as growth and photo-physiological performance and an increase in upper thermal limit have been shown to be possible, although the extent and rate of change differ between microalgal taxa. Studies employing multiple monoclonal replicates showed variation in responses among replicates and revealed the stochasticity of mutations. The work to date is already providing valuable information on species' climate sensitivity or resilience to managers and policymakers but extrapolating these insights to ecosystem- and community-level impacts continues to be a challenge. We recommend future work should include in situ experiments, diurnal and seasonal fluctuations, multiple drivers and multiple starting genotypes. Fitness trade-offs, stable versus plastic responses and the genetic bases of the changes also need investigating, and the incorporation of genome resequencing into experimental designs will be invaluable.
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Affiliation(s)
- Wing Yan Chan
- School of BioSciences, University of Melbourne, Melbourne, VIC, Australia
| | - John G Oakeshott
- CSIRO Synthetic Biology Future Science Platform, Land & Water, Canberra, ACT, Australia
- Applied Biosciences, Macquarie University, North Ryde, NSW, Australia
| | - Patrick Buerger
- School of BioSciences, University of Melbourne, Melbourne, VIC, Australia
- CSIRO Synthetic Biology Future Science Platform, Land & Water, Canberra, ACT, Australia
| | - Owain R Edwards
- CSIRO Synthetic Biology Future Science Platform, Land & Water, Canberra, ACT, Australia
- Applied Biosciences, Macquarie University, North Ryde, NSW, Australia
| | - Madeleine J H van Oppen
- School of BioSciences, University of Melbourne, Melbourne, VIC, Australia
- Australian Institute of Marine Science, Townsville, QLD, Australia
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22
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Marinov GK, Trevino AE, Xiang T, Kundaje A, Grossman AR, Greenleaf WJ. Transcription-dependent domain-scale three-dimensional genome organization in the dinoflagellate Breviolum minutum. Nat Genet 2021; 53:613-617. [PMID: 33927397 PMCID: PMC8110477 DOI: 10.1038/s41588-021-00848-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 03/17/2021] [Indexed: 11/09/2022]
Abstract
Dinoflagellate chromosomes represent a unique evolutionary experiment, as they exist in a permanently condensed, liquid crystalline state; are not packaged by histones; and contain genes organized into tandem gene arrays, with minimal transcriptional regulation. We analyze the three-dimensional genome of Breviolum minutum, and find large topological domains (dinoflagellate topologically associating domains, which we term 'dinoTADs') without chromatin loops, which are demarcated by convergent gene array boundaries. Transcriptional inhibition disrupts dinoTADs, implicating transcription-induced supercoiling as the primary topological force in dinoflagellates.
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Affiliation(s)
| | - Alexandro E Trevino
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.,Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Tingting Xiang
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA.,Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, CA, USA.,Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Arthur R Grossman
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University, Stanford, CA, USA. .,Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA. .,Department of Applied Physics, Stanford University, Stanford, CA, USA. .,Chan Zuckerberg Biohub, San Francisco, CA, USA.
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23
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Teh LSX, Poo JST, Boo MV, Chew SF, Ip YK. Using glutamine synthetase 1 to evaluate the symbionts' potential of ammonia assimilation and their responses to illumination in five organs of the giant clam, Tridacna squamosa. Comp Biochem Physiol A Mol Integr Physiol 2021; 255:110914. [PMID: 33540079 DOI: 10.1016/j.cbpa.2021.110914] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 01/23/2021] [Accepted: 01/25/2021] [Indexed: 11/16/2022]
Abstract
Nitrogen-deficient symbiotic dinoflagellates (zooxanthellae) living inside the fluted giant clam, Tridacna squamosa, need to obtain nitrogen from the host. Glutamine synthetase 1 (GS1) is a cytosolic enzyme that assimilates ammonia into glutamine. We determined the transcript levels of zooxanthellal GS1 (Zoox-GS1), which represented comprehensively GS1 transcripts of Symbiodinium, Cladocopium and Durusdinium, in five organs of T. squamosa. The outer mantle had significantly higher transcript level of Zoox-GS1 than the inner mantle, foot muscle, hepatopancreas and ctenidium, but the transcript ratios of Zoox-GS1 to zooxanthellal form II ribulose-1,5-bisphosphate carboxylase/oxygenase (Zoox-rbcII), which represented the potential of ammonia assimilation relative to the phototrophic potential, were comparable among these five organs. Based on transcript ratios of Zoox-GS1 to zooxanthellal Urease (Zoox-URE), the outer mantle had the highest potential of urea degradation relative to ammonia assimilation among the five organs, probably because urea degradation could furnish CO2 and NH3 for photosynthesis and amino acid synthesis, respectively, in the symbionts therein. The protein abundance of Zoox-GS1 was upregulated in the outer mantle and the inner mantle during illumination. Zoox-GS1 could catalyze light-enhanced glutamine formation using ammonia absorbed from the host or ammonia released through urea degradation in the cytoplasm. The glutamine produced could be used to synthesize other nitrogenous compounds, including amino acids in the cytoplasm or in the plastid of the dinoflagellates. Some of the amino acids synthesized by the symbionts in the inner mantle and foot muscle could be donated to the host to support shell organic matrix formation and muscle production, respectively.
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Affiliation(s)
- Leanne S X Teh
- Department of Biological Sciences, National University of Singapore, Kent Ridge, Singapore 117543, Republic of Singapore
| | - Jeslyn S T Poo
- Department of Biological Sciences, National University of Singapore, Kent Ridge, Singapore 117543, Republic of Singapore
| | - Mel V Boo
- Department of Biological Sciences, National University of Singapore, Kent Ridge, Singapore 117543, Republic of Singapore
| | - Shit F Chew
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, 1 Nanyang Walk, Singapore 637616, Republic of Singapore
| | - Yuen K Ip
- Department of Biological Sciences, National University of Singapore, Kent Ridge, Singapore 117543, Republic of Singapore.
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24
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Reich HG, Tu WC, Rodriguez IB, Chou Y, Keister EF, Kemp DW, LaJeunesse TC, Ho TY. Iron Availability Modulates the Response of Endosymbiotic Dinoflagellates to Heat Stress. JOURNAL OF PHYCOLOGY 2021; 57:3-13. [PMID: 32996595 DOI: 10.1111/jpy.13078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 09/03/2020] [Accepted: 09/11/2020] [Indexed: 06/11/2023]
Abstract
Warming and nutrient limitation are stressors known to weaken the health of microalgae. In situations of stress, access to energy reserves can minimize physiological damage. Because of its widespread requirements in biochemical processes, iron is an important trace metal, especially for photosynthetic organisms. Lowered iron availability in oceans experiencing rising temperatures may contribute to the thermal sensitivity of reef-building corals, which rely on mutualisms with dinoflagellates to survive. To test the influence of iron concentration on thermal sensitivity, the physiological responses of cultured symbiotic dinoflagellates (genus Breviolum; family Symbiodiniaceae) were evaluated when exposed to increasing temperatures (26 to 30°C) and iron concentrations ranging from replete (500 pM Fe') to limiting (50 pM Fe') under a diurnal light cycle with saturating radiance. Declines in photosynthetic efficiency at elevated temperatures indicated sensitivity to heat stress. Furthermore, five times the amount of iron was needed to reach exponential growth during heat stress (50 pM Fe' at 26-28°C vs. 250 pM Fe' at 30°C). In treatments where exponential growth was reached, Breviolum psygmophilum grew faster than B.minutum, possibly due to greater cellular contents of iron and other trace metals. The metal composition of B.psygmophilum shifted only at the highest temperature (30°C), whereas changes in B.minutum were observed at lower temperatures (28°C). The influence of iron availability in modulating each alga's response to thermal stress suggests the importance of trace metals to the health of coral-algal mutualisms. Ultimately, a greater ability to acquire scarce metals may improve the tolerance of corals to physiological stressors and contribute to the differences in performance associated with hosting one symbiont species over another.
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Affiliation(s)
- Hannah G Reich
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | - Wan-Chen Tu
- Research Center for Environmental Changes, Academia Sinica, Taipei, Taiwan
| | - Irene B Rodriguez
- Research Center for Environmental Changes, Academia Sinica, Taipei, Taiwan
| | - Yalan Chou
- Research Center for Environmental Changes, Academia Sinica, Taipei, Taiwan
| | - Elise F Keister
- Department of Biology, The University of Alabama at Birmingham, Birmingham, Alabama, 35294, USA
| | - Dustin W Kemp
- Department of Biology, The University of Alabama at Birmingham, Birmingham, Alabama, 35294, USA
| | - Todd C LaJeunesse
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | - Tung-Yuan Ho
- Research Center for Environmental Changes, Academia Sinica, Taipei, Taiwan
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan
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25
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Deng Y, Hu Z, Shang L, Chai Z, Tang YZ. Transcriptional Responses of the Heat Shock Protein 20 (Hsp20) and 40 (Hsp40) Genes to Temperature Stress and Alteration of Life Cycle Stages in the Harmful Alga Scrippsiella trochoidea (Dinophyceae). BIOLOGY 2020; 9:biology9110408. [PMID: 33233461 PMCID: PMC7700488 DOI: 10.3390/biology9110408] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/13/2020] [Accepted: 11/18/2020] [Indexed: 01/17/2023]
Abstract
Simple Summary As the greatest contributors to harmful algal blooms, dinoflagellates account for roughly 75% of bloom events, which become an escalating threat to coastal ecosystems and cause substantial economic loss worldwide. Resting cyst production and broad temperature tolerance are well proven as adaptive strategies for blooming dinoflagellates; however, to date, the underlying molecular information is scarce. In the present study, we characterized two heat shock protein genes from the representative dinoflagellate Scrippsiella trochoidea, with the aim to primarily determine their possible roles in response to temperature stress and alteration of the life cycle. The yielded results enhance our knowledge about the functions of cross-talk of different Hsp members in temperature adaptation of dinoflagellates and facilitate further exploration in their potential physiological relevance during different life-stage alternation in this ecological important lineage. Abstract The small heat shock protein (sHsp) and Hsp40 are Hsp members that have not been intensively investigated but are functionally important in most organisms. In this study, the potential roles of a Hsp20 (StHsp20) and a Hsp40 (StHsp40) in dinoflagellates during adaptation to temperature fluctuation and alteration of different life stages were explored using the representative harmful algal blooms (HABs)-causative dinoflagellate species, Scrippsiella trochoidea. We isolated the full-length cDNAs of the two genes via rapid amplification of cDNA ends (RACE) and tracked their differential transcriptions via real-time qPCR. The results revealed StHsp20 and StHsp40 exhibited mRNA accumulation patterns that were highly similar in response to heat stress but completely different toward cold stress, which implies that the mechanisms underlying thermal and cold acclimation in dinoflagellates are regulated by different sets of genes. The StHsp20 was probably related to the heat tolerance of the species, and StHsp40 was closely involved in the adaptation to both higher and lower temperature fluctuations. Furthermore, significantly higher mRNA abundance of StHsp40 was detected in newly formed resting cysts, which might be a response to intrinsic stress stemmed from encystment. This finding also implied StHsp40 might be engaged in resting cyst formation of S. trochoidea. Our findings enriched the knowledge about possible cross-talk of different Hsp members in dinoflagellates and provided clues to further explore the molecular underpinnings underlying resting cyst production and broad temperature tolerance of this group of HABs contributors.
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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 266071, China; (Y.D.); (Z.H.); (L.S.); (Z.C.)
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Zhangxi Hu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Y.D.); (Z.H.); (L.S.); (Z.C.)
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Lixia Shang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Y.D.); (Z.H.); (L.S.); (Z.C.)
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Zhaoyang Chai
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Y.D.); (Z.H.); (L.S.); (Z.C.)
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Ying Zhong Tang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Y.D.); (Z.H.); (L.S.); (Z.C.)
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
- Correspondence: ; Tel./Fax: +86-532-8289-6098
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26
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Boilard A, Dubé CE, Gruet C, Mercière A, Hernandez-Agreda A, Derome N. Defining Coral Bleaching as a Microbial Dysbiosis within the Coral Holobiont. Microorganisms 2020; 8:microorganisms8111682. [PMID: 33138319 PMCID: PMC7692791 DOI: 10.3390/microorganisms8111682] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 10/26/2020] [Accepted: 10/28/2020] [Indexed: 12/11/2022] Open
Abstract
Coral microbiomes are critical to holobiont health and functioning, but the stability of host–microbial interactions is fragile, easily shifting from eubiosis to dysbiosis. The heat-induced breakdown of the symbiosis between the host and its dinoflagellate algae (that is, “bleaching”), is one of the most devastating outcomes for reef ecosystems. Yet, bleaching tolerance has been observed in some coral species. This review provides an overview of the holobiont’s diversity, explores coral thermal tolerance in relation to their associated microorganisms, discusses the hypothesis of adaptive dysbiosis as a mechanism of environmental adaptation, mentions potential solutions to mitigate bleaching, and suggests new research avenues. More specifically, we define coral bleaching as the succession of three holobiont stages, where the microbiota can (i) maintain essential functions for holobiont homeostasis during stress and/or (ii) act as a buffer to mitigate bleaching by favoring the recruitment of thermally tolerant Symbiodiniaceae species (adaptive dysbiosis), and where (iii) environmental stressors exceed the buffering capacity of both microbial and dinoflagellate partners leading to coral death.
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Affiliation(s)
- Aurélie Boilard
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC G1V 0A6, Canada; (A.B.); (C.G.)
| | - Caroline E. Dubé
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC G1V 0A6, Canada; (A.B.); (C.G.)
- California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA 94118, USA;
- Correspondence: (C.E.D.); (N.D.)
| | - Cécile Gruet
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC G1V 0A6, Canada; (A.B.); (C.G.)
| | - Alexandre Mercière
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 66860 Perpignan CEDEX, France;
- Laboratoire d’Excellence “CORAIL”, 98729 Papetoai, Moorea, French Polynesia
| | | | - Nicolas Derome
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC G1V 0A6, Canada; (A.B.); (C.G.)
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec City, QC G1V 0A6, Canada
- Correspondence: (C.E.D.); (N.D.)
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27
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van Oppen MJH, Medina M. Coral evolutionary responses to microbial symbioses. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190591. [PMID: 32772672 PMCID: PMC7435167 DOI: 10.1098/rstb.2019.0591] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/09/2020] [Indexed: 12/19/2022] Open
Abstract
This review explores how microbial symbioses may have influenced and continue to influence the evolution of reef-building corals (Cnidaria; Scleractinia). The coral holobiont comprises a diverse microbiome including dinoflagellate algae (Dinophyceae; Symbiodiniaceae), bacteria, archaea, fungi and viruses, but here we focus on the Symbiodiniaceae as knowledge of the impact of other microbial symbionts on coral evolution is scant. Symbiosis with Symbiodiniaceae has extended the coral's metabolic capacity through metabolic handoffs and horizontal gene transfer (HGT) and has contributed to the ecological success of these iconic organisms. It necessitated the prior existence or the evolution of a series of adaptations of the host to attract and select the right symbionts, to provide them with a suitable environment and to remove disfunctional symbionts. Signatures of microbial symbiosis in the coral genome include HGT from Symbiodiniaceae and bacteria, gene family expansions, and a broad repertoire of oxidative stress response and innate immunity genes. Symbiosis with Symbiodiniaceae has permitted corals to occupy oligotrophic waters as the algae provide most corals with the majority of their nutrition. However, the coral-Symbiodiniaceae symbiosis is sensitive to climate warming, which disrupts this intimate relationship, causing coral bleaching, mortality and a worldwide decline of coral reefs. This article is part of the theme issue 'The role of the microbiome in host evolution'.
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Affiliation(s)
- Madeleine J. H. van Oppen
- School of BioSciences, The University of Melbourne, Parkville, 3010 Victoria, Australia
- Australian Institute of Marine Science, PMB No. 3, Townsville MC, 4810 Queensland, Australia
| | - Mónica Medina
- Department of Biology, The Pennsylvania State University, 208 Mueller Lab, University Park, PA 16802, USA
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28
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Mohamed AR, Andrade N, Moya A, Chan CX, Negri AP, Bourne DG, Ying H, Ball EE, Miller DJ. Dual RNA-sequencing analyses of a coral and its native symbiont during the establishment of symbiosis. Mol Ecol 2020; 29:3921-3937. [PMID: 32853430 DOI: 10.1111/mec.15612] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 08/16/2020] [Accepted: 08/17/2020] [Indexed: 12/14/2022]
Abstract
Despite the ecological significance of the mutualistic relationship between Symbiodiniaceae and reef-building corals, the molecular interactions during establishment of this relationship are not well understood. This is particularly true of the transcriptional changes that occur in the symbiont. In the current study, a dual RNA-sequencing approach was used to better understand transcriptional changes on both sides of the coral-symbiont interaction during the colonization of Acropora tenuis by a compatible Symbiodiniaceae strain (Cladocopium goreaui; ITS2 type C1). Comparison of transcript levels of the in hospite symbiont 3, 12, 48 and 72 hr after exposure to those of the same strain in culture revealed that extensive and generalized down-regulation of symbiont gene expression occurred during the infection process. Included in this "symbiosis-derived transcriptional repression" were a range of stress response and immune-related genes. In contrast, a suite of symbiont genes implicated in metabolism was upregulated in the symbiotic state. The coral data support the hypothesis that immune-suppression and arrest of phagosome maturation play important roles during the establishment of compatible symbioses, and additionally imply the involvement of some SCRiP family members in the colonization process. Consistent with previous ecological studies, the transcriptomic data suggest that active translocation of metabolites to the host may begin early in the colonization process, and thus that the mutualistic relationship can be established at the larval stage. This dual RNA-sequencing study provides insights into the transcriptomic remodelling that occurs in C. goreaui during transition to a symbiotic lifestyle and the novel coral genes implicated in symbiosis.
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Affiliation(s)
- Amin R Mohamed
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St Lucia, Qld, Australia.,Zoology Department, Faculty of Science, Benha University, Benha, Egypt.,ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, Australia.,Department of Molecular and Cell Biology, James Cook University, Townsville, Qld, Australia.,Department of Molecular and Cell Biology, AIMS@JCU, Australian Institute of Marine Science, James Cook University, Townsville, Qld, Australia
| | - Natalia Andrade
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, Australia.,Department of Molecular and Cell Biology, James Cook University, Townsville, Qld, Australia
| | - Aurelie Moya
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, Australia.,Department of Molecular and Cell Biology, James Cook University, Townsville, Qld, Australia
| | - Cheong Xin Chan
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Qld, Australia
| | - Andrew P Negri
- Australian Institute of Marine Science, Townsville, Qld, Australia
| | - David G Bourne
- Australian Institute of Marine Science, Townsville, Qld, Australia.,Department of Marine Ecosystems and Impacts, James Cook University, Townsville, Qld, Australia
| | - Hua Ying
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Acton, ACT, Australia
| | - Eldon E Ball
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, Australia.,Division of Ecology and Evolution, Research School of Biology, Australian National University, Acton, ACT, Australia
| | - David J Miller
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, Australia.,Department of Molecular and Cell Biology, James Cook University, Townsville, Qld, Australia
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29
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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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30
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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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Buerger P, Alvarez-Roa C, Coppin CW, Pearce SL, Chakravarti LJ, Oakeshott JG, Edwards OR, van Oppen MJH. Heat-evolved microalgal symbionts increase coral bleaching tolerance. SCIENCE ADVANCES 2020; 6:eaba2498. [PMID: 32426508 PMCID: PMC7220355 DOI: 10.1126/sciadv.aba2498] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 03/06/2020] [Indexed: 05/19/2023]
Abstract
Coral reefs worldwide are suffering mass mortalities from marine heat waves. With the aim of enhancing coral bleaching tolerance, we evolved 10 clonal strains of a common coral microalgal endosymbiont at elevated temperatures (31°C) for 4 years in the laboratory. All 10 heat-evolved strains had expanded their thermal tolerance in vitro following laboratory evolution. After reintroduction into coral host larvae, 3 of the 10 heat-evolved endosymbionts also increased the holobionts' bleaching tolerance. Although lower levels of secreted reactive oxygen species (ROS) accompanied thermal tolerance of the heat-evolved algae, reduced ROS secretion alone did not predict thermal tolerance in symbiosis. The more tolerant symbiosis exhibited additional higher constitutive expression of algal carbon fixation genes and coral heat tolerance genes. These findings demonstrate that coral stock with enhanced climate resilience can be developed through ex hospite laboratory evolution of their microalgal endosymbionts.
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Affiliation(s)
- P. Buerger
- CSIRO Synthetic Biology Future Science Platform, Land & Water, Black Mountain, ACT 2601, Australia
- School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - C. Alvarez-Roa
- Australian Institute of Marine Science, PMB #3, Townsville, QLD 4810, Australia
| | - C. W. Coppin
- CSIRO Synthetic Biology Future Science Platform, Land & Water, Black Mountain, ACT 2601, Australia
| | - S. L. Pearce
- CSIRO Synthetic Biology Future Science Platform, Land & Water, Black Mountain, ACT 2601, Australia
| | - L. J. Chakravarti
- Australian Institute of Marine Science, PMB #3, Townsville, QLD 4810, Australia
| | - J. G. Oakeshott
- CSIRO Synthetic Biology Future Science Platform, Land & Water, Black Mountain, ACT 2601, Australia
| | - O. R. Edwards
- CSIRO Synthetic Biology Future Science Platform, Land & Water, Black Mountain, ACT 2601, Australia
| | - M. J. H. van Oppen
- School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia
- Australian Institute of Marine Science, PMB #3, Townsville, QLD 4810, Australia
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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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Camp EF, Kahlke T, Nitschke MR, Varkey D, Fisher NL, Fujise L, Goyen S, Hughes DJ, Lawson CA, Ros M, Woodcock S, Xiao K, Leggat W, Suggett DJ. Revealing changes in the microbiome of Symbiodiniaceae under thermal stress. Environ Microbiol 2020; 22:1294-1309. [DOI: 10.1111/1462-2920.14935] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 01/08/2020] [Accepted: 01/27/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Emma F. Camp
- Climate Change ClusterUniversity of Technology Sydney Broadway NSW 2007 Australia
| | - Tim Kahlke
- Climate Change ClusterUniversity of Technology Sydney Broadway NSW 2007 Australia
| | - Matthew R. Nitschke
- Climate Change ClusterUniversity of Technology Sydney Broadway NSW 2007 Australia
- School of Biological SciencesVictoria University of Wellington Wellington New Zealand
| | - Deepa Varkey
- Climate Change ClusterUniversity of Technology Sydney Broadway NSW 2007 Australia
- Department of Molecular SciencesMacquarie University Sydney NSW 2109 Australia
| | - Nerissa L. Fisher
- Climate Change ClusterUniversity of Technology Sydney Broadway NSW 2007 Australia
| | - Lisa Fujise
- Climate Change ClusterUniversity of Technology Sydney Broadway NSW 2007 Australia
| | - Samantha Goyen
- Climate Change ClusterUniversity of Technology Sydney Broadway NSW 2007 Australia
| | - David J. Hughes
- Climate Change ClusterUniversity of Technology Sydney Broadway NSW 2007 Australia
| | - Caitlin A. Lawson
- Climate Change ClusterUniversity of Technology Sydney Broadway NSW 2007 Australia
| | - Mickael Ros
- Climate Change ClusterUniversity of Technology Sydney Broadway NSW 2007 Australia
| | - Stephen Woodcock
- Climate Change ClusterUniversity of Technology Sydney Broadway NSW 2007 Australia
| | - Kun Xiao
- Climate Change ClusterUniversity of Technology Sydney Broadway NSW 2007 Australia
| | - William Leggat
- School of Environmental and Life SciencesUniversity of Newcastle Ourimbah NSW 2308 Australia
| | - David J. Suggett
- Climate Change ClusterUniversity of Technology Sydney Broadway NSW 2007 Australia
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Alves Monteiro HJ, Brahmi C, Mayfield AB, Vidal-Dupiol J, Lapeyre B, Le Luyer J. Molecular mechanisms of acclimation to long-term elevated temperature exposure in marine symbioses. GLOBAL CHANGE BIOLOGY 2020; 26:1271-1284. [PMID: 31692206 DOI: 10.1111/gcb.14907] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 10/02/2019] [Indexed: 06/10/2023]
Abstract
Seawater temperature rise in French Polynesia has repeatedly resulted in the bleaching of corals and giant clams. Because giant clams possess distinctive ectosymbiotic features, they represent a unique and powerful model for comparing molecular pathways involved in (a) maintenance of symbiosis and (b) acquisition of thermotolerance among coral reef organisms. Herein, we explored the physiological and transcriptomic responses of the clam hosts and their photosynthetically active symbionts over a 65 day experiment in which clams were exposed to either normal or environmentally relevant elevated seawater temperatures. Additionally, we used metabarcoding data coupled with in situ sampling/survey data to explore the relative importance of holobiont adaptation (i.e., a symbiont community shift) versus acclimation (i.e., physiological changes at the molecular level) in the clams' responses to environmental change. We finally compared transcriptomic data to publicly available genomic datasets for Symbiodiniaceae dinoflagellates (both cultured and in hospite with the coral Pocillopora damicornis) to better tease apart the responses of both hosts and specific symbiont genotypes in this mutualistic association. Gene module preservation analysis revealed that the function of the symbionts' photosystem II was impaired at high temperature, and this response was also found across all holobionts and Symbiodiniaceae lineages examined. Similarly, epigenetic modulation appeared to be a key response mechanism for symbionts in hospite with giant clams exposed to high temperatures, and such modulation was able to distinguish thermotolerant from thermosensitive Cladocopium goreaui ecotypes; epigenetic processes may, then, represent a promising research avenue for those interested in coral reef conservation in this era of changing global climate.
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Affiliation(s)
| | - Chloé Brahmi
- Université de la Polynésie Française, UMR Ecosystèmes Insulaires Océaniens, Ifremer, ILM, IRD, Tahiti, Polynésie Française
| | - Anderson B Mayfield
- National Museum of Marine Biology and Aquarium, Checheng, Taiwan
- Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, FL, USA
| | | | - Bruno Lapeyre
- EPHE-CNRS-UPVD, USR3278-CRIOBE, Labex CORAIL, Moorea, Polynésie Française
| | - Jérémy Le Luyer
- IFREMER, UMR Ecosystèmes Insulaires Océaniens, UPF, ILM, IRD, Tahiti, Polynésie Française
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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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Li T, Yu L, Song B, Song Y, Li L, Lin X, Lin S. Genome Improvement and Core Gene Set Refinement of Fugacium kawagutii. Microorganisms 2020; 8:microorganisms8010102. [PMID: 31940756 PMCID: PMC7023079 DOI: 10.3390/microorganisms8010102] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 01/01/2020] [Accepted: 01/08/2020] [Indexed: 01/15/2023] Open
Abstract
Cataloging an accurate functional gene set for the Symbiodiniaceae species is crucial for addressing biological questions of dinoflagellate symbiosis with corals and other invertebrates. To improve the gene models of Fugacium kawagutii, we conducted high-throughput chromosome conformation capture (Hi-C) for the genome and Illumina combined with PacBio sequencing for the transcriptome to achieve a new genome assembly and gene prediction. A 0.937-Gbp assembly of F. kawagutii were obtained, with a N50 > 13 Mbp and the longest scaffold of 121 Mbp capped with telomere motif at both ends. Gene annotation produced 45,192 protein-coding genes, among which, 11,984 are new compared to previous versions of the genome. The newly identified genes are mainly enriched in 38 KEGG pathways including N-Glycan biosynthesis, mRNA surveillance pathway, cell cycle, autophagy, mitophagy, and fatty acid synthesis, which are important for symbiosis, nutrition, and reproduction. The newly identified genes also included those encoding O-methyltransferase (O-MT), 3-dehydroquinate synthase, homologous-pairing protein 2-like (HOP2) and meiosis protein 2 (MEI2), which function in mycosporine-like amino acids (MAAs) biosynthesis and sexual reproduction, respectively. The improved version of the gene set (Fugka_Geneset _V3) raised transcriptomic read mapping rate from 33% to 54% and BUSCO match from 29% to 55%. Further differential gene expression analysis yielded a set of stably expressed genes under variable trace metal conditions, of which 115 with annotated functions have recently been found to be stably expressed under three other conditions, thus further developing the "core gene set" of F. kawagutii. This improved genome will prove useful for future Symbiodiniaceae transcriptomic, gene structure, and gene expression studies, and the refined "core gene set" will be a valuable resource from which to develop reference genes for gene expression studies.
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Affiliation(s)
- Tangcheng Li
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (T.L.); (L.Y.); (L.L.)
- Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA
| | - Liying Yu
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (T.L.); (L.Y.); (L.L.)
| | - Bo Song
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China;
| | - Yue Song
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China;
| | - Ling Li
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (T.L.); (L.Y.); (L.L.)
| | - Xin Lin
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (T.L.); (L.Y.); (L.L.)
- Correspondence: (X.L.); (S.L.)
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (T.L.); (L.Y.); (L.L.)
- Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA
- Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory of Marine Science and Technology, Qingdao 266237, China
- Correspondence: (X.L.); (S.L.)
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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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Abstract
Endosymbiosis is found in all types of ecosystems and it can be sensitive to environmental changes due to the intimate interaction between the endosymbiont and the host. Indeed, global climate change disturbs the local ambient environment and threatens endosymbiotic species, and in some cases leads to local ecosystem collapse. Recent studies have revealed that the endosymbiont can affect holobiont (endosymbiont and host together) stress tolerance as much as the host does, and manipulation of the microbial partners in holobionts may mitigate the impacts of the environmental stress. Here, we first show how the endosymbiont presence affects holobiont stress tolerance by discussing three well-studied endosymbiotic systems, which include plant-fungi, aquatic organism-algae, and insect-bacteria systems. We then review how holobionts are able to alter their stress tolerance via associated endosymbionts by changing their endosymbiont composition, by adaptation of their endosymbionts, or by acclimation of their endosymbionts. Finally, we discuss how different transmission modes (vertical or horizontal transmission) might affect the adaptability of holobionts. We propose that the endosymbiont is a good target for modifying holobiont stress tolerance, which makes it critical to more fully investigate the role of endosymbionts in the adaptive responses of holobionts to stress.
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Suggett DJ, Smith DJ. Coral bleaching patterns are the outcome of complex biological and environmental networking. GLOBAL CHANGE BIOLOGY 2020; 26:68-79. [PMID: 31618499 DOI: 10.1111/gcb.14871] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 09/20/2019] [Indexed: 05/26/2023]
Abstract
Continued declines in coral reef health over the past three decades have been punctuated by severe mass coral bleaching-induced mortality events that have grown in intensity and frequency under climate change. Intensive global research efforts have therefore persistently focused on bleaching phenomena to understand where corals bleach, when and why-resulting in a large-yet still somewhat patchy-knowledge base. Particularly catastrophic bleaching-induced coral mortality events in the past 5 years have catalyzed calls for a more diverse set of reef management tools, extending far beyond climate mitigation and reef protection, to also include more aggressive interventions. However, the effectiveness of these various tools now rests on rapidly assimilating our knowledge base of coral bleaching into more integrated frameworks. Here, we consider how the past three decades of intensive coral bleaching research has established the basis for complex biological and environmental networks, which together regulate outcomes of bleaching severity. We discuss how we now have enough scaffold for conceptual biological and environmental frameworks underpinning bleaching susceptibility, but that new tools are urgently required to translate this to an operational system informing-and testing-bleaching outcomes. Specifically, adopting network models that can fully describe and predict metabolic functioning of coral holobionts, and how this functioning is regulated by complex doses and interactions among environmental factors. Identifying knowledge gaps limiting operation of such models is the logical step to immediately guide and prioritize future experiments and observations. We are at a time-critical point where we can implement new capacity to resolve how coral bleaching patterns emerge from complex biological-environmental networks, and so more effectively inform rapidly evolving ecological management and social adaptation frameworks aimed at securing the future of coral reefs.
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Affiliation(s)
- David J Suggett
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - David J Smith
- Coral Reef Research Unit, School of Biological Sciences, University of Essex, Colchester, UK
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Maor‐Landaw K, van Oppen MJH, McFadden GI. Symbiotic lifestyle triggers drastic changes in the gene expression of the algal endosymbiont Breviolum minutum (Symbiodiniaceae). Ecol Evol 2020; 10:451-466. [PMID: 31993121 PMCID: PMC6972872 DOI: 10.1002/ece3.5910] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 10/25/2019] [Accepted: 11/18/2019] [Indexed: 01/13/2023] Open
Abstract
Coral-dinoflagellate symbiosis underpins the evolutionary success of corals reefs. Successful exchange of molecules between the cnidarian host and the Symbiodiniaceae algae enables the mutualistic partnership. The algae translocate photosynthate to their host in exchange for nutrients and shelter. The photosynthate must traverse multiple membranes, most likely facilitated by transporters. Here, we compared gene expression profiles of cultured, free-living Breviolum minutum with those of the homologous symbionts freshly isolated from the sea anemone Exaiptasia diaphana, a widely used model for coral hosts. Additionally, we assessed expression levels of a list of candidate host transporters of interest in anemones with and without symbionts. Our transcriptome analyses highlight the distinctive nature of the two algal life stages, with many gene expression level changes correlating to the different morphologies, cell cycles, and metabolisms adopted in hospite versus free-living. Morphogenesis-related genes that likely underpin the metamorphosis process observed when symbionts enter a host cell were up-regulated. Conversely, many down-regulated genes appear to be indicative of the protective and confined nature of the symbiosome. Our results emphasize the significance of transmembrane transport to the symbiosis, and in particular of ammonium and sugar transport. Further, we pinpoint and characterize candidate transporters-predicted to be localized variously to the algal plasma membrane, the host plasma membrane, and the symbiosome membrane-that likely serve pivotal roles in the interchange of material during symbiosis. Our study provides new insights that expand our understanding of the molecular exchanges that underpin the cnidarian-algal symbiotic relationship.
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Affiliation(s)
- Keren Maor‐Landaw
- School of BioSciencesThe University of MelbourneMelbourneVic.Australia
| | - Madeleine J. H. van Oppen
- School of BioSciencesThe University of MelbourneMelbourneVic.Australia
- Australian Institute of Marine ScienceTownsvilleQldAustralia
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Raven JA, Beardall J, Quigg A. Light-Driven Oxygen Consumption in the Water-Water Cycles and Photorespiration, and Light Stimulated Mitochondrial Respiration. PHOTOSYNTHESIS IN ALGAE: BIOCHEMICAL AND PHYSIOLOGICAL MECHANISMS 2020. [DOI: 10.1007/978-3-030-33397-3_8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Bellantuono AJ, Dougan KE, Granados‐Cifuentes C, Rodriguez‐Lanetty M. Free‐living and symbiotic lifestyles of a thermotolerant coral endosymbiont display profoundly distinct transcriptomes under both stable and heat stress conditions. Mol Ecol 2019; 28:5265-5281. [DOI: 10.1111/mec.15300] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 10/22/2019] [Accepted: 10/25/2019] [Indexed: 02/06/2023]
Affiliation(s)
| | - Katherine E. Dougan
- Department of Biological Sciences Florida International University Miami FL USA
| | - Camila Granados‐Cifuentes
- Department of Biological Sciences Florida International University Miami FL USA
- Baruch College The City University of New York New York NY USA
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Omics Analysis for Dinoflagellates Biology Research. Microorganisms 2019; 7:microorganisms7090288. [PMID: 31450827 PMCID: PMC6780300 DOI: 10.3390/microorganisms7090288] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 08/20/2019] [Accepted: 08/21/2019] [Indexed: 01/13/2023] Open
Abstract
Dinoflagellates are important primary producers for marine ecosystems and are also responsible for certain essential components in human foods. However, they are also notorious for their ability to form harmful algal blooms, and cause shellfish poisoning. Although much work has been devoted to dinoflagellates in recent decades, our understanding of them at a molecular level is still limited owing to some of their challenging biological properties, such as large genome size, permanently condensed liquid-crystalline chromosomes, and the 10-fold lower ratio of protein to DNA than other eukaryotic species. In recent years, omics technologies, such as genomics, transcriptomics, proteomics, and metabolomics, have been applied to the study of marine dinoflagellates and have uncovered many new physiological and metabolic characteristics of dinoflagellates. In this article, we review recent application of omics technologies in revealing some of the unusual features of dinoflagellate genomes and molecular mechanisms relevant to their biology, including the mechanism of harmful algal bloom formations, toxin biosynthesis, symbiosis, lipid biosynthesis, as well as species identification and evolution. We also discuss the challenges and provide prospective further study directions and applications of dinoflagellates.
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Morse D. A Transcriptome-based Perspective of Meiosis in Dinoflagellates. Protist 2019; 170:397-403. [DOI: 10.1016/j.protis.2019.06.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 06/19/2019] [Accepted: 06/21/2019] [Indexed: 01/31/2023]
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Jiang J, Lu Y. Metabolite profiling of Breviolum minutum in response to acidification. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2019; 213:105215. [PMID: 31200330 DOI: 10.1016/j.aquatox.2019.05.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 05/28/2019] [Accepted: 05/28/2019] [Indexed: 06/09/2023]
Abstract
Coral reefs are in significant decline globally due to climate change and environmental pollution. The ocean is becoming more acidic due to rising atmospheric pCO2, and ocean acidification is considered a major threat to coral reefs. However, little is known about the exact mechanism by which acidification impacts coral symbiosis. As an important component of the symbiotic association, to explore the responses of symbionts could greatly enhance our understanding of this issue. The present work aimed to identify metabolomic changes of Breviolum minutum in acidification (low pH) condition, and investigate the underlying mechanisms responsible. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) was applied to determine metabolite profiles after exposure to ambient and acidic conditions. We analysed the resulting metabolite data, and acidification appeared to have little effect on photosynthetic parameters, but it inhibited growth. Marked alterations in metabolite pools were observed in response to acidification that may be important in acclimation to climate change. Acidification may affect the biosynthesis of amino acids and proteins, and thereby inhibit the growth of B. minutum. Metabolites identified using this approach provide targets for future analyses aimed at understanding the responses of Symbiodiniaceae to environmental disturbance.
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Affiliation(s)
- Jiaoyun Jiang
- State Key Laboratory of Marine Resource Utilization in South China Sea, College of Oceanology, Hainan University, Haikou 570228, Hainan, China; College of Life Sciences, Guangxi Normal University, Guilin 541004, Guangxi, China.
| | - Yandu Lu
- State Key Laboratory of Marine Resource Utilization in South China Sea, College of Oceanology, Hainan University, Haikou 570228, Hainan, China.
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Brian JI, Davy SK, Wilkinson SP. Multi-gene incongruence consistent with hybridisation in Cladocopium (Symbiodiniaceae), an ecologically important genus of coral reef symbionts. PeerJ 2019; 7:e7178. [PMID: 31289699 PMCID: PMC6598746 DOI: 10.7717/peerj.7178] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 05/22/2019] [Indexed: 12/23/2022] Open
Abstract
Coral reefs rely on their intracellular dinoflagellate symbionts (family Symbiodiniaceae) for nutritional provision in nutrient-poor waters, yet this association is threatened by thermally stressful conditions. Despite this, the evolutionary potential of these symbionts remains poorly characterised. In this study, we tested the potential for divergent Symbiodiniaceae types to sexually reproduce (i.e. hybridise) within Cladocopium, the most ecologically prevalent genus in this family. With sequence data from three organelles (cob gene, mitochondrion; psbAncr region, chloroplast; and ITS2 region, nucleus), we utilised the Incongruence Length Difference test, Approximately Unbiased test, tree hybridisation analyses and visual inspection of raw data in stepwise fashion to highlight incongruences between organelles, and thus provide evidence of reticulate evolution. Using this approach, we identified three putative hybrid Cladocopium samples among the 158 analysed, at two of the seven sites sampled. These samples were identified as the common Cladocopium types C40 or C1 with respect to the mitochondria and chloroplasts, but the rarer types C3z, C3u and C1# with respect to their nuclear identity. These five Cladocopium types have previously been confirmed as evolutionarily distinct and were also recovered in non-incongruent samples multiple times, which is strongly suggestive that they sexually reproduced to produce the incongruent samples. A concomitant inspection of next generation sequencing data for these samples suggests that other plausible explanations, such as incomplete lineage sorting or the presence of co-dominance, are much less likely. The approach taken in this study allows incongruences between gene regions to be identified with confidence, and brings new light to the evolutionary potential within Symbiodiniaceae.
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Affiliation(s)
- Joshua I Brian
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Simon K Davy
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Shaun P Wilkinson
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
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47
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Lin S, Yu L, Zhang H. Transcriptomic Responses to Thermal Stress and Varied Phosphorus Conditions in Fugacium kawagutii. Microorganisms 2019; 7:microorganisms7040096. [PMID: 30987028 PMCID: PMC6517890 DOI: 10.3390/microorganisms7040096] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 03/18/2019] [Accepted: 03/30/2019] [Indexed: 01/08/2023] Open
Abstract
Coral reef-associated Symbiodiniaceae live in tropical and oligotrophic environments and are prone to heat and nutrient stress. How their metabolic pathways respond to pulses of warming and phosphorus (P) depletion is underexplored. Here, we conducted RNA-seq analysis to investigate transcriptomic responses to thermal stress, phosphate deprivation, and organic phosphorus (OP) replacement in Fugacium kawagutii. Using dual-algorithm (edgeR and NOIseq) to remedy the problem of no replicates, we conservatively found 357 differentially expressed genes (DEGs) under heat stress, potentially regulating cell wall modulation and the transport of iron, oxygen, and major nutrients. About 396 DEGs were detected under P deprivation and 671 under OP utilization, both mostly up-regulated and potentially involved in photosystem and defensome, despite different KEGG pathway enrichments. Additionally, we identified 221 genes that showed relatively stable expression levels across all conditions (likely core genes), mostly catalytic and binding proteins. This study reveals a wide range of, and in many cases previously unrecognized, molecular mechanisms in F. kawagutii to cope with heat stress and phosphorus-deficiency stress. Their quantitative expression dynamics, however, requires further verification with triplicated experiments, and the data reported here only provide clues for generating testable hypotheses about molecular mechanisms underpinning responses and adaptation in F. kawagutii to temperature and nutrient stresses.
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Affiliation(s)
- Senjie Lin
- Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA.
| | - Liying Yu
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, Fujian, China.
| | - Huan Zhang
- Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA.
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48
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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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49
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Franzellitti S, Airi V, Calbucci D, Caroselli E, Prada F, Voolstra CR, Mass T, Falini G, Fabbri E, Goffredo S. Transcriptional response of the heat shock gene hsp70 aligns with differences in stress susceptibility of shallow-water corals from the Mediterranean Sea. MARINE ENVIRONMENTAL RESEARCH 2018; 140:444-454. [PMID: 30055833 DOI: 10.1016/j.marenvres.2018.07.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 07/09/2018] [Accepted: 07/13/2018] [Indexed: 06/08/2023]
Abstract
Shallow-water corals of the Mediterranean Sea are facing a dramatic increase in water temperature due to climate change, predicted to increase the frequency of bleaching and mass mortality events. However, supposedly not all corals are affected equally, as they show differences in stress susceptibility, as suggested by physiological outputs of corals along temperature gradients and under controlled conditions in terms of reproduction, demography, growth, calcification, and photosynthetic efficiency. In this study, gene expression and induction of a 70-kDa heat shock protein (HSP70) was analyzed in five common shallow-water hard corals in the Mediterranean Sea, namely Astroides calycularis, Balanophyllia europaea, Caryophyllia inornata, Cladocora caespitosa, and Leptopsammia pruvoti. The main aim was to assess the contribution of this evolutionary conserved cytoprotective mechanism to the physiological plasticity of these species that possess different growth modes (solitary vs colonial) and trophic strategies (zooxanthellate vs azooxanthellate). Using quantitative real-time PCR, in situ hsp70 baseline levels and expression profiles after a heat-shock exposure were assessed. Levels of hsp70 and heat stress induction were higher in zooxanthellate than in azooxanthellate species, and different heat stress transcriptional profiles were observed between colonial and solitary zooxanthellate corals. On the whole, the hsp70 transcriptional response to heat stress aligns with stress susceptibility of the species and suggests a contribution of trophic strategy and morphology in shaping coral resilience to stress. Understanding these molecular processes may contribute to assess the potential effects and relative resilience of Mediterranean corals under climate change.
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Affiliation(s)
- Silvia Franzellitti
- Animal and Environmental Physiology Laboratory, Department of Biological, Geological and Environmental Sciences, University of Bologna, via S. Alberto 163, I-48123, Ravenna, Italy.
| | - Valentina Airi
- Marine Science Group, Department of Biological, Geological and Environmental Sciences, University of Bologna, Via F. Selmi 3, I-40126, Bologna, Italy
| | - Diana Calbucci
- Animal and Environmental Physiology Laboratory, Department of Biological, Geological and Environmental Sciences, University of Bologna, via S. Alberto 163, I-48123, Ravenna, Italy
| | - Erik Caroselli
- Marine Science Group, Department of Biological, Geological and Environmental Sciences, University of Bologna, Via F. Selmi 3, I-40126, Bologna, Italy
| | - Fiorella Prada
- Marine Science Group, Department of Biological, Geological and Environmental Sciences, University of Bologna, Via F. Selmi 3, I-40126, Bologna, Italy
| | - 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
| | - Tali Mass
- Department of Marine Biology, The Leon H. Charney School of Marine Sciences, University of Haifa, Multi Purpose Boulevard, Mt. Carmel, Haifa, 3498838, Israel
| | - Giuseppe Falini
- Department of Chemistry "Giacomo Ciamician", University of Bologna, via F. Selmi 2, I-40126, Bologna, Italy
| | - Elena Fabbri
- Animal and Environmental Physiology Laboratory, Department of Biological, Geological and Environmental Sciences, University of Bologna, via S. Alberto 163, I-48123, Ravenna, Italy
| | - Stefano Goffredo
- Marine Science Group, Department of Biological, Geological and Environmental Sciences, University of Bologna, Via F. Selmi 3, I-40126, Bologna, Italy
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50
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Liu H, Stephens TG, González-Pech RA, Beltran VH, Lapeyre B, Bongaerts P, Cooke I, Aranda M, Bourne DG, Forêt S, Miller DJ, van Oppen MJH, Voolstra CR, Ragan MA, Chan CX. Symbiodinium genomes reveal adaptive evolution of functions related to coral-dinoflagellate symbiosis. Commun Biol 2018; 1:95. [PMID: 30271976 PMCID: PMC6123633 DOI: 10.1038/s42003-018-0098-3] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 06/21/2018] [Indexed: 12/20/2022] Open
Abstract
Symbiosis between dinoflagellates of the genus Symbiodinium and reef-building corals forms the trophic foundation of the world’s coral reef ecosystems. Here we present the first draft genome of Symbiodinium goreaui (Clade C, type C1: 1.03 Gbp), one of the most ubiquitous endosymbionts associated with corals, and an improved draft genome of Symbiodinium kawagutii (Clade F, strain CS-156: 1.05 Gbp) to further elucidate genomic signatures of this symbiosis. Comparative analysis of four available Symbiodinium genomes against other dinoflagellate genomes led to the identification of 2460 nuclear gene families (containing 5% of Symbiodinium genes) that show evidence of positive selection, including genes involved in photosynthesis, transmembrane ion transport, synthesis and modification of amino acids and glycoproteins, and stress response. Further, we identify extensive sets of genes for meiosis and response to light stress. These draft genomes provide a foundational resource for advancing our understanding of Symbiodinium biology and the coral-algal symbiosis. Huanle Liu et al. report draft genomes of two Symbiodinium species, one from the most dominant type of symbionts in reef-building corals. They find evidence of positive selection in genes related to stress response, meiosis and other traits required for forming successful symbiotic relationships.
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Affiliation(s)
- Huanle Liu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Timothy G Stephens
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Raúl A González-Pech
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Victor H Beltran
- Australian Institute of Marine Science, Townsville, QLD, 4810, Australia
| | - Bruno Lapeyre
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia.,Department of Molecular and Cell Biology, James Cook University, Townsville, QLD, 4811, Australia.,Laboratoire d'excellence CORAIL, Centre de Recherches Insulaires et Observatoire de l'Environnement, Moorea, 98729, French Polynesia
| | - Pim Bongaerts
- Global Change Institute, The University of Queensland, Brisbane, QLD, 4072, Australia.,Institute for Biodiversity Science and Sustainability, California Academy of Sciences, San Francisco, CA, 94118, USA
| | - Ira Cooke
- Department of Molecular and Cell Biology, James Cook University, Townsville, QLD, 4811, Australia
| | - Manuel Aranda
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - David G Bourne
- Australian Institute of Marine Science, Townsville, QLD, 4810, Australia.,College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia
| | - Sylvain Forêt
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia.,Research School of Biology, Australian National University, Canberra, ACT, 2601, Australia
| | - David J Miller
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia.,Department of Molecular and Cell Biology, James Cook University, Townsville, QLD, 4811, Australia
| | - Madeleine J H van Oppen
- Australian Institute of Marine Science, Townsville, QLD, 4810, Australia.,School of BioSciences, The University of Melbourne, VIC, 3010, Australia
| | - Christian R Voolstra
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - 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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