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Higuchi T, Tanaka K, Shirai K, Yuyama I, Mezaki T, Takahata N, Sano Y. Sulfur assimilation in corals with aposymbiotic and symbiotic zooxanthellae. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:98-103. [PMID: 33196142 DOI: 10.1111/1758-2229.12908] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 11/11/2020] [Accepted: 11/13/2020] [Indexed: 06/11/2023]
Abstract
Although sulfate ions are the main form of sulfur in the ocean, there is limited knowledge on their use by living organisms. Stable isotope labelling and NanoSIMS analysis were used in this study to clarify how sulfate, in seawater, is assimilated by corals and zooxanthellae at the cellular level. Aposymbiotic and symbiotic coral juveniles from the genus Acropora were incubated for 2 days in filtered seawater with 34 S-labelled sulfate. Further, the labelled corals were incubated for additional 2 days in natural seawater. Mapping of sulfur isotopes (34 S/32 S) showed that the 'hotspots' were enriched in 34 S on a sub-micro level and were heterogeneously distributed in the coral soft tissues. Specifically, 34 S hotspots were found in both the symbiotic zooxanthellae and coral host tissues. In aposymbiotic corals, 34 S was detected in the tissues, indicating that the host corals directly assimilated the sulfate ions without any aid from the zooxanthellae. Even after 2 days in normal seawater, the 34 S label was clearly seen in both symbiotic and aposymbiotic corals, indicating that the assimilated sulfur was retained for at least 2 days.
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Affiliation(s)
- Tomihiko Higuchi
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8564, Japan
| | - Kentaro Tanaka
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8564, Japan
| | - Kotaro Shirai
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8564, Japan
| | - Ikuko Yuyama
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
- Faculty of Science, Yamaguchi University, 1677-1 Yoshida, Yamaguchi City, Yamaguchi, 753-8512, Japan
| | - Takuma Mezaki
- Kuroshio Biological Research Foundation, Nishidomari, Otsuki, Kochi, 788-0333, Japan
| | - Naoto Takahata
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8564, Japan
| | - Yuji Sano
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8564, Japan
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Quigley KM, Bay LK, van Oppen MJH. Genome-wide SNP analysis reveals an increase in adaptive genetic variation through selective breeding of coral. Mol Ecol 2020; 29:2176-2188. [PMID: 32453867 DOI: 10.1111/mec.15482] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 05/13/2020] [Indexed: 12/18/2022]
Abstract
Marine heat waves are increasing in magnitude, duration, and frequency as a result of climate change and are the principal global driver of mortality in reef-building corals. Resilience-based genetic management may increase coral heat tolerance, but it is unclear how temperature responses are regulated at the genome level and thus how corals may adapt to warming naturally or through selective breeding. Here we combine phenotypic, pedigree, and genomic marker data from colonies sourced from a warm reef on the Great Barrier Reef reproductively crossed with conspecific colonies from a cooler reef to produce combinations of warm purebreds and warm-cool hybrid larvae and juveniles. Interpopulation breeding created significantly greater genetic diversity across the coral genome compared to breeding between populations and maintained diversity in key regions associated with heat tolerance and fitness. High-density genome-wide scans of single nucleotide polymorphisms (SNPs) identified alleles significantly associated with larval families reared at 27.5°C (87-2,224 loci), including loci putatively associated with proteins involved in responses to heat stress (cell membrane formation, metabolism, and immune responses). Underlying genetics of these families explained 43% of PCoA multilocus variation in survival, growth, and bleaching responses at 27.5°C and 31°C at the juvenile stage. Genetic marker contribution to total variation in fitness traits (narrow-sense heritability) was high for survival but not for growth and bleaching in juveniles, with heritability of these traits being higher at 31°C relative to 27.5°C. While based on only a limited number of crosses, the mechanistic understanding presented here demonstrates that allele frequencies are affected by one generation of selective breeding, key information for the assessments of genetic intervention feasibility and modelling of reef futures.
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Affiliation(s)
- Kate M Quigley
- Australian Institute of Marine Science, Townsville, Qld, Australia
| | - Line K Bay
- Australian Institute of Marine Science, Townsville, Qld, Australia
| | - Madeleine J H van Oppen
- Australian Institute of Marine Science, Townsville, Qld, Australia.,School of BioSciences, The University of Melbourne, Parkville, Vic, Australia
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Lin MF, Takahashi S, Forêt S, Davy SK, Miller DJ. Transcriptomic analyses highlight the likely metabolic consequences of colonization of a cnidarian host by native or non-native Symbiodinium species. Biol Open 2019; 8:bio.038281. [PMID: 30814067 PMCID: PMC6451341 DOI: 10.1242/bio.038281] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Reef-building corals and some other cnidarians form symbiotic relationships with members of the dinoflagellate family Symbiodinaceae. As Symbiodinaceae is a highly diverse taxon, the physiological interactions between its members and their hosts are assumed to differ between associations. The presence of different symbiont types is known to affect expression levels of specific host genes, but knowledge of the effects on the transcriptome more broadly remains limited. In the present study, transcriptome profiling was conducted on the tropical corallimorpharian, Ricordea yuma, following the establishment of symbiosis with either the ‘homologous’ symbiont Symbiodinium goreaui (also known as Cladocopium goreaui; ITS2 type C1) or ‘heterologous’ symbionts (predominantly S. trenchii, which is also known as Durusdinium trenchii; ITS2 type D1a) isolated from a different corallimorpharian host (Rhodactis indosinensis). Transcriptomic analyses showed that genes encoding host glycogen biosynthesis pathway components are more highly induced during colonization by the homologous symbiont than by the heterologous symbiont. Similar patterns were also observed for several other genes thought to facilitate symbiotic nutrient exchange, including those involved in lipid translocation/storage and metabolite transport. The gene expression results presented here imply that colonization by homologous or heterologous Symbiodinium types may have very different metabolic consequences for the Ricordea host, supporting the notion that even though some cnidarians may be able to form novel symbioses after bleaching, the metabolic performance of these may be compromised. This article has an associated First Person interview with the first author of the paper. Summary: Colonization by the homologous symbiont, Symbiodinium goreaui, resulted in greater glycogen synthesis and ammonium assimilation capacity in the host than when it was colonized by a heterologous symbiont (S. trenchii).
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Affiliation(s)
- Mei-Fang Lin
- Molecular and Cell Biology, James Cook University, Townsville, QLD 4811, Australia.,ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811, Australia.,Evolutionary Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Shunichi Takahashi
- Division of Environmental Photobiology, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki 444-8585, Japan
| | - Sylvain Forêt
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811, Australia.,Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
| | - Simon K Davy
- School of Biological Sciences, Victoria University of Wellington, Kelburn Parade, Wellington 6140, New Zealand
| | - David J Miller
- Molecular and Cell Biology, James Cook University, Townsville, QLD 4811, Australia .,ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811, Australia
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Yuyama I, Ishikawa M, Nozawa M, Yoshida MA, Ikeo K. Transcriptomic changes with increasing algal symbiont reveal the detailed process underlying establishment of coral-algal symbiosis. Sci Rep 2018; 8:16802. [PMID: 30429501 PMCID: PMC6235891 DOI: 10.1038/s41598-018-34575-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 10/19/2018] [Indexed: 12/21/2022] Open
Abstract
To clarify the establishment process of coral-algal symbiotic relationships, coral transcriptome changes during increasing algal symbiont densities were examined in juvenile corals following inoculation with the algae Symbiodinium goreaui (clade C) and S. trenchii (clade D), and comparison of their transcriptomes with aposymbiotic corals by RNA-sequencing. Since Symbiodinium clades C and D showed very different rates of density increase, comparisons were made of early onsets of both symbionts, revealing that the host behaved differently for each. RNA-sequencing showed that the number of differentially-expressed genes in corals colonized by clade D increased ca. two-fold from 10 to 20 days, whereas corals with clade C showed unremarkable changes consistent with a slow rate of density increase. The data revealed dynamic metabolic changes in symbiotic corals. In addition, the endocytosis pathway was also upregulated, while lysosomal digestive enzymes and the immune system tended to be downregulated as the density of clade D algae increased. The present dataset provides an enormous number of candidate symbiosis-related molecules that exhibit the detailed process by which coral-algal endosymbiosis is established.
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Affiliation(s)
- Ikuko Yuyama
- Faculty of Life and Environmental Sciences, University of Tsukuba, 111 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan.
| | - Masakazu Ishikawa
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, 17 177, Sweden
| | - Masafumi Nozawa
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji, Tokyo, 192-0397, Japan
- Center for Genomics and Bioinformatics, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji, Tokyo, 192-0397, Japan
| | - Masa-Aki Yoshida
- Marine Biological Science Section, Education and Research Center for Biological Resources, Faculty of Life and Environmental Science, Shimane University, 194 Kamo, Okinoshima-cho, Oki, Shimane, 685-0024, Japan
| | - Kazuho Ikeo
- Center for Information Biology, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan
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Quigley KM, Strader ME, Matz MV. Relationship between Acropora millepora juvenile fluorescence and composition of newly established Symbiodinium assemblage. PeerJ 2018; 6:e5022. [PMID: 29922515 PMCID: PMC6005160 DOI: 10.7717/peerj.5022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 05/30/2018] [Indexed: 11/20/2022] Open
Abstract
Coral-dinoflagellate symbiosis is the key biological interaction enabling existence of modern-type coral reefs, but the mechanisms regulating initial host-symbiont attraction, recognition and symbiont proliferation thus far remain largely unclear. A common reef-building coral, Acropora millepora, displays conspicuous fluorescent polymorphism during all phases of its life cycle, due to the differential expression of fluorescent proteins (FPs) of the green fluorescent protein family. In this study, we examine whether fluorescent variation in young coral juveniles exposed to natural sediments is associated with the uptake of disparate Symbiodinium assemblages determined using ITS-2 deep sequencing. We found that Symbiodinium assemblages varied significantly when redness values varied, specifically in regards to abundances of clades A and C. Whether fluorescence was quantified as a categorical or continuous trait, clade A was found at higher abundances in redder juveniles. These preliminary results suggest juvenile fluorescence may be associated with Symbiodinium uptake, potentially acting as either an attractant to ecologically specific types or as a mechanism to modulate the internal light environment to control Symbiodinium physiology within the host.
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Affiliation(s)
- Kate M. Quigley
- College of Marine and Environmental Sciences, and ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
- AIMS@JCU, Australian Institute of Marine Science, Townsville, Queensland, Australia
| | - Marie E. Strader
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA, United States of America
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States of America
| | - Mikhail V. Matz
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States of America
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6
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Merselis DG, Lirman D, Rodriguez-Lanetty M. Symbiotic immuno-suppression: is disease susceptibility the price of bleaching resistance? PeerJ 2018; 6:e4494. [PMID: 29682405 PMCID: PMC5909685 DOI: 10.7717/peerj.4494] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 02/22/2018] [Indexed: 12/11/2022] Open
Abstract
Accelerating anthropogenic climate change threatens to destroy coral reefs worldwide through the processes of bleaching and disease. These major contributors to coral mortality are both closely linked with thermal stress intensified by anthropogenic climate change. Disease outbreaks typically follow bleaching events, but a direct positive linkage between bleaching and disease has been debated. By tracking 152 individual coral ramets through the 2014 mass bleaching in a South Florida coral restoration nursery, we revealed a highly significant negative correlation between bleaching and disease in the Caribbean staghorn coral, Acropora cervicornis. To explain these results, we propose a mechanism for transient immunological protection through coral bleaching: removal of Symbiodinium during bleaching may also temporarily eliminate suppressive symbiont modulation of host immunological function. We contextualize this hypothesis within an ecological perspective in order to generate testable predictions for future investigation.
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Affiliation(s)
- Daniel G Merselis
- Department of Biological Sciences, Florida International University, Miami, FL, USA
| | - Diego Lirman
- Department of Marine Biology and Ecology, University of Miami, Miami, FL, USA
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Abstract
Sulfur-containing compounds are important components of all organisms, but few studies have explored sulfate utilization in corals. Our previous study found that the expression of a sulfur transporter (SLC26A11) was upregulated in the presence of Symbiodinium cells in juveniles of the reef-building coral Acropora tenuis. In this study, we performed autoradiography using 35S-labeled sulfate ions (35SO4 2−) to examine the localization and amount of incorporated radioactive sulfate in the coral tissues and symbiotic algae. Incorporated 35SO4 2− was detected in symbiotic algal cells, nematocysts, ectodermal cells and calicoblast cells. The combined results of 35S autoradiography and Alcian Blue staining showed that incorporated 35S accumulated as sulfated glycosaminoglycans (GAGs) in the ectodermal cell layer. We also compared the relative incorporation of 35SO4 2− into coral tissues and endosymbiotic algae, and their chemical fractions in dark versus light (photosynthetic) conditions. The amount of sulfur compounds, such as GAGs and lipids, generated from 35SO4 2− was higher under photosynthetic conditions. Together with the upregulation of sulfate transporters by symbiosis, our results suggest that photosynthesis of algal endosymbionts contributes to the synthesis and utilization of sulfur compounds in corals. Summary:35S-labeled sulfate incorporated into various cells of coral demonstrates that photosynthesis of endosymbiotic algae contributes to the synthesis and utilization of sulfur compounds.
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Affiliation(s)
- Ikuko Yuyama
- Center for Information Biology, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan Graduate School of Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Tomihiko Higuchi
- Graduate School of Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan
| | - Yoshio Takei
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan
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Balzano S, Corre E, Decelle J, Sierra R, Wincker P, Da Silva C, Poulain J, Pawlowski J, Not F. Transcriptome analyses to investigate symbiotic relationships between marine protists. Front Microbiol 2015; 6:98. [PMID: 25852650 PMCID: PMC4362344 DOI: 10.3389/fmicb.2015.00098] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 01/26/2015] [Indexed: 11/13/2022] Open
Abstract
Rhizaria are an important component of oceanic plankton communities worldwide. A number of species harbor eukaryotic microalgal symbionts, which are horizontally acquired in the environment at each generation. Although these photosymbioses are determinant for Rhizaria ability to thrive in oceanic ecosystems, the mechanisms for symbiotic interactions are unclear. Using high-throughput sequencing technology (i.e., 454), we generated large Expressed Sequence Tag (EST) datasets from four uncultured Rhizaria, an acantharian (Amphilonche elongata), two polycystines (Collozoum sp. and Spongosphaera streptacantha), and one phaeodarian (Aulacantha scolymantha). We assessed the main genetic features of the host/symbionts consortium (i.e., the holobiont) transcriptomes and found rRNA sequences affiliated to a wide range of bacteria and protists in all samples, suggesting that diverse microbial communities are associated with the holobionts. A particular focus was then carried out to search for genes potentially involved in symbiotic processes such as the presence of c-type lectins-coding genes, which are proteins that play a role in cell recognition among eukaryotes. Unigenes coding putative c-type lectin domains (CTLD) were found in the species bearing photosynthetic symbionts (A. elongata, Collozoum sp., and S. streptacantha) but not in the non-symbiotic one (A. scolymantha). More particularly, phylogenetic analyses group CTLDs from A. elongata and Collozoum sp. on a distinct branch from S. streptacantha CTLDs, which contained carbohydrate-binding motifs typically observed in other marine photosymbiosis. Our data suggest that similarly to other well-known marine photosymbiosis involving metazoans, the interactions of glycans with c-type lectins is likely involved in modulation of the host/symbiont specific recognition in Radiolaria.
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Affiliation(s)
- Sergio Balzano
- UMR 7144, Université Pierre et Marie Curie Université Paris 06, Sorbonne Universités, Station Biologique de Roscoff Roscoff, France ; Centre National de la Recherche Scientifique, UMR 7144, Station Biologique de Roscoff Roscoff, France
| | - Erwan Corre
- Centre National de la Recherche Scientifique and Université Pierre et Marie Curie, FR2424, ABiMS, Station Biologique Roscoff, France
| | - Johan Decelle
- UMR 7144, Université Pierre et Marie Curie Université Paris 06, Sorbonne Universités, Station Biologique de Roscoff Roscoff, France ; Centre National de la Recherche Scientifique, UMR 7144, Station Biologique de Roscoff Roscoff, France
| | - Roberto Sierra
- Department of Genetics and Evolution, University of Geneva Geneva, Switzerland
| | - Patrick Wincker
- Commissariat à l'Energie Atomique et aux Energies Alternatives Genoscope, France
| | - Corinne Da Silva
- Commissariat à l'Energie Atomique et aux Energies Alternatives Genoscope, France
| | - Julie Poulain
- Commissariat à l'Energie Atomique et aux Energies Alternatives Genoscope, France
| | - Jan Pawlowski
- Department of Genetics and Evolution, University of Geneva Geneva, Switzerland
| | - Fabrice Not
- UMR 7144, Université Pierre et Marie Curie Université Paris 06, Sorbonne Universités, Station Biologique de Roscoff Roscoff, France ; Centre National de la Recherche Scientifique, UMR 7144, Station Biologique de Roscoff Roscoff, France
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Hill MS. Production possibility frontiers in phototroph:heterotroph symbioses: trade-offs in allocating fixed carbon pools and the challenges these alternatives present for understanding the acquisition of intracellular habitats. Front Microbiol 2014; 5:357. [PMID: 25101064 PMCID: PMC4101577 DOI: 10.3389/fmicb.2014.00357] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 06/25/2014] [Indexed: 11/13/2022] Open
Abstract
Intracellular habitats have been invaded by a remarkable diversity of organisms, and strategies employed to successfully reside in another species' cellular space are varied. Common selective pressures may be experienced in symbioses involving phototrophic symbionts and heterotrophic hosts. Here I refine and elaborate the Arrested Phagosome Hypothesis that proposes a mechanism that phototrophs use to gain access to their host's intracellular habitat. I employ the economic concept of production possibility frontiers (PPF) as a useful heuristic to clearly define the trade-offs that an intracellular phototroph is likely to face as it allocates photosynthetically-derived pools of energy. Fixed carbon can fuel basic metabolism/respiration, it can support mitotic division, or it can be translocated to the host. Excess photosynthate can be stored for future use. Thus, gross photosynthetic productivity can be divided among these four general categories, and natural selection will favor phenotypes that best match the demands presented to the symbiont by the host cellular habitat. The PPF highlights trade-offs that exist between investment in growth (i.e., mitosis) or residency (i.e., translocating material to the host). Insights gained from this perspective might help explain phenomena such as coral bleaching because deficits in photosynthetic production are likely to diminish a symbiont's ability to "afford" the costs of intracellular residency. I highlight deficits in our current understanding of host:symbiont interactions at the molecular, genetic, and cellular level, and I also discuss how semantic differences among scientists working with different symbiont systems may diminish the rate of increase in our understanding of phototrophic-based associations. I argue that adopting interdisciplinary (in this case, inter-symbiont-system) perspectives will lead to advances in our general understanding of the phototrophic symbiont's intracellular niche.
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Affiliation(s)
- Malcolm S Hill
- Department of Biology, Gottwald Science Center, University of Richmond Richmond, VA, USA
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10
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Riesgo A, Peterson K, Richardson C, Heist T, Strehlow B, McCauley M, Cotman C, Hill M, Hill A. Transcriptomic analysis of differential host gene expression upon uptake of symbionts: a case study with Symbiodinium and the major bioeroding sponge Cliona varians. BMC Genomics 2014; 15:376. [PMID: 24885832 PMCID: PMC4144087 DOI: 10.1186/1471-2164-15-376] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 04/11/2014] [Indexed: 11/25/2022] Open
Abstract
Background We have a limited understanding of genomic interactions that occur among partners for many symbioses. One of the most important symbioses in tropical reef habitats involves Symbiodinium. Most work examining Symbiodinium-host interactions involves cnidarian partners. To fully and broadly understand the conditions that permit Symbiodinium to procure intracellular residency, we must explore hosts from different taxa to help uncover universal cellular and genetic strategies for invading and persisting in host cells. Here, we present data from gene expression analyses involving the bioeroding sponge Cliona varians that harbors Clade G Symbiodinium. Results Patterns of differential gene expression from distinct symbiont states (“normal”, “reinfected”, and “aposymbiotic”) of the sponge host are presented based on two comparative approaches (transcriptome sequencing and suppressive subtractive hybridization (SSH)). Transcriptomic profiles were different when reinfected tissue was compared to normal and aposymbiotic tissue. We characterized a set of 40 genes drawn from a pool of differentially expressed genes in “reinfected” tissue compared to “aposymbiotic” tissue via SSH. As proof of concept, we determined whether some of the differentially expressed genes identified above could be monitored in sponges grown under ecologically realistic field conditions. We allowed aposymbiotic sponge tissue to become re-populated by natural pools of Symbiodinium in shallow water flats in the Florida Keys, and we analyzed gene expression profiles for two genes found to be increased in expression in “reinfected” tissue in both the transcriptome and via SSH. These experiments highlighted the experimental tractability of C. varians to explore with precision the genetic events that occur upon establishment of the symbiosis. We briefly discuss lab- and field-based experimental approaches that promise to offer insights into the co-opted genetic networks that may modulate uptake and regulation of Symbiondinium populations in hospite. Conclusions This work provides a sponge transcriptome, and a database of putative genes and genetic pathways that may be involved in Symbiodinium interactions. The relative patterns of gene expression observed in these experiments will need to be evaluated on a gene-by-gene basis in controlled and natural re-infection experiments. We argue that sponges offer particularly useful characteristics for discerning essential dimensions of the Symbiodinium niche. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-376) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | - Malcolm Hill
- Department of Biology, University of Richmond, Richmond, VA, USA.
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11
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Extensive differences in gene expression between symbiotic and aposymbiotic cnidarians. G3-GENES GENOMES GENETICS 2014; 4:277-95. [PMID: 24368779 PMCID: PMC3931562 DOI: 10.1534/g3.113.009084] [Citation(s) in RCA: 116] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Coral reefs provide habitats for a disproportionate number of marine species relative to the small area of the oceans that they occupy. The mutualism between the cnidarian animal hosts and their intracellular dinoflagellate symbionts provides the nutritional foundation for coral growth and formation of reef structures, because algal photosynthesis can provide >90% of the total energy of the host. Disruption of this symbiosis (“coral bleaching”) is occurring on a large scale due primarily to anthropogenic factors and poses a major threat to the future of coral reefs. Despite the importance of this symbiosis, the cellular mechanisms involved in its establishment, maintenance, and breakdown remain largely unknown. We report our continued development of genomic tools to study these mechanisms in Aiptasia, a small sea anemone with great promise as a model system for studies of cnidarian–dinoflagellate symbiosis. Specifically, we have generated de novo assemblies of the transcriptomes of both a clonal line of symbiotic anemones and their endogenous dinoflagellate symbionts. We then compared transcript abundances in animals with and without dinoflagellates. This analysis identified >900 differentially expressed genes and allowed us to generate testable hypotheses about the cellular functions affected by symbiosis establishment. The differentially regulated transcripts include >60 encoding proteins that may play roles in transporting various nutrients between the symbiotic partners; many more encoding proteins functioning in several metabolic pathways, providing clues regarding how the transported nutrients may be used by the partners; and several encoding proteins that may be involved in host recognition and tolerance of the dinoflagellate.
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12
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Bay LK, Guérécheau A, Andreakis N, Ulstrup KE, Matz MV. Gene expression signatures of energetic acclimatisation in the reef building coral Acropora millepora. PLoS One 2013; 8:e61736. [PMID: 23671571 PMCID: PMC3650039 DOI: 10.1371/journal.pone.0061736] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Accepted: 03/13/2013] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Understanding the mechanisms by which natural populations cope with environmental stress is paramount to predict their persistence in the face of escalating anthropogenic impacts. Reef-building corals are increasingly exposed to local and global stressors that alter nutritional status causing reduced fitness and mortality, however, these responses can vary considerably across species and populations. METHODOLOGY/PRINCIPAL FINDINGS We compare the expression of 22 coral host genes in individuals from an inshore and an offshore reef location using quantitative Reverse Transcription-PCR (qRT-PCR) over the course of 26 days following translocation into a shaded, filtered seawater environment. Declines in lipid content and PSII activity of the algal endosymbionts (Symbiodinium ITS-1 type C2) over the course of the experiment indicated that heterotrophic uptake and photosynthesis were limited, creating nutritional deprivation conditions. Regulation of coral host genes involved in metabolism, CO2 transport and oxidative stress could be detected already after five days, whereas PSII activity took twice as long to respond. Opposing expression trajectories of Tgl, which releases fatty acids from the triacylglycerol storage, and Dgat1, which catalyses the formation of triglycerides, indicate that the decline in lipid content can be attributed, at least in part, by mobilisation of triacylglycerol stores. Corals from the inshore location had initially higher lipid content and showed consistently elevated expression levels of two genes involved in metabolism (aldehyde dehydrogenase) and calcification (carbonic anhydrase). CONCLUSIONS/SIGNIFICANCE Coral host gene expression adjusts rapidly upon change in nutritional conditions, and therefore can serve as an early signature of imminent coral stress. Consistent gene expression differences between populations indicate that corals acclimatize and/or adapt to local environments. Our results set the stage for analysis of these processes in natural coral populations, to better understand the responses of coral communities to global climate change and to develop more efficient management strategies.
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Affiliation(s)
- Line K Bay
- Climate Change and Ocean Acidification Team, Australian Institute of Marine Science, Townsville, Queensland, Australia.
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Hideno A, Inoue H, Fujii T, Yano S, Tsukahara K, Murakami K, Yunokawa H, Sawayama S. High-coverage gene expression profiling analysis of the cellulase-producing fungus Acremonium cellulolyticus cultured using different carbon sources. Appl Microbiol Biotechnol 2013; 97:5483-92. [DOI: 10.1007/s00253-013-4689-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 12/26/2012] [Accepted: 12/27/2012] [Indexed: 10/27/2022]
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Urbarova I, Karlsen BO, Okkenhaug S, Seternes OM, Johansen SD, Emblem Å. Digital marine bioprospecting: mining new neurotoxin drug candidates from the transcriptomes of cold-water sea anemones. Mar Drugs 2012; 10:2265-2279. [PMID: 23170083 PMCID: PMC3497022 DOI: 10.3390/md10102265] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 10/08/2012] [Accepted: 10/10/2012] [Indexed: 11/16/2022] Open
Abstract
Marine bioprospecting is the search for new marine bioactive compounds and large-scale screening in extracts represents the traditional approach. Here, we report an alternative complementary protocol, called digital marine bioprospecting, based on deep sequencing of transcriptomes. We sequenced the transcriptomes from the adult polyp stage of two cold-water sea anemones, Bolocera tuediae and Hormathia digitata. We generated approximately 1.1 million quality-filtered sequencing reads by 454 pyrosequencing, which were assembled into approximately 120,000 contigs and 220,000 single reads. Based on annotation and gene ontology analysis we profiled the expressed mRNA transcripts according to known biological processes. As a proof-of-concept we identified polypeptide toxins with a potential blocking activity on sodium and potassium voltage-gated channels from digital transcriptome libraries.
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Affiliation(s)
- Ilona Urbarova
- RNA and Transcriptomics Group, Department of Medical Biology, Faculty of Health Sciences, University of Tromsø, N9037 Tromsø, Norway; (I.U.); (B.O.K.); (S.O.); (A.E.)
| | - Bård Ove Karlsen
- RNA and Transcriptomics Group, Department of Medical Biology, Faculty of Health Sciences, University of Tromsø, N9037 Tromsø, Norway; (I.U.); (B.O.K.); (S.O.); (A.E.)
| | - Siri Okkenhaug
- RNA and Transcriptomics Group, Department of Medical Biology, Faculty of Health Sciences, University of Tromsø, N9037 Tromsø, Norway; (I.U.); (B.O.K.); (S.O.); (A.E.)
| | - Ole Morten Seternes
- Pharmacology Group, Department of Pharmacy, Faculty of Health Sciences, University of Tromsø, N9037 Tromsø, Norway;
| | - Steinar D. Johansen
- RNA and Transcriptomics Group, Department of Medical Biology, Faculty of Health Sciences, University of Tromsø, N9037 Tromsø, Norway; (I.U.); (B.O.K.); (S.O.); (A.E.)
- Marine Genomics Group, Faculty of Biosciences and Aquaculture, University of Nordland, N8049 Bodø, Norway
| | - Åse Emblem
- RNA and Transcriptomics Group, Department of Medical Biology, Faculty of Health Sciences, University of Tromsø, N9037 Tromsø, Norway; (I.U.); (B.O.K.); (S.O.); (A.E.)
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15
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Meyer E, Weis VM. Study of cnidarian-algal symbiosis in the "omics" age. THE BIOLOGICAL BULLETIN 2012; 223:44-65. [PMID: 22983032 DOI: 10.1086/bblv223n1p44] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The symbiotic associations between cnidarians and dinoflagellate algae (Symbiodinium) support productive and diverse ecosystems in coral reefs. Many aspects of this association, including the mechanistic basis of host-symbiont recognition and metabolic interaction, remain poorly understood. The first completed genome sequence for a symbiotic anthozoan is now available (the coral Acropora digitifera), and extensive expressed sequence tag resources are available for a variety of other symbiotic corals and anemones. These resources make it possible to profile gene expression, protein abundance, and protein localization associated with the symbiotic state. Here we review the history of "omics" studies of cnidarian-algal symbiosis and the current availability of sequence resources for corals and anemones, identifying genes putatively involved in symbiosis across 10 anthozoan species. The public availability of candidate symbiosis-associated genes leaves the field of cnidarian-algal symbiosis poised for in-depth comparative studies of sequence diversity and gene expression and for targeted functional studies of genes associated with symbiosis. Reviewing the progress to date suggests directions for future investigations of cnidarian-algal symbiosis that include (i) sequencing of Symbiodinium, (ii) proteomic analysis of the symbiosome membrane complex, (iii) glycomic analysis of Symbiodinium cell surfaces, and (iv) expression profiling of the gastrodermal cells hosting Symbiodinium.
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Affiliation(s)
- Eli Meyer
- Department of Zoology, Oregon State University, Corvallis, Oregon 97331, USA.
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Dorrell RG, Howe CJ. What makes a chloroplast? Reconstructing the establishment of photosynthetic symbioses. J Cell Sci 2012; 125:1865-75. [PMID: 22547565 DOI: 10.1242/jcs.102285] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Earth is populated by an extraordinary diversity of photosynthetic eukaryotes. Many eukaryotic lineages contain chloroplasts, obtained through the endosymbiosis of a wide range of photosynthetic prokaryotes or eukaryotes, and a wide variety of otherwise non-photosynthetic species form transient associations with photosynthetic symbionts. Chloroplast lineages are likely to be derived from pre-existing transient symbioses, but it is as yet poorly understood what steps are required for the establishment of permanent chloroplasts from photosynthetic symbionts. In the past decade, several species that contain relatively recently acquired chloroplasts, such as the rhizarian Paulinella chromatophora, and non-photosynthetic taxa that maintain photosynthetic symbionts, such as the sacoglossan sea slug Elysia, the ciliate Myrionecta rubra and the dinoflagellate Dinophysis, have emerged as potential model organisms in the study of chloroplast establishment. In this Commentary, we compare recent molecular insights into the maintenance of chloroplasts and photosynthetic symbionts from these lineages, and others that might represent the early stages of chloroplast establishment. We emphasise the importance in the establishment of chloroplasts of gene transfer events that minimise oxidative stress acting on the symbiont. We conclude by assessing whether chloroplast establishment is facilitated in some lineages by a mosaic of genes, derived from multiple symbiotic associations, encoded in the host nucleus.
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Affiliation(s)
- Richard G Dorrell
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK.
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Symbiodinium transcriptomes: genome insights into the dinoflagellate symbionts of reef-building corals. PLoS One 2012; 7:e35269. [PMID: 22529998 PMCID: PMC3329448 DOI: 10.1371/journal.pone.0035269] [Citation(s) in RCA: 163] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2011] [Accepted: 03/13/2012] [Indexed: 12/20/2022] Open
Abstract
Dinoflagellates are unicellular algae that are ubiquitously abundant in aquatic environments. Species of the genus Symbiodinium form symbiotic relationships with reef-building corals and other marine invertebrates. Despite their ecologic importance, little is known about the genetics of dinoflagellates in general and Symbiodinium in particular. Here, we used 454 sequencing to generate transcriptome data from two Symbiodinium species from different clades (clade A and clade B). With more than 56,000 assembled sequences per species, these data represent the largest transcriptomic resource for dinoflagellates to date. Our results corroborate previous observations that dinoflagellates possess the complete nucleosome machinery. We found a complete set of core histones as well as several H3 variants and H2A.Z in one species. Furthermore, transcriptome analysis points toward a low number of transcription factors in Symbiodinium spp. that also differ in the distribution of DNA-binding domains relative to other eukaryotes. In particular the cold shock domain was predominant among transcription factors. Additionally, we found a high number of antioxidative genes in comparison to non-symbiotic but evolutionary related organisms. These findings might be of relevance in the context of the role that Symbiodinium spp. play as coral symbionts. Our data represent the most comprehensive dinoflagellate EST data set to date. This study provides a comprehensive resource to further analyze the genetic makeup, metabolic capacities, and gene repertoire of Symbiodinium and dinoflagellates. Overall, our findings indicate that Symbiodinium possesses some unique characteristics, in particular the transcriptional regulation in Symbiodinium may differ from the currently known mechanisms of eukaryotic gene regulation.
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Dittmar T, Zänker KS. Horizontal gene transfers with or without cell fusions in all categories of the living matter. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2011; 714:5-89. [PMID: 21506007 PMCID: PMC7120942 DOI: 10.1007/978-94-007-0782-5_2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
This article reviews the history of widespread exchanges of genetic segments initiated over 3 billion years ago, to be part of their life style, by sphero-protoplastic cells, the ancestors of archaea, prokaryota, and eukaryota. These primordial cells shared a hostile anaerobic and overheated environment and competed for survival. "Coexist with, or subdue and conquer, expropriate its most useful possessions, or symbiose with it, your competitor" remain cellular life's basic rules. This author emphasizes the role of viruses, both in mediating cell fusions, such as the formation of the first eukaryotic cell(s) from a united crenarchaeon and prokaryota, and the transfer of host cell genes integrated into viral (phages) genomes. After rising above the Darwinian threshold, rigid rules of speciation and vertical inheritance in the three domains of life were established, but horizontal gene transfers with or without cell fusions were never abolished. The author proves with extensive, yet highly selective documentation, that not only unicellular microorganisms, but the most complex multicellular entities of the highest ranks resort to, and practice, cell fusions, and donate and accept horizontally (laterally) transferred genes. Cell fusions and horizontally exchanged genetic materials remain the fundamental attributes and inherent characteristics of the living matter, whether occurring accidentally or sought after intentionally. These events occur to cells stagnating for some 3 milliard years at a lower yet amazingly sophisticated level of evolution, and to cells achieving the highest degree of differentiation, and thus functioning in dependence on the support of a most advanced multicellular host, like those of the human brain. No living cell is completely exempt from gene drains or gene insertions.
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Affiliation(s)
- Thomas Dittmar
- Inst. Immunologie, Universität Witten/Herdecke, Stockumer Str. 10, Witten, 58448 Germany
| | - Kurt S. Zänker
- Institute of Immunologie, University of Witten/Herdecke, Stockumer Str. 10, Witten, 58448 Germany
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