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54 results for “Coral Symbionts”
Cophylogeny and specificity between cryptic coral species (Pocillopora spp.) at Mo'orea and their symbionts (Symbiodiniaceae)
<p>GENERAL INFORMATION</p> <p>1. Title of Dataset: Cophylogeny and specificity between cryptic coral species (Pocillopora spp.) at Mo'orea and their symbionts (Symbiodiniaceae)</p> <p>2. Author Information<br> A. Principal Investigator Contact Information<br> Name: Scott Burgess<br> Institution: Florida State University<br> Address: 319 Stadium Drive, Tallahassee, FL, USA 32306<br> Email: sburgess@bio.fsu.edu</p> <p><br> 3. Date of data collection (single date, range, approximate date): 2019-08</p> <p>4. Geographic location of data collection: Moorea, French Polynesia</p> <p>5. Information about funding sources that supported the collection of the data: National Science Foundation (NSF; OCE-1829867)</p> <p> </p> <p><br> DATA & FILE OVERVIEW</p> <p>1. File List:<br> Figure 2 Make.R<br> Figure 4 Make.R<br> Figure 5b Make.R<br> Figure 6 Make.R</p> <p>Figure 1 SNAPP species tree.xml<br> Figure 2.txt<br> Figure 2.vcf<br> Figure 3b - Pocillopora mt genomes.nex<br> Figure 4 and 6 data.csv<br> Figure 4 colors.csv<br> Figure 5a - Cladocopium_psbA.nex<br> Figure 5b - Clad clades.csv<br> Figure 5b_Cladocopium.nex<br> Figure 5b_Pocillopora.nex<br> Figure 5b.csv</p> <p><br> 2. Relationship between files:<br> Figure 2 Make.R uses Figure 2.txt and Figure 2.vcf<br> Figure 4 Make.R uses Figure 4 and 6 data.csv and Figure 4 colors.csv<br> Figure 5b Make.R uses Figure 5b - Clad clades.csv, Figure 5b_Cladocopium.nex, Figure 5b_Pocillopora.nex, and Figure 5b.csv<br> Figure 6 Make.R Figure 4 and 6 data.csv</p> <p> </p> <p>3. Metadata</p> <p>Figure 2 Make.R:<br> R code to produce Figure 2, and the accompanying analyses presented in the text, in:<br> Johnston EC, Cunning, Burgess SC. Cophylogeny and specificity between cryptic coral species (Pocillopora spp.) at Mo’orea and their symbionts (Symbiodiniaceae).<br> Uses 'Figure 2.txt', 'Figure 2.vcf'</p> <p><br> Figure 4 Make.R:<br> R code to produce Figure 4, and the accompanying analyses presented in the text, in:<br> Johnston EC, Cunning, Burgess SC. Cophylogeny and specificity between cryptic coral species (Pocillopora spp.) at Mo’orea and their symbionts (Symbiodiniaceae).<br> Uses 'Figure 4 and 4 data.csv', 'Figure 4 colors'</p> <p><br> Figure 5b Make.R:<br> R code to produce Figure 5b, and the accompanying analyses presented in the text, in:<br> Johnston EC, Cunning, Burgess SC. Cophylogeny and specificity between cryptic coral species (Pocillopora spp.) at Mo’orea and their symbionts (Symbiodiniaceae).<br> Uses 'Figure 5b - Clad clades.csv', 'Figure 5b_Cladocopium.nex', 'Figure 5b_Pocillopora.nex', 'Figure 5b.csv'</p> <p><br> Figure 6 Make.R:<br> R code to produce Figure 6, and the accompanying analyses presented in the text, in:<br> Johnston EC, Cunning, Burgess SC. Cophylogeny and specificity between cryptic coral species (Pocillopora spp.) at Mo’orea and their symbionts (Symbiodiniaceae).<br> Uses 'Figure 4 and 6 data.csv'</p> <p><br> Figure 1 SNAPP species tree.xml:<br> Data for species tree used in Figure 1</p> <p>Figure 2.txt:<br> Metadata<br> Sample_ID: Sample ID<br> Hap_Spp: Pocillopora species or haplotype</p> <p>Figure 2.vcf:<br> Linked dataset of 7,887 SNPs</p> <p>Figure 3b - Pocillopora mt genomes.nex:<br> Nexus tree of Pocillopora mitochondrial genomes used in Figure 3b</p> <p><br> Figure 4 and 6 data.csv:<br> Metadata<br> Species.haplotype: Pocillopora species or haplotype<br> Depth.m: Sampling depth in meters<br> Site: Sampling site, label corresponds to the site used in the Moorea Coral Reef Long-Term Ecological Research (MCR-LTER) program.<br> Coral.ID: Coral colony identifier<br> Type_profile: ITS2 type profile generated by SymPortal<br> Type_profile_Prop: Proportion of that given ITS2 type profile in colony sampled<br> Remaining columns: Proportion of ITS2 sequences in colony sampled</p> <p>Figure 4 colors.csv:<br> Metadata<br> my_colors: Custom colors for each ITS2 sequence<br> Symbio.clade: ITS2 sequences</p> <p>Figure 5a - Cladocopium_psbA.nex:<br> Nexus tree of Cladocopium taxa in figure 5a</p> <p>Figure 5b - Clad clades.csv:<br> Metadata<br> UCI_links: Sample ID that contains Pocillopora species or haplotype, sample ID, and ITS2 type profile<br> Clad_clades: Clade assignment from figure 5a</p> <p>Figure 5b_Cladocopium.nex:<br> Nexus tree of Cladocopium taxa in Figure 5b</p> <p>Figure 5b_Pocillopora.nex:<br> Nexus tree of Pocillopora taxa used in PACo analysis, Figure 5b</p> <p>Figure 5b.csv:<br> Matrix of Pocillopora host and Cladocopium symbiont links</p>
Exploring mechanisms that affect coral cooperation: symbiont transmission mode, cell density and community composition
<p>This repository contains code to accompany the manuscript titled</p> <p><strong>Exploring mechanisms that affect coral cooperation: symbiont transmission mode, cell density and community composition</strong></p> <p>by <strong>Carly D. Kenkel and Line K. Bay</strong><br> </p> <p>In this study, we used a phylogenetically controlled design to investigate the role of vertical symbiont transmission, an evolutionary mechanism predicted to enhance cooperation and holobiont fitness of reef-building corals. Six species of coral, three vertical transmitters and their closest horizontally transmitting relatives, were fragmented and subjected to a two-week thermal stress experiment. Symbiont cell density, photosynthetic function and translocation of photosynthetically fixed carbon between symbionts and hosts were quantified to assess changes in physiological metrics of fitness and cooperation. Amplicon sequencing of the <em>Symbiodinium</em> ITS-2 locus was used to investigate differences in symbiont community composition among focal species. We did not observe universally higher levels of cooperation in vertically transmitting species. However, the reduction in cooperation at the onset of bleaching was marginally associated with symbiont community diversity. Analysis of ITS2 amplicon sequence data suggest that it may not be vertical transmission <em>per se</em> that influences host-symbiont cooperation, but genetic uniformity of the symbiont community.</p> <p>Repository contents:</p> <ul> <li> <p><strong>TraitDataAnalysis.R:</strong> Annotated R script for generating figures and re-creating statistical analyses</p> <ul> <li> <p><strong>RsquaredGLMM.R:</strong> Accessory R script for running RsquaredGLMM analyses, called by <strong>TraitDataAnalysis.R</strong></p> </li> <li> <p><strong>NSF_RunningPam.csv</strong>: Input file for statistical analysis. Contains photophysiological data. Column headers are as follows:</p> <ul> <li> <p>Tank: Number of experimental tank in which experimental coral fragment was held</p> </li> <li> <p>Treatment: short-hand notation for sample treatments (e.g. ctrl1-5 = control temperature, genotypes 1-5)</p> </li> <li> <p>Water: source sump for temperature controlled water jackets for each set of treatment tanks</p> </li> <li> <p>Position: numerical rack position of coral fragment within experimental treatment tank</p> </li> <li> <p>Species: Coral species (Amil=<em>A. millepora</em>, Maqe=<em>M. aequituberculata</em>, Gast=<em>G. astreata</em>, Gach=<em>G. acrhelia</em>, Plob=<em>P. lobata</em>, Gcol=<em>G. columna</em>)</p> </li> <li> <p>Genotype: source colony origin of individual coral fragments within species</p> </li> <li> <p>Temp: experimental temperature treatment (ctrl: 27°C ; heat: 31°C)</p> </li> <li> <p>Treat: whether experimental corals received C14-labeled bicarbonate (bicarb), artemia or were sampled separately for Gene Expression Analysis (not presented in this manuscript)</p> </li> <li> <p>EQY: Effective quantum yield of <em>Symbiodinium</em> photosystem II as measured using PAM fluorometry</p> </li> <li> <p>Date: Actual calendar date of measure</p> </li> <li> <p>Transmission: coral symbiont transmission mode</p> </li> <li> <p>Reef: reef site of original coral collection</p> </li> <li> <p>Date: experimental date of measure</p> </li> </ul> </li> <li> <p><strong>TraitData.csv:</strong> Input file for statistical analysis. Contains all physiological trait data.</p> <ul> <li> <p>Includes columns as described above for the Running_Pam file in addition to columns containing raw trait data as described in the manuscript.</p> </li> </ul> </li> <li> <p><strong>TraitData_DaysAsCols.csv:</strong> Reformatted input file with trait data split by sampling day across columns</p> </li> </ul> </li> <li> <p><strong>DADA2Analysis.R:</strong> Annotated R script for generating figures and running ITS2 amplicon analyses</p> <ul> <li> <p>GeoSymbio_ITS2_LocalDatabase_verForPhyloseq.fasta: FASTA file of the GeoSymbio ITS2 reference database <a href="https://sites.google.com/site/geosymbio/">https://sites.google.com/site/geosymbio/</a>, formatted for use with the R prograom Phyloseq</p> </li> <li> <p>SeqVars_6Feb.fasta: FASTA file of identified sequence variants resulting from DADA2 analysis</p> </li> <li> <p>OutputDADA_6Feb.csv: Counts of sequence variants by sample</p> </li> <li> <p>Raw FASTQ paired end read files can be downloaded from NCBI's SRA: PRJNA338365</p> </li> </ul> </li> </ul>
Should I stay or should I go? Coral bleaching from the symbionts' perspective
<p>Code to replicate figures in Should I Stay or Should I Go?</p>
Variation in symbiont density is linked to changes in constitutive immunity in the facultatively symbiotic coral, Astrangia poculata
<p>Scleractinian corals are essential ecosystem engineers, forming the basis of coral reef ecosystems. However, these organisms are in decline globally, in part due to rising disease prevalence. Most corals are dependent on symbiotic interactions with single-celled algae from the family Symbiodiniaceae to meet their nutritional needs, however suppression of host immunity may be essential to this relationship. To explore immunological consequences of algal symbioses in scleractinian corals, we investigated constitutive immune activity in the facultatively symbiotic coral, <em>Astrangia poculata</em>. We compared immune metrics (melanin synthesis, antioxidant production, and antibacterial activity) between coral colonies of varying symbiont density. Symbiont density was positively correlated to both antioxidant activity and melanin concentration. Our results suggest that the relationship between algal symbiosis and host immunity may be more complex than originally hypothesized and highlight the need for nuanced approaches when considering these relationships.</p>
Variation in symbiont density is linked to changes in constitutive immunity in the facultatively symbiotic coral, Astrangia poculata
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Data from: Niche breadth and divergence in sympatric cryptic coral species (Pocillopora spp.) across habitats within reefs and among algal symbionts
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Corals adapted to extreme and fluctuating seawater pH increase calcification rates and have unique symbiont communities
<p>Ocean acidification (OA) is a severe threat to coral reefs mainly by reducing their calcification rate. Identifying the resilience factors of corals to decreasing seawater pH is of paramount importance to predict the survivability of coral reefs in the future. This study compared corals adapted to variable pH<sub>T</sub> (i.e., 7.23–8.06) from the semi-enclosed lagoon of Bouraké, New Caledonia, to corals adapted to more stable seawater pH<sub>T</sub> (i.e., 7.90-8.18). In a 100-day aquarium experiment, we examined the physiological response and genetic diversity of Symbiodiniaceae from three coral species (<em>Acropora tenuis</em>, <em>Montipora</em> <em>digitata</em> and <em>Porites</em> sp.) from both sites under three stable pH<sub>NBS</sub> conditions (8.11, 7.76, 7.54) and one fluctuating pHNBS regime (between 7.56 and 8.07). Bouraké corals consistently exhibited higher growth rates than corals from the stable pH environment. Interestingly, <em>A</em>. <em>tenuis</em> from Bouraké showed the highest growth rate under the 7.76 pH<sub>NBS</sub> condition, whereas for <em>M. digitata</em> and <em>Porites</em> sp. from Bouraké, growth was highest under the fluctuating regime and the 8.11 pH<sub>NBS</sub> conditions, respectively. While OA generally decreased coral calcification by ca. 16%, Bouraké corals showed higher growth rates than corals from the stable pH environment (21% increase for <em>A. tenuis</em> to 93% for <em>M. digitata</em>, with all pH conditions pooled). This superior performance coincided with divergent symbiont communities that were more homogenous for Bouraké corals. Corals adapted to variable pH conditions appear to have a better capacity to calcify under reduced pH compared to corals native to more stable pH conditions. This response was not gained by corals from the more stable environment exposed to variable pH during the 100-day experiment, suggesting that long-term exposure to pH fluctuations and/or differences in symbiont communities benefit calcification under OA.</p>
High physiological function for corals with thermally tolerant, host-adapted symbionts
<p>The flexibility to associate with more than one symbiont may considerably expand a host's niche breadth. Coral animals and dinoflagellate micro-algae represent one of the most functionally integrated and widespread mutualisms between two eukaryotic partners. Symbiont identity greatly affects a coral's ability to cope with extremes in temperature and light. Over its broad distribution across the Eastern Pacific, the ecologically dominant branching coral, <em>Pocillopora grandis</em>, depends on mutualisms with the dinoflagellates <em>Durusdinium glynnii</em> and <em>Cladocopium latusorum</em>. Measurements of skeletal growth, calcification rates, total mass increase, calyx dimensions, reproductive output and response to thermal stress were used to assess the functional performance of these partner combinations. The results show both host–symbiont combinations displayed similar phenotypes; however, significant functional differences emerged when exposed to increased temperatures. Negligible physiological differences in colonies hosting the more thermally tolerant <em>D. glynnii</em> refute the prevailing view that these mutualisms have considerable growth tradeoffs. Well beyond the Eastern Pacific, pocilloporid colonies with <em>D. glynnii</em> are found across the Pacific in warm, environmentally variable, near-shore lagoonal habitats. While rising ocean temperatures threaten the persistence of contemporary coral reefs, lessons from the Eastern Pacific indicate that co-evolved thermally tolerant host–symbiont combinations are likely to expand ecologically and spread geographically to dominate reef ecosystems in the future.</p>
Algal symbiont diversity in Acropora muricata from the extreme reef of Bouraké associated with resistance to coral bleaching
<p>Widespread coral bleaching has generally been linked to high water temperatures at larger geographic scale. However, teh bleaching response can be highly variable aming individuals of the same species, between different species, and across localities; what causes this variability remais unresolved. Here, we tracked bleached and non-bleached colonies of <em>Acropora muricata </em>to see if they recovered or died following a stress event inside the semi-enclosed lagoon of Bouraké (New Caledonia), where corals are long-term acclimatized to extreme conditions of temperature, pH and dissolved oxygen, and at a nearby control reef. We describe Symbiodiniaceae community changes, metabolic responses, and energetical reserves (12 physiological traits evaluated) during La Niña warm and rainy summer in 2021. Widespread coral bleaching (score 1 and 2 on coral colour health chart) was observed only in Bouraké, likely due to the combination of the high temperatures (up to 32 <sup>o</sup>C) and heavy rain. All colonies (i.e., Bouraké and reference site) had <em>Cladocopium </em> as their main genera. Unbleached colonies in Bouraké had a specific ITS2-type profile (proxies for Symbiodiniaceae genotypes), while the bleached colonies in Bouraké had the same ITS2-type profile of control colonies during the stress event. After four months, teh few bleached colonies thata survived acquired the same ITS2 type profiles of the unbleached resistant colonies. In terms of physiological performances, all bleached corals showed metabolic depression (e.g., P<sub>gross </sub>and R<sub>dark</sub>). In contrast, unbleahed colonies in Bouraké maintained higher metabolic rates and energetic reserves compared to control corals. Our study suggests that <em>Acropora muricata</em> enhanced their resistance to bleaching thanks to specific Symbiodiniaceae, while energetic reserves may increase their resilience after stress. </p>
Algal symbiont diversity in Acropora muricata from the extreme reef of Bouraké associated with resistance to coral bleaching
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High physiological function for corals with thermally tolerant, host-adapted symbionts
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Data from: Symbiont type and environmental factors affect transcriptome-wide gene expression in the coral Montipora capitata
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Corals adapted to extreme and fluctuating seawater pH increase calcification rates and have unique symbiont communities
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Sequence alignments of Corallicolids, apicomplexan symbionts of coral
<p class="BodyA">Corals (Metazoa; Cnidaria; Anthozoa) have recently been shown to play host to a widespread and diverse group of intracellular symbionts of the phylum Apicomplexa. These symbionts, colloquially called 'corallicolids', are mostly known through molecular analyses, and no formal taxonomy has been proposed. Another apicomplexan, <i>Gemmocystis cylindrus</i> (described from the coral <i>Dendrogyra cylindrus</i>), may be related to corallicolids, but lacks molecular data. Here, we isolate and describe motile trophozoite (feeding) corallicolids cells using microscopic (light, SEM, and TEM) and molecular phylogenetic analysis to provide the basis for a formal description. Phylogenetic analyses using nuclear and plastid rRNA operons, and three mitochondrial protein sequences derived from single-cell transcriptomes, all confirm that these organisms fall into a discrete deep-branching clade within the Apicomplexa not closely related to any known species or major subgroup. As a result, we assign this clade to a new order, Corallicolida ord. nov., and family, Corallicolidae fam. nov. We describe a type species, <i>Corallicola aquarius</i> gen. nov. sp. nov. from its <i>Rhodactis </i>sp.<i> </i>host, and also describe a second species, <i>Anthozoaphila gnarlus</i> gen. nov. sp. nov., from the coral host <i>Madracis mirabilis</i>. Finally, we propose reassigning the incertae sedis taxon <i>G. cylindrus</i> from the order Agamococcidiorida to the Corallicolida, based on similarities in morphology and host localization to that of the corallicolids.</p>
Data from: Acquisition of obligate mutualist symbionts during the larval stage is not beneficial for a coral host
Theory suggests that the direct transmission of endosymbionts from parents to offspring (vertical transmission) in animal hosts is advantageous and evolutionarily stable, yet many host species instead acquire their symbionts from the environment (horizontal acquisition). An outstanding question in marine biology is why some scleractinian corals do not provision their eggs and larvae with the endosymbiotic dinoflagellates that are necessary for a juvenile's ultimate survival. We tested whether the acquisition of photosynthetic endosymbionts (family Symbiodiniaceae) during the planktonic larval stage was advantageous, as is widely assumed, in the ecologically important and threatened Caribbean reef-building coral Orbicella faveolata. Following acquisition, similar changes occurred in larval energetic lipid use and gene expression regardless of whether their symbionts were photosynthesizing, suggesting the algae did not provide the energetic benefits characteristic of the mutualism in adults. Larvae that acquired photosymbionts isolated from conspecific adults on their natal reef exhibited a reduction in swimming, which may interfere with their ability to find suitable settlement substrate, and also a decrease in survival. Larvae exposed to two cultured algal species did not exhibit differences in survival, but decreased their swimming activity in response to one species. We conclude that acquiring photosymbionts during the larval stage confers no advantages and can in fact be disadvantageous to this coral host. The timing of symbiont acquisition appears to be a critical component of a host's life history strategy and overall reproductive fitness, and this timing itself appears to be under selective pressure.
Data from: Recovery from bleaching is mediated by threshold densities of background thermo-tolerant symbiont types in a reef-building coral
Sensitive molecular analyses show that most corals host a complement of Symbiodinium genotypes that includes thermo-tolerant types in low abundance. While tolerant symbiont types are hypothesized to facilitate tolerance to temperature and recovery from bleaching, empirical data on their distribution and relative abundance in corals under ambient and stress conditions are still rare. We quantified visual bleaching and mortality of coral hosts, along with relative abundance of C- and D-type Symbiodinium cells in 82 Acropora millepora colonies from three locations on the Great Barrier Reef transplanted to a central inshore site over a 13 month period. Our analyses reveal dynamic change in symbiont associations within colonies and among populations over time. Coral bleaching and declines in C- but not D-type symbionts were observed in transplanted corals. Survival and recovery of 25% of corals from one population was associated with either initial D-dominance or an increase in D-type symbionts that could be predicted by a minimum pre-stress D : C ratio of 0.003. One-third of corals from this population became D dominated at the bleached stage despite no initial detection of this symbiont type, but failed to recover and died in mid to late summer. These results provide a predictive threshold minimum density of background D-type symbionts in A. millepora, above which survival following extreme thermal stress is increased.
Data and code for: Photoacclimation dynamics in coral holobionts responding to thermal and irradiance changes correlate with photon pressure per symbiont
<p>Code and data used in the publication "Photoacclimation dynamics in coral holobionts responding to thermal and irradiance changes correlate with photon pressure per symbiont". For queries about this dataset please email robert.mason1@uq.net.au</p>
FIGURE 5 in A new species of the coral-symbiont crab genus Cymo de Haan, 1833 (Decapoda, Brachyura, Xanthidae) from Nansha Islands, the South China Sea
FIGURE 5. Diagnostic features of Cymo: A, F, K, P, C. mazu sp. nov.; B, G, L, Q, C. deplanatus; C, H, M, R, C. quadrilobatus; D, I, N, S, C. andreossyi; E, J, O, T, C. melanodactylus; A–E, overall morphology and live coloration; F–G, front; K–O, major cheliped; P–T, maxilliped 1. Scale bars: A, J, L, M = 2 mm; B–D, N, O = 5 mm; E = 10 mm; F, P = 0.5 mm; G–I, K, Q–T = 1 mm.
FIGURE 3 in A new species of the coral-symbiont crab genus Cymo de Haan, 1833 (Decapoda, Brachyura, Xanthidae) from Nansha Islands, the South China Sea
FIGURE 3. Cymo mazu sp. nov., holotype, male, CW 4.1 mm, CL 3.8 mm, MBM287035: A, carapace; B, front; C, maxilliped 1; D, maxilliped 3; E, pereopod 5; F, large cheliped; G, pleon; H, left G1, ventral view; I, left G1, distal part, ventral view; J, same, dorsal view; K, right G2, ventral view. Scale bar A, E, F = 1 mm, C, D, G = 0.5 mm, H = 0.2 mm, I–K = 0.1 mm.
FIGURE 4 in A new species of the coral-symbiont crab genus Cymo de Haan, 1833 (Decapoda, Brachyura, Xanthidae) from Nansha Islands, the South China Sea
FIGURE 4. Phylogenetic relationships among five species of Cymo based on COI sequences. The BI tree with posterior probabilities and ML bootstrap values labeled (PP/BS).
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