Coral Symbiodinium Community Composition Across the Belize Mesoamerican Barrier Reef System is Influenced by Host Species and Thermal Variability

Fatty acid production and associated gene pathways are altered by increased salinity and dimethyl sulfoxide treatments during cryopreservation of Symbiodinium pilosum (Symbiodiniaceae)

The Symbiodinium genus is ancestral among other Symbiodiniaceae lineages with species that are both symbiotic and free living. Changes in marine ecosystems threaten their existence and crucial ecological roles. Cryopreservation offers an avenue for their long-term storage for future habitat restoration after coral bleaching. In our previous study we demonstrated that high salinity treatments of Symbiodiniaceae isolates led to changes in their fatty acid (FA) profiles and higher cell viabilities after cryopreservation. In this study, we investigated the role of increased salinity on FA production and the genes involved in FA biosynthesis and degradation pathways during the cryopreservation of Symbiodinium pilosum. Overall, there was a twofold increase in mass of FAs produced by S. pilosum after being cultured in medium with increased salinity (54 parts per thousand; ppt). Dimethyl sulfoxide (Me2SO) led to a ninefold increase of FAs in standard salinity (SS) treatment, compared to a fivefold increase in increased salinity (IS) treatments. The mass of the FA classes returned to baseline during recovery. Transcriptomic analyses showed an acyl carrier protein gene was significantly upregulated after Me2SO treatment in the SS cultures. Cytochrome P450 reductase genes were significantly down regulated after Me2SO addition in SS treatment preventing FA degradation. These changes in the expression of FA biosynthesis and degradation genes contributed to more FAs in SS treated isolates. Understanding how increased salinity changes FA production and the roles of specific genes in regulating FA pathways will help improve current freezing protocols for Symbiodiniaceae and other marine microalgae.

Predictive models for the selection of thermally tolerant corals based on offspring survival

Finding coral reefs resilient to climate warming is challenging given the large spatial scale of reef ecosystems. Methods are needed to predict the location of corals with heritable tolerance to high temperatures. Here, we combine Great Barrier Reef-scale remote sensing with breeding experiments that estimate larval and juvenile coral survival under exposure to high temperatures. Using reproductive corals collected from the northern and central Great Barrier Reef, we develop forecasting models to locate reefs harbouring corals capable of producing offspring with increased heat tolerance of an additional 3.4° heating weeks (~3 °C). Our findings predict hundreds of reefs (~7.5%) may be home to corals that have high and heritable heat-tolerance in habitats with high daily and annual temperature ranges and historically variable heat stress. The locations identified represent targets for protection and consideration as a source of corals for use in restoration of degraded reefs given their potential to resist climate change impacts and repopulate reefs with tolerant offspring.

Adaptive Variation in Homolog Number Within Transcript Families Promotes Expression Divergence in Reef-Building Coral

Gene expression, especially in multi-species experiments, is used to gain insight into the genetic basis of how organisms adapt and respond to changing environments. However, evolutionary processes which can influence gene expression patterns between species such as the presence of paralogs which arise from gene duplication events are rarely accounted for. Paralogous transcripts can alter the transcriptional output of a gene and thus exclusion of these transcripts can obscure important biological differences between species. To address this issue, we investigated how differences in transcript family size is associated with divergent gene expression patterns in five species of Caribbean reef-building corals. We demonstrate that transcript families that are rapidly evolving in terms of size have increased levels of expression divergence. Additionally, these rapidly evolving transcript families are enriched for multiple biological processes, with genes involved in the coral innate immune system demonstrating pronounced variation in homolog number between species. Overall, this investigation demonstrates the importance of incorporating paralogous transcripts when comparing gene expression across species by influencing both transcriptional output and the number of transcripts within biological processes. As this investigation was based on transcriptome assemblies, additional insights into the relationship between gene duplications and expression patterns will likely emergence once more genome assemblies are available for study.

Cryoprotectant treatment tests on three morphologically diverse marine dinoflagellates and the cryopreservation of Breviolum sp. (Symbiodiniaceae)

Dinoflagellates are among the most diverse group of microalgae. Many dinoflagellate species have been isolated and cultured, and these are used for scientific, industrial, pharmaceutical, and agricultural applications. Maintaining cultures is time-consuming, expensive, and there is a risk of contamination or genetic drift. Cryopreservation offers an efficient means for their long-term preservation. Cryopreservation of larger dinoflagellate species is challenging and to date there has been only limited success. In this study, we explored the effect of cryoprotectant agents (CPAs) and freezing methods on three species: Vulcanodinium rugosum, Alexandrium pacificum and Breviolum sp. A total of 12 CPAs were assessed at concentrations between 5 and 15%, as well as in combination with dimethyl sulfoxide (DMSO) and other non-penetrating CPAs. Two freezing techniques were employed: rapid freezing and controlled-rate freezing. Breviolum sp. was successfully cryopreserved using 15% DMSO. Despite exploring different CPAs and optimizing the freezing techniques, we were unable to successfully cryopreserve V. rugosum and A. pacificum. For Breviolum sp. there was higher cell viability (45.4 ± 2.2%) when using the controlled-rate freezing compared to the rapid freezing technique (10.0 ± 2.8%). This optimized cryopreservation protocol will be of benefit for the cryopreservation of other species from the family Symbiodiniaceae.

Effect of Cryopreservation on Proteins from the Ubiquitous Marine Dinoflagellate Breviolum sp. (Family Symbiodiniaceae)

Coral reefs around the world are exposed to thermal stress from climate change, disrupting the delicate symbiosis between the coral host and its symbionts. Cryopreservation is an indispensable tool for the preservation of species, as well as the establishment of a gene bank. However, the development of cryopreservation techniques for application to symbiotic algae is limited, in addition to the scarceness of related studies on the molecular level impacts post-thawing. Hence, it is essential to set up a suitable freezing protocol for coral symbionts, as well as to analyze its cryo-injury at the molecular level. The objective of this study was to develop a suitable protocol for the coral symbiont Breviolum subjected to two-step freezing. The thawed Breviolum were then cultured for 3, 7, 14, and 28 days before they were analyzed by Western blot for protein expression, light-harvesting protein (LHP), and red fluorescent protein (RFP) and tested by adenosine triphosphate bioassay for cell viability. The results showed the highest cell viability for thawed Breviolum that was treated with 2 M propylene glycol (PG) and 2 M methanol (MeOH) and equilibrated with both cryoprotectants for 30 min and 20 min. Both treatment groups demonstrated a significant increase in cell population after 28 days of culture post-thawing, especially for the MeOH treatment group, whose growth rate was twice of the PG treatment group. Regarding protein expression, the total amounts of each type of protein were significantly affected by cryopreservation. After 28 days of culture, the protein expression for the MeOH treatment group showed no significant difference to that of the control group, whereas the protein expression for the PG treatment group showed a significant difference. Breviolum that were frozen with MeOH recovered faster upon thawing than those frozen with PG. LHP was positively and RFP was negatively correlated with Symbiodiniaceae viability and so could serve as health-informing biomarkers. This work represents the first time to document it in Symbiodiniaceae, and this study established a suitable protocol for the cryopreservation of Breviolum and further refined the current understanding of the impact of low temperature on its protein expression. By gaining further understanding of the use of cryopreservation as a way to conserve Symbiodiniaceae, we hope to make an effort in the remediation and conservation of the coral reef ecosystem and provide additional methods to rescue coral reefs.

Taxonomic profiling of Symbiodiniaceae and bacterial communities associated with Indo-Pacific corals in the Gulf of Thailand using PacBio sequencing of full-length ITS and 16S rRNA genes

Corals live with complex assemblages of microbes including bacteria, the dinoflagellate Symbiodiniaceae, fungi and viruses in a coral holobiont. These coral-associated microorganisms play an important role in their host fitness and survival. Here, we investigated the structure and diversity of algal and bacterial communities associated with five Indo-Pacific coral species, using full-length 16S rRNA and internal transcribed spacer sequences. While the dinoflagellate communities associated with Poriteslutea were dominated with Symbiodiniaceae genus Cladocopium, the other four coral hosts were associated mainly with members of the Durusdinium genus, suggesting that host species was one of the underlying factors influencing the structure and composition of dinoflagellate communities associated with corals in the Gulf of Thailand. Alphaproteobacteria dominated the microbiomes of Pocillopora spp. while Pavonafrondifera and P. lutea were associated primarily with Gammaproteobacteria. Finally, we demonstrated a superior performance of full-length 16S rRNA sequences in achieving species-resolution taxonomic classification of coral-associated microbiota.

Drivers of coral bleaching in a Marine Protected Area of the Southern Gulf of Mexico during the 2015 event

Here we report the bleached coral cover and its drivers observed at Alacranes Reef in 2015. Our results show that 2015 was an unprecedented heat stress event. However, we observed low coral bleaching, with the most substantial impact on sites with a 10-20% of coral cover with bleaching. Depth was the most relevant variable related to coral bleaching and the bleaching severity index, with deeper reefs being most affected. Further, our results show that reefs with higher structural complexity based on species composition were among the most affected. We identified that accumulated heat stress and thermal variation in the last 28 days were relevant drivers of coral bleaching. This work highlights the importance of multidimensional frameworks in assessing the spatial variation of coral bleaching, demonstrating the importance of structural habitat variables such as depth in high heat stress events and at a reef scale.

Patterns of environmental variability influence coral-associated bacterial and algal communities on the Mesoamerican Barrier Reef

A coral's capacity to alter its microbial symbionts may enhance its fitness in the face of climate change. Recent work predicts exposure to high environmental variability may increase coral resilience and adaptability to future climate conditions. However, how this heightened environmental variability impacts coral-associated microbial communities remains largely unexplored. Here, we examined the bacterial and algal symbionts associated with two coral species of the genus Siderastrea with distinct life history strategies from three reef sites on the Belize Mesoamerican Barrier Reef System with low or high environmental variability. Our results reveal bacterial community structure, as well as alpha- and beta-diversity patterns, vary by host species. Differences in bacterial communities between host species were partially explained by high abundance of Deltaproteobacteria and Rhodospirillales and high bacterial diversity in Siderastrea radians. Our findings also suggest Siderastrea spp. have dynamic core bacterial communities that likely drive differences observed in the entire bacterial community, which may play a critical role in rapid acclimatization to environmental change. Unlike the bacterial community, Symbiodiniaceae composition was only distinct between host species at high thermal variability sites, suggesting that different factors shape bacterial versus algal communities within the coral holobiont. Our findings shed light on how domain-specific shifts in dynamic microbiomes may allow for unique methods of enhanced host fitness.

Resistance and robustness of the global coral-symbiont network

Increasing ocean temperatures have widespread consequences for coral reefs, one of which is coral bleaching. We analyzed a global network of associations between coral species and Symbiodiniaceae for resistance to temperature stress and robustness to perturbations. Null networks were created by changing either the physiological parameters of the nodes or the structures of the networks. We developed a bleaching model in which each link, association, is given a weight based on temperature thresholds for specific host-symbiont pairs and links are removed as temperature increases. Resistance to temperature stress was determined from the response of the networks to the bleaching model. Ecological robustness, defined by how much perturbation is needed to decrease the number of nodes by 50%, was determined for multiple removal models that considered traits of the hosts, symbionts, and their associations. Network resistance to bleaching and robustness to perturbations differed from the null networks and varied across spatial scales, supporting that thermal tolerances, local association patterns, and environment play an important role in network persistence. Networks were more robust to attacks on associations than to attacks on species. Although the global network was fairly robust to random link removals, when links are removed according to the bleaching model, robustness decreases by about 20%. Specific environmental attacks, in the form of increasing temperatures, destabilize the global network of coral species and Symbiodiniaceae. On a global scale, the network was more robust to removals of links with susceptible Symbiodiniaceae than it was to removals of links with susceptible hosts. Thus, the symbionts convey more stability to the symbiosis than the hosts when the system is under an environmental attack. However, our results also provide evidence that the environment of the networks affects robustness to link perturbations. Our work shows that ecological resistance and robustness can be assessed through network analysis that considers specific biological traits and functional weaknesses. The global network of associations between corals and Symbiodiniaceae and its distribution of thermal tolerances are non-random, and the evolution of this architecture has led to higher sensitivity to environmental perturbations.

Depth Influences Symbiodiniaceae Associations Among Montastraea cavernosa Corals on the Belize Barrier Reef

In Belize, shallow populations (10 and 16 m) of the coral species Montastraea cavernosa from the back reef and reef crest are genetically differentiated from deeper populations on the fore reef and reef wall (25 and 35 m). Like many species of scleractinian corals, M. cavernosa has an obligate symbiosis with dinoflagellate microalgae from the family Symbiodiniaceae. Here, we describe the Symbiodiniaceae taxa found within previously sampled and genotyped M. cavernosa populations along a depth gradient on the Belize Barrier Reef by implementing high-throughput sequencing of the ITS2 region of Symbiodiniaceae ribosomal DNA and the SymPortal analysis framework. While Symbiodiniaceae ITS2 type profiles across all sampling depths were almost entirely (99.99%) from the genus Cladocopium (formerly Symbiodinium Clade C), shallow (10 and 16 m) populations had a greater diversity of ITS2 type profiles in comparison to deeper (25 and 35 m) populations. Permutational multivariate analysis of variance (PERMANOVA) confirmed significant differences in ITS2 type profiles between shallow and deep sample populations. Overall Symbiodiniaceae communities changed significantly with depth, following patterns similar to the coral host's population genetic structure. Though physiological differences among species in the cosmopolitan genus Cladocopium are not well-described, our results suggest that although some members of Cladocopium are depth-generalists, shallow M. cavernosa populations in Belize may harbor shallow-specialized Symbiodiniaceae not found in deeper populations.

Searching for phylogenetic patterns of Symbiodiniaceae community structure among Indo-Pacific Merulinidae corals

Over half of all extant stony corals (Cnidaria: Anthozoa: Scleractinia) harbour endosymbiotic dinoflagellates of the family Symbiodiniaceae, forming the foundational species of modern shallow reefs. However, whether these associations are conserved on the coral phylogeny remains unknown. Here we aim to characterise Symbiodiniaceae communities in eight closely-related species in the genera Merulina, Goniastrea and Scapophyllia, and determine if the variation in endosymbiont community structure can be explained by the phylogenetic relatedness among hosts. We perform DNA metabarcoding of the nuclear internal transcribed spacer 2 using Symbiodiniaceae-specific primers on 30 coral colonies to recover three major endosymbiont clades represented by 23 distinct types. In agreement with previous studies on Southeast Asian corals, we find an abundance of Cladocopium and Durusdinium, but also detect Symbiodinium types in three of the eight coral host species. Interestingly, differences in endosymbiont community structure are dominated by host variation at the intraspecific level, rather than interspecific, intergeneric or among-clade levels, indicating a lack of phylogenetic constraint in the coral-endosymbiont association among host species. Furthermore, the limited geographic sampling of four localities spanning the Western and Central Indo-Pacific preliminarily hints at large-scale spatial structuring of Symbiodiniaceae communities. More extensive collections of corals from various regions and environments will help us better understand the specificity of the coral-endosymbiont relationship.

Thermal plasticity of a freshwater cnidarian holobiont: detection of trans-generational effects in asexually reproducing hosts and symbionts

Understanding factors affecting the susceptibility of organisms to thermal stress is of enormous interest in light of our rapidly changing climate. When adaptation is limited, thermal acclimation and deacclimation abilities of organisms are critical for population persistence through a period of thermal stress. Holobionts (hosts plus associated symbionts) are key components of various ecosystems, such as coral reefs, yet the contributions of their two partners to holobiont thermal plasticity are poorly understood. Here, we tested thermal plasticity of the freshwater cnidarian Hydra viridissima (green hydra) using individual behavior and population responses. We found that algal presence initially reduced hydra thermal tolerance. Hydra with algae (symbiotic hydra) had comparable acclimation rates, deacclimation rates, and thermal tolerance after acclimation to those without algae (aposymbiotic hydra) but they had higher acclimation capacity. Acclimation of the host (hydra) and/or symbiont (algae) to elevated temperatures increased holobiont thermal tolerance and these effects persisted for multiple asexual generations. In addition, acclimated algae presence enhanced hydra fitness under prolonged sublethal thermal stress, especially when food was limited. Our study indicates while less intense but sublethal stress may favor symbiotic organisms by allowing them to acclimate, sudden large, potentially lethal fluctuations in climate stress likely favor aposymbiotic organisms. It also suggests that thermally stressed colonies of holobionts could disperse acclimated hosts and/or symbionts to other colonies, thereby reducing their vulnerability to climate change.

Thermal Tolerance in Green Hydra: Identifying the Roles of Algal Endosymbionts and Hosts in a Freshwater Holobiont Under Stress

It has been proposed that holobionts (host-symbiont units) could swap endosymbionts, rapidly alter the hologenome (host plus symbiont genome), and increase their stress tolerance. However, experimental tests of individual and combined contributions of hosts and endosymbionts to holobiont stress tolerance are needed to test this hypothesis. Here, we used six green hydra (Hydra viridissima) strains to tease apart host (hydra) and symbiont (algae) contributions to thermal tolerance. Heat shock experiments with (1) hydra with their original symbionts, (2) aposymbiotic hydra (algae removed), (3) novel associations (a single hydra strain hosting different algae individually), and (4) control hydra (aposymbiotic hydra re-associated with their original algae) showed high variation in thermal tolerance in each group. Relative tolerances of strains were the same within original, aposymbiotic, and control treatments, but reversed in the novel associations group. Aposymbiotic hydra had similar or higher thermal tolerance than hydra with algal symbionts. Selection on the holobiont appears to be stronger than on either partner alone, suggesting endosymbiosis could become an evolutionary trap under climate change. Our results suggest that green hydra thermal tolerance is strongly determined by the host, with a smaller, non-positive role for the algal symbiont. Once temperatures exceed host tolerance limits, swapping symbionts is unlikely to allow these holobionts to persist. Rather, increases in host tolerance through in situ adaptation or migration of pre-adapted host strains appear more likely to increase local thermal tolerance. Overall, our results indicate green hydra is a valuable system for studying aquatic endosymbiosis under changing environmental conditions, and demonstrate how the host and the endosymbiont contribute to holobiont stress tolerance.