Coral microbiome diversity reflects mass coral bleaching susceptibility during the 2016 El Niño heat wave

Antibiotics alter development and gene expression in the model cnidarian Nematostella vectensis

Background

Antibiotics are commonly used for controlling microbial growth in diseased organisms. However, antibiotic treatments during early developmental stages can have negative impacts on development and physiology that could offset the positive effects of reducing or eliminating pathogens. Similarly, antibiotics can shift the microbial community due to differential effectiveness on resistant and susceptible bacteria. Though antibiotic application does not typically result in mortality of marine invertebrates, little is known about the developmental and transcriptional effects. These sublethal effects could reduce the fitness of the host organism and lead to negative changes after removal of the antibiotics. Here, we quantify the impact of antibiotic treatment on development, gene expression, and the culturable bacterial community of a model cnidarian, Nematostella vectensis.

Methods

Ampicillin, streptomycin, rifampicin, and neomycin were compared individually at two concentrations, 50 and 200 µg mL-1, and in combination at 50 µg mL-1 each, to assess their impact on N. vectensis. First, we determined the impact antibiotics have on larval development. Next Amplicon 16S rDNA gene sequencing was used to compare the culturable bacteria that persist after antibiotic treatment to determine how these treatments may differentially select against the native microbiome. Lastly, we determined how acute (3-day) and chronic (8-day) antibiotic treatments impact gene expression of adult anemones.

Results

Under most exposures, the time of larval settlement extended as the concentration of antibiotics increased and had the longest delay of 3 days in the combination treatment. Culturable bacteria persisted through a majority of exposures where we identified 359 amplicon sequence variants (ASVs). The largest proportion of bacteria belonged to Gammaproteobacteria, and the most common ASVs were identified as Microbacterium and Vibrio. The acute antibiotic exposure resulted in differential expression of genes related to epigenetic mechanisms and neural processes, while constant application resulted in upregulation of chaperones and downregulation of mitochondrial genes when compared to controls. Gene Ontology analyses identified overall depletion of terms related to development and metabolism in both antibiotic treatments.

Discussion

Antibiotics resulted in a significant increase to settlement time of N. vectensis larvae. Culturable bacterial species after antibiotic treatments were taxonomically diverse. Additionally, the transcriptional effects of antibiotics, and after their removal result in significant differences in gene expression that may impact the physiology of the anemone, which may include removal of bacterial signaling on anemone gene expression. Our research suggests that impacts of antibiotics beyond the reduction of bacteria may be important to consider when they are applied to aquatic invertebrates including reef building corals.

Comprehensive insights into the differences of fungal communities at taxonomic and functional levels in stony coral Acropora intermedia under a natural bleaching event

Previous studies have reported the correlations between bacterial communities and coral bleaching, but the knowledge of fungal roles in coral bleaching is still limited. In this study, the taxonomic and functional diversities of fungi in unbleached, partly bleached and bleached stony coral Acropora intermedia were investigated through the ITS-rRNA gene next-generation sequencing. An unexpected diversity of successfully classified fungi (a total of 167 fungal genera) was revealed in this study, and the partly bleached coral samples gained the highest fungal diversity, followed by bleached and unbleached coral samples. Among these fungi, 122 genera (nearly 73.2%) were rarely found in corals in previous studies, such as Calostoma and Morchella, which gave us a more comprehensive understanding of coral-associated fungi. Positively correlated fungal genera (Calostoma, Corticium, Derxomyces, Fusicolla, Penicillium and Vishniacozyma) and negative correlated fungal genera (Blastobotrys, Exophiala and Dacryopinax) with the coral bleaching were both detected. It was found that a series of fungal genera, dominant by Apiotrichum, a source of opportunistic infections, was significantly enriched; while another fungal group majoring in Fusicolla, a probiotic fungus, was distinctly depressed in the bleached coral. It was also noteworthy that the abundance of pathogenic fungi, including Fusarium, Didymella and Trichosporon showed a rising trend; while the saprotrophic fungi, including Tricladium, Botryotrichum and Scleropezicula demostrated a declining trend as the bleaching deteriorating. The rising of pathogenic fungi and the declining of saprotrophic fungi revealed the basic rules of fungal community transitions in the coral bleaching, but the mechanism of coral-associated fungal interactions still lacks further investigation. Overall, this is an investigation focused on the differences of fungal communities at taxonomic and functional levels in stony coral A. intermedia under different bleaching statuses, which provides a better comprehension of the correlations between fungal communities and the coral bleaching.

Dynamic changes in bacterial communities in three species of corals during the 2017 bleaching event in subtropical Hong Kong waters

Bacteria play important roles in coral health, yet little is known about the dynamics of coral-associated bacterial communities during coral bleaching. Here, we reported the dynamic changes of bacterial communities in three scleractinian corals (Montipora peltiformis, Pavona decussata and Platygyra carnosa) during and after bleaching through amplicon sequencing. Our results revealed that the bacterial composition and dominant bacteria varied among the three coral species. The higher susceptibility of M. peltiformis to bleaching corresponded to a lower bacterial community diversity, and the dominant Synechococcus shifted in abundance during the bleaching and coral recovery phases. The resilient P. decussata and P. carnosa had higher bacterial diversity and a more similar bacterial composition between the healthy and bleached conditions. Overall, our study reveals the dynamic changes in coral-associated microbial diversity under different conditions, contributing to explaining the differential susceptibility of corals to extreme climate conditions.

A gauge of coral physiology: re-examining temporal changes in Endozoicomonas abundance correlated with natural coral bleaching

Bacteria contribute to many physiological functions of coral holobionts, including responses to bleaching. The bacterial genus, Endozoicomonas, dominates the microbial flora of many coral species and its abundance appears to be correlated with coral bleaching. However, evidences for decoupling of bleaching and Endozoicomonas abundance changes have also been reported. In 2020, a severe bleaching event was recorded at reefs in Taiwan, providing a unique opportunity to re-examine bleaching-Endozoicomonas association using multiple stony corals in natural environments. In this study, we monitored tissue color and microbiome changes in three coral species (Montipora sp., Porites sp., and Stylophora pistillata) in Kenting National Park, following the bleaching event. All tagged Montipora sp. and Porites sp. recovered from bleaching within 1 year, while high mortality occurred in S. pistillata. Microbiome analysis found no correlation of Endozoicomonas relative abundance and bleaching severity during the sampling period, but found a stronger correlation when the month in which bleaching occurred was excluded. Moreover, Endozoicomonas abundance increased during recovery months in Montipora sp. and Porites sp., whereas in S. pistillata it was nearly depleted. These results suggest that Endozoicomonas abundance may represent a gauge of coral health and reflect recovery of some corals from stress. Interestingly, even though different Endozoicomonas strains predominated in the three corals, these Endozoicomonas strains were also shared among coral taxa. Meanwhile, several Endozoicomonas strains showed secondary emergence during coral recovery, suggesting possible symbiont switching in Endozoicomonas. These findings indicate that it may be possible to introduce Endozoicomonas to non-native coral hosts as a coral probiotic.

Species-specific coral microbiome assemblages support host bleaching resistance during an extreme marine heatwave

Scleractinian assemblages are threatened by marine heat waves with coral survivorship depending on host genetics and microbiome composition. We documented an extreme marine heat wave in Fiji and the response of corals in two thermally stressed reef flats. Through high-throughput amplicon sequencing of 16S and ITS rDNA phylogenetic markers, we assessed coral microbiomes (Symbiodiniaceae, prokaryotes, fungi, and Apicomplexa) of paired bleached and unbleached colonies of four common coral species representative of dominant genera in the South Pacific. While all coral species exhibited one or more pathways to bleaching resistance, harboring assemblages composed primarily of thermally tolerant photosymbionts did not always result in host bleaching resistance. Montipora and Pocillopora species, which associate with diverse Symbiodiniaceae and vertically transmit their photosymbionts, fared better than Acropora, which acquire their photosymbionts from the environment, and Porites, which associate with a narrow photosymbiont assemblage. Prokaryotic and fungal beta diversity did not differ between bleached and unbleached conspecifics, however, the relative abundance of the fungus Malassezia globosa was significantly greater in unbleached colonies of Montipora digitata. Each coral species harbored distinct assemblages of Symbiodiniaceae, prokaryotes, and Apicomplexa, but not fungi, reiterating the importance of host genetics in structuring components of its microbiome. Terrestrial fungal and prokaryotic taxa were detected at low abundance across coral microbiomes, indicating that allochthonous microbial inputs occur, but that coral microbiomes remain dominated by marine microbial taxa. Our study offers valuable insights into the microbiome assemblages associated with coral tolerance to extreme water temperatures.

Microbial shifts associated to ENSO-derived thermal anomalies reveal coral acclimation at holobiont level

The coral microbiome conforms a proxy to study effects of changing environmental conditions. However, scarce information exists regarding microbiome dynamics and host acclimation in response to environmental changes associated to global-scale disturbances. We assessed El Niño Southern Oscillation (ENSO)-derived thermal anomalies shifts in the bacterial microbiome of Pacifigorgia cairnsi (Gorgoniidae: Octocorallia) from the remote island of Malpelo in the Tropical Eastern Pacific. Malpelo is a hot spot of biodiversity and lacks direct coastal anthropogenic impacts. We evaluated the community composition and predicted functional profiles of the microbiome during 2015, 2017 and 2018, including different phases of ENSO cycle. The bacterial community diversity and composition between the warming and cooling phase were similar, but differed from the neutral phase. Relative abundances of different microbiome core members such as Endozoicomonas and Mycoplasma mainly drove these differences. An acclimated coral holobiont is suggested not just to warm but also to cold stress by embracing similar microbiome shifts and functional redundancy that allow maintaining coral's viability under thermal stress. Responses of the microbiome of unperturbed sea fans such as P. cairnsi in Malpelo could be acting as an extended phenotype facilitating the acclimation at the holobiont level.

Meta-analysis reveals variations in microbial communities from diverse stony coral taxa at different geographical distances

Coral-associated microbial communities play a vital role in underpinning the health and resilience of reef ecosystems. Previous studies have demonstrated that the microbial communities of corals are affected by multiple factors, mainly focusing on host species and geolocation. However, up-to-date, insight into how the coral microbiota is structured by vast geographic distance with rich taxa is deficient. In the present study, the coral microbiota in six stony coral species collected from the coastal area of three countries, including United States of America (USA), Australia and Fiji, was used for analysis. It was found that the geographic influence on the coral microbiota was stronger than the coral host influence, even though both were significant. Interestingly, the contribution of the deterministic process to bacterial community composition increased as geographical distance grew. A total of 65 differentially abundant features of functions in coral microbial communities were identified to be associated with three geolocations. While in the same coastal area of USA, the similar relationship of coral microbiota was consistent with the phylogenetic relationship of coral hosts. In contrast to the phylum Proteobacteria, which was most abundant in other coral species in USA, Cyanobacteria was the most abundant phylum in Orbicella faveolata. The above findings may help to better understand the multiple natural driving forces shaping the coral microbial community to contribute to defining the healthy baseline of the coral microbiome.

Corals at the edge of environmental limits: A new conceptual framework to re-define marginal and extreme coral communities

The worldwide decline of coral reefs has renewed interest in coral communities at the edge of environmental limits because they have the potential to serve as resilience hotspots and climate change refugia, and can provide insights into how coral reefs might function in future ocean conditions. These coral communities are often referred to as marginal or extreme but few definitions exist and usage of these terms has therefore been inconsistent. This creates significant challenges for categorising these often poorly studied communities and synthesising data across locations. Furthermore, this impedes our understanding of how coral communities can persist at the edge of their environmental limits and the lessons they provide for future coral reef survival. Here, we propose that marginal and extreme coral communities are related but distinct and provide a novel conceptual framework to redefine them. Specifically, we define coral reef extremeness solely based on environmental conditions (i.e., large deviations from optimal conditions in terms of mean and/or variance) and marginality solely based on ecological criteria (i.e., altered community composition and/or ecosystem functioning). This joint but independent assessment of environmental and ecological criteria is critical to avoid common pitfalls where coral communities existing outside the presumed optimal conditions for coral reef development are automatically considered inferior to coral reefs in more traditional settings. We further evaluate the differential potential of marginal and extreme coral communities to serve as natural laboratories, resilience hotspots and climate change refugia, and discuss strategies for their conservation and management as well as priorities for future research. Our new classification framework provides an important tool to improve our understanding of how corals can persist at the edge of their environmental limits and how we can leverage this knowledge to optimise strategies for coral reef conservation, restoration and management in a rapidly changing ocean.

Consistent responses of coral microbiome to acute and chronic heat stress exposures

Frequent and intense heat waves lead to bleaching and even death of reef-building corals, and the thermal tolerance ultimately depends on the genetic composition of the holobiont. Here, we compared the effects of acute and chronic heat stress exposures on coral Porites cylindrica holobiont. Regardless of the temperature treatment, corals at 33 °C showed signs of bleaching and a significant decrease in photochemical efficiency (Fv/Fm). However, Symbiodiniaceae communities were relatively stable and all dominated by the same genus Cladocopium (C15). The relative abundanbce of core microbiome varied significantly, and they may provide several functions important to holobiont fitness. Both heat stress exposures induced the significant structural reorganization of coral-associated bacteria, with bacterial diversity and community heterogeneity significantly increasing with the temperature treatment. The modified stochasticity ratio (MST) revealed that stochastic processes dominated bacterial community assembly in thermally stressed corals. Certain core bacterial members that were hypothesized to fulfil functional niche decreased significantly, with the enrichment of potentially pathogenic and opportunistic bacteria in heat stress exposures. Thermally stressed corals had more positive correlation, higher network complexity and tighter associations among microbial taxa, relative to healthy corals. Overall, the coral microbiome exhibits similar responses to acute and chronic heat stress, and our study provides new insights about the deleterious impacts of complex warming oceans on coral holobiont.

Microbiota of healthy and bleached corals of the species Siderastrea stellata in response to river influx and seasonality in Brazilian northeast

Although coral bleaching is increasing worldwide due to warming oceans exacerbated by climate change, there has been a growing recognition that local stressors may play an additional role. Important stressors include the physicochemical and microbiological influences that are related to river runoff. Here, we investigated the microbiota associated to mucus and tissue of endemic coral Siderastrea stellata, collected from Brazilian northeast coral reefs of Barra de Santo Antônio (subject to river runoff) and Maragogi (minimal river runoff) during both the rainy and dry seasons. We sequenced the V4 region of 16S rDNA and used multiple R packages to process raw data and performed statistical analysis to reveal the microbial community structure composition and functional predictions. Major dissimilarities between microbial communities were related to seasonality, while healthy and bleached specimens were mainly associated with the enrichment of several less abundant taxa involved in specific metabolic functions, mainly related to the nitrogen cycle. We were not able to observe the dominance of groups that has been previously associated with bleachings, such as Vibrionaceae or Burkholderiaceae. The influx of freshwater appears to increase the homogeneity between individuals in Barra de Santo Antonio, especially during the rainy season. By contrast, we observed an increased homogeneity between samples in Maragogi during the dry season. Understanding the dynamics of the coral microbiota and how bleaching appears in response to specific environmental variables, in addition to determining the conditions that lead to a more robust coral microbiota, is essential for choosing the most appropriate area and conservation methods, for example.

Toxicological effects of oxybenzone on the growth and bacterial composition of Symbiodiniaceae

Oxybenzone, a common ultraviolet (UV) filter, is a growing environmental concern due to its ecotoxicological effects. However, the responses of Symbiodiniaceae and their bacterial communities to oxybenzone are largely unknown. In this study, the effects of oxybenzone on Effrenium voratum and Cladocopium goreaui were investigated. The results revealed that sensitivity of Symbiodiniaceae to oxybenzone was species-dependent. 50 μg L^-1 of oxybenzone significantly impacted the cell density of C. goreaui, causing a 36.73% decrease. When oxybenzone concentration increased to 500 μg L^-1 and 5000 μg L^-1, cell division was completely suppressed; meanwhile, chl-a content declined to zero. Compared to C. goreaui, E. voratum had higher resistance to oxybenzone. There was no significant difference in cell density between 50 μg L^-1 group and control group. At higher dosage of oxybenzone (500 μg L^-1 and 5000 μg L^-1), the cell density declined 32.02% and 45.45% compared to the control group, respectively. Additionally, we revealed that the diversity and structure of bacterial community were affected by oxybenzone. Briefly, 500 μg L^-1 and 5000 μg L^-1 of oxybenzone altered the diversity of bacterial community in C. goreau. Furthermore, the relative abundances of Costertonia, Roseitalea, Rhodopirellula, and Roseobacter were negatively affected by oxybenzone ranging 50 μg L^-1 to 5000 μg L^-1. Compare to C. goreaui, the bacterial community composition associated with E. voratum was more stable. As revealed by KEGG pathway analysis, oxybenzone affected energy metabolism and inhibited the metabolism of cofactors and vitamins in C. goreaui, while 5000 μg L^-1 of oxybenzone significantly altered the carbohydrate metabolism, membrane transport and amino acid metabolism in E. voratum. The changes of bacterial composition may contribute to the variation in algal growth. These results indicated that oxybenzone pollution could injury Symbiodiniaceae, even threaten coral reef ecosystems.

Stable Symbiodiniaceae composition in three coral species during the 2017 natural bleaching event in subtropical Hong Kong

Adaptive changes in endosymbiotic Symbiodiniaceae communities have been reported during and after bleaching events in tropical coral species, but little is known about such shifts in subtropical species. Here we examined the Symbiodiniaceae communities in three coral species (Montipora peltiformis, Pavona decussata, and Platygyra carnosa) based on samples collected during and after the 2017 bleaching event in subtropical Hong Kong waters. In all of the collected samples, ITS2 meta-sequencing revealed that P. decussata and P. carnosa were predominantly associated with Cladocopium C1 and C1c, whereas M. peltiformis was mainly associated with two Cladocopium C21 types and C1. For each species, the predominant endosymbionts exhibited high fidelity, and the relatively low abundance ITS2-types showed minor changes between the bleached and recovered corals. Our study provided the first details of coral-algal association in Hong Kong waters, suggesting the selection of certain genotypes as a potential adaptive mechanism to the marginal environmental conditions.

Full-Length Transcriptome Maps of Reef-Building Coral Illuminate the Molecular Basis of Calcification, Symbiosis, and Circa-Dian Genes

Coral transcriptomic data largely rely on short-read sequencing, which severely limits the understanding of coral molecular mechanisms and leaves many important biological questions unresolved. Here, we sequence the full-length transcriptomes of four common and frequently dominant reef-building corals using the PacBio Sequel II platform. We obtain information on reported gene functions, structures, and expression profiles. Among them, a comparative analysis of biomineralization-related genes provides insights into the molecular basis of coral skeletal density. The gene expression profiles of the symbiont Symbiodiniaceae are also isolated and annotated from the holobiont sequence data. Finally, a phylogenetic analysis of key circadian clock genes among 40 evolutionarily representative species indicates that there are four key members in early metazoans, including cry genes; Clock or Npas2; cyc or Arntl; and tim, while per, as the fifth member, occurs in Bilateria. In summary, this work provides a foundation for further work on the manipulation of skeleton production or symbiosis to promote the survival of these important organisms.

Towards standardized and reproducible research in skin microbiomes

Skin is a complex organ serving a critical role as a barrier and mediator of interactions between the human body and its environment. Recent studies have uncovered how resident microbial communities play a significant role in maintaining the normal healthy function of the skin and the immune system. In turn, numerous host-associated and environmental factors influence these communities' composition and diversity across the cutaneous surface. In addition, specific compositional changes in skin microbiota have also been connected to the development of several chronic diseases. The current era of microbiome research is characterized by its reliance on large data sets of nucleotide sequences produced with high-throughput sequencing of sample-extracted DNA. These approaches have yielded new insights into many previously uncharacterized microbial communities. Application of standardized practices in the study of skin microbial communities could help us understand their complex structures, functional capacities, and health associations and increase the reproducibility of the research. Here, we overview the current research in human skin microbiomes and outline challenges specific to their study. Furthermore, we provide perspectives on recent advances in methods, analytical tools and applications of skin microbiomes in medicine and forensics.

A roadmap to integrating resilience into the practice of coral reef restoration

Recent warm temperatures driven by climate change have caused mass coral bleaching and mortality across the world, prompting managers, policymakers, and conservation practitioners to embrace restoration as a strategy to sustain coral reefs. Despite a proliferation of new coral reef restoration efforts globally and increasing scientific recognition and research on interventions aimed at supporting reef resilience to climate impacts, few restoration programs are currently incorporating climate change and resilience in project design. As climate change will continue to degrade coral reefs for decades to come, guidance is needed to support managers and restoration practitioners to conduct restoration that promotes resilience through enhanced coral reef recovery, resistance, and adaptation. Here, we address this critical implementation gap by providing recommendations that integrate resilience principles into restoration design and practice, including for project planning and design, coral selection, site selection, and broader ecosystem context. We also discuss future opportunities to improve restoration methods to support enhanced outcomes for coral reefs in response to climate change. As coral reefs are one of the most vulnerable ecosystems to climate change, interventions that enhance reef resilience will help to ensure restoration efforts have a greater chance of success in a warming world. They are also more likely to provide essential contributions to global targets to protect natural biodiversity and the human communities that rely on reefs.

Microbial Associations of Abyssal Gorgonians and Anemones (>4,000 m Depth) at the Clarion-Clipperton Fracture Zone

Deep coral-dominated communities play paramount roles in benthic environments by increasing their complexity and biodiversity. Coral-associated microbes are crucial to maintain fitness and homeostasis at the holobiont level. However, deep-sea coral biology and their associated microbiomes remain largely understudied, and less from remote and abyssal environments such as those in the Clarion-Clipperton Fracture Zone (CCZ) in the tropical Northeast (NE) Pacific Ocean. Here, we study microbial-associated communities of abyssal gorgonian corals and anemones (>4,000 m depth) in the CCZ; an area harboring the largest known global reserve of polymetallic nodules that are commercially interesting for the deep-sea nodule mining. Coral samples (n = 25) belonged to Isididae and Primnoidae families, while anemones (n = 4) to Actinostolidae family. Significant differences in bacterial community compositions were obtained between these three families, despite sharing similar habitats. Anemones harbored bacterial microbiomes composed mainly of Hyphomicrobiaceae, Parvibaculales, and Pelagibius members. Core microbiomes of corals were mainly dominated by different Spongiibacteraceae and Terasakiellaceae bacterial members, depending on corals' taxonomy. Moreover, the predicted functional profiling suggests that deep-sea corals harbor bacterial communities that allow obtaining additional energy due to the scarce availability of nutrients. This study presents the first report of microbiomes associated with abyssal gorgonians and anemones and will serve as baseline data and crucial insights to evaluate and provide guidance on the impacts of deep-sea mining on these key abyssal communities.

Best practices for generating and analyzing 16S rRNA amplicon data to track coral microbiome dynamics

Over the past two decades, researchers have searched for methods to better understand the relationship between coral hosts and their microbiomes. Data on how coral-associated bacteria are involved in their host's responses to stressors that cause bleaching, disease, and other deleterious effects can elucidate how they may mediate, ameliorate, and exacerbate interactions between the coral and the surrounding environment. At the same time tracking coral bacteria dynamics can reveal previously undiscovered mechanisms of coral resilience, acclimatization, and evolutionary adaptation. Although modern techniques have reduced the cost of conducting high-throughput sequencing of coral microbes, to explore the composition, function, and dynamics of coral-associated bacteria, it is necessary that the entire procedure, from collection to sequencing, and subsequent analysis be carried out in an objective and effective way. Corals represent a difficult host with which to work, and unique steps in the process of microbiome assessment are necessary to avoid inaccuracies or unusable data in microbiome libraries, such as off-target amplification of host sequences. Here, we review, compare and contrast, and recommend methods for sample collection, preservation, and processing (e.g., DNA extraction) pipelines to best generate 16S amplicon libraries with the aim of tracking coral microbiome dynamics. We also discuss some basic quality assurance and general bioinformatic methods to analyze the diversity, composition, and taxonomic profiles of the microbiomes. This review aims to be a generalizable guide for researchers interested in starting and modifying the molecular biology aspects of coral microbiome research, highlighting best practices and tricks of the trade.

Coastal corals during heat stress and eutrophication: A case study in Northwest Hainan coastal areas

This study initially investigated the coral status during the unexpected bleaching event in three coastal areas in Northwest Hainan coastal areas and analyzed changes in coral holobionts of the healthy and bleached Galaxea fascicularis. Coral coverage had declined severely, and the bleaching rate was extremely high during heat stress. The bleached corals had lower maximum photosynthetic yield, actual photosynthetic yield, zooxanthellae density, and chlorophyll a content than the healthy G. fascicularis, but there was no significant difference in protein, carbohydrate and lipid in eutrophic waters. The diversity and community composition of Symbiodiniaceae and symbiotic bacteria between healthy and bleached G. fascicularis showed no difference. Function prediction of the symbiotic bacteria revealed that the metabolism process was the main pathway of annotation. Present findings suggested that energy reserve functioning and high stability of the holobiont structure and might provide opportunities to G. fascicularis to adapt to eutrophication and heat stress.

Contrasting microbiome dynamics of putative denitrifying bacteria in two octocoral species exposed to dissolved organic carbon (DOC) and warming

Mutualistic nutrient cycling in the coral-algae symbiosis depends on limited nitrogen (N) availability for algal symbionts. Denitrifying prokaryotes capable of reducing nitrate or nitrite to dinitrogen could thus support coral holobiont functioning by limiting N availability. Octocorals show some of the highest denitrification rates among reef organisms; however, little is known about the community structures of associated denitrifiers and their response to environmental fluctuations. Combining 16S rRNA gene amplicon sequencing with nirS in-silico PCR and quantitative PCR, we found differences in bacterial community dynamics between two octocorals exposed to excess dissolved organic carbon (DOC) and concomitant warming. Although bacterial communities of the gorgonian Pinnigorgia flava remained largely unaffected by DOC and warming, the soft coral Xenia umbellata exhibited a pronounced shift toward Alphaproteobacteria dominance under excess DOC. Likewise, the relative abundance of denitrifiers was not altered in P. flava but decreased by 1 order of magnitude in X. umbellata under excess DOC, likely due to decreased proportions of Ruegeria spp. Given that holobiont C:N ratios remained stable in P. flava but showed a pronounced increase with excess DOC in X. umbellata, our results suggest that microbial community dynamics may reflect the nutritional status of the holobiont. Hence, denitrifier abundance may be directly linked to N availability. This suggests a passive regulation of N cycling microbes based on N availability, which could help stabilize nutrient limitation in the coral-algal symbiosis and thereby support holobiont functioning in a changing environment.

IMPORTANCE Octocorals are important members of reef-associated benthic communities that can rapidly replace scleractinian corals as the dominant ecosystem engineers on degraded reefs. Considering the substantial change in the (a)biotic environment that is commonly driving reef degradation, maintaining a dynamic and metabolically diverse microbial community might contribute to octocoral acclimatization. Nitrogen (N) cycling microbes, in particular denitrifying prokaryotes, may support holobiont functioning by limiting internal N availability, but little is known about the identity and (a)biotic drivers of octocoral-associated denitrifiers. Here, we show contrasting dynamics of bacterial communities associated with two common octocoral species, the soft coral Xenia umbellata and the gorgonian Pinnigorgia flava after a 6-week exposure to excess dissolved organic carbon under concomitant warming conditions. The specific responses of denitrifier communities of the two octocoral species aligned with the nutritional status of holobiont members. This suggests a passive regulation based on N availability in the coral holobiont.

Rapid Shifts in Bacterial Communities and Homogeneity of Symbiodiniaceae in Colonies of Pocillopora acuta Transplanted Between Reef and Mangrove Environments

It has been proposed that an effective approach for predicting whether and how reef-forming corals persist under future climate change is to examine populations thriving in present day extreme environments, such as mangrove lagoons, where water temperatures can exceed those of reef environments by more than 3°C, pH levels are more acidic (pH < 7.9, often below 7.6) and O₂ concentrations are regularly considered hypoxic (<2 mg/L). Defining the physiological features of these “extreme” corals, as well as their relationships with the, often symbiotic, organisms within their microbiome, could increase our understanding of how corals will persist into the future. To better understand coral-microbe relationships that potentially underpin coral persistence within extreme mangrove environments, we therefore conducted a 9-month reciprocal transplant experiment, whereby specimens of the coral Pocillopora acuta were transplanted between adjacent mangrove and reef sites on the northern Great Barrier Reef. Bacterial communities associated with P. acuta specimens native to the reef environment were dominated by Endozoicomonas, while Symbiodiniaceae communities were dominated by members of the Cladocopium genus. In contrast, P. acuta colonies native to the mangrove site exhibited highly diverse bacterial communities with no dominating members, and Symbiodiniaceae communities dominated by Durusdinium. All corals survived for 9 months after being transplanted from reef-to-mangrove, mangrove-to-reef environments (as well as control within environment transplants), and during this time there were significant changes in the bacterial communities, but not in the Symbiodiniaceae communities or their photo-physiological functioning. In reef-to-mangrove transplanted corals, there were varied, but sometimes rapid shifts in the associated bacterial communities, including a loss of “core” bacterial members after 9 months where coral bacterial communities began to resemble those of the native mangrove corals. Bacterial communities associated with mangrove-to-reef P. acuta colonies also changed from their original composition, but remained different to the native reef corals. Our data demonstrates that P. acuta associated bacterial communities are strongly influenced by changes in environmental conditions, whereas Symbiodiniaceae associated communities remain highly stable.

Blowing Hot and Cold: Body Temperature and the Microbiome

The intestinal microbiome influences host health, and its responsiveness to diet and disease is increasingly well studied. However, our understanding of the factors driving microbiome variation remain limited. Temperature is a core factor that controls microbial growth, but its impact on the microbiome remains to be fully explored. Although commonly assumed to be a constant 37°C, normal body temperatures vary across the animal kingdom, while individual body temperature is affected by multiple factors, including circadian rhythm, age, environmental temperature stress, and immune activation. Changes in body temperature via hypo- and hyperthermia have been shown to influence the gut microbiota in a variety of animals, with consistent effects on community diversity and stability. It is known that temperature directly modulates the growth and virulence of gastrointestinal pathogens; however, the effect of temperature on gut commensals is not well studied. Further, body temperature can influence other host factors, such as appetite and immunity, with indirect effects on the microbiome. In this minireview, we discuss the evidence linking body temperature and the intestinal microbiome and their implications for microbiome function during hypothermia, heat stress, and fever.

Seasonal fluctuations in symbiotic bacteria and their role in environmental adaptation of the scleractinian coral Acropora pruinosa in high-latitude coral reef area of the South China Sea

Coral-associated bacterial communities are paramount for coral ecosystems and holobiont health. However, the role of symbiotic bacteria in the adaptation of high-latitude corals to seasonal fluctuations remains underexplored. Therefore, we used 16S rRNA-based high-throughput sequencing to analyze the symbiotic bacterial diversity, composition, and core bacterial community in high-latitude coral and explored the seasonal fluctuation characteristics of symbiotic bacterial communities. We found that bacterial richness and α-diversity changed significantly across different seasons. Additionally, the community structure recombined seasonally, with different dominant bacterial phyla and genera in different seasons. However, the symbiotic bacterial community structures of Acropora pruinosa in winter and spring were similar. Proteobacteria were the dominant bacteria in spring, autumn, and winter. In summer, the dominant bacterial taxa were Bacteroidota and Proteobacteria. Ralstonia was the dominant bacterial genus in spring and winter, whereas in autumn, BD1-7_clade was dominant. Linear discriminant analysis effect size identified 20 abundant genera between the different groups. Core microbiome analysis revealed that 12 core bacterial operational taxonomic units were associated with A. pruinosa in all seasons, seven of which varied with the seasons, changing between dominant and rare. Distance-based redundancy and variation partitioning analyses revealed that sea surface temperature was the major contributor of variation in the microbial community structure. We hypothesized that the high diversity and abundance of symbiotic bacteria and the increase in Prosthecochloris abundance in coral in summer can help A. pruinosa maintain its physiological functions, ameliorating the negative physiological effects of the decrease in Symbiodiniaceae density under high-temperature stress. Thus, the rapid reorganization of the symbiotic bacterial community structure and core microflora in different seasons may allow the corals to adapt to large seasonal environmental fluctuations. In conclusion, seasonal variation of bacteria plays an important role in coral adaptation to large environmental fluctuations.

Testing cophylogeny between coral reef invertebrates and their bacterial and archaeal symbionts

Marine invertebrates harbour a complex suite of bacterial and archaeal symbionts, a subset of which are probably linked to host health and homeostasis. Within a complex microbiome it can be difficult to tease apart beneficial or parasitic symbionts from nonessential commensal or transient microorganisms; however, one approach is to detect strong cophylogenetic patterns between microbial lineages and their respective hosts. We employed the Procrustean approach to cophylogeny (PACo) on 16S rRNA gene derived microbial community profiles paired with COI, 18S rRNA and ITS1 host phylogenies. Second, we undertook a network analysis to identify groups of microbes that were co-occurring within our host species. Across 12 coral, 10 octocoral and five sponge species, each host group and their core microbiota (50% prevalence within host species replicates) had a significant fit to the cophylogenetic model. Independent assessment of each microbial genus and family found that bacteria and archaea affiliated to Endozoicomonadaceae, Spirochaetaceae and Nitrosopumilaceae have the strongest cophylogenetic signals. Further, local Moran's I measure of spatial autocorrelation identified 14 ASVs, including Endozoicomonadaceae and Spirochaetaceae, whose distributions were significantly clustered by host phylogeny. Four co-occurring subnetworks were identified, each of which was dominant in a different host group. Endozoicomonadaceae and Spirochaetaceae ASVs were abundant among the subnetworks, particularly one subnetwork that was exclusively comprised of these two bacterial families and dominated the octocoral microbiota. Our results disentangle key microbial interactions that occur within complex microbiomes and reveal long-standing, essential microbial symbioses in coral reef invertebrates.

Fast and pervasive transcriptomic resilience and acclimation of extremely heat-tolerant coral holobionts from the northern Red Sea

Corals from the northern Red Sea and Gulf of Aqaba exhibit extreme thermal tolerance. To examine the underlying gene expression dynamics, we exposed Stylophora pistillata from the Gulf of Aqaba to short-term (hours) and long-term (weeks) heat stress with peak seawater temperatures ranging from their maximum monthly mean of 27 °C (baseline) to 29.5 °C, 32 °C, and 34.5 °C. Corals were sampled at the end of the heat stress as well as after a recovery period at baseline temperature. Changes in coral host and symbiotic algal gene expression were determined via RNA-sequencing (RNA-Seq). Shifts in coral microbiome composition were detected by complementary DNA (cDNA)-based 16S ribosomal RNA (rRNA) gene sequencing. In all experiments up to 32 °C, RNA-Seq revealed fast and pervasive changes in gene expression, primarily in the coral host, followed by a return to baseline gene expression for the majority of coral (>94%) and algal (>71%) genes during recovery. At 34.5 °C, large differences in gene expression were observed with minimal recovery, high coral mortality, and a microbiome dominated by opportunistic bacteria (including Vibrio species), indicating that a lethal temperature threshold had been crossed. Our results show that the S. pistillata holobiont can mount a rapid and pervasive gene expression response contingent on the amplitude and duration of the thermal stress. We propose that the transcriptomic resilience and transcriptomic acclimation observed are key to the extraordinary thermal tolerance of this holobiont and, by inference, of other northern Red Sea coral holobionts, up to seawater temperatures of at least 32 °C, that is, 5 °C above their current maximum monthly mean.

Ecotoxico Linking of Phthalates and Flame-Retardant Combustion Byproducts with Coral Solar Bleaching

Persian Gulf coral reefs are unique biota communities in the global sunbelts in being able to survive in multiple stressful fields during summertime (>36 °C). Despite the high-growth emerging health-hazard microplastic additive type of contaminants, its biological interactions with coral-algal symbiosis and/or its synergistic effects linked to solar-bleaching events remain unknown. This study investigated the bioaccumulation patterns of polybrominated diphenyl ether (PBDE) and phthalate ester (PAE) pollutants in six genera of living/bleached corals in Larak Island, Persian Gulf, and their ambient abiotic matrixes. Results showed that the levels of ∑₁₈PBDEs and ∑₁₃PAEs in abiotic matrixes followed the order of SPMs > surface sediments > seawater, and the cnidarian POP-uptake patterns (soft corals > hard corals) were as follows: coral mucus (138.49 ± 59.98 and 71.57 ± 47.39 ng g^-1 dw) > zooxanthellae (82.05 ± 28.27 and 20.14 ± 12.65 ng g^-1 dw) ≥ coral tissue (66.26 ± 21.42 and 34.97 ± 26.10 ng g^-1 dw) > bleached corals (45.19 ± 8.73 and 13.83 ± 7.05 ng g^-1 dw) > coral skeleton (35.66 ± 9.58 and 6.47 ± 6.47 ng g^-1 dw, respectively). Overall, findings suggest that mucus checking is a key^/facile diagnostic approach for fast detection of POP bioaccumulation (PB) in tropical corals. Although studied corals exhibited no consensus concerning hazardous levels of PB (log BSAF < 3.7), our bleaching evidence showed soft corals as the ultimate "summer winners" due to their flexibility/recovering ability.

Flexibility in Red Sea Tridacna maxima-Symbiodiniaceae associations supports environmental niche adaptation

Giant clams (Tridacninae) are important members of Indo-Pacific coral reefs and among the few bivalve groups that live in symbiosis with unicellular algae (Symbiodiniaceae). Despite the importance of these endosymbiotic dinoflagellates for clam ecology, the diversity and specificity of these associations remain relatively poorly studied, especially in the Red Sea. Here, we used the internal transcribed spacer 2 (ITS2) rDNA gene region to investigate Symbiodiniaceae communities associated with Red Sea Tridacna maxima clams. We sampled five sites spanning 1,300 km (10° of latitude, from the Gulf of Aqaba, 29°N, to the Farasan Banks, 18°N) along the Red Sea's North-South environmental gradient. We detected a diverse and structured assembly of host-associated algae with communities demonstrating region and site-specificity. Specimens from the Gulf of Aqaba harbored three genera of Symbiodiniaceae, Cladocopium, Durusdinium, and Symbiodinium, while at all other sites clams associated exclusively with algae from the Symbiodinium genus. Of these exclusively Symbiodinium-associating sites, the more northern (27° and 22°) and more southern sites (20° and 18°) formed two separate groupings despite site-specific algal genotypes being resolved at each site. These groupings were congruent with the genetic break seen across multiple marine taxa in the Red Sea at approximately 19°, and along with our documented site-specificity of algal communities, contrasted the panmictic distribution of the T. maxima host. As such, our findings indicate flexibility in T. maxima-Symbiodiniaceae associations that may explain its relatively high environmental plasticity and offers a mechanism for environmental niche adaptation.

Heat stress decreases the diversity, abundance and functional potential of coral gas emissions

Terrestrial ecosystems emit large quantities of biogenic volatile organic compounds (BVOCs), many of which play important roles in abiotic stress responses, pathogen and grazing defences, inter- and intra-species communications, and climate regulation. Conversely, comparatively little is known about the diversity and functional potential of BVOCs produced in the marine environment, especially in highly productive coral reefs. Here we describe the first 'volatilomes' of two common reef-building corals, Acropora intermedia and Pocillopora damicornis, and how the functional potential of their gaseous emissions is altered by heat stress events that are driving rapid deterioration of coral reef ecosystems worldwide. A total of 87 BVOCs were detected from the two species and the chemical richness of both coral volatilomes-particularly the chemical classes of alkanes and carboxylic acids-decreased during heat stress by 41% and 62% in A. intermedia and P. damicornis, respectively. Across both coral species, the abundance of individual compounds changed significantly during heat stress, with the majority (>86%) significantly decreasing compared to control conditions. Additionally, almost 60% of the coral volatilome (or 52 BVOCs) could be assigned to four key functional groups based on their activities in other species or systems, including stress response, chemical signalling, climate regulation and antimicrobial activity. The total number of compounds assigned to these functions decreased significantly under heat stress for both A. intermedia (by 35%) and P. damicornis (by 64%), with most dramatic losses found for climatically active BVOCs in P. damicornis and antimicrobial BVOCs in A. intermedia. Together, our observations suggest that future heat stress events predicted for coral reefs will reduce the diversity, quantity and functional potential of BVOCs emitted by reef-building corals, potentially further compromising the healthy functioning of these ecosystems.

Unlocking the phylogenetic diversity, primary habitats, and abundances of free-living Symbiodiniaceae on a coral reef

Dinoflagellates of the family Symbiodiniaceae form mutualistic symbioses with marine invertebrates such as reef-building corals, but also inhabit reef environments as free-living cells. Most coral species acquire Symbiodiniaceae horizontally from the surrounding environment during the larval and/or recruitment phase, however the phylogenetic diversity and ecology of free-living Symbiodiniaceae on coral reefs is largely unknown. We coupled environmental DNA sequencing and genus-specific qPCR to resolve the community structure and cell abundances of free-living Symbiodiniaceae in the water column, sediment, and macroalgae and compared these to coral symbionts. Sampling was conducted at two time points, one of which coincided with the annual coral spawning event when recombination between hosts and free-living Symbiodiniaceae is assumed to be critical. Amplicons of the internal transcribed spacer (ITS2) region were assigned to 12 of the 15 Symbiodiniaceae genera or genera-equivalent lineages. Community compositions were separated by habitat, with water samples containing a high proportion of sequences corresponding to coral symbionts of the genus Cladocopium, potentially as a result of cell expulsion from in hospite populations. Sediment-associated Symbiodiniaceae communities were distinct, potentially due to the presence of exclusively free-living species. Intriguingly, macroalgal surfaces displayed the highest cell abundances of Symbiodiniaceae, suggesting a key role for macroalgae in ensuring the ecological success of corals through maintenance of a continuum between environmental and symbiotic populations of Symbiodiniaceae.

Defining Coral Bleaching as a Microbial Dysbiosis within the Coral Holobiont

Coral microbiomes are critical to holobiont health and functioning, but the stability of host–microbial interactions is fragile, easily shifting from eubiosis to dysbiosis. The heat-induced breakdown of the symbiosis between the host and its dinoflagellate algae (that is, “bleaching”), is one of the most devastating outcomes for reef ecosystems. Yet, bleaching tolerance has been observed in some coral species. This review provides an overview of the holobiont’s diversity, explores coral thermal tolerance in relation to their associated microorganisms, discusses the hypothesis of adaptive dysbiosis as a mechanism of environmental adaptation, mentions potential solutions to mitigate bleaching, and suggests new research avenues. More specifically, we define coral bleaching as the succession of three holobiont stages, where the microbiota can (i) maintain essential functions for holobiont homeostasis during stress and/or (ii) act as a buffer to mitigate bleaching by favoring the recruitment of thermally tolerant Symbiodiniaceae species (adaptive dysbiosis), and where (iii) environmental stressors exceed the buffering capacity of both microbial and dinoflagellate partners leading to coral death.

Distinct fungal communities associated with different organs of the mangrove Sonneratia alba in the Malay Peninsula

Mangrove forests are key tropical marine ecosystems that are rich in fungi, but our understanding of fungal communities associated with mangrove trees and their various organs remains limited because much of the diversity lies within the microbiome. In this study, we investigated the fungal communities associated with the mangrove tree Sonneratia alba throughout Peninsular Malaysia and Singapore. At each sampling location, we collected leaves, fruits, pneumatophores and sediment samples and performed amplicon sequencing of the ribosomal internal transcribed spacer 1 to characterise the associated communities. Results show distinct fungal communities at each sampled location with further differentiation according to the plant part. We find a significant distance decay of similarity, particularly for sediment samples due to the greater variability of sediment environments relative to the more stable fungal habitats provided by living plant organs. We are able to assign taxonomy to the majority of sequences from leaves and fruits, but a much larger portion of the sequences recovered from pneumatophores and sediment samples could not be identified. This pattern underscores the limited mycological research performed in marine environments and demonstrates the need for a concerted research effort on multiple species to fully characterise the coastal microbiome and its role in the functioning of marine ecosystems.

Adding insult to injury: Effects of chronic oxybenzone exposure and elevated temperature on two reef-building corals

Coral bleaching due to global warming currently is the largest threat to coral reefs, which may be exacerbated by altered water quality. Elevated levels of the UV filter oxybenzone in coastal waters as a result of sunscreen use have recently been demonstrated. We studied the effect of chronic oxybenzone exposure and elevated water temperature on coral health. Microcolonies of Stylophora pistillata and Acropora tenuis were cultured in 20 flow-through aquaria, of which 10 were exposed to oxybenzone at a field-relevant concentration of ~0.06 μg L^-1 at 26 °C. After two weeks, half of the corals experienced a heat wave culminating at 33 °C. All S. pistillata colonies survived the heat wave, although heat reduced growth and zooxanthellae density, irrespective of oxybenzone. Acropora tenuis survival decreased to 0% at 32 °C, and oxybenzone accelerated mortality. Oxybenzone and heat significantly impacted photosynthetic yield in both species, causing a 5% and 22-33% decrease, respectively. In addition, combined oxybenzone and temperature stress altered the abundance of five bacterial families in the microbiome of S. pistillata. Our results suggest that oxybenzone adds insult to injury by further weakening corals in the face of global warming.

Microbiomes of Caribbean Octocorals Vary Over Time but Are Resistant to Environmental Change

The bacterial microbiome is an essential component of many corals, although knowledge of the microbiomes in scleractinian corals far exceeds that for octocorals. This study characterized the bacterial communities present in shallow water Caribbean gorgonian octocorals over time and space, in addition to determining the bacterial assemblages in gorgonians exposed to environmental perturbations. We found that seven shallow water Caribbean gorgonian species maintained distinct microbiomes and predominantly harbored two bacterial genera, Mycoplasma and Endozoicomonas. Representatives of these taxa accounted for over 70% of the sequences recovered, made up the three most common operational taxonomic units (OTUs), and were present in most of the gorgonian species. Gorgonian species sampled in different seasons and/or in different years, exhibited significant shifts in the abundances of these bacterial OTUs, though there were few changes to overall bacterial diversity, or to the specific OTUs present. These shifts had minimal impact on the relative abundance of inferred functional proteins within the gorgonian corals. Sequences identified as Escherichia were ubiquitous in gorgonian colonies sampled from a lagoon but not in colonies sampled from a back reef. Exposure to increased temperature and/or ultraviolet radiation (UVR) or nutrient enrichment led to few significant changes in the gorgonian coral microbiomes. While there were some shifts in the abundance of the prevalent bacteria, more commonly observed was “microbial switching” between different OTUs identified within the same bacterial genus. The relative stability of gorgonian coral bacterial microbiome may potentially explain some of the resistance and resilience of Caribbean gorgonian corals against changing environmental conditions.

Correlations Between Prokaryotic Microbes and Stress-Resistant Algae in Different Corals Subjected to Environmental Stress in Hong Kong

Coral reefs are extremely vulnerable to global climate change, as evidenced by increasing bleaching events. Previous studies suggest that both algal and microbial partners benefit coral hosts, but the nature of interactions between Symbiodiniaceae and prokaryotic microbes and their effects on coral hosts remains unclear. In the present study, we examined correlations between Symbiodiniaceae and prokaryotic microbes in Montipora spp. and Porites lutea sampled from two sites in Hong Kong with contrasting environmental conditions in March and October 2014. The results showed that the prokaryotic microbial communities had adaptable structures in both Montipora spp. and P. lutea, and environmental conditions had greater effects on the algal/microbial communities in Montipora spp. than in P. lutea. Further network analysis revealed a greater number of prokaryotic microbes were significantly correlated with potentially stress-resistant Symbiodiniaceae in P. lutea than in Montipora spp. Stress-resistant Symbiodiniaceae played more important roles in the community and in the algal–microbial correlations in P. lutea than in Montipora spp. Since P. lutea is faring better in Hong Kong as the seawater temperature gradually increases, the results suggest that the correlations between stress-resistant algae and prokaryotic microbes could provide a compensation mechanism allowing coral hosts to adapt to higher temperatures, particularly as the prokaryotic microbes correlated with Symbiodiniaceae provide the ecological functions of photosynthesis and nitrogen fixation.

Coral microbiome composition along the northern Red Sea suggests high plasticity of bacterial and specificity of endosymbiotic dinoflagellate communities

BACKGROUND

The capacity of reef-building corals to tolerate (or adapt to) heat stress is a key factor determining their resilience to future climate change. Changes in coral microbiome composition (particularly for microalgal endosymbionts and bacteria) is a potential mechanism that may assist corals to thrive in warm waters. The northern Red Sea experiences extreme temperatures anomalies, yet corals in this area rarely bleach suggesting possible refugia to climate change. However, the coral microbiome composition, and how it relates to the capacity to thrive in warm waters in this region, is entirely unknown.

RESULTS

We investigated microbiomes for six coral species (Porites nodifera, Favia favus, Pocillopora damicornis, Seriatopora hystrix, Xenia umbellata, and Sarcophyton trocheliophorum) from five sites in the northern Red Sea spanning 4° of latitude and summer mean temperature ranges from 26.6 °C to 29.3 °C. A total of 19 distinct dinoflagellate endosymbionts were identified as belonging to three genera in the family Symbiodiniaceae (Symbiodinium, Cladocopium, and Durusdinium). Of these, 86% belonged to the genus Cladocopium, with notably five novel types (19%). The endosymbiont community showed a high degree of host-specificity despite the latitudinal gradient. In contrast, the diversity and composition of bacterial communities of the surface mucus layer (SML)-a compartment particularly sensitive to environmental change-varied significantly between sites, however for any given coral was species-specific.

CONCLUSION

The conserved endosymbiotic community suggests high physiological plasticity to support holobiont productivity across the different latitudinal regimes. Further, the presence of five novel algal endosymbionts suggests selection of certain genotypes (or genetic adaptation) within the semi-isolated Red Sea. In contrast, the dynamic composition of bacteria associated with the SML across sites may contribute to holobiont function and broaden the ecological niche. In doing so, SML bacterial communities may aid holobiont local acclimatization (or adaptation) by readily responding to changes in the host environment. Our study provides novel insight about the selective and endemic nature of coral microbiomes along the northern Red Sea refugia.

Revealing the impact of global mass bleaching on coral microbiome through 16S rRNA gene-based metagenomic analysis

Coral bleaching, a phenomenon by which the expulsion of corals' alveolate endosymbiont (zooxanthellae) occurs when experiencing thermal stress is the major cause for devastation of corals. However, apart from this obligate symbiont of Scleractinian corals, there are different kinds of microbes that exist as stable, transient or sporadic members of the holobiont which reside within various microhabitats in the coral structures. Thus, this study aims to profile the coral bacterial community composition among different coral genera (thermally-sensitive (Acropora digetifera and A. noblis) and thermally resistant (Favites abdita) coral genera analyzed by field monitoring surveys) and also in a particular coral genus (thermally sensitive coral-A. digetifera) at two different sampling times (March 2016 and January 2017). A total of about 608695 paired end reads were obtained through Illumina MiSeq Sequencing platform. The alpha diversity indices (ACE, Chao1 and Shannon) were found to be higher in A. nobilis, followed by A. digetifera and Favites abdita, and the corresponding Simpson values were also found to follow the same trend, indicating that the samples are both rich in species diversity and species evenness. Proteobacteria was found to be the most dominant phylum and Gammaproteobacteria was the predominant class present in all the coral genera studied as also during different sampling time periods. As Vibrionaceae was previously reported to increase its abundance during bleaching stress conditions, bacterial profiling among different coral genera showed the presence of 86 % Vibrionaceae in A. digetifera colonies, and it was 93 % in A. digetifera samples collected during March 2016 whereas, it was found to decrease significantly (7 %) in same tagged colonies collected during January 2017. Thus, profiling of microbiome is of prime importance while studying the holobiont organism like the corals. Stress levels experienced by Palk Bay are even depicted in this microbiome study showing high alpha diversity indices that should alarm reef managers to pay attention to this precious stress tolerant reef community.

Heat-induced shift in coral microbiome reveals several members of the Rhodobacteraceae family as indicator species for thermal stress in Porites lutea

The coral holobiont is a complex ecosystem consisting of coral animals and a highly diverse consortium of associated microorganisms including algae, fungi, and bacteria. Several studies have highlighted the importance of coral‐associated bacteria and their potential roles in promoting the host fitness and survival. Recently, dynamics of coral‐associated microbiomes have been demonstrated to be linked to patterns of coral heat tolerance. Here, we examined the effect of elevated seawater temperature on the structure and diversity of bacterial populations associated with Porites lutea, using full‐length 16S rRNA sequences obtained from Pacific Biosciences circular consensus sequencing. We observed a significant increase in alpha diversity indices and a distinct shift in microbiome composition during thermal stress. There was a marked decline in the apparent relative abundance of Gammaproteobacteria family Endozoicomonadaceae after P. lutea had been exposed to elevated seawater temperature. Concomitantly, the bacterial community structure shifted toward the predominance of Alphaproteobacteria family Rhodobacteraceae. Interestingly, we did not observe an increase in relative abundance of Vibrio‐related sequences in our heat‐stressed samples even though the appearance of Vibrio spp. has often been detected in parallel with the increase in the relative abundance of Rhodobacteraceae during thermal bleaching in other coral species. The ability of full‐length 16S rRNA sequences in resolving taxonomic uncertainty of associated bacteria at a species level enabled us to identify 24 robust indicator bacterial species for thermally stressed corals. It is worth noting that the majority of those indicator species were members of the family Rhodobacteraceae. The comparison of bacterial community structure and diversity between corals in ambient water temperature and thermally stressed corals may provide a better understanding on how bacteria symbionts contribute to the resilience of their coral hosts to ocean warming.