Coral transcriptome and bacterial community profiles reveal distinct Yellow Band Disease states in Orbicella faveolata

Microbial and transcriptional response of Acropora valida and Turbinaria peltata to Vibrio coralliilyticus challenge: insights into corals disease resistance

BACKGROUND

Coral diseases are significant drivers of global coral reef degradation, with pathogens dominated by Vibrio coralliilyticus playing a prominent role in the development of coral diseases. Coral phenotype, symbiotic microbial communities, and host transcriptional regulation have been well-established as factors involved in determining coral disease resistance, but the underlying mechanisms remain incompletely understood.

METHODS

This study employs high-throughput sequencing to analyse the symbiotic microbial and transcriptional response of the hosts in order to evaluate the disease resistance of Acropora valida and Turbinaria peltata exposed to Vibrio coralliilyticus.

RESULTS

A. valida exhibited pronounced bleaching and tissue loss within 7 h of pathogen infection, whereas T. peltata showed no signs of disease throughout the experiment. Microbial diversity analyses revealed that T. peltata had a more flexible microbial community and a higher relative abundance of potential beneficial bacteria compared to A. valida. Although Vibrio inoculation resulted in a more significant decrease in the Symbiodiniaceae density of A. valida compared to that of T. peltata, it did not lead to recombination of the coral host and Symbiodiniaceae in either coral species. RNA-seq analysis revealed that the interspecific differences in the transcriptional regulation of hosts after Vibrio inoculation. Differentially expressed genes in A. valida were mainly enriched in the pathways associated with energy supply and immune response, such as G protein-coupled receptor signaling, toll-like receptor signaling, regulation of TOR signaling, while these genes in T. peltata were mainly involved in the pathway related to immune homeostasis and ion transport, such as JAK-STAT signaling pathway and regulation of ion transport.

CONCLUSIONS

Pathogenic challenges elicit different microbial and transcriptional shifts across coral species. This study offers novel insights into molecular mechanisms of coral resistance to disease.

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.

Spatial extent of dysbiosis in the branching coral Pocillopora damicornis during an acute disease outbreak

Globally, coral reefs face increasing disease prevalence and large-scale outbreak events. These outbreaks offer insights into microbial and functional patterns of coral disease, including early indicators of disease that may be present in visually-healthy tissues. Outbreak events also allow investigation of how reef-building corals, typically colonial organisms, respond to disease. We studied Pocillopora damicornis during an acute tissue loss disease outbreak on Guam to determine whether dysbiosis was present in visually-healthy tissues ahead of advancing disease lesions. These data reveal that coral fragments with visual evidence of disease are expectedly dysbiotic with high microbial and metabolomic variability. However, visually-healthy tissues from the same colonies lacked dysbiosis, suggesting disease containment near the affected area. These results challenge the idea of using broad dysbiosis as a pre-visual disease indicator and prompt reevaluation of disease assessment in colonial organisms such as reef-building corals.

Different disease inoculations cause common responses of the host immune system and prokaryotic component of the microbiome in Acropora palmata

Reef-building corals contain a complex consortium of organisms, a holobiont, which responds dynamically to disease, making pathogen identification difficult. While coral transcriptomics and microbiome communities have previously been characterized, similarities and differences in their responses to different pathogenic sources has not yet been assessed. In this study, we inoculated four genets of the Caribbean branching coral Acropora palmata with a known coral pathogen (Serratia marcescens) and white band disease. We then characterized the coral's transcriptomic and prokaryotic microbiomes' (prokaryiome) responses to the disease inoculations, as well as how these responses were affected by a short-term heat stress prior to disease inoculation. We found strong commonality in both the transcriptomic and prokaryiomes responses, regardless of disease inoculation. Differences, however, were observed between inoculated corals that either remained healthy or developed active disease signs. Transcriptomic co-expression analysis identified that corals inoculated with disease increased gene expression of immune, wound healing, and fatty acid metabolic processes. Co-abundance analysis of the prokaryiome identified sets of both healthy-and-disease-state bacteria, while co-expression analysis of the prokaryiomes' inferred metagenomic function revealed infected corals' prokaryiomes shifted from free-living to biofilm states, as well as increasing metabolic processes. The short-term heat stress did not increase disease susceptibility for any of the four genets with any of the disease inoculations, and there was only a weak effect captured in the coral hosts' transcriptomic and prokaryiomes response. Genet identity, however, was a major driver of the transcriptomic variance, primarily due to differences in baseline immune gene expression. Despite genotypic differences in baseline gene expression, we have identified a common response for components of the coral holobiont to different disease inoculations. This work has identified genes and prokaryiome members that can be focused on for future coral disease work, specifically, putative disease diagnostic tools.

Seaweeds influence oyster microbiota and disease susceptibility

A growing awareness of role that microbiota can play in mediating the effects of pathogens on hosts has given rise to the concept of the pathobiome. Recently, we demonstrated that the Pacific oyster mortality syndrome affecting Crassostrea gigas oysters is caused by infection with the Ostreid herpesvirus type 1 (OsHV-1) followed by infection with multiple bacterial taxa. Here we extend the concept of this pathobiome beyond the host species and its bacterial microbiota by investigating how seaweed living in association with oysters influences their response to the disease. We hypothesized that by their mere presence in the environment, different species of seaweeds can positively or negatively influence the risk of disease in oysters by shaping their bacterial microbiota and their immune response. Although seaweed and oysters do not have direct ecological interactions, they are connected by seawater and likely share microbes. To test our hypothesis, oysters were acclimated with green, brown or red algae for 2 weeks and then challenged with OsHV-1. We monitored host survival and pathogen proliferation and performed bacterial microbiota and transcriptome analyses. We found that seaweeds can alter the bacterial microbiota of the host and its response to the disease. More particularly, green algae belonging to the genus Ulva spp. induced bacterial microbiota dysbiosis in oyster and modification of its transcriptional immune response leading to increased susceptibility to the disease. This work provides a better understanding of a marine disease and highlights the importance of considering both macrobiotic and microbiotic interactions for conservation, management and exploitation of marine ecosystems and resources.

The rice foot rot pathogen Dickeya zeae alters the in-field plant microbiome

Studies on bacterial plant diseases have thus far been focused on the single bacterial species causing the disease, with very little attention given to the many other microorganisms present in the microbiome. This study intends to use pathobiome analysis of the rice foot rot disease, caused by Dickeya zeae, as a case study to investigate the effects of this bacterial pathogen to the total resident microbiome and to highlight possible interactions between the pathogen and the members of the community involved in the disease process. The microbiome of asymptomatic and the pathobiome of foot‐rot symptomatic field‐grown rice plants over two growing periods and belonging to two rice cultivars were determined via 16S rRNA gene amplicon sequencing. Results showed that the presence of D. zeae is associated with an alteration of the resident bacterial community in terms of species composition, abundance and richness, leading to the formation of microbial consortia linked to the disease state. Several bacterial species were significantly co‐presented with the pathogen in the two growing periods suggesting that they could be involved in the disease process. Besides, culture‐dependent isolation and in planta inoculation studies of a bacterial member of the pathobiome, identified as positive correlated with the pathogen in our in silico analysis, indicated that it benefits from the presence of D. zeae. A similar microbiome/pathobiome experiment was also performed in a symptomatically different rice disease evidencing that not all plant diseases have the same consequence/relationship with the plant microbiome. This study moves away from a pathogen‐focused stance and goes towards a more ecological perception considering the effect of the entire microbial community which could be involved in the pathogenesis, persistence, transmission and evolution of plant pathogens.

The microbial profile of a tissue necrosis affecting the Atlantic invasive coral Tubastraea tagusensis

The Southwestern Atlantic rocky reef ecosystems are undergoing significant changes due to sun-corals (Tubastraea tagusensis and T. coccinea) invasion. At Búzios Island, on the northern coast of São Paulo State, where the abundance of T. tagusensis is particularly high, some colonies are displaying tissue necrosis, a phenomenon never reported for this invasive nor any other azooxanthellate coral species. Using next-generation sequencing, we sought to understand the relationship between T. tagusensis tissue necrosis and its microbiota. Thus, through amplicon sequencing, we studied both healthy and diseased coral colonies. Results indicate a wide variety of bacteria associated with healthy colonies and an even higher diversity associated with those corals presenting tissue necrosis, which displayed nearly 25% more microorganisms. Also, as the microbial community associated with the seven healthy colonies did not alter composition significantly, it was possible to verify the microbial succession during different stages of tissue necrosis (i.e., initial, intermediate, and advanced). Comparing the microbiome from healthy corals to those in early tissue necrosis suggests 21 potential pathogens, which might act as the promoters of such disease.

Characterization of the microbiome and immune response in corals with chronic Montipora white syndrome

Coral diseases have increased in frequency and intensity around the tropics worldwide. However, in many cases, little is known about their etiology. Montipora white syndrome (MWS) is a common disease affecting the coral Montipora capitata, a major reef builder in Hawai'i. Chronic Montipora white syndrome (cMWS) is a slow-moving form of the disease that affects M. capitata throughout the year. The effects of this chronic disease on coral immunology and microbiology are currently unknown. In this study, we use prophenoloxidase immune assays and 16S rRNA gene amplicon sequencing to characterize the microbiome and immunological response associated with cMWS. Our results show that immunological and microbiological responses are highly localized. Relative to diseased samples, apparently healthy portions of cMWS corals differed in immune activity and in the relative abundance of microbial taxa. Coral tissues with cMWS showed decreased tyrosinase-type catecholase and tyrosinase-type cresolase activity and increased laccase-type activity. Catecholase and cresolase activity were negatively correlated across all tissue types with microbiome richness. The localized effect of cMWS on coral microbiology and immunology is probably an important reason for the slow progression of the disease. This local confinement may facilitate interventions that focus on localized treatments on tissue types. This study provides an important baseline to understand the interplay between the microbiome and immune system and the mechanisms used by corals to manage chronic microbial perturbations associated with white syndrome.

Ecological Factors Mediate Immunity and Parasitic Co-Infection in Sea Fan Octocorals

The interplay among environment, demography, and host-parasite interactions is a challenging frontier. In the ocean, fundamental changes are occurring due to anthropogenic pressures, including increased disease outbreaks on coral reefs. These outbreaks include multiple parasites, calling into question how host immunity functions in this complex milieu. Our work investigates the interplay of factors influencing co-infection in the Caribbean sea fan octocoral, Gorgonia ventalina, using metrics of the innate immune response: cellular immunity and expression of candidate immune genes. We used existing copepod infections and live pathogen inoculation with the Aspergillus sydowii fungus, detecting increased expression of the immune recognition gene Tachylectin 5A (T5A) in response to both parasites. Cellular immunity increased by 8.16% in copepod infections compared to controls and single Aspergillus infections. We also detected activation of cellular immunity in reef populations, with a 13.6% increase during copepod infections. Cellular immunity was similar in the field and in the lab, increasing with copepod infections and not the fungus. Amoebocyte density and the expression of T5A and a matrix metalloproteinase (MMP) gene were also positively correlated across all treatments and colonies, irrespective of parasitic infection. We then assessed the scaling of immune metrics to population-level disease patterns and found random co-occurrence of copepods and fungus across 15 reefs in Puerto Rico. The results suggest immune activation by parasites may not alter parasite co-occurrence if factors other than immunity prevail in structuring parasite infection. We assessed non-immune factors in the field and found that sea fan colony size predicted infection by the copepod parasite. Moreover, the effect of infection on immunity was small relative to that of site differences and live coral cover, and similar to the effect of reproductive status. While additional immune data would shed light on the extent of this pattern, ecological factors may play a larger role than immunity in controlling parasite patterns in the wild. Parsing the effects of immunity and ecological factors in octocoral co-infection shows how disease depends on more than one host and one parasite and explores the application of co-infection research to a colonial marine organism.

Innate immune gene expression in Acropora palmata is consistent despite variance in yearly disease events

Coral disease outbreaks are expected to increase in prevalence, frequency and severity due to climate change and other anthropogenic stressors. This is especially worrying for the Caribbean branching coral Acropora palmata which has already seen an 80% decrease in cover primarily due to disease. Despite the importance of this keystone species, there has yet to be a characterization of its transcriptomic response to disease exposure. In this study we provide the first transcriptomic analysis of 12 A. palmata genotypes and their symbiont Symbiodiniaceae exposed to disease in 2016 and 2017. Year was the primary driver of gene expression variance for A. palmata and the Symbiodiniaceae. We hypothesize that lower expression of ribosomal genes in the coral, and higher expression of transmembrane ion transport genes in the Symbiodiniaceae indicate that a compensation or dysbiosis may be occurring between host and symbiont. Disease response was the second driver of gene expression variance for A. palmata and included a core set of 422 genes that were significantly differentially expressed. Of these, 2 genes (a predicted cyclin-dependent kinase 11b and aspartate 1-decarboxylase) showed negative Log2 fold changes in corals showing transmission of disease, and positive Log2 fold changes in corals showing no transmission of disease, indicating that these may be important in disease resistance. Co-expression analysis identified two modules positively correlated to disease exposure, one enriched for lipid biosynthesis genes, and the other enriched in innate immune genes. The hub gene in the immune module was identified as D-amino acid oxidase, a gene implicated in phagocytosis and microbiome homeostasis. The role of D-amino acid oxidase in coral immunity has not been characterized but could be an important enzyme for responding to disease. Our results indicate that A. palmata mounts a core immune response to disease exposure despite differences in the disease type and virulence between 2016 and 2017. These identified genes may be important for future biomarker development in this Caribbean keystone species.

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.

A place for taxonomic profiling in the study of the coral prokaryotic microbiome

The enormous variability in richness, abundance and diversity of unknown bacterial organisms inhabiting the coral microbiome have challenged our understanding of their functional contribution to coral health. Identifying the attributes of the healthy meta-organism is paramount for contemporary approaches aiming to manipulate dysbiotic stages of the coral microbiome. This review evaluates the current knowledge on the structure and mechanisms driving bacterial communities in the coral microbiome and discusses two topics requiring further research to define the healthy coral microbiome. (i) We examine the necessity to establish microbial baselines to understand the spatial and temporal dynamics of the healthy coral microbiome and summarise conceptual and logistic challenges to consider in the design of these baselines. (ii) We propose potential mechanical, physical and chemical mechanisms driving bacterial distribution within coral compartments and suggest experiments to test them. Finally, we highlight aspects of the use of 16S amplicon sequencing requiring standardization and discuss its contribution to other multi-omics approaches.

Ecology, histopathology, and microbial ecology of a white-band disease outbreak in the threatened staghorn coral Acropora cervicornis

This study is a multi-pronged description of a temperature-induced outbreak of white-band disease (WBD) that occurred in Acropora cervicornis off northern Miami Beach, Florida (USA), from July to October 2014. We describe the ecology of the disease and examine diseased corals using both histopathology and next-generation bacterial 16S gene sequencing, making it possible to better understand the effect this disease has on the coral holobiont, and to address some of the seeming contradictions among previous studies of WBD that employed either a purely histological or molecular approach. The outbreak began in July 2014, as sea surface temperatures reached 29°C, and peaked in mid-September, a month after the sea surface temperature maximum. The microscopic anatomy of apparently healthy portions of colonies displaying active disease signs appeared normal except for some tissue atrophy and dissociation of mesenterial filaments deep within the branch. Structural changes were more pronounced in visibly diseased fragments, with atrophy, necrosis, and lysing of surface and basal body wall and polyp structures at the tissue-loss margin. The only bacteria evident microscopically in both diseased and apparently healthy tissues with Giemsa staining was a Rickettsiales-like organism (RLO) occupying mucocytes. Sequencing also identified bacteria belonging to the order Rickettsiales in all fragments. When compared to apparently healthy fragments, diseased fragments had more diverse bacterial communities made up of many previously suggested potential primary pathogens and secondary (opportunistic) colonizers. Interactions between elevated seawater temperatures, the coral host, and pathogenic members of the diseased microbiome all contribute to the coral displaying signs of WBD.

The Effect of Thermal Stress on the Bacterial Microbiome of Exaiptasia diaphana

Coral bleaching linked to climate change has generated interest in the response of coral’s bacterial microbiome to thermal stress. The sea anemone, Exaiptasia diaphana, is a popular coral model, but the response of its bacteria to thermal stress has been barely explored. To address this, we compared the bacterial communities of Great Barrier Reef (GBR) E. diaphana maintained at 26 °C or exposed to increasing temperature (26–33 °C) over two weeks. Communities were analyzed by metabarcoding of the bacterial 16S rRNA gene. Bleaching and Symbiodiniaceae health were assessed by Symbiodiniaceae cell density and dark-adapted quantum yield (F_v/F_m), respectively. Significant bleaching and reductions in F_v/F_m occurred in the heat-treated anemones above 29 °C. Overall declines in bacterial alpha diversity in all anemones were also observed. Signs of bacterial change emerged above 31 °C. Some initial outcomes may have been influenced by relocation or starvation, but collectively, the bacterial community and taxa-level data suggested that heat was the primary driver of change above 32 °C. Six bacterial indicator species were identified as potential biomarkers for thermal stress. We conclude that the bacterial microbiome of GBR E. diaphana is generally stable until a thermal threshold is surpassed, after which significant changes occur.

Technical pitfalls that bias comparative microbial community analyses of aquatic disease Ian Hewson

The accessibility of high-throughput DNA sequencing technologies has attracted the application of comparative microbial analyses to study diseases. These studies present a window into host microbiome diversity and composition that can be used to address ecological theory in the context of host biology and behavior. Recently, comparative microbiome studies have been used to study non-vertebrate aquatic diseases to elucidate microorganisms potentially involved in disease processes or in disease prevention. These investigations suffer from many well-described biases, especially prior to sequence analyses, that could lead to misleading conclusions. Microbiome-focused studies of aquatic metazoan diseases provide valuable documentation of microbial ecology, although, they are only a starting point for establishing disease etiology, which demands quantitative validation through targeted approaches. The microbiome approach to understanding disease is most useful after laboratory diagnostics guided by pathology have failed to identify a causative agent. This opinion piece presents several technical pitfalls which may affect wider interpretation of microbe-host interactions through comparative microbial community analyses and provides recommendations, based on studies in non-aquatic systems, for incorporation into future aquatic disease research.

Acquisition of obligate mutualist symbionts during the larval stage is not beneficial for a coral host

Theory suggests that the direct transmission of beneficial endosymbionts (mutualists) 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 larval acquisition, similar changes occurred in host energetic lipid use and gene expression regardless of whether their symbionts were photosynthesizing, suggesting the symbionts did not provide the energetic benefit 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.

Disease Specific Bacterial Communities in a Coralline Algae of the Northwestern Mediterranean Sea: A Combined Culture Dependent and -Independent Approach

Crustose coralline red algae (CCA) are important components of marine ecosystems thriving from tropical waters and up to the poles. They fulfill important ecological services including framework building and induction of larval settlement. Like other marine organisms, CCAs have not been spared by the increase in marine disease outbreaks. The white-band syndrome has been recently observed in corallines from the Mediterranean Sea indicating that the disease threat has extended from tropical to temperate waters. Here, we examined the microbiome and the pathobiome of healthy and diseased Neogoniolithon brassica-florida coralline algae in the Mediterranean Sea by combining culture-dependent and -independent approaches. The coralline white-band syndrome was associated with a distinct pathobiome compared to healthy tissues and showed similarities with the white-band syndrome described in the Caribbean Sea. A sequence related to the genus Hoeflea, order Rhizobiales, characterized the white-band disease pathobiome described by amplicon sequencing. No representative of this genus was isolated by culture. We, however, successfully isolated an abundant member of the healthy CCA microbiome, an Alphaproteobateria of the family Rhodobacteraceae. In conclusion, we did not identify a potential causative agent of the disease, but through the complementarity of culture dependent and independent approaches we characterized the healthy microbiome of the coralline and the possible opportunistic bacteria colonizing diseased tissues.

Development of a transcriptomic database for 14 species of scleractinian corals

BACKGROUND

Scleractinian corals are important reef builders, but around the world they are under the threat of global climate change as well as local stressors. Molecular resources are critical for understanding a species' stress responses and resilience to the changing environment, but such resources are unavailable for most scleractinian corals, especially those distributed in the South China Sea. We therefore aimed to provide transcriptome resources for 14 common species, including a few structure forming species, in the South China Sea.

DESCRIPTION

We sequenced the transcriptome of 14 species of scleractinian corals using high-throughput RNA-seq and conducted de novo assembly. For each species, we produced 7.4 to 12.0 gigabases of reads, and assembled them into 271 to 762 thousand contigs with a N50 value of 629 to 1427 bp. These contigs included 66 to 114 thousand unigenes with a predicted open reading frame, and 74.3 to 80.5% of the unigenes were functionally annotated. In the azooxanthelate species Tubastraea coccinea, 41.5% of the unigenes had at least a best-hit sequence from corals. In the other thirteen species, 20.2 to 48.9% of the annotated unigenes had best-hit sequences from corals, and 28.3 to 51.6% from symbiotic algae belonging to the family Symbiodinaceae. With these resources, we developed a transcriptome database (CoralTBase) which features online BLAST and keyword search for unigenes/functional terms through a user friendly Internet interface.

SHORT CONCLUSION

We developed comprehensive transcriptome resources for 14 species of scleractinian corals and constructed a publicly accessible database ( www.comp.hkbu.edu.hk/~db/CoralTBase ). CoralTBase will facilitate not only functional studies using these corals to understand the molecular basis of stress responses and adaptation, but also comparative transcriptomic studies with other species of corals and more distantly related cnidarians.

Long-Term Temperature Stress in the Coral Model Aiptasia Supports the "Anna Karenina Principle" for Bacterial Microbiomes

The understanding of host-microbial partnerships has become a hot topic during the last decade as it has been shown that associated microbiota play critical roles in the host physiological functions and susceptibility to diseases. Moreover, the microbiome may contribute to host resilience to environmental stressors. The sea anemone Aiptasia is a good laboratory model system to study corals and their microbial symbiosis. In this regard, studying its bacterial microbiota provides a better understanding of cnidarian metaorganisms as a whole. Here, we investigated the bacterial communities of different Aiptasia host-symbiont combinations under long-term heat stress in laboratory conditions. Following a 16S rRNA gene sequencing approach we were able to detect significant differences in the bacterial composition and structure of Aiptasia reared at different temperatures. A higher number of taxa (i.e., species richness), and consequently increased α-diversity and β-dispersion, were observed in the microbiomes of heat-stressed individuals across all host strains and experimental batches. Our findings are in line with the recently proposed Anna Karenina principle (AKP) for animal microbiomes, which states that dysbiotic or stressed organisms have a more variable and unstable microbiome than healthy ones. Microbial interactions affect the fitness and survival of their hosts, thus exploring the AKP effect on animal microbiomes is important to understand host resilience. Our data contributes to the current knowledge of the Aiptasia holobiont and to the growing field of study of host-associated microbiomes.

Coral-associated bacteria demonstrate phylosymbiosis and cophylogeny

Scleractinian corals’ microbial symbionts influence host health, yet how coral microbiomes assembled over evolution is not well understood. We survey bacterial and archaeal communities in phylogenetically diverse Australian corals representing more than 425 million years of diversification. We show that coral microbiomes are anatomically compartmentalized in both modern microbial ecology and evolutionary assembly. Coral mucus, tissue, and skeleton microbiomes differ in microbial community composition, richness, and response to host vs. environmental drivers. We also find evidence of coral-microbe phylosymbiosis, in which coral microbiome composition and richness reflect coral phylogeny. Surprisingly, the coral skeleton represents the most biodiverse coral microbiome, and also shows the strongest evidence of phylosymbiosis. Interactions between bacterial and coral phylogeny significantly influence the abundance of four groups of bacteria–including Endozoicomonas-like bacteria, which divide into host-generalist and host-specific subclades. Together these results trace microbial symbiosis across anatomy during the evolution of a basal animal lineage.

Associations between corals and symbiotic microorganisms could be driven by the environment or shared evolutionary history. Here, the authors examine relationships between coral phylogenies and associated microbiomes, finding evidence of phylosymbiosis in microbes from coral skeleton and tissue, but not mucus.

Plankton community assessment in anthropogenic-impacted oligotrophic coastal regions

Microbial planktonic communities are critical components of marine biogeochemical pathways. Despite this, there is still limited knowledge on the dynamics of this group in warm and oligotrophic waters. We used high-throughput sequencing to characterise the bacterial (16S rRNA) and eukaryotic (18S rRNA) microbial plankton communities in two regions under the influence of anthropogenic impacts (a port and sewage outflow) and a coastal region with no direct anthropogenic disturbances in the central Red Sea. Overall, bacterial and eukaryotic components responded in a similar way to the environmental conditions. Community composition and structure were more sensitive than alpha diversity measures to environmental impacts. With the exception of eukaryotes, for which the number of OTU differed significantly between sampling periods in all the regions, environmental changes associated with anthropogenic pressures seem to be better reflected by variations in the relative dominance of microbial groups. For example, elevated proportional abundances of nitrifying and sewage-/faecal-related bacteria at the impacted sites were observed compared with the coastal region. The recently developed microgAMBI also appeared to correlate well with the level of anthropogenic impact the regions experienced, showing the potential to be applied in oligotrophic waters.

Local confinement of disease-related microbiome facilitates recovery of gorgonian sea fans from necrotic-patch disease

Microbiome disruptions triggering disease outbreaks are increasingly threatening corals worldwide. In the Tropical Eastern Pacific, a necrotic-patch disease affecting gorgonian corals (sea fans, Pacifigorgia spp.) has been observed in recent years. However, the composition of the microbiome and its disease-related disruptions remain unknown in these gorgonian corals. Therefore, we analysed 16S rRNA gene amplicons from tissues of healthy colonies (n = 19) and from symptomatic-asymptomatic tissues of diseased colonies (n = 19) of Pacifigorgia cairnsi (Gorgoniidae: Octocorallia) in order to test for disease-related changes in the bacterial microbiome. We found that potential endosymbionts (mostly Endozoicomonas spp.) dominate the core microbiome in healthy colonies. Moreover, healthy tissues differed in community composition and functional profile from those of the symptomatic tissues but did not show differences to asymptomatic tissues of the diseased colonies. A more diverse set of bacteria was observed in symptomatic tissues, together with the decline in abundance of the potential endosymbionts from the healthy core microbiome. Furthermore, according to a comparative taxonomy-based functional profiling, these symptomatic tissues were characterized by the increase in heterotrophic, ammonia oxidizer and dehalogenating bacteria and by the depletion of nitrite and sulphate reducers. Overall, our results suggest that the bacterial microbiome associated with the disease behaves opportunistically and is likely in a state of microbial dysbiosis. We also conclude that the confinement of the disease-related consortium to symptomatic tissues may facilitate colony recovery.

Testing methods to mitigate Caribbean yellow-band disease on Orbicella faveolata

Outbreaks of coral diseases continue to reduce global coral populations. In the Caribbean, yellow band is a severe and wide-spread disease that commonly affects corals of the Orbicella spp. complex, significantly impeding coral reproduction, and hindering the natural recovery of Orbicella spp. populations. Caribbean yellow-band disease (CYBD) lesions may be severe, and often result in the complete loss of coral tissue. The slow spread of CYBD, however, provides an opportunity to test methods to mitigate the disease. Here we report the results of in situ experiments, conducted within Buck Island Reef National Monument in St. Croix, USVI, to test the effectiveness of three techniques to minimize disease impact on Orbicella faveolata: (1) shading, (2) aspirating, and (3) chiseling a “firebreak” to isolate the lesion. Neither shading nor aspirating the diseased tissue significantly reduced CYBD tissue loss. However, chiseling reduced the rate and amount of tissue lost by 31%. While 30–40% of the chiseled lesions appeared to be free of disease signs 12–16 months after treatment, success significantly and steadily declined over 23 months, indicating a possible lack of long-term viability of the technique. The results of this study demonstrate that creating a “firebreak” between diseased and healthy-appearing tissue slows the spread of the disease and may prolong the life of O. faveolata colonies. The firebreak method yielded the best results of all the techniques tested, and also required the least amount of effort and resources. However, we do not recommend that this treatment alone be used for long-term disease mitigation. Rather, we propose that modifications of this and other treatment options be sought. The results also highlight the need for extended monitoring of CYBD after any treatment, due to the slow but variable rate and pattern of tissue loss in this disease.

Reef-Building Corals as a Tool for Climate Change Research in the Genomics Era

Coral reef ecosystems are among the most biodiverse habitats in the marine realm. They not only contribute with a plethora of ecosystem services, but they also are beneficial to humankind via nurturing marine fisheries and sustaining recreational activities. We will discuss the biology of coral reefs and their ecophysiology including the complex bacterial microbiota associated with them.

Complex interactions between potentially pathogenic, opportunistic, and resident bacteria emerge during infection on a reef-building coral

Increased bacterial diversity on diseased corals can obscure disease etiology and complicate our understanding of pathogenesis. To untangle microbes that may cause white band disease signs from microbes responding to disease, we inoculated healthy Acropora cervicornis corals with an infectious dose from visibly diseased corals. We sampled these dosed corals and healthy controls over time for sequencing of the bacterial 16S region. Endozoicomonas were associated with healthy fragments from 4/10 colonies, dominating microbiomes before dosing and decreasing over time only in corals that displayed disease signs, suggesting a role in disease resistance. We grouped disease-associated bacteria by when they increased in abundance (primary vs secondary) and whether they originated in the dose (colonizers) or the previously healthy corals (responders). We found that all primary responders increased in all dosed corals regardless of final disease state and are therefore unlikely to cause disease signs. In contrast, primary colonizers in the families Pasteurellaceae and Francisellaceae increased solely in dosed corals that ultimately displayed disease signs, and may be infectious foreign bacteria involved in the development of disease signs. Moving away from a static comparison of diseased and healthy bacterial communities, we provide a framework to identify key players in other coral diseases.

Pathobiomes Differ between Two Diseases Affecting Reef Building Coralline Algae

Crustose coralline algae (CCA) are major benthic calcifiers that play crucial roles in coral reef ecosystems. Two diseases affecting CCA have recently been investigated: coralline white band syndrome (CWBS) and coralline white patch disease (CWPD). These diseases can trigger major losses in CCA cover on tropical coral reefs, but their causative agents remain unknown. Here, we provide data from the first investigation of the bacterial communities associated with healthy and diseased CCA tissues. We show that Neogoniolithon mamillare diseased tissues had distinct microbial communities compared to healthy tissues and demonstrate that CWBS and CWPD were associated with different pathobiomes, indicating that they had different disease causations. CWBS tissues were composed of opportunistic bacteria, and the origin of the disease was undetermined. In contrast, a vibrio related to Vibrio tubiashii characterized the CWPD pathobiome, suggesting that it could be a putative disease agent and supporting the case of a temperature dependent disease associated with global warming.

Intraspecific differences in molecular stress responses and coral pathobiome contribute to mortality under bacterial challenge in Acropora millepora

Disease causes significant coral mortality worldwide; however, factors responsible for intraspecific variation in disease resistance remain unclear. We exposed fragments of eight Acropora millepora colonies (genotypes) to putatively pathogenic bacteria (Vibrio spp.). Genotypes varied from zero to >90% mortality, with bacterial challenge increasing average mortality rates 4–6 fold and shifting the microbiome in favor of stress-associated taxa. Constitutive immunity and subsequent immune and transcriptomic responses to the challenge were more prominent in high-mortality individuals, whereas low-mortality corals remained largely unaffected and maintained expression signatures of a healthier condition (i.e., did not launch a large stress response). Our results suggest that lesions appeared due to changes in the coral pathobiome (multiple bacterial species associated with disease) and general health deterioration after the biotic disturbance, rather than the direct activity of any specific pathogen. If diseases in nature arise because of weaknesses in holobiont physiology, instead of the virulence of any single etiological agent, environmental stressors compromising coral condition might play a larger role in disease outbreaks than is currently thought. To facilitate the diagnosis of compromised individuals, we developed and independently cross-validated a biomarker assay to predict mortality based on genes whose expression in asymptomatic individuals coincides with mortality rates.

Compositional shifts in bacterial communities associated with the coral Palythoa caribaeorum due to anthropogenic effects

Corals harbor abundant and diverse prokaryotic communities that may be strongly influenced by human activities, which in turn compromise the normal functioning of coral species and predispose them to opportunistic infections. In this study, we investigated the effect of sewage dumping on the bacterial communities associated with the soft coral Palythoa caribaeorum at two sites in the Brazilian coast. We observed a dominance of bacterial species classified as human pathogens at sites exposed to untreated sewage discharge. The microbial diversity of undisturbed sites was more homogeneous and diverse and showed greater abundance. In addition, bacterial communities differed substantially between the exposed and undisturbed areas. The microbial community associated with the samples collected from the exposed sites revealed the anthropogenic effect caused by organic matter from untreated sewage dumping, with an abundance of pathogenic bacterial species.

Viruses and the origin of microbiome selection and immunity

The last common metazoan ancestor (LCMA) emerged over half a billion years ago. These complex metazoans provided newly available niche space for viruses and microbes. Modern day contemporaries, such as cnidarians, suggest that the LCMA consisted of two cell layers: a basal endoderm and a mucus-secreting ectoderm, which formed a surface mucus layer (SML). Here we propose a model for the origin of metazoan immunity based on external and internal microbial selection mechanisms. In this model, the SML concentrated bacteria and their associated viruses (phage) through physical dynamics (that is, the slower flow fields near a diffusive boundary layer), which selected for mucin-binding capabilities. The concentration of phage within the SML provided the LCMA with an external microbial selective described by the bacteriophage adherence to mucus (BAM) model. In the BAM model, phage adhere to mucus protecting the metazoan host against invading, potentially pathogenic bacteria. The same fluid dynamics that concentrated phage and bacteria in the SML also concentrated eukaryotic viruses. As eukaryotic viruses competed for host intracellular niche space, those viruses that provided the LCMA with immune protection were maintained. If a resident virus became pathogenic or if a non-beneficial infection occurred, we propose that tumor necrosis factor (TNF)-mediated programmed cell death, as well as other apoptosis mechanisms, were utilized to remove virally infected cells. The ubiquity of the mucosal environment across metazoan phyla suggest that both BAM and TNF-induced apoptosis emerged during the Precambrian era and continue to drive the evolution of metazoan immunity.

Seasonal changes in bacterial communities associated with healthy and diseasedPoritescoral in southern Taiwan

We compared the bacterial communities associated with healthy scleractinian coral Porites sp. with those associated with coral infected with pink spot syndrome harvested during summer and winter from waters off the coast of southern Taiwan. Members of the bacterial community associated with the coral were characterized by means of denaturing gradient gel electrophoresis (DGGE) of a short region of the 16S rRNA gene and clone library analysis. Of 5 different areas of the 16S rRNA gene, we demonstrated that the V3 hypervariable region is most suited to represent the coral-associated bacterial community. The DNA sequences of 26 distinct bands extracted from DGGE gels and 269 sequences of the 16S rRNA gene from clone libraries were determined. We found that the communities present in diseased coral were more heterogeneous than the bacterial communities of uninfected coral. In addition, bacterial communities associated with coral harvested in the summer were more diverse than those associated with coral collected in winter, regardless of the health status of the coral. Our study suggested that the compositions of coral-associated bacteria communities are complex, and the population of bacteria varies greatly between seasons and in coral of differing health status.

Multiple opportunistic pathogens can cause a bleaching disease in the red seaweed Delisea pulchra

While macroalgae (or seaweeds) are increasingly recognized to suffer from disease, in most cases the causative agents are unknown. The model macroalga Delisea pulchra is susceptible to a bleaching disease and previous work has identified two epiphytic bacteria, belonging to the Roseobacter clade, that cause bleaching under laboratory conditions. However, recent environmental surveys have shown that these in vitro pathogens are not abundant in naturally bleached D. pulchra, suggesting the presence of other pathogens capable of causing this algal disease. To test this hypothesis, we cultured bacteria that were abundant on bleached tissue across multiple disease events and assessed their ability to cause bleaching disease. We identified the new pathogens Alteromonas sp. BL110, Aquimarina sp. AD1 and BL5 and Agarivorans sp BL7 that are phylogenetically diverse, distinct from the previous two pathogens and can also be found in low abundance in healthy individuals. Moreover, we found that bacterial communities of diseased individuals that were infected with these pathogens were less diverse and more divergent from each other than those of healthy algae. This study demonstrates that multiple and opportunistic pathogens can cause the same disease outcome for D. pulchra and we postulate that such pathogens are more common in marine systems than previously anticipated.

Microbial Dysbiosis: Rethinking Disease in Marine Ecosystems

With growing environmental pressures placed on our marine habitats there is concern that the prevalence and severity of diseases affecting marine organisms will increase. Yet relative to terrestrial systems, we know little about the underlying causes of many of these diseases. Moreover, factors such as saprophytic colonizers and a lack of baseline data on healthy individuals make it difficult to accurately assess the role of specific microbial pathogens in disease states. Emerging evidence in the field of medicine suggests that a growing number of human diseases result from a microbiome imbalance (or dysbiosis), questioning the traditional view of a singular pathogenic agent. Here we discuss the possibility that many diseases seen in marine systems are, similarly, the result of microbial dysbiosis and the rise of opportunistic or polymicrobial infections. Thus, understanding and managing disease in the future will require us to also rethink definitions of disease and pathogenesis for marine systems. We suggest that a targeted, multidisciplinary approach that addresses the questions of microbial symbiosis in both healthy and diseased states, and at that the level of the holobiont, will be key to progress in this area.

Spirochaetes dominate the microbial community associated with the red coral Corallium rubrum on a broad geographic scale

Mass mortality events in populations of the iconic red coral Corallium rubrum have been related to seawater temperature anomalies that may have triggered microbial disease development. However, very little is known about the bacterial community associated with the red coral. We therefore aimed to provide insight into this species’ bacterial assemblages using Illumina MiSeq sequencing of 16S rRNA gene amplicons generated from samples collected at five locations distributed across the western Mediterranean Sea. Twelve bacterial species were found to be consistently associated with the red coral, forming a core microbiome that accounted for 94.6% of the overall bacterial community. This core microbiome was particularly dominated by bacteria of the orders Spirochaetales and Oceanospirillales, in particular the ME2 family. Bacteria belonging to these orders have been implicated in nutrient cycling, including nitrogen, carbon and sulfur. While Oceanospirillales are common symbionts of marine invertebrates, our results identify members of the Spirochaetales as other important dominant symbiotic bacterial associates within Anthozoans.

Caribbean yellow band disease compromises the activity of catalase and glutathione S-transferase in the reef-building coral Orbicella faveolata exposed to anthracene

Healthy and diseased corals are threatened by different anthropogenic sources, such as pollution, a problem expected to become more severe in the near future. Despite the fact that coastal pollution and coral diseases might represent a serious threat to coral reef health, there is a paucity of controlled experiments showing whether the response of diseased and healthy corals to xenobiotics differs. In this study, we exposed healthy and Caribbean yellow band disease (CYBD)-affected Orbicella faveolata colonies to 3 sublethal concentrations of anthracene to test if enzymatic responses to this hydrocarbon were compromised in CYBD-affected tissues. For this, a 2-factorial fully orthogonal design was used in a controlled laboratory bioassay, using tissue condition (2 levels: apparently healthy and diseased) and pollutant concentration (4 levels: experimental control, 10, 30 and 100 ppb concentration) as fixed factors. A permutation-based ANOVA (PERMANOVA) was used to test the effects of condition and concentration on the specific activity of 3 enzymatic biomarkers: catalase, glutathione S-transferase, and glutathione peroxidase. We found a significant interaction between the concentration of anthracene and the colony condition for catalase (Pseudo-F = 3.84, df = 3, p < 0.05) and glutathione S-transferase (Pseudo-F = 3.29, df = 3, p < 0.05). Moreover, our results indicated that the enzymatic response to anthracene in CYBD-affected tissues was compromised, as the activity of these enzymes decreased 3- to 4-fold compared to healthy tissues. These results suggest that under a potential scenario of increasing hydrocarbon coastal pollution, colonies of O. faveolata affected with CYBD might become more vulnerable to the deleterious effects of chemical pollution.

Coral microbial community dynamics in response to anthropogenic impacts near a major city in the central Red Sea

Coral-associated bacteria play an increasingly recognized part in coral health. We investigated the effect of local anthropogenic impacts on coral microbial communities on reefs near Jeddah, the largest city on the Saudi Arabian coast of the central Red Sea. We analyzed the bacterial community structure of water and corals (Pocillopora verrucosa and Acropora hemprichii) at sites that were relatively unimpacted, exposed to sedimentation & local sewage, or in the discharge area of municipal wastewaters. Coral microbial communities were significantly different at impacted sites: in both corals the main symbiotic taxon decreased in abundance. In contrast, opportunistic bacterial families, such as e.g. Vibrionaceae and Rhodobacteraceae, were more abundant in corals at impacted sites. In conclusion, microbial community response revealed a measurable footprint of anthropogenic impacts to coral ecosystems close to Jeddah, even though the corals appeared visually healthy.

Coral-Associated Bacterial Diversity Is Conserved across Two Deep-Sea Anthothela Species

Cold-water corals, similar to tropical corals, contain diverse and complex microbial assemblages. These bacteria provide essential biological functions within coral holobionts, facilitating increased nutrient utilization and production of antimicrobial compounds. To date, few cold-water octocoral species have been analyzed to explore the diversity and abundance of their microbial associates. For this study, 23 samples of the family Anthothelidae were collected from Norfolk (n = 12) and Baltimore Canyons (n = 11) from the western Atlantic in August 2012 and May 2013. Genetic testing found that these samples comprised two Anthothela species (Anthothela grandiflora and Anthothela sp.) and Alcyonium grandiflorum. DNA was extracted and sequenced with primers targeting the V4–V5 variable region of the 16S rRNA gene using 454 pyrosequencing with GS FLX Titanium chemistry. Results demonstrated that the coral host was the primary driver of bacterial community composition. Al. grandiflorum, dominated by Alteromonadales and Pirellulales had much higher species richness, and a distinct bacterial community compared to Anthothela samples. Anthothela species (A. grandiflora and Anthothela sp.) had very similar bacterial communities, dominated by Oceanospirillales and Spirochaetes. Additional analysis of core-conserved bacteria at 90% sample coverage revealed genus level conservation across Anthothela samples. This core included unclassified Oceanospirillales, Kiloniellales, Campylobacterales, and genus Spirochaeta. Members of this core were previously recognized for their functional capabilities in nitrogen cycling and suggest the possibility of a nearly complete nitrogen cycle within Anthothela species. Overall, many of the bacterial associates identified in this study have the potential to contribute to the acquisition and cycling of nutrients within the coral holobiont.

Ostracod (Ostracoda, Crustacea) genomics - Promises and challenges

Ostracods are well-suited model organisms for evolutionary research. Classic genetic techniques have mostly been used for phylogenetic studies on Ostracoda and were somewhat affected by the lack of large numbers of suitable markers. Genomic methods with their huge potential have so far rarely been applied to this group of crustaceans. We provide relevant examples of genomic studies on other organisms to propose future avenues of genomic ostracod research. At the same time, we suggest solutions to the potential problems in ostracods that the application of genomic techniques might present.

Low regeneration of lesions produced by coring in Orbicella faveolata

The extraction of tissue-skeleton cores from coral colonies is a common procedure to study diverse aspects of their biology, water quality or to obtain environmental proxies. Coral species preferred for such studies in Caribbean reefs belong to the genera Orbicella. The long term effects of coring in the coral colony are seldom evaluated and in many Caribbean countries this practice is not regulated. We monitored 50 lesions produced on Orbicella faveolata colonies by the extraction of two centimeter-diameter cores to determine if they were able to heal after a four year period. At the end of the study 4% of the lesions underwent full regeneration, 52% underwent partial regeneration, 14% suffered additional tissue loss but remained surrounded by live tissue, and 30% merged with dead areas of the colonies. Given the low capacity of Orbicella faveolata to regenerate tissue-skeleton lesions, studies that use coring should be regulated and mitigation actions, such as using less destructive techniques and remediation measures after extraction, should be conducted to facilitate tissue regeneration.

RNA-Seq of the Caribbean reef-building coral Orbicella faveolata (Scleractinia-Merulinidae) under bleaching and disease stress expands models of coral innate immunity

Climate change-driven coral disease outbreaks have led to widespread declines in coral populations. Early work on coral genomics established that corals have a complex innate immune system, and whole-transcriptome gene expression studies have revealed mechanisms by which the coral immune system responds to stress and disease. The present investigation expands bioinformatic data available to study coral molecular physiology through the assembly and annotation of a reference transcriptome of the Caribbean reef-building coral, Orbicella faveolata. Samples were collected during a warm water thermal anomaly, coral bleaching event and Caribbean yellow band disease outbreak in 2010 in Puerto Rico. Multiplex sequencing of RNA on the Illumina GAIIx platform and de novo transcriptome assembly by Trinity produced 70,745,177 raw short-sequence reads and 32,463 O. faveolata transcripts, respectively. The reference transcriptome was annotated with gene ontologies, mapped to KEGG pathways, and a predicted proteome of 20,488 sequences was generated. Protein families and signaling pathways that are essential in the regulation of innate immunity across Phyla were investigated in-depth. Results were used to develop models of evolutionarily conserved Wnt, Notch, Rig-like receptor, Nod-like receptor, and Dicer signaling. O. faveolata is a coral species that has been studied widely under climate-driven stress and disease, and the present investigation provides new data on the genes that putatively regulate its immune system.

Microbial transcriptome profiling of black band disease in a Faviid coral during a seasonal disease peak

The etiology of black band disease (BBD), a persistent, globally distributed coral disease characterized by a dark microbial mat, is still unclear. A metatranscriptomics approach was used to unravel the roles of the major mat constituents in the disease process. By comparing the transcriptomes of the mat constituents with those of the surface microbiota of diseased and healthy corals, we showed a shift in bacterial composition and function in BBD-affected corals. mRNA reads of Cyanobacteria, Bacteroidetes and Firmicutes phyla were prominent in the BBD mat. Cyanobacterial adenosylhomocysteinase, involved in cyanotoxin production, was the most transcribed gene in the band consortium. Pathogenic and non-pathogenic forms of Vibrio spp., mainly transcribing the thiamine ABC transporter, were abundant and highly active in both the band and surface tissues. Desulfovibrio desulfuricans was the primary producer of sulfide in the band. Members of the Bacilli class expressed high levels of rhodanese, an enzyme responsible for cyanide and sulfide detoxification. These results offer a first look at the varied functions of the microbiota in the disease mat and surrounding coral surface and enabled us to develop an improved functional model for this disease.

Spatial Homogeneity of Bacterial Communities Associated with the Surface Mucus Layer of the Reef-Building Coral Acropora palmata

Coral surface mucus layer (SML) microbiota are critical components of the coral holobiont and play important roles in nutrient cycling and defense against pathogens. We sequenced 16S rRNA amplicons to examine the structure of the SML microbiome within and between colonies of the threatened Caribbean reef-building coral Acropora palmata in the Florida Keys. Samples were taken from three spatially distinct colony regions—uppermost (high irradiance), underside (low irradiance), and the colony base—representing microhabitats that vary in irradiance and water flow. Phylogenetic diversity (PD) values of coral SML bacteria communities were greater than surrounding seawater and lower than adjacent sediment. Bacterial diversity and community composition was consistent among the three microhabitats. Cyanobacteria, Bacteroidetes, Alphaproteobacteria, and Proteobacteria, respectively were the most abundant phyla represented in the samples. This is the first time spatial variability of the surface mucus layer of A. palmata has been studied. Homogeneity in the microbiome of A. palmata contrasts with SML heterogeneity found in other Caribbean corals. These findings suggest that, during non-stressful conditions, host regulation of SML microbiota may override diverse physiochemical influences induced by the topographical complexity of A. palmata. Documenting the spatial distribution of SML microbes is essential to understanding the functional roles these microorganisms play in coral health and adaptability to environmental perturbations.

Development and application of molecular biomarkers for characterizing Caribbean Yellow Band Disease in Orbicella faveolata

Molecular stress responses associated with coral diseases represent an under-studied area of cnidarian transcriptome investigations. Caribbean Yellow Band Disease (CYBD) is considered a disease of Symbiodinium within the tissues of the coral host Orbicella faveolata. There is a paucity of diagnostic tools to assist in the early detection and characterization of coral diseases. The validity of a diagnostic test is determined by its ability to distinguish host organisms that have the disease from those that do not. The ability to detect and identify disease-affected tissue before visible signs of the disease are evident would then be a useful diagnostic tool for monitoring and managing disease outbreaks. Representational Difference Analysis (RDA) was utilized to isolate differentially expressed genes in O. faveolata exhibiting CYBD. Preliminary screening of RDA products identified a small number of genes of interest (GOI) which included an early growth response factor and ubiquitin ligase from the coral host as well as cytochrome oxidase from the algal symbiont. To further characterize the specificity of response, quantitative real-time PCR (qPCR) was utilized to compare the expression profiles of these GOIs within diseased tissues (visible lesions), tissues that precede visible lesions by 2–4 cm (transition area), and tissues from healthy-looking colonies with no signs of disease. Results show there are distinctive differences in the expression profiles of these three GOIs within each tissue examined. Collectively, this small suite of GOIs can provide a molecular “finger print” which is capable of differentiating between infected and uninfected colonies on reefs where CYBD is known to occur.

Microbiome shifts and the inhibition of quorum sensing by Black Band Disease cyanobacteria

Disruption of the microbiome often correlates with the appearance of disease symptoms in metaorganisms such as corals. In Black Band Disease (BBD), a polymicrobial disease consortium dominated by the filamentous cyanobacterium Roseofilum reptotaenium displaces members of the epibiotic microbiome. We examined both normal surface microbiomes and BBD consortia on Caribbean corals and found that the microbiomes of healthy corals were dominated by Gammaproteobacteria, in particular Halomonas spp., and were remarkably stable across spatial and temporal scales. In contrast, the microbial community structure in black band consortia was more variable and more diverse. Nevertheless, deep sequencing revealed that members of the disease consortium were present in every sampled surface microbiome of Montastraea, Orbicella and Pseudodiploria corals, regardless of the health status. Within the BBD consortium, we identified lyngbic acid, a cyanobacterial secondary metabolite. It strongly inhibited quorum sensing (QS) in the Vibrio harveyi QS reporters. The effects of lyngbic acid on the QS reporters depended on the presence of the CAI-1 receptor CqsS. Lyngbic acid inhibited luminescence in native coral Vibrio spp. that also possess the CAI-1-mediated QS. The effects of this naturally occurring QS inhibitor on bacterial regulatory networks potentially contribute to the structuring of the interactions within BBD consortia.

Pyrosequencing of the bacteria associated with Platygyra carnosus corals with skeletal growth anomalies reveals differences in bacterial community composition in apparently healthy and diseased tissues

Corals are rapidly declining globally due to coral diseases. Skeletal growth anomalies (SGA) or "coral tumors" are a group of coral diseases that affect coral reefs worldwide, including Hong Kong waters in the Indo-Pacific region. To better understand how bacterial communities may vary in corals with SGA, for the first time, we examined the bacterial composition associated with the apparently healthy and the diseased tissues of SGA-affected Platgyra carnosus using 16S ribosomal rRNA gene pyrosequencing. Taxonomic analysis revealed Proteobacteria, Bacteroidetes, Cyanobacteria, and Actinobacteria as the main phyla in both the apparently healthy and the diseased tissues. A significant difference in the bacterial community composition was observed between the two conditions at the OTU level. Diseased tissues were associated with higher abundances of Acidobacteria and Gemmatimonadetes, and a lower abundance of Spirochaetes. Several OTUs belonging to Rhodobacteraceae, Rhizobiales, Gammaproteobacteria, and Cytophaga-Flavobacterium-Bacteroidetes (CFB) were strongly associated with the diseased tissues. These groups of bacteria may contain potential pathogens involved with the development of SGA or opportunistic secondary or tertiary colonizers that proliferated upon the health-compromised coral host. We suggest that these bacterial groups to be further studied based on inoculation experiments and testing of Koch's postulates in efforts to understand the etiology and progression of SGA.

De Novo Assembly and Characterization of Four Anthozoan (Phylum Cnidaria) Transcriptomes

Many nonmodel species exemplify important biological questions but lack the sequence resources required to study the genes and genomic regions underlying traits of interest. Reef-building corals are famously sensitive to rising seawater temperatures, motivating ongoing research into their stress responses and long-term prospects in a changing climate. A comprehensive understanding of these processes will require extending beyond the sequenced coral genome (Acropora digitifera) to encompass diverse coral species and related anthozoans. Toward that end, we have assembled and annotated reference transcriptomes to develop catalogs of gene sequences for three scleractinian corals (Fungia scutaria, Montastraea cavernosa, Seriatopora hystrix) and a temperate anemone (Anthopleura elegantissima). High-throughput sequencing of cDNA libraries produced ~20-30 million reads per sample, and de novo assembly of these reads produced ~75,000-110,000 transcripts from each sample with size distributions (mean ~1.4 kb, N50 ~2 kb), comparable to the distribution of gene models from the coral genome (mean ~1.7 kb, N50 ~2.2 kb). Each assembly includes matches for more than half the gene models from A. digitifera (54-67%) and many reasonably complete transcripts (~5300-6700) spanning nearly the entire gene (ortholog hit ratios ≥0.75). The catalogs of gene sequences developed in this study made it possible to identify hundreds to thousands of orthologs across diverse scleractinian species and related taxa. We used these sequences for phylogenetic inference, recovering known relationships and demonstrating superior performance over phylogenetic trees constructed using single mitochondrial loci. The resources developed in this study provide gene sequences and genetic markers for several anthozoan species. To enhance the utility of these resources for the research community, we developed searchable databases enabling researchers to rapidly recover sequences for genes of interest. Our analysis of de novo assembly quality highlights metrics that we expect will be useful for evaluating the relative quality of other de novo transcriptome assemblies. The identification of orthologous sequences and phylogenetic reconstruction demonstrates the feasibility of these methods for clarifying the substantial uncertainties in the existing scleractinian phylogeny.

Identification of Candidate Coral Pathogens on White Band Disease-Infected Staghorn Coral

Bacterial diseases affecting scleractinian corals pose an enormous threat to the health of coral reefs, yet we still have a limited understanding of the bacteria associated with coral diseases. White band disease is a bacterial disease that affects the two Caribbean acroporid corals, the staghorn coral Acropora cervicornis and the elkhorn coral A. palmate. Species of Vibrio and Rickettsia have both been identified as putative WBD pathogens. Here we used Illumina 16S rRNA gene sequencing to profile the bacterial communities associated with healthy and diseased A. cervicornis collected from four field sites during two different years. We also exposed corals in tanks to diseased and healthy (control) homogenates to reduce some of the natural variation of field-collected coral bacterial communities. Using a combination of multivariate analyses, we identified community-level changes between diseased and healthy corals in both the field-collected and tank-exposed datasets. We then identified changes in the abundances of individual operational taxonomic units (OTUs) between diseased and healthy corals. By comparing the diseased and healthy-associated bacteria in field-collected and tank-exposed corals, we were able to identify 16 healthy-associated OTUs and 106 consistently disease-associated OTUs, which are good candidates for putative WBD pathogens. A large percentage of these disease-associated OTUs belonged to the order Flavobacteriales. In addition, two of the putative pathogens identified here belong to orders previously suggested as WBD pathogens: Vibronales and Rickettsiales.

Dual Transcriptomic Profiling of Host and Microbiota during Health and Disease in Pediatric Asthma

BACKGROUND

High-throughput sequencing (HTS) analysis of microbial communities from the respiratory airways has heavily relied on the 16S rRNA gene. Given the intrinsic limitations of this approach, airway microbiome research has focused on assessing bacterial composition during health and disease, and its variation in relation to clinical and environmental factors, or other microbiomes. Consequently, very little effort has been dedicated to describing the functional characteristics of the airway microbiota and even less to explore the microbe-host interactions. Here we present a simultaneous assessment of microbiome and host functional diversity and host-microbe interactions from the same RNA-seq experiment, while accounting for variation in clinical metadata.

METHODS

Transcriptomic (host) and metatranscriptomic (microbiota) sequences from the nasal epithelium of 8 asthmatics and 6 healthy controls were separated in silico and mapped to available human and NCBI-NR protein reference databases. Human genes differentially expressed in asthmatics and controls were then used to infer upstream regulators involved in immune and inflammatory responses. Concomitantly, microbial genes were mapped to metabolic databases (COG, SEED, and KEGG) to infer microbial functions differentially expressed in asthmatics and controls. Finally, multivariate analysis was applied to find associations between microbiome characteristics and host upstream regulators while accounting for clinical variation.

RESULTS AND DISCUSSION

Our study showed significant differences in the metabolism of microbiomes from asthmatic and non-asthmatic children for up to 25% of the functional properties tested. Enrichment analysis of 499 differentially expressed host genes for inflammatory and immune responses revealed 43 upstream regulators differentially activated in asthma. Microbial adhesion (virulence) and Proteobacteria abundance were significantly associated with variation in the expression of the upstream regulator IL1A; suggesting that microbiome characteristics modulate host inflammatory and immune systems during asthma.