In-situ effects of eutrophication and overfishing on physiology and bacterial diversity of the red sea coral Acropora hemprichii

The microbiome dynamics and interaction of endosymbiotic Symbiodiniaceae and fungi are associated with thermal bleaching susceptibility of coral holobionts

The thermal bleaching percentage of coral holobionts shows interspecific differences under heat-stress conditions, which are closely related to the coral-associated microbiome. However, the ecological effects of community dynamics and interactions between Symbiodiniaceae and fungi on coral thermal bleaching susceptibility remain unclear. In this study, we analyzed the diversity, community structure, functions, and potential interaction of Symbiodiniaceae and fungi among 18 coral species from a high thermal bleaching risk atoll using next-generation sequencing. The results showed that heat-tolerant C3u sub-clade and Durusdinium dominated the Symbiodiniaceae community of corals and that there were no core amplicon sequence variants in the coral-associated fungal community. Fungal richness and the abundance of confirmed functional animal-plant pathogens were significantly positively correlated with the coral thermal bleaching percentage. Fungal indicators, including Didymellaceae, Chaetomiaceae, Schizophyllum, and Colletotrichum, were identified in corals. Each coral species had a complex Symbiodiniaceae-fungi interaction network (SFIN), which was driven by the dominant Symbiodiniaceae sub-clades. The SFINs of coral holobionts with low thermal bleaching susceptibility exhibited low complexity and high betweenness centrality. These results indicate that the extra heat tolerance of coral in Huangyan Island may be linked to the high abundance of heat-tolerant Symbiodiniaceae. Fungal communities have high interspecific flexibility, and the increase of fungal diversity and pathogen abundance was correlated with higher thermal bleaching susceptibility of corals. Moreover, fungal indicators were associated with the degrees of coral thermal bleaching susceptibility, including both high and intermediate levels. The topological properties of SFINs suggest that heat-tolerant coral have limited fungal parasitism and strong microbial network resilience.IMPORTANCEGlobal warming and enhanced marine heatwaves have led to a rapid decline in coral reef ecosystems worldwide. Several studies have focused on the impact of coral-associated microbiomes on thermal bleaching susceptibility in corals; however, the ecological functions and interactions between Symbiodiniaceae and fungi remain unclear. We investigated the microbiome dynamics and potential interactions of Symbiodiniaceae and fungi among 18 coral species in Huangyan Island. Our study found that the Symbiodiniaceae community of corals was mainly composed of heat-tolerant C3u sub-clade and Durusdinium. The increase in fungal diversity and pathogen abundance has close associations with higher coral thermal bleaching susceptibility. We first constructed an interaction network between Symbiodiniaceae and fungi in corals, which indicated that restricting fungal parasitism and strong interaction network resilience would promote heat acclimatization of corals. Accordingly, this study provides insights into the role of microorganisms and their interaction as drivers of interspecific differences in coral thermal bleaching.

Water depth outweighs reef condition in shaping non-geniculate coralline algae-associated microbial communities in coral reefs: A case study from Thailand

Red calcified non-geniculate coralline algae (NGCA) provide habitat structures, stabilize reef structures, and foster coral larval settlement and metamorphosis. Moreover, the microbes associated with NGCA are dependent on the NGCA host species and are affected by environmental factors; however, little is known about the influence of reef conditions and depth gradients on the associated microbial communities and NGCA. In this study, we collected NGCA under different reef conditions and depth gradients and characterized the microbial communities using the V3-V4 hypervariable regions of the 16S rRNA gene. Metagenomic analysis revealed 2 domains, 51 phyla, 123 classes, and 210 genera. The NGCA-associated bacterial communities were dominated by Proteobacteria, Bacteroidetes, Chloroflexi, Actinobacteria, and Acidobacteriota. Gammaproteobacteria and Alphaproteobacteria were the most abundant bacterial classes. Differences in microbial diversity and richness were not apparent between reef conditions and depth gradients. However, there was a significant difference in bacterial evenness among the depth gradients. The bacterial abundance associated with NGCA was greater in deep zones than in shallow zones. The shallow zone exhibited a greater relative abundance of all gene functions than the deep zone, indicating differences in the distribution of gene functions. This study showed that the microbial communities associated with red calcified NGCA are diverse, and that the depth gradient affects their abundance and evenness, highlighting the need for further research to understand the functional roles of these microbial communities in coral reef conservation.

Unveiling microbiome changes in Mediterranean octocorals during the 2022 marine heatwaves: quantifying key bacterial symbionts and potential pathogens

BACKGROUND

Climate change has accelerated the occurrence and severity of heatwaves in the Mediterranean Sea and poses a significant threat to the octocoral species that form the foundation of marine animal forests (MAFs). As coral health intricately relies on the symbiotic relationships established between corals and microbial communities, our goal was to gain a deeper understanding of the role of bacteria in the observed tissue loss of key octocoral species following the unprecedented heatwaves in 2022.

RESULTS

Using amplicon sequencing and taxon-specific qPCR analyses, we unexpectedly found that the absolute abundance of the major bacterial symbionts, Spirochaetaceae (C. rubrum) and Endozoicomonas (P. clavata), remained, in most cases, unchanged between colonies with 0% and 90% tissue loss. These results suggest that the impairment of coral health was not due to the loss of the main bacterial symbionts. However, we observed a significant increase in the total abundance of bacterial opportunists, including putative pathogens such as Vibrio, which was not evident when only their relative abundance was considered. In addition, there was no clear relation between bacterial symbiont loss and the intensity of thermal stress, suggesting that factors other than temperature may have influenced the differential response of octocoral microbiomes at different sampling sites.

CONCLUSIONS

Our results indicate that tissue loss in octocorals is not directly caused by the decline of the main bacterial symbionts but by the proliferation of opportunistic and pathogenic bacteria. Our findings thus underscore the significance of considering both relative and absolute quantification approaches when evaluating the impact of stressors on coral microbiome as the relative quantification does not accurately depict the actual changes in the microbiome. Consequently, this research enhances our comprehension of the intricate interplay between host organisms, their microbiomes, and environmental stressors, while offering valuable insights into the ecological implications of heatwaves on marine animal forests. Video Abstract.

Holobiont responses of mesophotic precious red coral Corallium rubrum to thermal anomalies

Marine heat waves (MHWs) have increased in frequency and intensity worldwide, causing mass mortality of benthic organisms and loss of biodiversity in shallow waters. The Mediterranean Sea is no exception, with shallow populations of habitat-forming octocorals facing the threat of local extinction. The mesophotic zone, which is less affected by MHWs, may be of ecological importance in conservation strategies for these species. However, our understanding of the response of mesophotic octocoral holobionts to changes in seawater temperature remains limited. To address this knowledge gap, we conducted a study on an iconic Mediterranean octocoral, the red coral Corallium rubrum sampled at 60 m depth and 15 °C. We exposed the colonies to temperatures they occasionally experience (18 °C) and temperatures that could occur at the end of the century if global warming continues (21 °C). We also tested their response to extremely cold and warm temperatures (12 °C and 24 °C). Our results show a high tolerance of C. rubrum to a two-month long exposure to temperatures ranging from 12 to 21 °C as no colony showed signs of tissue loss, reduced feeding ability, stress-induced gene expression, or disruption of host-bacterial symbioses. At 24 °C, however, we measured a sharp decrease in the relative abundance of Spirochaetaceae, which are the predominant bacterial symbionts under healthy conditions, along with a relative increase in Vibrionaceae. Tissue loss and overexpression of the tumor necrosis factor receptor 1 gene were also observed after two weeks of exposure. In light of ongoing global warming, our study helps predict the consequences of MHWs on mesophotic coralligenous reefs and the biodiversity that depends on them.

Ecology of Endozoicomonadaceae in three coral genera across the Pacific Ocean

Health and resilience of the coral holobiont depend on diverse bacterial communities often dominated by key marine symbionts of the Endozoicomonadaceae family. The factors controlling their distribution and their functional diversity remain, however, poorly known. Here, we study the ecology of Endozoicomonadaceae at an ocean basin-scale by sampling specimens from three coral genera (Pocillopora, Porites, Millepora) on 99 reefs from 32 islands across the Pacific Ocean. The analysis of 2447 metabarcoding and 270 metagenomic samples reveals that each coral genus harbored a distinct new species of Endozoicomonadaceae. These species are composed of nine lineages that have distinct biogeographic patterns. The most common one, found in Pocillopora, appears to be a globally distributed symbiont with distinct metabolic capabilities, including the synthesis of amino acids and vitamins not produced by the host. The other lineages are structured partly by the host genetic lineage in Pocillopora and mainly by the geographic location in Porites. Millepora is more rarely associated to Endozoicomonadaceae. Our results show that different coral genera exhibit distinct strategies of host-Endozoicomonadaceae associations that are defined at the bacteria lineage level.

Prevalence of differential microbiome in healthy, diseased and nipped colonies of corals, Porites lutea in the Gulf of Kachchh, north-west coast of India

Coral reefs are constantly subjected to multiple stresses like diseases and fish predation, which can profoundly influence the coral microbiome. This study investigated the differences in bacterial community structure of healthy, white syndrome affected and blenny nipped coral colonies of Porites lutea, collected from the coral reefs of Gulf of Kachchh, north-west coast of India. Present study observed that the stressed coral colonies harbored more OTUs and contained higher diversity values compared to healthy corals colonies. Similarly, beta diversity analysis indicated the dissimilarities among the three coral samples analyzed. Though the taxonomy analysis indicated bacterial phyla like Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria among the entire coral samples studied, there was a variation in their relative abundances. Huge variations were observed in the relative dominance at the bacterial genera level. About 13phyla and 11 genera was identified in healthy coral. The PBN sample was found to contain Proteobacteria, Cyanobacteria, Verrucomicrobia, and Lentisphaerae as dominant phyla and Endozoicomonas, Dyella, Woeseia, and Winogradskyella as dominant genera. The PWS sample contained Proteobacteria, Lentisphaerae, Spirochaetes, and Tenericutes as dominant phyla and Endozoicomonas, Arcobacter, Sunxiuqinia, and Carboxylicivirgia as dominant genera. Among the healthy samples, sequences belonging to Uncultured Rhodospirillaceae were dominant, while Woeseia and sequences belonging to Uncultured Rhodovibrionaceae were dominant among the blenny nipped white syndrome infected corals. Although any previously established pathogen was not identified, present study revealed the presence of a potentially pathogenic bacterium, Arcobacter, among the diseased corals. It also demonstrated a dynamic microbiome among the Porites lutea colonies on subjecting to various stresses.

The widely distributed soft coral Xenia umbellata exhibits high resistance against phosphate enrichment and temperature increase

Both global and local factors affect coral reefs worldwide, sometimes simultaneously. An interplay of these factors can lead to phase shifts from hard coral dominance to algae or other invertebrates, particularly soft corals. However, most studies have targeted the effects of single factors, leaving pronounced knowledge gaps regarding the effects of combined factors on soft corals. Here, we investigated the single and combined effects of phosphate enrichment (1, 2, and 8 μM) and seawater temperature increase (26 to 32 °C) on the soft coral Xenia umbellata by quantifying oxygen fluxes, protein content, and stable isotope signatures in a 5-week laboratory experiment. Findings revealed no significant effects of temperature increase, phosphate enrichment, and the combination of both factors on oxygen fluxes. However, regardless of the phosphate treatment, total protein content and carbon stable isotope ratios decreased significantly by 62% and 7% under temperature increase, respectively, suggesting an increased assimilation of their energy reserves. Therefore, we hypothesize that heterotrophic feeding may be important for X. umbellata to sustain their energy reserves under temperature increase, highlighting the advantages of a mixotrophic strategy. Overall, X. umbellata shows a high tolerance towards changes in global and local factors, which may explain their competitive advantage observed at many Indo-Pacific reef locations.

The Effect of Co-Culture of Two Coral Species on Their Bacterial Composition Under Captive Environments

Coral symbionts are important members of the coral holobiont, and coral bacterial flora are essential in host health maintenance and coral conservation. Coral symbionts are affected by various environmental factors, such as seawater temperature, pH, and salinity. Although physicochemical and chemical factors have been highlighted as possible causes of these effects, the effects of water flow and the co-culture of different species corals have not been elucidated. In this study, we designed an artificial rearing environment to examine the impact of environmental and biological factors on Acropora tenuis, one of the major coral species in Okinawa, and Montipora digitata, during their co-culture. We intervened with the water flow to reveal that the movement of the rearing environment alters the bacterial flora of A. tenuis. During the rearing under captive environment, the alpha diversity of the coral microbiota increased, suggesting the establishment of rare bacteria from the ocean. No differences in the bacterial composition between the control and water flow groups were observed under the rearing conditions. However, the structure of the bacterial flora was significantly different in the co-culture group. Comparison of bacterial community succession strongly suggested that the differences observed were due to the suppressed transmission of bacteria from the ocean in the co-culture group. These results enhance our understanding of interactions between corals and shed light on the importance of regional differences and bacterial composition of coral flora.

Population Differences and Host Species Predict Variation in the Diversity of Host-Associated Microbes in Hydra

Most animals co-exist with diverse host-associated microbial organisms that often form complex communities varying between individuals, habitats, species and higher taxonomic levels. Factors driving variation in the diversity of host-associated microbes are complex and still poorly understood. Here, we describe the bacterial composition of field-collected Hydra, a freshwater cnidarian that forms stable associations with microbial species in the laboratory and displays complex interactions with components of the microbiota. We sampled Hydra polyps from 21 Central European water bodies and identified bacterial taxa through 16S rRNA sequencing. We asked whether diversity and taxonomic composition of host-associated bacteria depends on sampling location, habitat type, host species or host reproductive mode (sexual vs. asexual). Bacterial diversity was most strongly explained by sampling location, suggesting that the source environment plays an important role in the assembly of bacterial communities associated with Hydra polyps. We also found significant differences between host species in their bacterial composition that partly mirrored variations observed in lab strains. Furthermore, we detected a minor effect of host reproductive mode on bacterial diversity. Overall, our results suggest that extrinsic (habitat identity) factors predict the diversity of host-associated bacterial communities more strongly than intrinsic (species identity) factors, however, only a combination of both factors determines microbiota composition in Hydra.

Determining the Composition of Resident and Transient Members of the Oyster Microbiome

To better understand how complex microbial communities become assembled on eukaryotic hosts, it is essential to disentangle the balance between stochastic and deterministic processes that drive their assembly. Deterministic processes can create consistent patterns of microbiome membership that result in persistent resident communities, while stochastic processes can result in random fluctuation of microbiome members that are transient with regard to their association to the host. We sampled oyster reefs from six different populations across the east coast of the United States. At each site we collected gill tissues for microbial community analysis and additionally collected and shipped live oysters to Northeastern University where they were held in a common garden experiment. We then examined the microbiome shifts in gill tissues weekly for 6 weeks using 16S rRNA gene amplicon sequencing. We found a strong population-specific signal in the microbial community composition of field-sampled oysters. Surprisingly, the oysters sampled during the common garden experiment maintained compositionally distinct gill-associated microbial communities that reflected their wild population of origin, even after rearing them in a common garden for several weeks. This indicates that oyster gill-associated microbiota are predominantly composed of resident microbes specific to host population, rather than being a reflection of their immediate biotic and abiotic surroundings. However, certain bacterial taxa tended to appear more frequently on individuals from different populations than on individuals from the same population, indicating that there is a small portion of the gill microbiome that is transient and is readily exchanged with the environmental pool of microbes. Regardless, the majority of gill-associated microbes were resident members that were specific to each oyster population, suggesting that there are strong deterministic factors that govern a large portion of the gill microbiome. A small portion of the microbial communities, however, was transient and moved among oyster populations, indicating that stochastic assembly also contributes to the oyster gill microbiome. Our results are relevant to the oyster aquaculture industry and oyster conservation efforts because resident members of the oyster microbiome may represent microbes that are important to oyster health and some of these key members vary depending on oyster population.

The effect of thermal stress on the physiology and bacterial communities of two key Mediterranean gorgonians

Gorgonians are important habitat-providing species in the Mediterranean Sea, but their populations are declining due to microbial diseases and repeated mass mortality events caused by summer heat waves. Elevated seawater temperatures may impact the stress tolerance and disease resistance of gorgonians and lead to disturbances in their microbiota. However, our knowledge of the biological response of the gorgonian holobiont (i.e., the host and its microbiota) to thermal stress remains limited. Here, we investigated how the holobiont of two gorgonian species (Paramuricea clavata and Eunicella cavolini) are affected throughout a 7-week thermal stress event by following both the corals’ physiology and the composition of their bacterial communities. We found that P. clavata was more sensitive to elevated seawater temperatures than E. cavolini, showing a greater loss in energy reserves, reduced feeding ability, and partial mortality. This lower thermotolerance may be linked to the ∼20× lower antioxidant defense capacity in P. clavata compared with E. cavolini. In the first 4 weeks of thermal stress, we also observed minor shifts in the microbiota of both species, suggesting that the microbiota likely plays a limited role in thermal acclimation of the holobiont. However, major stochastic changes occurred later on in some colonies, which were of a transient nature in E. cavolini, but were linked to partial colony mortality in P. clavata. Overall, our results show significant, but differential, effects of thermal stress on the holobionts of both E. cavolini and P. clavata and predict potentially severe impacts on gorgonian populations under future climate scenarios.

IMPORTANCE In the Mediterranean Sea, the tree-shaped gorgonian corals form large forests that provide a place to live for many species. Because of this important ecological role, it is crucial to understand how common habitat-forming gorgonians, like Eunicella cavolini and Paramuricea clavata, are affected by high seawater temperatures that are expected in the future due to climate change. We found that both species lost biomass, but P. clavata was more affected, being also unable to feed and showing signs of mortality. The microbiota of both gorgonians also changed substantively under high temperatures. Although this could be linked to partial colony mortality in P. clavata, the changes were temporary in E. cavolini. The overall higher resistance of E. cavolini may be related to its much higher antioxidant defense levels than P. clavata. Climate change may thus have severe impacts on gorgonian populations and the habitats they provide.

Extra high superoxide dismutase in host tissue is associated with improving bleaching resistance in "thermal adapted" and Durusdinium trenchii-associating coral

Global warming threatens reef-building corals with large-scale bleaching events; therefore, it is important to discover potential adaptive capabilities for increasing their temperature resistance before it is too late. This study presents two coral species (Platygyra verweyi and Isopora palifera) surviving on a reef having regular hot water influxes via a nearby nuclear power plant that exhibited completely different bleaching susceptibilities to thermal stress, even though both species shared several so-called "winner" characteristics (e.g., containing Durusdinium trenchii, thick tissue, etc.). During acute heating treatment, algal density did not decline in P. verweyi corals within three days of being directly transferred from 25 to 31 °C; however, the same treatment caused I. palifera to lose < 70% of its algal symbionts within 24 h. The most distinctive feature between the two coral species was an overwhelmingly higher constitutive superoxide dismutase (ca. 10-fold) and catalase (ca. 3-fold) in P. verweyi over I. palifera. Moreover, P. verweyi also contained significantly higher saturated and lower mono-unsaturated fatty acids, especially a long-chain saturated fatty acid (C22:0), than I. palifera, and was consistently associated with the symbiotic bacteria Endozoicomonas, which was not found in I. palifera. However, antibiotic treatment and inoculation tests did not support Endozoicomonas having a direct contribution to thermal resistance. This study highlights that, besides its association with a thermally tolerable algal symbiont, a high level of constitutive antioxidant enzymes in the coral host is crucial for coral survivorship in the more fluctuating and higher temperature environments.

Naturally occurring fire coral clones demonstrate a genetic and environmental basis of microbiome composition

Coral microbiomes are critical to holobiont functioning, but much remains to be understood about how prevailing environment and host genotype affect microbial communities in ecosystems. Resembling human identical twin studies, we examined bacterial community differences of naturally occurring fire coral clones within and between contrasting reef habitats to assess the relative contribution of host genotype and environment to microbiome structure. Bacterial community composition of coral clones differed between reef habitats, highlighting the contribution of the environment. Similarly, but to a lesser extent, microbiomes varied across different genotypes in identical habitats, denoting the influence of host genotype. Predictions of genomic function based on taxonomic profiles suggest that environmentally determined taxa supported a functional restructuring of the microbial metabolic network. In contrast, bacteria determined by host genotype seemed to be functionally redundant. Our study suggests microbiome flexibility as a mechanism of environmental adaptation with association of different bacterial taxa partially dependent on host genotype.

The diversity and metabolic potential of the microbial functional gene associated with Porites pukoensis

Coral reef ecosystems usually distribute in oligotrophic tropical and subtropical marine environments, but they possess great biodiversity and high productivity. It may attribute to its efficient internal nutrient cycle system. However, the knowledge of functional microbial community structure is still limited. In this study, both functional gene array (Geochip 5.0) and nifH Illumina sequencing were used to profile the overall functional genes and diazotrophic communities associated with coral Porites pukoensis. More than 7500 microbial functional genes were detected from archaea, bacteria, and fungi. Most of these genes are related to the transformation of carbon, nitrogen, sulfur, and phosphorus, providing evidence that microbes in the coral holobiont play important roles in the biogeochemical cycle of coral reef ecosystems. Our results indicated a high diversity of diazotrophs associated with corals. The dominant diazotrophic groups were related to phyla Alphaproteobacteria, Deltaproteobacteria, Cyanobacteria, and Gammaproteobacteria. And the dominant diazotrophic communities were divided into four clusters. They were affiliated with nifH sequences from genera Zymomonas, Halorhodospira, Leptolyngbya, Trichormus, and Desulfovibrio, indicating these groups may play a more important role in the nitrogen-fixing process in the coral holobiont. This study revealed functional gene diversity and suggested the roles they played in the biogeochemical cycling of the coral holobiont.

Symbiotic Associations in Ascidians: Relevance for Functional Innovation and Bioactive Potential

Associations between different organisms have been extensively described in terrestrial and marine environments. These associations are involved in roles as diverse as nutrient exchanges, shelter or adaptation to adverse conditions. Ascidians are widely dispersed marine invertebrates associated to invasive behaviours. Studying their microbiomes has interested the scientific community, mainly due to its potential for bioactive compounds production-e.g., ET-73 (trabectedin, Yondelis), an anticancer drug. However, these symbiotic interactions embrace several environmental and biological functions with high ecological relevance, inspiring diverse biotechnological applications. We thoroughly reviewed microbiome studies (microscopic to metagenomic approaches) of around 171 hosts, worldwide dispersed, occurring at different domains of life (Archaea, Bacteria, Eukarya), to illuminate the functions and bioactive potential of associated organisms in ascidians. Associations with Bacteria are the most prevalent, namely with Cyanobacteria, Proteobacteria, Bacteroidetes, Actinobacteria and Planctomycetes phyla. The microbiomes of ascidians belonging to Aplousobranchia order have been the most studied. The integration of worldwide studies characterizing ascidians' microbiome composition revealed several functions including UV protection, bioaccumulation of heavy metals and defense against fouling or predators through production of natural products, chemical signals or competition. The critical assessment and characterization of these communities is extremely valuable to comprehend their biological/ecological role and biotechnological potential.

Shifts in abundance and network complexity of coral bacteria in response to elevated ammonium stress

Coral bacteria are highly dynamic and acutely affected by host health and environmental conditions. However, there is limited knowledge of how the dynamics of coral-associated bacterial communities and interactions among bacterial members change in response to dissolved inorganic nutrient stressors. Here, we used high-throughput sequencing of the 16S rRNA gene to examine dynamic changes in coral-associated bacterial communities under elevated ammonium stress. Short-term exposure to high levels of ammonium does not significantly harm coral holobiont. Physiological parameters such as carbohydrate, chlorophyll a, and lipid content of coral holobiont were not affected. After three weeks of elevated ammonium stress, however, the coral-associated bacterial community changed significantly. The abundance of certain bacterial populations increased significantly, with enrichment of pathogenic and opportunistic bacteria and a decrease in defensive and core bacteria. Keystone bacterial species in the co-occurrence network changed considerably. Under elevated ammonium stress, the abundance of keystone species associated with corals was lower and the complexity of keystone bacterial relationships decreased significantly. Our results indicate that bacteria respond to elevated ammonium stress through changes in abundance and co-occurrence among bacterial members. This precedes visual symptoms of changes in coral physiological conditions and could be used as an early warning indicator of elevated ammonium stress in coastal coral reef management.

Calcified macroalgae and their bacterial community in relation to larval settlement and metamorphosis of reef-building coral Pocillopora damicornis

Calcified macroalgae play an important role in the settlement and metamorphosis of invertebrate larvae in coral reef ecosystems. However, little is known about the algal-associated bacterial communities and their effects on larval settlement. In this study, the responses of larvae of the coral Pocillopora damicornis to calcified algae (Porolithon onkodes, Halimeda cylindracea, Halimeda opuntia and Amphiroa fragilissima) were evaluated. The results revealed that Por. onkodes and H. cylindracea significantly enhanced the rates of settlement and metamorphosis, whereas fewer larvae settled on Am. fragilissima and H. opuntia. Amplicon pyrosequencing of the V3-V4 region of 16S rDNA was applied to investigate the relationship between algal bacterial community and larval settlement. Principal coordinates analysis demonstrated that the bacterial community composition of H. opuntia was more similar to that of Am. fragilissima, but clearly distinct from those of H. cylindracea and Por. onkodes. Furthermore, the relative abundances of bacteria were highly diverse among different algae. H. opuntia had higher percentages of Thalassobius, Pelagibius and SM1A02, whereas the abundances of Mycoplasma and Suttonella were significantly higher in H. cylindracea than other algae. Our results showed that larval settlement/metamorphosis was strongly correlated with the bacterial community composition and with the relative abundance of a few operational taxonomic units.

High summer temperatures amplify functional differences between coral- and algae-dominated reef communities

Shifts from coral to algal dominance are expected to increase in tropical coral reefs as a result of anthropogenic disturbances. The consequences for key ecosystem functions such as primary productivity, calcification, and nutrient recycling are poorly understood, particularly under changing environmental conditions. We used a novel in situ incubation approach to compare functions of coral‐ and algae‐dominated communities in the central Red Sea bimonthly over an entire year. In situ gross and net community primary productivity, calcification, dissolved organic carbon fluxes, dissolved inorganic nitrogen fluxes, and their respective activation energies were quantified to describe the effects of seasonal changes. Overall, coral‐dominated communities exhibited 30% lower net productivity and 10 times higher calcification than algae‐dominated communities. Estimated activation energies indicated a higher thermal sensitivity of coral‐dominated communities. In these communities, net productivity and calcification were negatively correlated with temperature (>40% and >65% reduction, respectively, with +5°C increase from winter to summer), whereas carbon losses via respiration and dissolved organic carbon release more than doubled at higher temperatures. In contrast, algae‐dominated communities doubled net productivity in summer, while calcification and dissolved organic carbon fluxes were unaffected. These results suggest pronounced changes in community functioning associated with coral‐algal phase shifts. Algae‐dominated communities may outcompete coral‐dominated communities because of their higher productivity and carbon retention to support fast biomass accumulation while compromising the formation of important reef framework structures. Higher temperatures likely amplify these functional differences, indicating a high vulnerability of ecosystem functions of coral‐dominated communities to temperatures even below coral bleaching thresholds. Our results suggest that ocean warming may not only cause but also amplify coral–algal phase shifts in coral reefs.

Nitrogen eutrophication particularly promotes turf algae in coral reefs of the central Red Sea

While various sources increasingly release nutrients to the Red Sea, knowledge about their effects on benthic coral reef communities is scarce. Here, we provide the first comparative assessment of the response of all major benthic groups (hard and soft corals, turf algae and reef sands—together accounting for 80% of the benthic reef community) to in-situ eutrophication in a central Red Sea coral reef. For 8 weeks, dissolved inorganic nitrogen (DIN) concentrations were experimentally increased 3-fold above environmental background concentrations around natural benthic reef communities using a slow release fertilizer with 15% total nitrogen (N) content. We investigated which major functional groups took up the available N, and how this changed organic carbon (C_org) and N contents using elemental and stable isotope measurements. Findings revealed that hard corals (in their tissue), soft corals and turf algae incorporated fertilizer N as indicated by significant increases in δ¹⁵N by 8%, 27% and 28%, respectively. Among the investigated groups, C_org content significantly increased in sediments (+24%) and in turf algae (+33%). Altogether, this suggests that among the benthic organisms only turf algae were limited by N availability and thus benefited most from N addition. Thereby, based on higher C_org content, turf algae potentially gained competitive advantage over, for example, hard corals. Local management should, thus, particularly address DIN eutrophication by coastal development and consider the role of turf algae as potential bioindicator for eutrophication.

Insights on aquatic microbiome of the Indian Sundarbans mangrove areas

BACKGROUND

Anthropogenic perturbations have strong impact on water quality and ecological health of mangrove areas of Indian Sundarbans. Diversity in microbial community composition is important causes for maintaining the health of the mangrove ecosystem. However, microbial communities of estuarine water in Indian Sundarbans mangrove areas and environmental determinants that contribute to those communities were seldom studied.

METHODS

Nevertheless, this study attempted first to report bacterial and archaeal communities simultaneously in the water from Matla River and Thakuran River of Maipith coastal areas more accurately using 16S rRNA gene-based amplicon approaches. Attempt also been made to assess the capability of the environmental parameters for explaining the variation in microbial community composition.

RESULTS

Our investigation indicates the dominancy of halophilic marine bacteria from families Flavobacteriaceae and OM1 clade in the water with lower nutrient load collected from costal regions of a small Island of Sundarban Mangroves (ISM). At higher eutrophic conditions, changes in bacterial communities in Open Marine Water (OMW) were detected, where some of the marine hydrocarbons degrading bacteria under families Oceanospirillaceae and Spongiibacteraceae were dominated. While most abundant bacterial family Rhodobacteracea almost equally (18% of the total community) dominated in both sites. Minor variation in the composition of archaeal community was also observed between OMW and ISM. Redundancy analysis indicates a combination of total nitrogen and dissolved inorganic nutrients for OMW and for ISM, salinity and total nitrogen was responsible for explaining the changes in their respective microbial community composition.

CONCLUSIONS

Our study contributes the first conclusive overview on how do multiple environmental/anthropogenic stressors (salinity, pollution, eutrophication, land-use) affect the Sundarban estuary water and consequently the microbial communities in concert. However, systematic approaches with more samples for evaluating the effect of environmental pollutions on mangrove microbial communities are recommended.

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.

Metagenomic analysis of microbial community associated with coral mucus from the Gulf of Aqaba

Coral-associated microbial communities contribute to a wide variety of useful roles regarding the their host, and therefore, the arrangement of the general microbiome network can emphatically impact coral wellbeing and survival. Various pollution sources can interfere and disrupt the microbial relationship with corals. Here, we adopted the bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP®) technique to investigate the shift of microbial communities associated with the mucus of the coral Stylophora pistillata collected from five sites (Marine Science Station, Industrial Complex, Oil Terminal, Public Beach, and Phosphate Port) along the Gulf of Aqaba (Red Sea). Our results revealed a high diversity in bacterial populations associated with coral mucus. Proteobacteria were observed to be the dominating phylum among all sampling sites. The identified bacterial taxa belong to the pathogenic bacteria from the genus Vibrio was presented in varying abundances at all sampling sites. Diversity and similarity analysis of microbial communists based on rarefaction curve and UniFrac cluster respectively demonstrated that there are variances in microbial groups associated with coral mucus along sites. The pollution sources among different locations along the Gulf of Aqaba seem to affect the coral-associated holobiont leading to changes in bacterial populations due to increasing human activities.

Tissue-Specific Microbiomes of the Red Sea Giant Clam Tridacna maxima Highlight Differential Abundance of Endozoicomonadaceae

Giant clams (subfamily Tridacninae) are prevalent members of coral reef communities and engage in symbioses with algal photosymbionts of the family Symbiodiniaceae, similar to their scleractinian coral counterparts. However, we know little about their associated bacterial microbiome members. Here, we explored bacterial community diversity of digestive system, gill, and mantle tissues associated with the giant clam Tridacna maxima across a cross-shelf gradient (inshore, midshore, and offshore reef sites) in the central Red Sea using 16S rRNA gene amplicon sequencing. Different tissues harbor spatially stable and distinct microbial communities. Notably, diverse assemblages of bacteria affiliated to the family Endozoicomonadaceae were prevalent in all tissues, but particularly abundant in gills and to a lesser extent in digestive tissues. Besides Endozoicomonadaceae, bacteria in the families Pasteurellaceae, Alteromonadaceae, and Comamonadaceae were common associates, depending on the tissue queried. Taxonomy-based functional inference identified processes related to nitrogen cycling (among others) to be enriched in giant clam tissues and contributed by Endozoicomonadaceae. Our study highlights the tissue-specificity and broad taxonomic range of Endozoicomonadaceae associates, similar to other marine invertebrates, and suggests their contribution to nitrogen-related pathways. The investigation of bivalve-associated microbiome communities provides an important addition to the pathogen-focused studies for commercially important bivalves (e.g., oysters).

Different nitrogen sources speed recovery from corallivory and uniquely alter the microbiome of a reef-building coral

Corals are in decline worldwide due to local anthropogenic stressors, such as nutrient loading, and global stressors, such as ocean warming. Anthropogenic nutrient loading, which is often rich in nitrate, inhibits coral growth and worsens corals' response to warming while natural sources of nitrogen, such as ammonium from fish excretion, promotes coral growth. Although the effects of nutrient loading and ocean warming have been well-studied, it remains unclear how these factors may interact with biotic processes, such as corallivory, to alter coral health and the coral microbiome. This study examined how nitrate vs. ammonium enrichment altered the effects of increased seawater temperature and simulated parrotfish corallivory on the health of Pocillopora meandrina and its microbial community. We tested the effects of nitrogen source on the response to corallivory under contrasting temperatures (control: 26 °C, warming: 29 °C) in a factorial mesocosm experiment in Moorea, French Polynesia. Corals were able to maintain growth rates despite simultaneous stressors. Seawater warming suppressed wound healing rates by nearly 66%. However, both ammonium and nitrate enrichment counteracted the effect of higher temperatures on would healing rates. Elevated seawater temperature and ammonium enrichment independently increased Symbiodiniaceae densities relative to controls, yet there was no effect of nitrate enrichment on algal symbiont densities. Microbiome variability increased with the addition of nitrate or ammonium. Moreover, microbial indicator analysis showed that Desulfovibrionaceae Operational taxonomic units (OTUs) are indicators of exclusively temperature stress while Rhodobacteraceae and Saprospiraceae OTUs were indicators of high temperature, wounding, and nitrogen enrichment. Overall, our results suggest that nitrogen source may not alter the response of the coral host to simultaneous stressors, but that the associated microbial community may be distinct depending on the source of enrichment.

Seagrass-associated fungal communities show distance decay of similarity that has implications for seagrass management and restoration

Marine fungal biodiversity remains vastly understudied, and even less is known of their biogeography and the processes responsible for driving these distributions in marine environments. We investigated the fungal communities associated with the seagrass Enhalus acoroides collected from Singapore and Peninsular Malaysia to test the hypothesis that fungal communities are homogeneous throughout the study area. Seagrass samples were separated into different structures (leaves, roots, and rhizomes), and a sediment sample was collected next to each plant. Amplicon sequencing of the fungal internal transcribed spacer 1 and subsequent analysis revealed significant differences in fungal communities collected from different locations and different structures. We show a significant pattern of distance decay, with samples collected close to each other having more similar fungal communities in comparison with those that are more distant, indicating dispersal limitations and/or differences in habitat type are contributing to the observed biogeographic patterns. These results add to our understanding of the seagrass ecosystem in an understudied region of the world that is also the global epicenter of seagrass diversity. This work has implications for seagrass management and conservation initiatives, and we recommend that fungal community composition be a consideration for any seagrass transplant or restoration programme.

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.

The Tara Pacific expedition-A pan-ecosystemic approach of the "-omics" complexity of coral reef holobionts across the Pacific Ocean

Coral reefs are the most diverse habitats in the marine realm. Their productivity, structural complexity, and biodiversity critically depend on ecosystem services provided by corals that are threatened because of climate change effects-in particular, ocean warming and acidification. The coral holobiont is composed of the coral animal host, endosymbiotic dinoflagellates, associated viruses, bacteria, and other microeukaryotes. In particular, the mandatory photosymbiosis with microalgae of the family Symbiodiniaceae and its consequences on the evolution, physiology, and stress resilience of the coral holobiont have yet to be fully elucidated. The functioning of the holobiont as a whole is largely unknown, although bacteria and viruses are presumed to play roles in metabolic interactions, immunity, and stress tolerance. In the context of climate change and anthropogenic threats on coral reef ecosystems, the Tara Pacific project aims to provide a baseline of the "-omics" complexity of the coral holobiont and its ecosystem across the Pacific Ocean and for various oceanographically distinct defined areas. Inspired by the previous Tara Oceans expeditions, the Tara Pacific expedition (2016-2018) has applied a pan-ecosystemic approach on coral reefs throughout the Pacific Ocean, drawing an east-west transect from Panama to Papua New Guinea and a south-north transect from Australia to Japan, sampling corals throughout 32 island systems with local replicates. Tara Pacific has developed and applied state-of-the-art technologies in very-high-throughput genetic sequencing and molecular analysis to reveal the entire microbial and chemical diversity as well as functional traits associated with coral holobionts, together with various measures on environmental forcing. This ambitious project aims at revealing a massive amount of novel biodiversity, shedding light on the complex links between genomes, transcriptomes, metabolomes, organisms, and ecosystem functions in coral reefs and providing a reference of the biological state of modern coral reefs in the Anthropocene.

Coral bacterial community structure responds to environmental change in a host-specific manner

The global decline of coral reefs heightens the need to understand how corals respond to changing environmental conditions. Corals are metaorganisms, so-called holobionts, and restructuring of the associated bacterial community has been suggested as a means of holobiont adaptation. However, the potential for restructuring of bacterial communities across coral species in different environments has not been systematically investigated. Here we show that bacterial community structure responds in a coral host-specific manner upon cross-transplantation between reef sites with differing levels of anthropogenic impact. The coral Acropora hemprichii harbors a highly flexible microbiome that differs between each level of anthropogenic impact to which the corals had been transplanted. In contrast, the microbiome of the coral Pocillopora verrucosa remains remarkably stable. Interestingly, upon cross-transplantation to unaffected sites, we find that microbiomes become indistinguishable from back-transplanted controls, suggesting the ability of microbiomes to recover. It remains unclear whether differences to associate with bacteria flexibly reflects different holobiont adaptation mechanisms to respond to environmental change.

The flexibility of corals to associate with different bacteria in different environments has not been systematically investigated. Here, the authors study bacterial community dynamics for two coral species and show that bacterial community structure responds to environmental changes in a host-specific manner.

Diversity of deep-water coral-associated bacteria and comparison across depth gradients

Environmental conditions influence species composition, including the microbial communities that associate with benthic organisms such as corals. In this study we identified and compared bacteria that associate with three common deep-water corals, Lophelia pertusa, Madrepora oculata and Paragorgia arborea, from a reef habitat on the mid-Norwegian shelf. The 16S rRNA gene amplicon sequencing data obtained revealed that >50% of sequences were represented by only five operational taxonomic units. Three were host-specific and unclassified below class level, belonging to Alphaproteobacteria with affiliation to members of the Rhizobiales order (L. pertusa), Flavobacteria affiliated with members of the Elisabethkingia genus (M. oculata) and Mollicutes sequences affiliated with the Mycoplasma genus (P. arborea). In addition, gammaproteobacterial sequences within the genera Sulfitobacter and Oleispira were found across all three deep-water coral taxa. Although highly abundant in the coral microbiomes, these sequences accounted for <0.1% of the surrounding bacterioplankton, supporting specific relationships. We combined this information with previous studies, undertaking a meta-data analysis of 165 widespread samples across coral hosts and habitats. Patterns in bacterial diversity indicated enrichment of distinct uncultured species in coral microbiomes that differed among deep (>200 m), mesophotic (30–200 m) and shallow (<30 m) reefs.

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.

Atmospheric Deposition Impact on Bacterial Community Composition in the NW Mediterranean

Atmospheric deposition is a source of inorganic nutrients and organic matter to the ocean, and can favor the growth of some planktonic species over others according to their nutrient requirements. Atmospheric inputs from natural and anthropogenic sources are nowadays increasing due to desertification and industrialization, respectively. While the impact of mineral dust (mainly from the Saharan desert) on phytoplankton and bacterial community composition has been previously assessed, the effect of anthropogenic aerosols on marine bacterial assemblages remains poorly studied. Since marine bacteria play a range of roles in the biogeochemical cycles of inorganic nutrients and organic carbon, it is important to determine which taxa of marine bacteria may benefit from aerosol fertilization and which not. Here, we experimentally assessed the effect of Saharan dust and anthropogenic aerosols on marine bacterioplankton community composition across a spatial and temporal range of trophic conditions in the northwestern Mediterranean Sea. Results from 16S rDNA sequencing showed that bacterial diversity varied significantly with seasonality and geographical location. While atmospheric deposition did not yield significant changes in community composition when all the experiments where considered together, it did produce changes at certain places and during certain times of the year. These effects accounted for shifts in the bacterial community's relative abundance of up to 28%. The effect of aerosols was overall greatest in summer, both types of atmospheric particles stimulating the groups Alphaproteobacteria, Betaproteobacteria, and Cyanobacteria in the location with the highest anthropogenic footprint. Other bacterial groups benefited from one or the other aerosol depending on the season and location. Anthropogenic aerosols increased the relative abundance of groups belonging to the phylum Bacteriodetes (Cytophagia, Flavobacteriia, and Sphingobacteriia), while Saharan dust stimulated most the phytoplanktonic group of Cyanobacteria and, more specifically, Synechococcus.

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

Repeat marine heat wave-induced mass coral bleaching has decimated reefs in Seychelles for 35 years, but how coral-associated microbial diversity (microalgal endosymbionts of the family Symbiodiniaceae and bacterial communities) potentially underpins broad-scale bleaching dynamics remains unknown. We assessed microbiome composition during the 2016 heat wave peak at two contrasting reef sites (clear vs. turbid) in Seychelles, for key coral species considered bleaching sensitive (Acropora muricata, Acropora gemmifera) or tolerant (Porites lutea, Coelastrea aspera). For all species and sites, we sampled bleached versus unbleached colonies to examine how microbiomes align with heat stress susceptibility. Over 30% of all corals bleached in 2016, half of which were from Acropora sp. and Pocillopora sp. mass bleaching that largely transitioned to mortality by 2017. Symbiodiniaceae ITS2-sequencing revealed that the two Acropora sp. and P. lutea generally associated with C3z/C3 and C15 types, respectively, whereas C. aspera exhibited a plastic association with multiple D types and two C3z types. 16S rRNA gene sequencing revealed that bacterial communities were coral host-specific, largely through differences in the most abundant families, Hahellaceae (comprising Endozoicomonas), Rhodospirillaceae, and Rhodobacteraceae. Both Acropora sp. exhibited lower bacterial diversity, species richness, and community evenness compared to more bleaching-resistant P. lutea and C. aspera. Different bleaching susceptibility among coral species was thus consistent with distinct microbiome community profiles. These profiles were conserved across bleached and unbleached colonies of all coral species. As this pattern could also reflect a parallel response of the microbiome to environmental changes, the detailed functional associations will need to be determined in future studies. Further understanding such microbiome-environmental interactions is likely critical to target more effective management within oceanically isolated reefs of Seychelles.

A Newly Designed Primer Revealed High Phylogenetic Diversity of Endozoicomonas in Coral Reefs

Endozoicomonas bacteria are commonly regarded as having a potentially symbiotic relationship with their coral hosts. However, their diversity and phylogeny in samples collected from various sources remain unclear. Therefore, we designed an Endozoicomonas-specific primer paired with a bacterial universal primer to detect the 16S ribosomal RNA (rRNA) genes of this taxon and conducted an in-depth investigation of the Endozoicomonas community structure in reef-building corals. The primer had high specificity in the V3-V4 region (95.6%) and its sensitivity was high, particularly when Endozoicomonas was rare in samples (e.g., in seawater, which had a higher alpha diversity of Endozoicomonas than corals). In coral samples, predominant V3-V4 ribotypes had greater divergence than predominant V1-V2 ribotypes, and were grouped into at least 9 novel clades in a phylogenetic tree, indicating Endozoicomonas had high phylogenetic diversity. Divergence within this genus was potentially higher than that among 7 outgroup genera based on the phylogenetic distances of partial 16S rDNA sequences, suggesting that the taxonomy of this genus needs to be revised. In conclusion, dominant Endozoicomonas populations had variable phylogenies; furthermore, the newly designed primers may be useful molecular tools for the reliable detection of the Endozoicomonas community in marine environments.

In situ observations of coral bleaching in the central Saudi Arabian Red Sea during the 2015/2016 global coral bleaching event

Coral bleaching continues to be one of the most devastating and immediate impacts of climate change on coral reef ecosystems worldwide. In 2015, a major bleaching event was declared as the "3rd global coral bleaching event" by the United States National Oceanic and Atmospheric Administration, impacting a large number of reefs in every major ocean. The Red Sea was no exception, and we present herein in situ observations of the status of coral reefs in the central Saudi Arabian Red Sea from September 2015, following extended periods of high temperatures reaching upwards of 32.5°C in our study area. We examined eleven reefs using line-intercept transects at three different depths, including all reefs that were surveyed during a previous bleaching event in 2010. Bleaching was most prevalent on inshore reefs (55.6% ± 14.6% of live coral cover exhibited bleaching) and on shallower transects (41% ± 10.2% of live corals surveyed at 5m depth) within reefs. Similar taxonomic groups (e.g., Agariciidae) were affected in 2015 and in 2010. Most interestingly, Acropora and Porites had similar bleaching rates (~30% each) and similar relative coral cover (~7% each) across all reefs in 2015. Coral genera with the highest levels of bleaching (>60%) were also among the rarest (<1% of coral cover) in 2015. While this bodes well for the relative retention of coral cover, it may ultimately lead to decreased species richness, often considered an important component of a healthy coral reef. The resultant long-term changes in these coral reef communities remain to be seen.

Draft Genome Sequence of Endozoicomonas acroporae Strain Acr-14T, Isolated from Acropora Coral

A lacuna exists in our understanding of the genetic makeup of Endozoicomonas bacteria, due to scarcity of genome sequences. We report here the first draft genome sequence of Endozoicomonas acroporae Acr-14, a type strain isolated from the coral Acropora. This sequence will foster an understanding of the genetic makeup and role of hosts in shaping gene repertoires.

Dominance of Endozoicomonas bacteria throughout coral bleaching and mortality suggests structural inflexibility of the Pocillopora verrucosa microbiome

The importance of Symbiodinium algal endosymbionts and a diverse suite of bacteria for coral holobiont health and functioning are widely acknowledged. Yet, we know surprisingly little about microbial community dynamics and the stability of host-microbe associations under adverse environmental conditions. To gain insight into the stability of coral host-microbe associations and holobiont structure, we assessed changes in the community structure of Symbiodinium and bacteria associated with the coral Pocillopora verrucosa under excess organic nutrient conditions. Pocillopora-associated microbial communities were monitored over 14 days in two independent experiments. We assessed the effect of excess dissolved organic nitrogen (DON) and excess dissolved organic carbon (DOC). Exposure to excess nutrients rapidly affected coral health, resulting in two distinct stress phenotypes: coral bleaching under excess DOC and severe tissue sloughing (>90% tissue loss resulting in host mortality) under excess DON. These phenotypes were accompanied by structural changes in the Symbiodinium community. In contrast, the associated bacterial community remained remarkably stable and was dominated by two Endozoicomonas phylotypes, comprising on average 90% of 16S rRNA gene sequences. This dominance of Endozoicomonas even under conditions of coral bleaching and mortality suggests the bacterial community of P. verrucosa may be rather inflexible and thereby unable to respond or acclimatize to rapid changes in the environment, contrary to what was previously observed in other corals. In this light, our results suggest that coral holobionts might occupy structural landscapes ranging from a highly flexible to a rather inflexible composition with consequences for their ability to respond to environmental change.

Seasonal Stability in the Microbiomes of Temperate Gorgonians and the Red Coral Corallium rubrum Across the Mediterranean Sea

Populations of key benthic habitat-forming octocoral species have declined significantly in the Mediterranean Sea due to mass mortality events caused by microbial disease outbreaks linked to high summer seawater temperatures. Recently, we showed that the microbial communities of these octocorals are relatively structured; however, our knowledge on the seasonal dynamics of these microbiomes is still limited. To investigate their seasonal stability, we collected four soft gorgonian species (Eunicella singularis, Eunicella cavolini, Eunicella verrucosa and Leptogorgia sarmentosa) and the precious red coral (Corallium rubrum) from two coastal locations with different terrestrial impact levels in the Mediterranean Sea, and used next-generation amplicon sequencing of the 16S rRNA gene. The microbiomes of all soft gorgonian species were dominated by the same 'core microbiome' bacteria belonging to the Endozoicomonas and the Cellvibrionales clade BD1-7, whereas the red coral microbiome was primarily composed of 'core' Spirochaetes, Oceanospirillales ME2 and Parcubacteria. The associations with these bacterial taxa were relatively consistent over time at each location for each octocoral species. However, differences in microbiome composition and seasonal dynamics were observed between locations and could primarily be attributed to locally variant bacteria. Overall, our data provide further evidence of the intricate symbiotic relationships that exist between Mediterranean octocorals and their associated microbes, which are ancient and highly conserved over both space and time, and suggest regulation of the microbiome composition by the host, depending on local conditions.

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.

Spatial variation in coral reef fish and benthic communities in the central Saudi Arabian Red Sea

Local-scale ecological information is critical as a sound basis for spatial management and conservation and as support for ongoing research in relatively unstudied areas. We conducted visual surveys of fish and benthic communities on nine reefs (3–24 km from shore) in the Thuwal area of the central Saudi Arabian Red Sea. Fish biomass increased with increasing distance from shore, but was generally low compared to reefs experiencing minimal human influence around the world. All reefs had a herbivore-dominated trophic structure and few top predators, such as sharks, jacks, or large groupers. Coral cover was considerably lower on inshore reefs, likely due to a 2010 bleaching event. Community analyses showed inshore reefs to be characterized by turf algae, slower-growing corals, lower herbivore diversity, and highly abundant turf-farming damselfishes. Offshore reefs had more planktivorous fishes, a more diverse herbivore assemblage, and faster-growing corals. All reefs appear to be impacted by overfishing, and inshore reefs seem more vulnerable to thermal bleaching. The study provides a description of the spatial variation in biomass and community structure in the central Saudi Arabian Red Sea and provides a basis for spatial prioritization and subsequent marine protected area design in Thuwal.

High resolution profiling of coral-associated bacterial communities using full-length 16S rRNA sequence data from PacBio SMRT sequencing system

Coral reefs are a complex ecosystem consisting of coral animals and a vast array of associated symbionts including the dinoflagellate Symbiodinium, fungi, viruses and bacteria. Several studies have highlighted the importance of coral-associated bacteria and their fundamental roles in fitness and survival of the host animal. The scleractinian coral Porites lutea is one of the dominant reef-builders in the Indo-West Pacific. Currently, very little is known about the composition and structure of bacterial communities across P. lutea reefs. The purpose of this study is twofold: to demonstrate the advantages of using PacBio circular consensus sequencing technology in microbial community studies and to investigate the diversity and structure of P. lutea-associated microbiome in the Indo-Pacific. This is the first metagenomic study of marine environmental samples that utilises the PacBio sequencing system to capture full-length 16S rRNA sequences. We observed geographically distinct coral-associated microbial profiles between samples from the Gulf of Thailand and Andaman Sea. Despite the geographical and environmental impacts on the coral-host interactions, we identified a conserved community of bacteria that were present consistently across diverse reef habitats. Finally, we demonstrated the superior performance of full-length 16S rRNA sequences in resolving taxonomic uncertainty of coral associates at the species level.

Stable mucus-associated bacterial communities in bleached and healthy corals of Porites lobata from the Arabian Seas

Coral reefs are subject to coral bleaching manifested by the loss of endosymbiotic algae from coral host tissue. Besides algae, corals associate with bacteria. In particular, bacteria residing in the surface mucus layer are thought to mediate coral health, but their role in coral bleaching is unknown. We collected mucus from bleached and healthy Porites lobata colonies in the Persian/Arabian Gulf (PAG) and the Red Sea (RS) to investigate bacterial microbiome composition using 16S rRNA gene amplicon sequencing. We found that bacterial community structure was notably similar in bleached and healthy corals, and the most abundant bacterial taxa were identical. However, fine-scale differences in bacterial community composition between the PAG and RS were present and aligned with predicted differences in sulfur- and nitrogen-cycling processes. Based on our data, we argue that bleached corals benefit from the stable composition of mucus bacteria that resemble their healthy coral counterparts and presumably provide a conserved suite of protective functions, but monitoring of post-bleaching survival is needed to further confirm this assumption. Conversely, fine-scale site-specific differences highlight flexibility of the bacterial microbiome that may underlie adjustment to local environmental conditions and contribute to the widespread success of Porites lobata.

Transcriptome profiling of Galaxea fascicularis and its endosymbiont Symbiodinium reveals chronic eutrophication tolerance pathways and metabolic mutualism between partners

In the South China Sea, coastal eutrophication in the Beibu Gulf has seriously threatened reef habitats by subjecting corals to chronic physiological stress. To determine how coral holobionts may tolerate such conditions, we examined the transcriptomes of healthy colonies of the galaxy coral Galaxea fascicularis and its endosymbiont Symbiodinium from two reef sites experiencing pristine or eutrophied nutrient regimes. We identified 236 and 205 genes that were differentially expressed in eutrophied hosts and symbionts, respectively. Both gene sets included pathways related to stress responses and metabolic interactions. An analysis of genes originating from each partner revealed striking metabolic integration with respect to vitamins, cofactors, amino acids, fatty acids, and secondary metabolite biosynthesis. The expression levels of these genes supported the existence of a continuum of mutualism in this coral-algal symbiosis. Additionally, large sets of transcription factors, cell signal transduction molecules, biomineralization components, and galaxin-related proteins were expanded in G. fascicularis relative to other coral species.

Comparative Assessment of Mediterranean Gorgonian-Associated Microbial Communities Reveals Conserved Core and Locally Variant Bacteria

Gorgonians are key habitat-forming species of Mediterranean benthic communities, but their populations have suffered from mass mortality events linked to high summer seawater temperatures and microbial disease. However, our knowledge on the diversity, dynamics and function of gorgonian-associated microbial communities is limited. Here, we analysed the spatial variability of the microbiomes of five sympatric gorgonian species (Eunicella singularis, Eunicella cavolini, Eunicella verrucosa, Leptogorgia sarmentosa and Paramuricea clavata), collected from the Mediterranean Sea over a scale of ∼1100 km, using next-generation amplicon sequencing of the 16S rRNA gene. The microbiomes of all gorgonian species were generally dominated by members of the genus Endozoicomonas, which were at very low abundance in the surrounding seawater. Although the composition of the core microbiome (operational taxonomic units consistently present in a species) was found to be unique for each host species, significant overlap was observed. These spatially consistent associations between gorgonians and their core bacteria suggest intricate symbiotic relationships and regulation of the microbiome composition by the host. At the same time, local variations in microbiome composition were observed. Functional predictive profiling indicated that these differences could be attributed to seawater pollution. Taken together, our data indicate that gorgonian-associated microbiomes are composed of spatially conserved bacteria (core microbiome members) and locally variant members, and that local pollution may influence these local associations, potentially impacting gorgonian health.

Endozoicomonas genomes reveal functional adaptation and plasticity in bacterial strains symbiotically associated with diverse marine hosts

Endozoicomonas bacteria are globally distributed and often abundantly associated with diverse marine hosts including reef-building corals, yet their function remains unknown. In this study we generated novel Endozoicomonas genomes from single cells and metagenomes obtained directly from the corals Stylophora pistillata, Pocillopora verrucosa, and Acropora humilis. We then compared these culture-independent genomes to existing genomes of bacterial isolates acquired from a sponge, sea slug, and coral to examine the functional landscape of this enigmatic genus. Sequencing and analysis of single cells and metagenomes resulted in four novel genomes with 60–76% and 81–90% genome completeness, respectively. These data also confirmed that Endozoicomonas genomes are large and are not streamlined for an obligate endosymbiotic lifestyle, implying that they have free-living stages. All genomes show an enrichment of genes associated with carbon sugar transport and utilization and protein secretion, potentially indicating that Endozoicomonas contribute to the cycling of carbohydrates and the provision of proteins to their respective hosts. Importantly, besides these commonalities, the genomes showed evidence for differential functional specificity and diversification, including genes for the production of amino acids. Given this metabolic diversity of Endozoicomonas we propose that different genotypes play disparate roles and have diversified in concert with their hosts.

Year-Long Monitoring of Physico-Chemical and Biological Variables Provide a Comparative Baseline of Coral Reef Functioning in the Central Red Sea

Coral reefs in the central Red Sea are sparsely studied and in situ data on physico-chemical and key biotic variables that provide an important comparative baseline are missing. To address this gap, we simultaneously monitored three reefs along a cross-shelf gradient for an entire year over four seasons, collecting data on currents, temperature, salinity, dissolved oxygen (DO), chlorophyll-a, turbidity, inorganic nutrients, sedimentation, bacterial communities of reef water, and bacterial and algal composition of epilithic biofilms. Summer temperature (29–33°C) and salinity (39 PSU) exceeded average global maxima for coral reefs, whereas DO concentration was low (2–4 mg L^-1). While temperature and salinity differences were most pronounced between seasons, DO, chlorophyll-a, turbidity, and sedimentation varied most between reefs. Similarly, biotic communities were highly dynamic between reefs and seasons. Differences in bacterial biofilms were driven by four abundant families: Rhodobacteraceae, Flavobacteriaceae, Flammeovirgaceae, and Pseudanabaenaceae. In algal biofilms, green crusts, brown crusts, and crustose coralline algae were most abundant and accounted for most of the variability of the communities. Higher bacterial diversity of biofilms coincided with increased algal cover during spring and summer. By employing multivariate matching, we identified temperature, salinity, DO, and chlorophyll-a as the main contributing physico-chemical drivers of biotic community structures. These parameters are forecast to change most with the progression of ocean warming and increased nutrient input, which suggests an effect on the recruitment of Red Sea benthic communities as a result of climate change and anthropogenic influence. In conclusion, our study provides insight into coral reef functioning in the Red Sea and a comparative baseline to support coral reef studies in the region.

Diversity and function of prevalent symbiotic marine bacteria in the genus Endozoicomonas

Endozoicomonas bacteria are emerging as extremely diverse and flexible symbionts of numerous marine hosts inhabiting oceans worldwide. Their hosts range from simple invertebrate species, such as sponges and corals, to complex vertebrates, such as fish. Although widely distributed, the functional role of Endozoicomonas within their host microenvironment is not well understood. In this review, we provide a summary of the currently recognized hosts of Endozoicomonas and their global distribution. Next, the potential functional roles of Endozoicomonas, particularly in light of recent microscopic, genomic, and genetic analyses, are discussed. These analyses suggest that Endozoicomonas typically reside in aggregates within host tissues, have a free-living stage due to their large genome sizes, show signs of host and local adaptation, participate in host-associated protein and carbohydrate transport and cycling, and harbour a high degree of genomic plasticity due to the large proportion of transposable elements residing in their genomes. This review will finish with a discussion on the methodological tools currently employed to study Endozoicomonas and host interactions and review future avenues for studying complex host-microbial symbioses.

Caribbean corals house shared and host-specific microbial symbionts over time and space

The rise of coral diseases has triggered a surge of interest in coral microbial communities. But to fully understand how the coral microbiome may cause or respond to disease, we must first understand structure and variation in the healthy coral microbiome. We used 16S rRNA sequencing to characterize the microbiomes of 100 healthy coral colonies from six Caribbean coral species (Acropora cervicornis, A. palmata, Diploria labyrinthiformis, Diploria strigosa, Porites astreoides and P. furcata) across four reefs and three time points over 1 year. We found host species to be the strongest driver of coral microbiome structure across site and time. Analysis of the core microbiome revealed remarkable similarity in the bacterial taxa represented across coral hosts and many bacterial phylotypes shared across all corals sampled. Some of these widespread bacterial taxa have been identified in Pacific corals, indicating that a core coral microbiome may extend across oceans. Core bacterial phylotypes that were unique to each coral were taxonomically diverse, suggesting that different coral hosts provide persistent, divergent niches for bacteria.

Differential specificity between closely related corals and abundant Endozoicomonas endosymbionts across global scales

Reef-building corals are well regarded not only for their obligate association with endosymbiotic algae, but also with prokaryotic symbionts, the specificity of which remains elusive. To identify the central microbial symbionts of corals, their specificity across species and conservation over geographic regions, we sequenced partial SSU ribosomal RNA genes of Bacteria and Archaea from the common corals Stylophora pistillata and Pocillopora verrucosa across 28 reefs within seven major geographical regions. We demonstrate that both corals harbor Endozoicomonas bacteria as their prevalent symbiont. Importantly, catalyzed reporter deposition–fluorescence in situ hybridization (CARD–FISH) with Endozoicomonas-specific probes confirmed their residence as large aggregations deep within coral tissues. Using fine-scale genotyping techniques and single-cell genomics, we demonstrate that P. verrucosa harbors the same Endozoicomonas, whereas S. pistillata associates with geographically distinct genotypes. This specificity may be shaped by the different reproductive strategies of the hosts, potentially uncovering a pattern of symbiont selection that is linked to life history. Spawning corals such as P. verrucosa acquire prokaryotes from the environment. In contrast, brooding corals such as S. pistillata release symbiont-packed planula larvae, which may explain a strong regional signature in their microbiome. Our work contributes to the factors underlying microbiome specificity and adds detail to coral holobiont functioning.

Overfishing and nutrient pollution interact with temperature to disrupt coral reefs down to microbial scales

Losses of corals worldwide emphasize the need to understand what drives reef decline. Stressors such as overfishing and nutrient pollution may reduce resilience of coral reefs by increasing coral–algal competition and reducing coral recruitment, growth and survivorship. Such effects may themselves develop via several mechanisms, including disruption of coral microbiomes. Here we report the results of a 3-year field experiment simulating overfishing and nutrient pollution. These stressors increase turf and macroalgal cover, destabilizing microbiomes, elevating putative pathogen loads, increasing disease more than twofold and increasing mortality up to eightfold. Above-average temperatures exacerbate these effects, further disrupting microbiomes of unhealthy corals and concentrating 80% of mortality in the warmest seasons. Surprisingly, nutrients also increase bacterial opportunism and mortality in corals bitten by parrotfish, turning normal trophic interactions deadly for corals. Thus, overfishing and nutrient pollution impact reefs down to microbial scales, killing corals by sensitizing them to predation, above-average temperatures and bacterial opportunism.

Overfishing and nutrient pollution can damage coral reefs in part by increasing coral-algal competition. Here the authors simulate these stressors in a three year field experiment, and show that they interact to enhance sensitivity to temperature, predation and bacterial opportunism.