Coral transplantation triggers shift in microbiome and promotion of coral disease associated potential pathogens

Identification of quorum sensing-regulated Vibrio fortis as potential pathogenic bacteria for coral bleaching and the effects on the microbial shift

Coastal pollution, global warming, ocean acidification, and other reasons lead to the imbalance of the coral reef ecosystem, resulting in the increasingly serious problem of coral degradation. Coral bleaching is often accompanied by structural abnormalities of coral symbiotic microbiota, among which Vibrio is highly concerned. In this study, Vibrio fortis S10-1 (MCCC 1H00104), isolated from sea cucumber, was used for the bacterial infection on coral Seriatopora guttatus and Pocillopora damicornis. The infection of S10-1 led to coral bleaching and a significant reduction of photosynthetic function in coral holobiont, and the pathogenicity of V. fortis was regulated by quorum sensing. Meanwhile, Vibrio infection also caused a shift of coral symbiotic microbial community, with significantly increased abundant Proteobacteria and Actinobacteria and significantly reduced abundant Firmicutes; on genus level, the abundance of Bacillus decreased significantly and the abundance of Rhodococcus, Ralstonia, and Burkholderia-Caballeronia-Paraburkholderia increased significantly; S10-1 infection also significantly impacted the water quality in the micro-ecosystem. In contrast, S10-1 infection showed less effect on the microbial community of the live stone, which reflected that the microbes in the epiphytic environment of the live stone might have a stronger ability of self-regulation; the algal symbionts mainly consisted of Cladocopium sp. and showed no significant effect by the Vibrio infection. This study verified that V. fortis is the primary pathogenic bacterium causing coral bleaching, revealed changes in the microbial community caused by its infection, provided strong evidence for the "bacterial bleaching" hypothesis, and provided an experimental experience for the exploration of the interaction mechanism among microbial communities, especially coral-associated Vibrio in the coral ecosystem, and potential probiotic strategy or QS regulation on further coral disease control.

The bacterial signature offers vision into the machinery of coral fitness across high-latitude coral reef in the South China Sea

Coral-bacterial interaction is a major driver in coral acclimatization to the stressful environment. 16S rRNA High-throughput sequencing was used to classify the role of different coral reef compartments; sediment, water, and tissue; in the South China Sea (SCS), as well as different locations in shaping the microbial community. The majority of OTUs significantly shifted at impacted sites and indicated distinction in the relative abundance of bacteria compartment/site-wise. Richness and diversity were higher, and more taxa were enriched in the sediment communities. Proteobacteria dominated sediment samples, while Cyanobacteria dominated water samples. Coral tissue showed a shift among different sites with Proteobacteria remaining the dominant Phylum. Moreover, we report a dominance of Chlorobium genus in the healthy coral tissue sample collected from the severely damaged Site B, suggesting a contribution to tolerance and adaptation to the disturbing environment. Thus, revealing the complex functionally diverse microbial patterns associated with biotic and abiotic disturbed coral reefs will deliver understanding of the symbiotic connections and competitive benefit inside the hosts niche and can reveal a measurable footprint of the environmental impacts on coral ecosystems. We hence, urge scientists to draw more attention towards using coral microbiome as a self-sustaining tool in coral restoration.

Diversity and Distribution of Microbial Communities Associated with Reef Corals of the Malay Peninsula

Coral-associated bacteria play critical roles in the regulation of coral health and function. Environmental perturbations that alter the bacterial community structure can render the coral holobiont more susceptible and less resilient to disease. Understanding the natural variation of the coral microbiome across space and host species provides a baseline that can be used to distinguish shifts in community structure. Using a 16S rRNA gene metabarcoding approach, this study examines bacterial community structure across three scleractinian coral hosts. Our results show that corals of three regions-eastern and western Peninsular Malaysia and Singapore-host distinct bacterial communities; despite these differences, we were able to identify a core microbiome shared across all three species. This core microbiome was also present in samples previously collected in Thailand, suggesting that these core microbes play an important role in promoting and maintaining host health. For example, several have been identified as dimethylsulfoniopropionate (DMSP) metabolizers that have roles in sulfur cycling and the suppression of bacterial pathogens. Pachyseris speciosa has the most variable microbiome, followed by Porites lutea, with the composition of the Diploastrea heliopora microbiome the least variable throughout all locations. Microbial taxa associated with each region or site are likely shaped by local environmental conditions. Taken together, host identity is a major driver of differences in microbial community structure, while environmental heterogeneity shapes communities at finer scales.

Assessing the potential for demographic restoration and assisted evolution to build climate resilience in coral reefs

Interest is growing in developing conservation strategies to restore and maintain coral reef ecosystems in the face of mounting anthropogenic stressors, particularly climate warming and associated mass bleaching events. One such approach is to propagate coral colonies ex situ and transplant them to degraded reef areas to augment habitat for reef-dependent fauna, prevent colonization from spatial competitors, and enhance coral reproductive output. In addition to such "demographic restoration" efforts, manipulating the thermal tolerance of outplanted colonies through assisted relocation, selective breeding, or genetic engineering is being considered for enhancing rates of evolutionary adaptation to warming. Although research into such "assisted evolution" strategies has been growing, their expected performance remains unclear. We evaluated the potential outcomes of demographic restoration and assisted evolution in climate change scenarios using an eco-evolutionary simulation model. We found that supplementing reefs with pre-existing genotypes (demographic restoration) offers little climate resilience benefits unless input levels are large and maintained for centuries. Supplementation with thermally resistant colonies was successful at improving coral cover at lower input levels, but only if maintained for at least a century. Overall, we found that, although demographic restoration and assisted evolution have the potential to improve long-term coral cover, both approaches had a limited impact in preventing severe declines under climate change scenarios. Conversely, with sufficient natural genetic variance and time, corals could readily adapt to warming temperatures, suggesting that restoration approaches focused on building genetic variance may outperform those based solely on introducing heat-tolerant genotypes.

Intestinal Microbiome Richness of Coral Reef Damselfishes (Actinopterygii: Pomacentridae)

Fish gastro-intestinal system harbors diverse microbiomes that affect the host's digestion, nutrition, and immunity. Despite the great taxonomic diversity of fish, little is understood about fish microbiome and the factors that determine its structure and composition. Damselfish are important coral reef species that play pivotal roles in determining algae and coral population structures of reefs. Broadly, damselfish belong to either of two trophic guilds based on whether they are planktivorous or algae-farming. In this study, we used 16S rRNA gene sequencing to investigate the intestinal microbiome of 5 planktivorous and 5 algae-farming damselfish species (Pomacentridae) from the Great Barrier Reef. We detected Gammaproteobacteria ASVs belonging to the genus Actinobacillus in 80% of sampled individuals across the 2 trophic guilds, thus, bacteria in this genus can be considered possible core members of pomacentrid microbiomes. Algae-farming damselfish had greater bacterial alpha-diversity, a more diverse core microbiome and shared 35 ± 22 ASVs, whereas planktivorous species shared 7 ± 3 ASVs. Our data also highlight differences in microbiomes associated with both trophic guilds. For instance, algae-farming damselfish were enriched in Pasteurellaceae, whilst planktivorous damselfish in Vibrionaceae. Finally, we show shifts in bacterial community composition along the intestines. ASVs associated with the classes Bacteroidia, Clostridia, and Mollicutes bacteria were predominant in the anterior intestinal regions while Gammaproteobacteria abundance was higher in the stomach. Our results suggest that the richness of the intestinal bacterial communities of damselfish reflects host species diet and trophic guild.

Differential Response of the Microbiome of Pocillopora acuta to Reciprocal Transplantation Within Singapore

As corals continue to decline globally, particularly due to climate change, it is vital to understand the extent to which their microbiome may confer an adaptive resilience against environmental stress. Corals that survive on the urban reefs of Singapore are ideal candidates to study the association of scleractinians with their microbiome, which in turn can inform reef conservation and management. In this study, we monitored differences in the microbiome of Pocillopora acuta colonies reciprocally transplanted between two reefs, Raffles and Kusu, within the Port of Singapore, where corals face intense anthropogenic impacts. Pocillopora acuta had previously been shown to host distinct microbial communities between these two reefs. Amplicon sequencing (16S rRNA) was used to assess the coral microbiomes at 1, 2, 4, and 10 days post-transplantation. Coral microbiomes responded rapidly to transplantation, becoming similar to those of the local corals at the destination reef within one day at Raffles and within two days at Kusu. Elevated nitrate concentrations were detected at Raffles for the duration of the study, potentially influencing the microbiome's response to transplantation. The persistence of corals within the port of Singapore highlights the ability of corals to adapt to stressful environments. Further, coral resilience appears to coincide with a dynamic microbiome which can undergo shifts in composition without succumbing to dysbiosis.

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.

Population differentiation of Rhodobacteraceae along with coral compartments

Coral mucus, tissue, and skeleton harbor compositionally different microbiota, but how these coral compartments shape the microbial evolution remains unexplored. Here, we sampled bacteria inhabiting a prevalent coral species Platygyra acuta and sequenced genomes of 234 isolates comprising two populations in Rhodobacteraceae, an alphaproteobacterial lineage representing a significant but variable proportion (5-50%) of the coral microbiota. The Ruegeria population (20 genomes) contains three clades represented by eight, six, and six isolates predominantly sampled from the skeleton (outgroup), mucus (clade-M), and skeleton (clade-S), respectively. The clade-M possesses functions involved in the utilization of coral osmolytes abundant in the mucus (e.g., methylamines, DMSP, taurine, and L-proline), whereas the clade-S uniquely harbors traits that may promote adaptation to the low-energy and diurnally anoxic skeleton (e.g., sulfur oxidation and swimming motility). These between-clade genetic differences were largely supported by physiological assays. Expanded analyses by including genomes of 24 related isolates (including seven new genomes) from other marine environments suggest that clade-M and clade-S may have diversified in non-coral habitats, but they also consolidated a key role of distinct coral compartments in diversifying many of the above-mentioned traits. The unassigned Rhodobacteraceae population (214 genomes) varies only at a few dozen nucleotide sites across the whole genomes, but the number of between-compartment migration events predicted by the Slatkin-Maddison test supported that dispersal limitation between coral compartments is another key mechanism diversifying microbial populations. Collectively, our results suggest that different coral compartments represent ecologically distinct and microgeographically separate habitats that drive the evolution of the coral microbiota.

Nutrient Enrichment Predominantly Affects Low Diversity Microbiomes in a Marine Trophic Symbiosis between Algal Farming Fish and Corals

While studies show that nutrient pollution shifts reef trophic interactions between fish, macroalgae, and corals, we know less about how the microbiomes associated with these organisms react to such disturbances. To investigate how microbiome dynamics are affected during nutrient pollution, we exposed replicate Porites lobata corals colonized by the fish Stegastes nigricans, which farm an algal matrix on the coral, to a pulse of nutrient enrichment over a two-month period and examined the microbiome of each partner using 16S amplicon analysis. We found 51 amplicon sequence variants (ASVs) shared among the three hosts. Coral microbiomes had the lowest diversity with over 98% of the microbiome dominated by a single genus, Endozoicomonas. Fish and algal matrix microbiomes were ~20 to 70× more diverse and had higher evenness compared to the corals. The addition of nutrients significantly increased species richness and community variability between samples of coral microbiomes but not the fish or algal matrix microbiomes, demonstrating that coral microbiomes are less resistant to nutrient pollution than their trophic partners. Furthermore, the 51 common ASVs within the 3 hosts indicate microbes that may be shared or transmitted between these closely associated organisms, including Vibrionaceae bacteria, many of which can be pathogenic to corals.

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.

The microbiota of intertidal macroalgae Fucus distichus is site-specific and resistant to change following transplant

It is unclear how host-associated microbial communities will be affected by future environmental change. Characterizing how microbiota differ across sites with varying environmental conditions and assessing the stability of the microbiota in response to abiotic variation are critical steps towards predicting outcomes of environmental change. Intertidal organisms are valuable study systems because they experience extreme variation in environmental conditions on tractable timescales such as tide cycles and across small spatial gradients in the intertidal zone. Here we show a widespread intertidal macroalgae, Fucus distichus, hosts site-specific microbiota over small (meters to kilometres) spatial scales. We demonstrate stability of site-specific microbial associations by manipulating the host environment and microbial species pool with common garden and reciprocal transplant experiments. We hypothesized that F. distichus microbiota would readily shift to reflect the contemporary environment due to selective filtering by abiotic conditions and/or colonization by microbes from the new environment or nearby hosts. Instead, F. distichus microbiota was stable for days after transplantation in both the laboratory and field. Our findings expand the current understanding of microbiota dynamics on an intertidal foundation species. These results may also point to adaptations for withstanding short-term environmental variation, in hosts and/or microbes, facilitating stable host-microbial associations.

Aberrations in the microbiome of cyanobacteria from a tropical estuary polluted by heavy metals

The effect of heavy metal pollution on the microbiome of cyanobacteria in Cochin estuary (CE) on the southwest coast of India is reported in the study. Statistically significant difference in heavy metal concentration was observed between water, suspended particulate matter (SPM) and sediment. The Zn, Cd, Cu, Ni and Cr were 2-6 times higher in the SPM compared with the sediment, while Pb was 10 to 25 times higher. Although nearly 60% of the species diversity of microbiome was common between cyanobacteria enriched from the upstream (S1S) and downstream (S11B), there was a difference in the major groups of heterotrophic bacterial associates. Proteobacteria was the dominant phylum (>80%) in S1S, while it was second only (27.5%) after Planctomycetes (37.4%) in S11B. The results of the current study indicate that the pollution can influence an ecosystem at the micro-niche level.

Vulnerability of global coral reef habitat suitability to ocean warming, acidification and eutrophication

Coral reefs are threatened by global and local stressors. Yet, reefs appear to respond differently to different environmental stressors. Using a global dataset of coral reef occurrence as a proxy for the long-term adaptation of corals to environmental conditions in combination with global environmental data, we show here how global (warming: sea surface temperature; acidification: aragonite saturation state, Ω_arag ) and local (eutrophication: nitrate concentration, and phosphate concentration) stressors influence coral reef habitat suitability. We analyse the relative distance of coral communities to their regional environmental optima. In addition, we calculate the expected change of coral reef habitat suitability across the tropics in relation to an increase of 0.1°C in temperature, an increase of 0.02 μmol/L in nitrate, an increase of 0.01 μmol/L in phosphate and a decrease of 0.04 in Ω_arag . Our findings reveal that only 6% of the reefs worldwide will be unaffected by local and global stressors and can thus act as temporary refugia. Local stressors, driven by nutrient increase, will affect 22% of the reefs worldwide, whereas global stressors will affect 11% of these reefs. The remaining 61% of the reefs will be simultaneously affected by local and global stressors. Appropriate wastewater treatments can mitigate local eutrophication and could increase areas of temporary refugia to 28%, allowing us to 'buy time', while international agreements are found to abate global stressors.

Coral cover and rubble cryptofauna abundance and diversity at outplanted reefs in Okinawa, Japan

Global climate change is leading to damage and loss of coral reef ecosystems. On subtropical Okinawa Island in southwestern Japan, the prefectural government is working on coral reef restoration by outplanting coral colonies from family Acroporidae back to reefs after initially farming colonies inside protected nurseries. In order to establish a baseline for future comparisons, in this study we documented the current status of reefs undergoing outplanting at Okinawa Island, and nearby locations where no human manipulation has occurred. We examined three sites on the coast of Onna Village on the west coast of the island; each site included an outplanted and control location. We used (1) coral rubble sampling to measure and compare abundance and diversity of rubble cryptofauna; and (2) coral reef monitoring using Line Intercept Transects to track live coral coverage. Results showed that rubble shape had a positive correlation with the numbers of animals found within rubble themselves and may therefore constitute a reliable abundance predictor. Each outplanted location did not show differences with the corresponding control location in terms of rubble cryptofauna abundance, but outplanted locations had significantly lower coral coverage. Overall, differences between sites (Maeganeku1, Maeganeku2 and Manza, each including both outplanted and control locations) were significant, for both rubble cryptofauna and coral coverage. We recommend (1) to outplant colonies from more stress-resistant genera in place of Acropora, and (2) to conduct regular surveys to monitor the situation closely. With a lack of baseline data preceding impacts, rigorous monitoring over time can highlight trends towards increases or decreases in evaluated variables, allowing to obtain a clearer idea of the effects of transplants and on the trajectory of impacts due to climate change and local stressors . Finally, we also recommend (3) to establish conservation and sustainable practices that could aid the ongoing restoration efforts such as installing anchoring buoys to reduce impacts from anchoring, which could reduce coral mortality of both outplanted and native coral colonies.

Interactions between coral restoration and fish assemblages: implications for reef management

Corals create complex reef structures that provide both habitat and food for many fish species. Because of numerous natural and anthropogenic threats, many coral reefs are currently being degraded, endangering the fish assemblages they support. Coral reef restoration, an active ecological management tool, may help reverse some of the current trends in reef degradation through the transplantation of stony corals. Although restoration techniques have been extensively reviewed in relation to coral survival, our understanding of the effects of adding live coral cover and complexity on fishes is in its infancy with a lack of scientifically validated research. This study reviews the limited data on reef restoration and fish assemblages, and complements this with the more extensive understanding of complex interactions between natural reefs and fishes and how this might inform restoration efforts. It also discusses which key fish species or functional groups may promote, facilitate or inhibit restoration efforts and, in turn, how restoration efforts can be optimised to enhance coral fish assemblages. By highlighting critical knowledge gaps in relation to fishes and restoration interactions, the study aims to stimulate research into the role of reef fishes in restoration projects. A greater understanding of the functional roles of reef fishes would also help inform whether restoration projects can return fish assemblages to their natural compositions or whether alternative species compositions develop, and over what timeframe. Although alleviation of local and global reef stressors remains a priority, reef restoration is an important tool; an increased understanding of the interactions between replanted corals and the fishes they support is critical for ensuring its success for people and nature.

Coral Disease Causes, Consequences, and Risk within Coral Restoration

As a result of increased reef degradation, restoration efforts are now being widely applied on coral reefs. However, outplanted coral survival in restoration zones varies substantially, and coral mortality can be a significant limitation to the success of restoration efforts. With reef restoration now occurring within, and adjacent to, nationally preserved and managed marine parks, the potential risks of mortality events and disease spread to adjacent marine populations need to be considered, particularly as these ecosystems continue to decline. We review the causes and consequences of coral mortality and disease outbreaks within the context of coral restoration, highlighting knowledge gaps in our understanding of the restored coral microbiome and discussing management practices for assessing coral disease. We identify the need for research efforts into monitoring and diagnostics of disease within coral restoration, as well as practices to mitigate and manage coral disease risks in restoration.

A horizon scan of priorities for coastal marine microbiome research

Research into the microbiomes of natural environments is changing the way ecologists and evolutionary biologists view the importance of microorganisms in ecosystem function. This is particularly relevant in ocean environments, where microorganisms constitute the majority of biomass and control most of the major biogeochemical cycles, including those that regulate Earth's climate. Coastal marine environments provide goods and services that are imperative to human survival and well-being (for example, fisheries and water purification), and emerging evidence indicates that these ecosystem services often depend on complex relationships between communities of microorganisms (the 'microbiome') and the environment or their hosts - termed the 'holobiont'. Understanding of coastal ecosystem function must therefore be framed under the holobiont concept, whereby macroorganisms and their associated microbiomes are considered as a synergistic ecological unit. Here, we evaluate the current state of knowledge on coastal marine microbiome research and identify key questions within this growing research area. Although the list of questions is broad and ambitious, progress in the field is increasing exponentially, and the emergence of large, international collaborative networks and well-executed manipulative experiments are rapidly advancing the field of coastal marine microbiome research.

Expanding walls and shrinking beaches: loss of natural coastline in Okinawa Island, Japan

Okinawa is the largest and most populated island of the Ryukyu Archipelago in southern Japan and is renowned for its natural resources and beauty. Similar as to what has been happening in the rest of the country, Okinawa Island has been affected by an increasing amount of development and construction work. The trend has been particularly acute after reversion to Japanese sovereignty in 1972, following 27 years of post-war American administration. A coastline once characterized by extended sandy beaches surrounded by coral reefs now includes tracts delimited by seawalls, revetments, and other human-made hardening structures. Additionally, part of coastal Okinawa Island was obtained by land-filling shallow ocean areas (land reclamation). Nevertheless, the current extension of the artificial coastline, as well as the level of fragmentation of the natural coastline are unclear, due to the lack of both published studies and easily accessible and updated datasets. The aims of this research were to quantify the extension of coastline alterations in Okinawa Island, including the amount of land-filling performed over the last 41 years, and to describe the coastlines that have been altered the most as well as those that are still relatively pristine. The analyses were performed using a reference map of Okinawa Island based on GIS vector data extracted from the OpenStreetMap (OSM) coastline dataset (average node distance for Okinawa Island = 24 m), in addition to satellite and aerial photography from multiple providers. We measured 431.8 km of altered coastline, equal to about 63% of the total length of coastline in Okinawa Island. Habitat fragmentation is also an issue as the remaining natural coastline was broken into 239 distinct tracts (mean length = 1.05 km). Finally, 21.03 km² of the island’s surface were of land reclaimed over the last 41 years. The west coast has been altered the most, while the east coast is in relatively more natural conditions, particularly the northern part, which has the largest amount of uninterrupted natural coastline. Given the importance of the ecosystem services that coastal and marine ecosystems provide to local populations of subtropical islands, including significant economic income from tourism, conservation of remaining natural coastlines should be given high priority.

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.

Microbial indicators of environmental perturbations in coral reef ecosystems

BACKGROUND

Coral reefs are facing unprecedented pressure on local and global scales. Sensitive and rapid markers for ecosystem stress are urgently needed to underpin effective management and restoration strategies. Although the fundamental contribution of microbes to the stability and functioning of coral reefs is widely recognised, it remains unclear how different reef microbiomes respond to environmental perturbations and whether microbiomes are sensitive enough to predict environmental anomalies that can lead to ecosystem stress. However, the lack of coral reef microbial baselines hinders our ability to study the link between shifts in microbiomes and ecosystem stress. In this study, we established a comprehensive microbial reference database for selected Great Barrier Reef sites to assess the diagnostic value of multiple free-living and host-associated reef microbiomes to infer the environmental state of coral reef ecosystems.

RESULTS

A comprehensive microbial reference database, originating from multiple coral reef microbiomes (i.e. seawater, sediment, corals, sponges and macroalgae), was generated by 16S rRNA gene sequencing for 381 samples collected over the course of 16 months. By coupling this database to environmental parameters, we showed that the seawater microbiome has the greatest diagnostic value to infer shifts in the surrounding reef environment. In fact, 56% of the observed compositional variation in the microbiome was explained by environmental parameters, and temporal successions in the seawater microbiome were characterised by uniform community assembly patterns. Host-associated microbiomes, in contrast, were five-times less responsive to the environment and their community assembly patterns were generally less uniform. By applying a suite of indicator value and machine learning approaches, we further showed that seawater microbial community data provide an accurate prediction of temperature and eutrophication state (i.e. chlorophyll concentration and turbidity).

CONCLUSION

Our results reveal that free-living microbial communities have a high potential to infer environmental parameters due to their environmental sensitivity and predictability. This highlights the diagnostic value of microorganisms and illustrates how long-term coral reef monitoring initiatives could be enhanced by incorporating assessments of microbial communities in seawater. We therefore recommend timely integration of microbial sampling into current coral reef monitoring initiatives.

Ruegeria sp. Strains Isolated from the Reef-Building Coral Galaxea fascicularis Inhibit Growth of the Temperature-Dependent Pathogen Vibrio coralliilyticus

The coral microbiome has attracted increased attention because of its potential roles in host protection against deadly diseases. However, little is known about the role of coral-associated bacteria against the temperature-dependent opportunistic pathogen Vibrio coralliilyticus. In this study, we tested whether bacteria associated with the reef-building coral Galaxea fascicularis could inhibit the growth of V. coralliilyticus. Twenty-nine cultivable bacteria were successfully isolated from a healthy colony of G. fascicularis kept in an aquarium. Among the bacterial isolates, three Ruegeria sp. strains inhibited the growth of V. coralliilyticus P1 as a reference strain and Vibrio sp. isolated in this study. Ruegeria sp. strains were also detected from other G. fascicularis colonies in the aquarium and in previous field studies by 16S rRNA amplicon sequencing, suggesting that Ruegeria sp. strains are common among G. fascicularis colonies. These results illuminate the potential role of Ruegeria sp. in protecting corals against pathogenic Vibrio species.

Metagenomics of Coral Reefs Under Phase Shift and High Hydrodynamics

Local and global stressors have affected coral reef ecosystems worldwide. Switches from coral to algal dominance states and microbialization are the major processes underlying the global decline of coral reefs. However, most of the knowledge concerning microbialization has not considered physical disturbances (e.g., typhoons, waves, and currents). Southern Japan reef systems have developed under extreme physical disturbances. Here, we present analyses of a three-year investigation on the coral reefs of Ishigaki Island that comprised benthic and fish surveys, water quality analyses, metagenomics and microbial abundance data. At the four studied sites, inorganic nutrient concentrations were high and exceeded eutrophication thresholds. The dissolved organic carbon (DOC) concentration (up to 233.3 μM) and microbial abundance (up to 2.5 × 105 cell/mL) values were relatively high. The highest vibrio counts coincided with the highest turf cover (∼55-85%) and the lowest coral cover (∼4.4-10.2%) and fish biomass (0.06 individuals/m2). Microbiome compositions were similar among all sites and were dominated by heterotrophs. Our data suggest that a synergic effect among several regional stressors are driving coral decline. In a high hydrodynamics reef environment, high algal/turf cover, stimulated by eutrophication and low fish abundance due to overfishing, promote microbialization. Together with crown-of-thorns starfish (COTS) outbreaks and possible of climate changes impacts, theses coral reefs are likely to collapse.

Microbiomes of gall-inducing copepod crustaceans from the corals Stylophora pistillata (Scleractinia) and Gorgonia ventalina (Alcyonacea)

Corals harbor complex and diverse microbial communities that strongly impact host fitness and resistance to diseases, but these microbes themselves can be influenced by stresses, like those caused by the presence of macroscopic symbionts. In addition to directly influencing the host, symbionts may transmit pathogenic microbial communities. We analyzed two coral gall-forming copepod systems by using 16S rRNA gene metagenomic sequencing: (1) the sea fan Gorgonia ventalina with copepods of the genus Sphaerippe from the Caribbean and (2) the scleractinian coral Stylophora pistillata with copepods of the genus Spaniomolgus from the Saudi Arabian part of the Red Sea. We show that bacterial communities in these two systems were substantially different with Actinobacteria, Alphaproteobacteria, and Betaproteobacteria more prevalent in samples from Gorgonia ventalina, and Gammaproteobacteria in Stylophora pistillata. In Stylophora pistillata, normal coral microbiomes were enriched with the common coral symbiont Endozoicomonas and some unclassified bacteria, while copepod and gall-tissue microbiomes were highly enriched with the family ME2 (Oceanospirillales) or Rhodobacteraceae. In Gorgonia ventalina, no bacterial group had significantly different prevalence in the normal coral tissues, copepods, and injured tissues. The total microbiome composition of polyps injured by copepods was different. Contrary to our expectations, the microbial community composition of the injured gall tissues was not directly affected by the microbiome of the gall-forming symbiont copepods.

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.

Effectiveness of coral relocation as a mitigation strategy in Kāne'ohe Bay, Hawai'i

Coral reef restoration and management techniques are in ever-increasing demand due to the global decline of coral reefs in the last several decades. Coral relocation has been established as an appropriate restoration technique in select cases, particularly where corals are scheduled for destruction. However, continued long-term monitoring of recovery of transplanted corals is seldom sustained. Removal of coral from a navigation channel and relocation to a similar nearby dredged site occurred in 2005. Coral recovery at the donor site and changes in fish populations at the receiving site were tracked periodically over the following decade. Coral regrowth at the donor site was rapid until a recent bleaching event reduced coral cover by more than half. The transplant of mature colonies increased spatial complexity at the receiving site, immediately increasing fish biomass, abundance, and species that was maintained throughout subsequent surveys. Our research indicates that unlike the majority of historical accounts of coral relocation in the Pacific, corals transplanted into wave-protected areas with similar conditions as the original site can have high survival rates. Data on long-term monitoring of coral transplants in diverse environments is central in developing management and mitigation strategies.

The Hologenome Across Environments and the Implications of a Host-Associated Microbial Repertoire

Our understanding of the diverse interactions between hosts and microbes has grown profoundly over the past two decades and, as a product, has revolutionized our knowledge of the life sciences. Through primarily laboratory experiments, the current framework for holobionts and their respective hologenomes aims to decipher the underpinnings and implications of symbioses between host and microbiome. However, the laboratory setting restricts the full spectrum of host-associated symbionts as compared to those found in nature; thus, limiting the potential for a holistic interpretation of the functional roles the microbiome plays in host biology. When holobionts are studied in nature, associated microbial communities vary considerably between conditions, resulting in more microbial associates as part of the "hologenome" across environments than in either environment alone. We review and synthesize empirical evidence suggesting that hosts may associate with a larger microbial network that, in part, corresponds to experiencing diverse environmental conditions. To conceptualize the interactions between host and microbiome in an ecological context, we suggest the "host-associated microbial repertoire," which is the sum of microbial species a host may associate with over the course of its life-history under all encountered environmental circumstances. Furthermore, using examples from both terrestrial and marine ecosystems, we discuss how this concept may be used as a framework to compare the ability of the holobiont to acclimate and adapt to environmental variation, and propose three "signatures" of the concept.