Development of a transcriptomic database for 14 species of scleractinian corals.

BACKGROUND: Scleractinian corals are important reef builders, but around the world they are under the threat of global climate change as well as local stressors. Molecular resources are critical for understanding a species' stress responses and resilience to the changing environment, but such resources are unavailable for most scleractinian corals, especially those distributed in the South China Sea. We therefore aimed to provide transcriptome resources for 14 common species, including a few structure forming species, in the South China Sea. DESCRIPTION: We sequenced the transcriptome of 14 species of scleractinian corals using high-throughput RNA-seq and conducted de novo assembly. For each species, we produced 7.4 to 12.0 gigabases of reads, and assembled them into 271 to 762 thousand contigs with a N50 value of 629 to 1427 bp. These contigs included 66 to 114 thousand unigenes with a predicted open reading frame, and 74.3 to 80.5% of the unigenes were functionally annotated. In the azooxanthelate species Tubastraea coccinea, 41.5% of the unigenes had at least a best-hit sequence from corals. In the other thirteen species, 20.2 to 48.9% of the annotated unigenes had best-hit sequences from corals, and 28.3 to 51.6% from symbiotic algae belonging to the family Symbiodinaceae. With these resources, we developed a transcriptome database (CoralTBase) which features online BLAST and keyword search for unigenes/functional terms through a user friendly Internet interface. SHORT CONCLUSION: We developed comprehensive transcriptome resources for 14 species of scleractinian corals and constructed a publicly accessible database ( www.comp.hkbu.edu.hk/~db/CoralTBase ). CoralTBase will facilitate not only functional studies using these corals to understand the molecular basis of stress responses and adaptation, but also comparative transcriptomic studies with other species of corals and more distantly related cnidarians.

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

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

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

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

Comparative transcriptomics of two coral holobionts collected during the 2017 El Niño heat wave reveal differential stress response mechanisms.

Although coral species exhibit differential susceptibility to stressors, little is known about the underlying molecular mechanisms. Here we compared scleractinian corals Montipora peltiformis and Platygyra carnosa collected during the 2017 El Niño heat wave. Zooxanthellae density and chlorophyll a content declined and increased substantially during and after heat stress event, respective. However, the magnitude of change was larger in M. peltiformis. Transcriptome analysis showed that heat-stressed corals corresponded to metabolic depression and catabolism of amino acids in both hosts which might promote their survival. However, only M. peltiformis has developed the bleached coral phenotype with corresponding strong stress- and immune-related responses in the host and symbiont, and strong suppression of photosynthesis-related genes in the symbiont. Overall, our study reveals differences among species in the homeostatic capacity to prevent the development of the bleached phenotype under environmental stressors, eventually determining their likelihood of survival in the warming ocean.

Host-symbiont transcriptomic changes during natural bleaching and recovery in the leaf coral Pavona decussata.

Coral bleaching has become a major threat to coral reefs worldwide, but for most coral species little is known about their resilience to environmental changes. We aimed to understand the gene expressional regulation underlying natural bleaching and recovery in Pavona decussata, a dominant species of scleractinian coral in the northern South China Sea. Analyzing samples collected in 2017 from the field revealed distinct zooxanthellae density, chlorophyll a concentration and transcriptomic signatures corresponding to changes in health conditions of the coral holobiont. In the host, normal-looking tissues of partially bleached colonies were frontloaded with stress responsive genes, as indicated by upregulation of immune defense, response to endoplasmic reticulum, and oxidative stress genes. Bleaching was characterized by upregulation of apoptosis-related genes which could cause a reduction in algal symbionts, and downregulation of genes involved in stress responses and metabolic processes. The transcription factors stat5b and irf1 played key roles in bleaching by regulating immune and apoptosis pathways. Recovery from bleaching was characterized by enrichment of pathways involved in mitosis, DNA replication, and recombination for tissue repairing, as well as restoration of energy and metabolism. In the symbionts, bleaching corresponded to imbalance in photosystems I and II activities which enhanced oxidative stress and limited energy production and nutrient assimilation. Overall, our study revealed distinct gene expressional profiles and regulation in the different phases of the bleaching and recovery process, and provided new insight into the molecular mechanisms underlying the holobiont's resilience that may determine the species' fate in response to global and regional environmental changes.

Rapid external erosion of coral substrate in subtropical Hong Kong waters.

Erosion of coral substrate plays a crucial role in reef calcium carbonate budget, but little is known about erosion in subtropical corals. In a 2-year study of coral substrate erosion, we deployed Porites skeletal blocks at nine sites across subtropical Hong Kong waters. External erosion varied from 0.05 to 3.07 kg m-2 yr-1 and accounted for 23.4-99.2% of the total erosion. More than half of the study sites had substantial external erosion (> 1 kg m-2 yr-1), and the values were positively correlated with density of the sea urchin Diadema setosum. Excluding urchins from access to the skeletal blocks using cages reduced external erosion by more than 90%. Overall, our study revealed that external erosion caused by urchin grazing contributed predominantly to the total coral skeletal loss in Hong Kong waters. Control of sea urchin population is needed to reduce coral erosion in places with high urchin density. (149 words).

Hong Kong's subtropical scleractinian coral communities: Baseline, environmental drivers and management implications.

We surveyed 41 sites to provide an updated baseline of Hong Kong coral communities. Five community types were identified, among them the most common one inhabited oceanic waters and dominated by both massive and upward-plating corals. The 41 sites had 2.1-⁠79% coral cover; among them 21 in the eastern waters had >40% coral cover. Corals in several sites showed signs of external bioerosion or bleaching-induced damage. Sites in the southern waters had low coral cover. Both coral cover and generic richness correlated negatively with several water quality parameters including total inorganic nitrogen concentration and turbidity, indicating the development of Hong Kong's coral communities is constrained by water quality parameters. Management actions are proposed to reduce bioerosion, and to monitor sites affected by bleaching.

Localized bleaching and quick recovery in Hong Kong's coral communities.

During the summer of 2017 we visited 33 sites with substantial coral cover across Hong Kong waters. At six sites where coral bleaching was observed, video-transect surveys were conducted, which revealed 18.7% to 56.1% bleached colonies and 5.9% to 57.6% bleached coral covered area per site. Mainly affected were three plate-like and three massive coral species. Water quality parameters were analyzed, which indicated that hyposalinity might have triggered the bleaching event. Tagging and follow-up field observation revealed a pattern of recovery depending on coral growth form, with high recovery rates (>93%) at five sites dominated by massive and submassive corals, but moderate (70%) at a site dominated by plate-like corals. Our study shows that the corals of Hong Kong exhibit differential susceptibility to bleaching and ability to recover, therefore it is imperative to establish a long-term monitoring programme to detect the changes in community structure over time.

Coral reef diversity losses in China's Greater Bay Area were driven by regional stressors.

Observations of coral reef losses to climate change far exceed our understanding of historical degradation before anthropogenic warming. This is a critical gap to fill as conservation efforts simultaneously work to reverse climate change while restoring coral reef diversity and function. Here, we focused on southern China's Greater Bay Area, where coral communities persist despite centuries of coral mining, fishing, dredging, development, and pollution. We compared subfossil assemblages with modern-day communities and revealed a 40% decrease in generic diversity, concomitant to a shift from competitive to stress-tolerant species dominance since the mid-Holocene. Regions with characteristically poor water quality-high chl-a, dissolved inorganic nitrogen, and turbidity-had lower contemporary diversity and the greatest community composition shift observed in the past, driven by the near extirpation of Acropora These observations highlight the urgent need to mitigate local stressors from development in concert with curbing greenhouse gas emissions.

Exploring coral microbiome assemblages in the South China Sea.

Coral reefs are significant ecosystems. The ecological success of coral reefs relies on not only coral-algal symbiosis but also coral-microbial partnership. However, microbiome assemblages in the South China Sea corals remain largely unexplored. Here, we compared the microbiome assemblages of reef-building corals Galaxea (G. fascicularis) and Montipora (M. venosa, M. peltiformis, M. monasteriata) collected from five different locations in the South China Sea using massively-parallel sequencing of 16S rRNA gene and multivariate analysis. The results indicated that microbiome assemblages for each coral species were unique regardless of location and were different from the corresponding seawater. Host type appeared to drive the coral microbiome assemblages rather than location and seawater. Network analysis was employed to explore coral microbiome co-occurrence patterns, which revealed 61 and 80 co-occurring microbial species assembling the Galaxea and Montipora microbiomes, respectively. Most of these co-occurring microbial species were commonly found in corals and were inferred to play potential roles in host nutrient metabolism; carbon, nitrogen, sulfur cycles; host detoxification; and climate change. These findings suggest that the co-occurring microbial species explored might be essential to maintain the critical coral-microbial partnership. The present study provides new insights into coral microbiome assemblages in the South China Sea.

The 2014 summer coral bleaching event in subtropical Hong Kong.

We reported a coral bleaching event that occurred in August-September 2014 in Hong Kong waters based on video transect surveys conducted at eight sites. The bleaching affected eight species of corals with different growth forms. Bleaching at seven of the eight study sites was minor, affecting only 0.4-5.2% colonies and 0.8-10.0% coral-covered area. Sharp Island East, however, suffered from a moderate level of bleaching, with 13.1% colonies and 30.1% coral-covered area affected. Examination of the government's environmental monitoring data indicated abnormal water quality conditions preceding and during the bleaching event. Follow-up field surveys of tagged colonies showed that 76% of them had fully recovered, 12% partially recovered, and 12% suffered from mortality. These results indicate that the subtropical corals of Hong Kong are not immune to bleaching, and there is a need to study their responses under climate change scenarios.

Metagenomic analysis reveals a green sulfur bacterium as a potential coral symbiont.

Coral reefs are ecologically significant habitats. Coral-algal symbiosis confers ecological success on coral reefs and coral-microbial symbiosis is also vital to coral reefs. However, current understanding of coral-microbial symbiosis on a genomic scale is largely unknown. Here we report a potential microbial symbiont in corals revealed by metagenomics-based genomic study. Microbial cells in coral were enriched for metagenomic analysis and a high-quality draft genome of "Candidatus Prosthecochloris korallensis" was recovered by metagenome assembly and genome binning. Phylogenetic analysis shows "Ca. P. korallensis" belongs to the Prosthecochloris clade and is clustered with two Prosthecochloris clones derived from Caribbean corals. Genomic analysis reveals "Ca. P. korallensis" has potentially important ecological functions including anoxygenic photosynthesis, carbon fixation via the reductive tricarboxylic acid (rTCA) cycle, nitrogen fixation, and sulfur oxidization. Core metabolic pathway analysis suggests "Ca. P. korallensis" is a green sulfur bacterium capable of photoautotrophy or mixotrophy. Potential host-microbial interaction reveals a symbiotic relationship: "Ca. P. korallensis" might provide organic and nitrogenous nutrients to its host and detoxify sulfide for the host; the host might provide "Ca. P. korallensis" with an anaerobic environment for survival, carbon dioxide and acetate for growth, and hydrogen sulfide as an electron donor for photosynthesis.

Borehole density on the surface of living Porites corals as an indicator of sedimentation in Hong Kong.

Borehole density on the surface of Porites has been used as an indicator of water quality in the Great Barrier Reef. We assessed the relationship between borehole density on Porites and eight water quality parameters across 26 sites in Hong Kong. We found that total borehole densities on the surface of Porites at 16 of the studied sites were high (>1000individualsm(-2)), with polychaetes being the dominant bioeroders. Sedimentation rate was correlated positively with total borehole density and polychaete borehole density, with the latter relationship having a substantially higher correlation of determination. None of the environmental factors used were significantly correlated with bivalve borehole density. These results provide a baseline for assessing future changes in coral bioerosion in Hong Kong. This present study also indicates that polychaete boreholes can be used as a bioindicator of sedimentation in the South China Sea region where polychaetes are numerically dominant bioeroders.