Temperature-Driven Local Acclimatization of Symbiodnium Hosted by the Coral Galaxea fascicularis at Hainan Island, China

Higher genotypic diversity and distinct assembly mechanism of free-living Symbiodiniaceae assemblages than sympatric coral-endosymbiotic assemblages in a tropical coral reef

While in hospite Symbiodiniaceae dinoflagellates are essential for coral health, ambient free-living counterparts are crucial for coral recruitment and resilience. Comparing free-living and in hospite Symbiodiniaceae communities can potentially provide insights into endosymbiont acquisition and recurrent recruitment in bleaching recovery. In this study, we studied coral-endosymbiotic and ambient free-living Symbiodiniaceae communities in the South China Sea. We collected samples from 183 coral and ambient plankton samples and conducted metabarcoding to investigate the diversity distribution, driving factors, and assembly mechanisms of the two groups of Symbiodiniaceae. Results revealed Cladocopium C1 and Durusdinium D1 as dominant genotypes. We detected a higher genotypic diversity in free-living than in hospite symbiodiniacean communities, but with shared dominant genotypes. This indicates a genetically diverse pool of Symbiodiniaceae available for recruitment by corals. Strikingly, we found that the cooler area had more Symbiodiniaceae thermosensitive genotypes, whereas the warmer area had more Symbiodiniaceae thermotolerant genotypes. Furthermore, in hospite and free-living Symbiodiniaceae communities were similarly affected by environmental factors, but shaped by different assembly mechanisms. The in hospite communities were controlled mainly by deterministic processes, whereas the ambient communities by stochastic processes. This study sheds light on the genetic diversity of source environmental Symbiodiniaceae and differential assembly mechanisms influencing Symbiodiniaceae inside and outside corals.IMPORTANCESymbiodiniaceae dinoflagellates play a pivotal role as key primary producers within coral reef ecosystems. Coral-endosymbiotic Symbiodiniaceae communities have been extensively studied, but relatively little work has been reported on the free-living Symbiodiniaceae community. Conducting a comparative analysis between sympatric coral-endosymbiotic and free-living Symbiodiniaceae communities can potentially enhance the understanding of how endosymbiont communities change in response to changing environments and the mechanisms driving these changes. Our findings shed light on the genetic diversity of source environmental Symbiodiniaceae and differential assembly mechanisms shaping free-living and in hospite Symbiodiniaceae communities, with implications in evaluating the adaptive and resilient capacity of corals in response to future climate change.

Adaptive changes of coral Galaxea fascicularis holobiont in response to nearshore stress

Global change and local stressors are simultaneously affecting the nearshore corals, and microbiome flexibility may assist corals in thriving under such multiple stressors. Here, we investigated the effects of various environmental variables on Galaxea fascicularis holobiont from nearshore and offshore reefs. These nearshore reefs were more turbid, eutrophic, and warm than offshore reefs. However, coral physiological parameters did not differ significantly. Corals under stressful nearshore environments had low symbiont diversity and selected more tolerant Symbiodiniaceae. The bacterial diversity of offshore corals was significantly higher, and their community composition varied obviously. Diffusion limitations and environmental heterogeneity were essential in structuring microbial communities. Functional annotation analysis demonstrated significant differences between nearshore and offshore corals in bacterial functional groups. Environmental stress significantly reduced the complexity and connectivity of bacterial networks, and the abundances of keystone taxa altered considerably. These results indicated that corals could thrive nearshore through holobiont plasticity to cope with multiple environmental stresses.

Molecular diversity and assemblages of coral symbionts (Symbiodiniaceae) in diverse scleractinian coral species

The scleractinian coral-associated symbiotic algae Symbiodiniaceae plays an important role in bleaching tolerance and coral resilience. In this study, coral-associated Symbiodiniaceae communities of 14 reef sites of Perhentian and Redang Islands Marine Parks (Malaysia, South China Sea) were characterized using the high-throughput next-generation amplicon sequencing on the ITS2 rDNA marker to inventory the Symbiodiniaceae diversity from a healthy tropical reef system and to generate a baseline for future studies. A total of 64 coral-Symbiodiniaceae associations were characterized in 18 genera (10 families) of scleractinian corals using the SymPortal analytical framework. The results revealed the predominance of Symbiodiniaceae genera Cladocopium (average 82%) and Durusdinium (18%), while Symbiodinium, Breviolum, Fugacium, and Gerakladium were found as minor groups (<0.01%). Of the 39 Cladocopium and Durusdinium major ITS2 sequences, 14 were considered dominant/sub-dominant, with C3u as the predominant type (63.3%), followed by D1 (15%), C27 (10.1%), and C15 (6.9%). A total of 19 and 13 Cladocopium and Durusdinium ITS2-type profiles were detected across the coral species, respectively. Symbiodiniaceae diversity and richness recorded in this study were higher when compared to other reefs in the proximity. With the increasing coral-Symbiodiniaceae associations archived, the database would provide a baseline to assess the changes of Symbiodiniaceae communities in the coral hosts and to explore the potential adaptive roles of this coral-algal association.

Impact of Ocean Warming and Acidification on Symbiosis Establishment and Gene Expression Profiles in Recruits of Reef Coral Acropora intermedia

The onset of symbiosis and the early development of most broadcast spawning corals play pivotal roles in recruitment success, yet these critical early stages are threatened by multiple stressors. However, molecular mechanisms governing these critical processes under ocean warming and acidification are still poorly understood. The present study investigated the interactive impact of elevated temperature (∼28.0°C and ∼30.5°C) and partial pressure of carbon dioxide (pCO₂) (∼600 and ∼1,200 μatm) on early development and the gene expression patterns in juvenile Acropora intermedia over 33 days. The results showed that coral survival was >89% and was unaffected by high temperature, pCO₂, or the combined treatment. Notably, high temperature completely arrested successful symbiosis establishment and the budding process, whereas acidification had a negligible effect. Moreover, there was a positive exponential relationship between symbiosis establishment and budding rates (y = 0.0004e^6.43x, R = 0.72, P < 0.0001), which indicated the importance of symbiosis in fueling asexual budding. Compared with corals at the control temperature (28°C), those under elevated temperature preferentially harbored Durusdinium spp., despite unsuccessful symbiosis establishment. In addition, compared to the control, 351 and 153 differentially expressed genes were detected in the symbiont and coral host in response to experimental conditions, respectively. In coral host, some genes involved in nutrient transportation and tissue fluorescence were affected by high temperature. In the symbionts, a suite of genes related to cell growth, ribosomal proteins, photosynthesis, and energy production was downregulated under high temperatures, which may have severely hampered successful cell proliferation of the endosymbionts and explains the failure of symbiosis establishment. Therefore, our results suggest that the responses of symbionts to future ocean conditions could play a vital role in shaping successful symbiosis in juvenile coral.

Dispersal, genetic variation, and symbiont interaction network of heat-tolerant endosymbiont Durusdinium trenchii: Insights into the adaptive potential of coral to climate change

Global warming has degraded coral reef ecosystems worldwide. Some corals develop thermal tolerance by associating with heat-tolerant Symbiodiniaceae. Here, we studied the mechanisms surrounding the dispersal, genetic variation and symbionts interaction of heat-tolerant Durusdinium trenchii across 13° latitudes in the South China Sea (SCS), to explore the possible mechanisms underlying these changes. Our results showed that Durusdinium trenchii are widely distributed in the seawater from the SCS. Our analyses of microsatellite loci revealed that D. trenchii has a high genetic diversity in the SCS; STRUCTURE analysis indicated that D. trenchii can be divided into four populations within the SCS; There exist positive correlations between genetic variation and geographic isolation, average sea surface temperature (SST) and variations in SST. Network modelling inferences showed that D. trenchii is a key species in the Symbiodiniaceae communities in the tropical SCS and contributes the greatest number of co-exclusion relationships. These results indicated that D. trenchii can affect the rare Symbiodiniaceae community. The long lifespan and the monsoon-driven ocean currents have shaped the wide distribution of D. trenchii. But low SST limits the ability of D. trenchii to establish stable symbioses with coral in the subtropical habitats. Geographical isolation and SST have shaped significant genetic variation of D.trenchii around the SCS. Our data reveals the biogeography and genetic population characteristics of D. trenchii in the Indo-Pacific region, and suggests that heat-tolerance and high genetic diversity of D. trenchii aid the corals with their adaptation to climate change.

Differences in Symbiodiniaceae communities and photosynthesis following thermal bleaching of massive corals in the northern part of the South China Sea

Although many achievements have been made in studies on the relationship between Symbiodiniaceae and coral bleaching, there is little information on the responses of Symbiodiniaceae to coral thermal bleaching in the South China Sea (SCS). In this study, Symbiodiniaceae communities and the effective quantum yield (Ф_PSII) of healthy and bleached massive corals from the SCS were compared. The results indicated that the Symbiodiniaceae communities and Ф_PSII values showed coral bleaching-dependent variations. Specifically, the relative abundances of the rare putatively thermally tolerant Durusdinium sp. (D1) and the Symbiochlorum hainanensis increased significantly in the bleached corals. In addition, bleached Porites lutea was mainly associated with the putatively thermally tolerant Cladocopium sp. (C15 and C91) and exhibited the highest Ф_PSII value compared with other bleached corals. These results highlight that the rare putatively thermally tolerant algae and coral species-specific algae may be important for understanding thermal bleaching of corals.

Latitudinal Variation in the Molecular Diversity and Community Composition of Symbiodiniaceae in Coral From the South China Sea

Coral reefs are continuing to decline worldwide due to anthropogenic climate change. The study of the molecular diversity and biogeographical patterns of Symbiodiniaceae, is essential to understand the adaptive potential and resilience of coral–algal symbiosis. Next generation sequencing was used to analyze the Symbiodiniaceae rDNA internal transcribed spacer 2 marker genes from 178 reef-building coral samples in eight coral habitats across approximately 13° of latitude in the South China Sea (SCS). A total of three Symbiodiniaceae genera, Cladocopium, Durusdinium, and Gerakladium, as well as 31 dominant Symbiodiniaceae types, were identified. Symbiodiniaceae richness, diversity, and community composition varied according to latitude; intermediate and low latitude coral reefs (IR and LR) have higher Symbiodiniaceae richness and diversity than high latitude coral habitats (HC and HR). A PERMANOVA analysis found significant differences in the Symbiodiniaceae community composition in the SCS (F = 14.75, R² = 0.20, p = 0.001 < 0.01). The major dominant Symbiodiniaceae types were C1 in the HC and the HR, C1/Cspc/C50/C15 and D1 in the IR, and C3u and C15 in the LR. Canonical correspondence analysis showed that the relative abundance of different Symbiodiniaceae types is affected by multiple environmental factors. Phylogenetic analysis indicated that the Symbiodiniaceae type Cladocopium, which shared common ancestors, shows similar environmental adaptability. Based on these results, we suggest that coral host species played a relatively small role in the identity of the dominant Symbiodiniaceae type. Therefore, the biogeographical patterns of Symbiodiniaceae may be mainly affected by environmental factors. Our research provides a comprehensive overview of the biogeography of Symbiodiniaceae in the SCS, where coral communities and reefs are widely distributed across different latitude regions and have variable environmental conditions. Our data will provide support for further study of the regional diversification of Symbiodiniaceae and the ecological resilience of the coral-Symbiodiniaceae symbioses.

Flexible Symbiotic Associations of Symbiodinium With Five Typical Coral Species in Tropical and Subtropical Reef Regions of the Northern South China Sea

The coral symbiont Symbiodinium plays important roles in the adaptation of coral to environmental changes. However, coral-Symbiodinium symbiotic associations are not well-understood in the South China Sea (SCS) whilst considering environmental factors and host taxa. In this study, next-generation sequencing of the internal transcribed spacer region 2 (ITS2) marker gene was used to explore the symbiotic associations between Symbiodinium and five typical coral species across tropical and subtropical reef regions of the SCS. The results showed that Acropora sp., Galaxea fascicularis, Platygyra lamellina, and Sarcophyton glaucum exhibited distinct Symbiodinium compositions between tropical and subtropical reef regions, whereas Porites lutea had stable Symbiodinium compositions. More heterogeneous Symbiodinium compositions among different coral species were observed in the tropical region, but there were no statistically significant differences in Symbiodinium compositions among different coral species in subtropical reef regions. There was a correlation between the Symbiodinium compositions and environmental factors, except for the composition of P. lutea. Symbiodinium subclades D1, D2, C71, C71a, C21, C3b, and C161 were primarily explained by the seawater temperature, nitrate, ammonia, and phosphate. Several host-specific Symbiodinium subclades (e.g., C15, C15.6, and C91) were observed in P. lutea as well. The findings of this study demonstrate the relationship of Symbiodinium diversity with coral hosts and the environment are helpful for elucidating the adaptation of corals to global climate change and anthropogenic disturbance.

Season structures prokaryotic partners but not algal symbionts in subtropical hard corals

Coral reef ecosystems have great economic, social, and ecological value. The ecological success of coral reef ecosystems critically depends on coral-algal symbiosis and coral-prokaryotic partnership. However, seasonal changes underlying these relationships in subtropical hard corals of Hong Kong are poorly studied. Here, we compared the community changes of algal symbionts and prokaryotic partners in Platygyra carnosa and Galaxea fascicularis from Hong Kong collected at two seasonal time points of winter and summer via massively parallel sequencing of genetic markers and multivariate analysis. The results indicated that algal symbionts showed no significant changes between the two seasonal time points but prokaryotic partners changed substantially. Prokaryotic partners putatively involved in photosynthesis, nitrogen fixation, and sulfur oxidation increased significantly from winter to summer, while prokaryotic partners potentially associated with chemosynthesis, ammonia oxidation, and nitrite oxidation decreased significantly from winter to summer. Dissolved oxygen and pH served as the main contributors influencing prokaryotic partners in winter, while temperature, turbidity, and salinity played a dominant role in shaping prokaryotic partners in summer. The findings of the present study suggest that season structures prokaryotic partners but not algal symbionts in subtropical hard corals.