Highly infectious symbiont dominates initial uptake in coral juveniles

The majority of reef-building corals acquire their obligate algal symbionts ( Symbiodinium ) from the environment. However, factors shaping the initial establishment of coral–algal symbioses, including parental effects, local environmental conditions and local availability of symbionts, are not well understood. This study monitored the uptake and maintenance of Symbiodinium in juveniles of two common corals, Acropora tenuis and Acropora millepora , that were reciprocally explanted between sites where adult colonies host different types of Symbiodinium . We found that coral juveniles were rapidly dominated by type D Symbiodinium , even though this type is not found in adult colonies (including the parental colonies) in four out of the five study populations. Furthermore, type D Symbiodinium was found in less than one-third of a wide range of coral species ( n  > 50) sampled at the two main study sites, suggesting that its dominance in the acroporid juveniles is not because it is the most abundant local endosymbiotic type. Moreover, dominance by type D was observed irrespective of the light intensity to which juveniles were exposed in a field study. In summary, despite its relatively low abundance in coral assemblages at the study sites and irrespective of the surrounding light environment, type D Symbiodinium is the main symbiont type initially acquired by juveniles of A. millepora and A. tenuis . We conclude that during early ontogeny in these corals, there are few barriers to the uptake of Symbiodinium types which differ from those found in parental colonies, resulting in dominance by a highly infectious and potentially opportunistic symbiont.     

Species-specific interactions between algal endosymbionts and coral hosts define their bleaching response to heat and light stress

The impacts of warming seas on the frequency and severity of bleaching events are well documented, but the potential for different Symbiodinium types to enhance the physiological tolerance of reef corals is not well understood. Here we compare the functionality and physiological properties of juvenile corals when experimentally infected with one of two homologous Symbiodinium types and exposed to combined heat and light stress. A suite of physiological indicators including chlorophyll a fluorescence, oxygen production and respiration, as well as pigment concentration consistently demonstrated lower metabolic costs and enhanced physiological tolerance of Acropora tenuis juveniles when hosting Symbiodinium type C1 compared with type D. In other studies, the same D-type has been shown to confer higher thermal tolerance than both C2 in adults and C1 in juveniles of the closely related species Acropora millepora. Our results challenge speculations that associations with type D are universally most robust to thermal stress. Although the heat tolerance of corals may be contingent on the Symbiodinium strain in hospite, our results highlight the complexity of interactions between symbiotic partners and a potential role for host factors in determining the physiological performance of reef corals.     

Diversities of coral-associated bacteria differ with location, but not species, for three acroporid corals on the Great Barrier Reef

Patterns in the diversity of bacterial communities associated with three species of Acropora ( Acropora millepora, Acropora tenuis and Acropora valida ) were compared at two locations (Magnetic Island and Orpheus Island) on the Great Barrier Reef to better understand the nature and specificity of coral–microbial symbioses. Three culture-independent techniques demonstrated consistent bacterial communities among replicate samples of each coral species, confirming that corals associate with specific microbiota. Profiles were also conserved among all three species of Acropora within each location, suggesting that closely related corals of the same genus harbor similar bacterial types. Bacterial community profiles of A. millepora at Orpheus Island were consistent in samples collected throughout the year, indicating a stable community despite temporal changes. However, DGGE and T-RFLP profiles differed on corals from different reefs. Nonmetric multidimensional scaling of T-RFLP profiles showed that samples grouped according to location rather than coral species. Although similar sequences were retrieved from clone libraries of corals at both Magnetic and Orpheus Island, differences in the relative dominant bacterial ribotypes within the libraries drive bacterial community structure at different geographical locations. These results indicate certain bacterial groups associated specifically with corals, but the dominant bacterial genera differ between geographically-spaced corals.     

A community change in the algal endosymbionts of a scleractinian coral following a natural bleaching event: field evidence of acclimatization

The symbiosis between reef-building corals and their algal endosymbionts (zooxanthellae of the genus Symbiodinium) is highly sensitive to temperature stress, which makes coral reefs vulnerable to climate change. Thermal tolerance in corals is known to be substantially linked to the type of zooxanthellae they harbour and, when multiple types are present, the relative abundance of types can be experimentally manipulated to increase the thermal limits of individual corals. Although the potential exists for this to translate into substantial thermal acclimatization of coral communities, to date there is no evidence to show that this takes place under natural conditions. In this study, we show field evidence of a dramatic change in the symbiont community of Acropora millepora, a common and widespread Indo-Pacific hard coral species, after a natural bleaching event in early 2006 in the Keppel Islands (Great Barrier Reef). Before bleaching, 93.5% (n=460) of the randomly sampled and tagged colonies predominantly harboured the thermally sensitive Symbiodinium type C2, while the remainder harboured a tolerant Symbiodinium type belonging to clade D or mixtures of C2 and D. After bleaching, 71% of the surviving tagged colonies that were initially C2 predominant changed to D or C1 predominance. Colonies that were originally C2 predominant suffered high mortality (37%) compared with D-predominant colonies (8%). We estimate that just over 18% of the original A. millepora population survived unchanged leaving 29% of the population C2 and 71% D or C1 predominant six months after the bleaching event. This change in the symbiont community structure, while it persists, is likely to have substantially increased the thermal tolerance of this coral population. Understanding the processes that underpin the temporal changes in symbiont communities is key to assessing the acclimatization potential of reef corals.     

Resistance to thermal stress in corals without changes in symbiont composition

Discovering how corals can adjust their thermal sensitivity in the context of global climate change is important in understanding the long-term persistence of coral reefs. In this study, we showed that short-term preconditioning to higher temperatures, 3°C below the experimentally determined bleaching threshold, for a period of 10 days provides thermal tolerance for the symbiosis stability between the scleractinian coral, Acropora millepora and Symbiodinium. Based on genotypic analysis, our results indicate that the acclimatization of this coral species to thermal stress does not come down to simple changes in Symbiodinium and/or the bacterial communities that associate with reef-building corals. This suggests that the physiological plasticity of the host and/or symbiotic components appears to play an important role in responding to ocean warming. The further study of host and symbiont physiology, both of Symbiodinium and prokaryotes, is of paramount importance in the context of global climate change, as mechanisms for rapid holobiont acclimatization will become increasingly important to the long-standing persistence of coral reefs.     

Corals form characteristic associations with symbiotic nitrogen-fixing bacteria

The complex symbiotic relationship between corals and their dinoflagellate partner Symbiodinium is believed to be sustained through close associations with mutualistic bacterial communities, though little is known about coral associations with bacterial groups able to fix nitrogen (diazotrophs). In this study, we investigated the diversity of diazotrophic bacterial communities associated with three common coral species (Acropora millepora, Acropora muricata, and Pocillopora damicormis) from three midshelf locations of the Great Barrier Reef (GBR) by profiling the conserved subunit of the nifH gene, which encodes the dinitrogenase iron protein. Comparisons of diazotrophic community diversity among coral tissue and mucus microenvironments and the surrounding seawater revealed that corals harbor diverse nifH phylotypes that differ between tissue and mucus microhabitats. Coral mucus nifH sequences displayed high heterogeneity, and many bacterial groups overlapped with those found in seawater. Moreover, coral mucus diazotrophs were specific neither to coral species nor to reef location, reflecting the ephemeral nature of coral mucus. In contrast, the dominant diazotrophic bacteria in tissue samples differed among coral species, with differences remaining consistent at all three reefs, indicating that coral-diazotroph associations are species specific. Notably, dominant diazotrophs for all coral species were closely related to the bacterial group rhizobia, which represented 71% of the total sequences retrieved from tissue samples. The species specificity of coral-diazotroph associations further supports the coral holobiont model that bacterial groups associated with corals are conserved. Our results suggest that, as in terrestrial plants, rhizobia have developed a mutualistic relationship with corals and may contribute fixed nitrogen to Symbiodinium.     

The role of zooxanthellae in the thermal tolerance of corals: a 'nugget of hope' for coral reefs in an era of climate change

The ability of coral reefs to survive the projected increases in temperature due to global warming will depend largely on the ability of corals to adapt or acclimatize to increased temperature extremes over the next few decades. Many coral species are highly sensitive to temperature stress and the number of stress (bleaching) episodes has increased in recent decades. We investigated the acclimatization potential of Acropora millepora, a common and widespread Indo-Pacific hard coral species, through transplantation and experimental manipulation. We show that adult corals, at least in some circumstances, are capable of acquiring increased thermal tolerance and that the increased tolerance is a direct result of a change in the symbiont type dominating their tissues from Symbiodinium type C to D. Our data suggest that the change in symbiont type in our experiment was due to a shuffling of existing types already present in coral tissues, not through exogenous uptake from the environment. The level of increased tolerance gained by the corals changing their dominant symbiont type to D (the most thermally resistant type known) is around 1-1.5 degrees C. This is the first study to show that thermal acclimatization is causally related to symbiont type and provides new insight into the ecological advantage of corals harbouring mixed algal populations. While this increase is of huge ecological significance for many coral species, in the absence of other mechanisms of thermal acclimatization/adaptation, it may not be sufficient to survive climate change under predicted sea surface temperature scenarios over the next 100 years. However, it may be enough to 'buy time' while greenhouse reduction measures are put in place.     

Identification of fast-evolving genes in the scleractinian coral Acropora using comparative EST analysis

To identify fast-evolving genes in reef-building corals, we performed direct comparative sequence analysis with expressed sequence tag (EST) datasets from two acroporid species: Acropora palmata from the Caribbean Sea and A. millepora from the Great Barrier Reef in Australia. Comparison of 589 independent sequences from 1,421 A. palmata contigs, with 10,247 A. millepora contigs resulted in the identification of 196 putative homologues. Most of the homologous pairs demonstrated high amino acid similarities (over 90%). Comparisons of putative homologues showing low amino acid similarities (under 90%) among the Acropora species to the near complete datasets from two other cnidarians (Hydra magnipapillata and Nematostella vectensis) implied that some were non-orthologous. Within 86 homologous pairs, 39 exhibited dN/dS ratios significantly less than 1, suggesting that these genes are under purifying selection associated with functional constraints. Eight independent genes showed dN/dS ratios exceeding 1, while three deviated significantly from 1, suggesting that these genes may play important roles in the adaptive evolution of Acropora. Our results also indicated that CEL-III lectin was under positive selection, consistent with a possible role in immunity or symbiont recognition. Further studies are needed to clarify the possible functions of the genes under positive selection to provide insight into the evolutionary process of corals.     

Patterns of coral-dinoflagellate associations in Acropora: significance of local availability and physiology of Symbiodinium strains and host-symbiont selectivity

Like other reef-building corals, members of the genus Acropora form obligate endosymbioses with dinoflagellates (zooxanthellae) belonging to the genus Symbiodinium. Both Symbiodinium and its hosts are diverse assemblages, and the relationships between host and algal genotypes are unclear. In this study, we determined phylogenetic relationships between Symbiodinium isolates from a wide range of Acropora species and plotted the algal genotypes onto a molecular phylogeny of 28 Acropora species, using the same samples for the host and symbiont genotyping. In addition, we performed a preliminary survey of zooxanthella distribution in Acropora species from the central Great Barrier Reef. Three of the four known major zooxanthellae clades were represented in the 168 samples examined, and within the major clade C, three distinct subclades were identified. No evidence was found for coevolution, but several clear patterns of specificity were identified. Moreover, composition of the zooxanthella pool varied among locales and in one host species we found light-related patterns of zooxanthella distribution.     

Acquisition of symbiotic dinoflagellates (Symbiodinium) by juveniles of the coral Acropora longicyathus

Scleractinian corals may acquire Symbiodinium from their parents (vertically) or from the environment (horizontally). In the present study, adult colonies of the coral Acropora longicyathus from One Tree Island (OTI) on the southern Great Barrier Reef (Australia) acquired two distinct varieties of symbiotic dinoflagellates (Symbiodinium) from the environment. Adult colonies had either Symbiodinium from clade C (86.7%) or clade A (5.3%), or a mixture of both clades A and C (8.0% of all colonies). In contrast, all 10-day-old juveniles were associated with Symbiodinium from clade A, while 83-day-old colonies contained clades A, C and D even though they were growing at the same location. Symbiodinium from clade A were dominant in both 10- and 83-day-old juveniles (99 and 97% of all recruits, respectively), while clade D was also found in 31% of 83-day-old juveniles. Experimental manipulation also revealed that parental association (with clade A or C), or the location within the OTI reef, did not influence which clade of symbiont was acquired by juvenile corals. The differences between the genetic identity of populations of Symbiodinium resident in juveniles and adult A. longicyathus suggest that ontogenetic changes in the symbiosis may occur during the development of scleractinian corals. Whether or not these changes are due to host selective processes or differences in the physical environment associated with juvenile versus adult colonies remains to be determined.     

Habitat utilization by coral reef fish: implications for specialists vs. generalists in a changing environment

1. The impact of environmental disturbance and habitat loss on associated species is expected to be dependent on a species' level of specialization. We examined habitat use and specialization of coral reef fish from the diverse and ecologically important family Pomacentridae, and determined which species are susceptible to declines in coral cover due to disturbance induced by crown-of-thorns seastar (COTS, Acanthaster planci L.). 2. A high proportion of pomacentrid species live in association with live coral as adults (40%) or juveniles (53%). Adults of many species had strong affiliations with branching corals, while juveniles favoured plating growth forms, reflecting the sizes of refuge provided by coral types. 3. Juveniles of species that associated with coral had narrower niche breadths than adult conspecifics, due to associations with specific coral types. The especially high coral association and narrower niche breadth of juveniles suggest that the presence of live coral is crucial for many species during early life history, and that disturbance-induced coral loss may have serious flow-on effects on adult abundance. 4. Microhabitat availability was a poor predictor of fish species abundance. Significant correlations between coverage of coral types and abundance of five adults and two juvenile species were detected; however, these relationships explained <35% and <10% of the variation in abundance of adult and juvenile species, respectively. 5. Niche breadth explained 74% of the variation in species' mean response to coral decline and it is clear that disturbance has a greater impact on resource specialists, suggesting that increasing frequency and intensity of coral loss will cause reef fish communities to become dominated by habitat generalists at the expense of coral-dwelling specialists.     

Geographic and habitat partitioning of genetically distinct zooxanthellae (Symbiodinium) in Acropora corals on the Great Barrier Reef

Intra- and intercolony diversity and distribution of zooxanthellae in acroporid corals is largely uncharted. In this study, two molecular methods were applied to determine the distribution of zooxanthellae in the branching corals Acropora tenuis and A. valida at several reef locations in the central section of the Great Barrier Reef. Sun-exposed and shaded parts of all colonies were examined. Single-stranded conformational polymorphism analysis showed that individual colonies of A. tenuis at two locations harbour two strains of Symbiodinium belonging to clade C (C1 and C2), whereas conspecific colonies at two other reefs harboured a single zooxanthella strain. A. valida was found to simultaneously harbour strains belonging to two distinct phylogenetic clades (C and D) at all locations sampled. A novel method with improved sensitivity (quantitative polymerase chain reaction using Taqman fluorogenic probes) was used to map the relative abundance distribution of the two zooxanthella clades. At two of the five sampling locations both coral species were collected. At these two locations, composition of the zooxanthella communities showed the same pattern in both coral species, i.e. correlation with ambient light in Pioneer Bay and an absence thereof in Nelly Bay. The results show that the distribution of genetically distinct zooxanthellae is correlated with light regime and possibly temperature in some (but not all) colonies of A. tenuis and A. valida and at some reef locations, which we interpret as acclimation to local environmental conditions.     

Diversity and distribution of symbiodinium associated with seven common coral species in the Chagos Archipelago, central Indian Ocean

The Chagos Archipelago designated as a no-take marine protected area in 2010, lying about 500 km south of the Maldives in the Indian Ocean, has a high conservation priority, particularly because of its fast recovery from the ocean-wide massive coral mortality following the 1998 coral bleaching event. The aims of this study were to examine Symbiodinium diversity and distribution associated with scleractinian corals in five atolls of the Chagos Archipelago, spread over 10,000 km(2). Symbiodinium clade diversity in 262 samples of seven common coral species, Acropora muricata, Isopora palifera, Pocillopora damicornis, P. verrucosa, P. eydouxi, Seriatopora hystrix, and Stylophora pistillata were determined using PCR-SSCP of the ribosomal internal transcribed spacer 1 (ITS1), PCR-DDGE of ITS2, and phylogenetic analyses. The results indicated that Symbiodinium in clade C were the dominant symbiont group in the seven coral species. Our analysis revealed types of Symbiodinium clade C specific to coral species. Types C1 and C3 (with C3z and C3i variants) were dominant in Acroporidae and C1 and C1c were the dominant types in Pocilloporidae. We also found 2 novel ITS2 types in S. hystrix and 1 novel ITS2 type of Symbiodinium in A. muricata. Some colonies of A. muricata and I. palifera were also associated with Symbiodinium A1. These results suggest that corals in the Chagos Archipelago host different assemblages of Symbiodinium types then their conspecifics from other locations in the Indian Ocean; and that future research will show whether these patterns in Symbiodinium genotypes may be due to local adaptation to specific conditions in the Chagos.     

Microhabitat use and prey selection of the coral-feeding snail <Emphasis Type="Italic">Drupella cornus</Emphasis> in the northern Red Sea

Corallivorous gastropods of the genus Drupella are known for population outbreaks throughout the Indo-Pacific region. Despite their potential to destroy wide areas of coral reef, prey preferences have never been analyzed with respect to prey availability, and juvenile ecology and food selectivity remain largely unknown. Here, the influence of water depth, coral abundance, colony shape, prey species, and intraspecific attraction among snails on distribution patterns, prey selection, and microhabitat use of D. cornus was studied in the northern Red Sea. Special emphasis was put on ontogenetic differences. The snails were most abundant in the shallowest reef zone (1 m depth). Adults were associated with several substrates and coral growth forms, whereas juveniles were highly cryptic and restricted to live branching corals. The genus Acropora was significantly preferred over other acroporid and pocilloporid corals. As revealed by resource selection ratios, Acropora acuminata was preferred by juveniles, A. selago by adults. In aquarium experiments, intraspecific attraction was high among both life stages. Overall, significant differences in juvenile and adult microhabitat and prey use suggest that juveniles have more specific habitat requirements, and indicate ecological impacts on coral communities different from that of adults. Prey preferences seem to depend on both coral genus and colony shape. Acropora corals provide the best combination of food and shelter and therefore determine distribution patterns of D. cornus.     

Restriction Fragment Length Polymorphism Analysis of Large Subunit rDNA of Symbiotic Dinoflagellates from Scleractinian Corals in the Zhubi Coral Reef of the Nansha Islands

Zooxanthellae are very important for the coral reef ecosystem. The diversity of coral hosts Is high in the South China Sea, but the diversity of zooxanthellae has not yet been investigated. We chose the Zhubi Coral Reef of the Nansha Islands as the region to be surveyed in the present study because it represents a typical tropical coral reef of the South China Sea and we investigated zooxanthellae diversity In 10 host scleractinlan coral species using polymerase chain reaction （PCR） of the large subunit rRNA and restriction fragment length polymorphlsm （RFLP） patterns. Poclllopora verrucosa, Acropora pefifera, Acropora mlllepora, Fungla fungltes, Galaxea fasclcularls, and Acropora pruinosa harbor Clade C, Goniastrea aspera harbors Clade D, and Acropora formosa harbors Clades D and C. Therefore, the Clade C is the dominant type in the Zhubi Coral Reef of the Nansha Islands. Furthermore, the results of the present also disprove what has been widely accepted, namely that one coral host harbors only one algal symblont. The coral-algal symbiosis Is flexible, which may be an Important mechanism for surviving coral bleaching. Meanwhile, on the basis of the results of the present study, we think that Symblodlnium Clade D may be more tolerant to stress than Symbiodlnlum Clade C.     

The roles of age,parentage and environment on bacterial and algal endosymbiont communities in Acropora corals

The bacterial and microalgal endosymbiont (Symbiodiniaceae spp.) communities associated with corals have important roles in their health and resilience, yet little is known about the factors driving their succession during early coral life stages. Using 16S rRNA gene and ITS2 metabarcoding, we compared these communities in four Acropora coral species and their hybrids obtained from two laboratory crosses (Acropora tenuis × Acropora loripes and Acropora sarmentosa × Acropora florida) across the parental, recruit (7 months old) and juvenile (2 years old) life stages. We tested whether microbiomes differed between (a) life stages, (b) hybrids and purebreds, and (c) treatment conditions (ambient/elevated temperature and pCO₂). Microbial communities of early life stage corals were highly diverse, lacked host specificity and were primarily determined by treatment conditions. Over time, a winnowing process occurred, and distinct microbial communities developed between the two species pair crosses by 2 years of age, irrespective of hybrid or purebred status. These findings suggest that the microbial communities of corals have a period of flexibility prior to adulthood, which can be valuable to future research aimed at the manipulation of coral microbial communities.     

Habitat associations of juvenile versus adult butterflyfishes

Many coral reef fishes exhibit distinct ontogenetic shifts in habitat use while some species settle directly in adult habitats, but there is not any general explanation to account for these differences in settlement strategies among coral reef fishes. This study compared distribution patterns and habitat associations of juvenile (young of the year) butterflyfishes to those of adult conspecifics. Three species, Chaetodon auriga, Chaetodon melannotus, and Chaetodon vagabundus, all of which have limited reliance on coral for food, exhibited marked differences in habitat association of juvenile versus adult individuals. Juveniles of these species were consistently found in shallow-water habitats, whereas adult conspecifics were widely distributed throughout a range of habitats. Juveniles of seven other species (Chaetodon aureofasciatus, Chaetodon baronessa, Chaetodon citrinellus, Chaetodon lunulatus, Chaetodon plebeius, Chaetodon rainfordi, and Chaetodon trifascialis), all of which feed predominantly on live corals, settled directly into habitat occupied by adult conspecifics. Butterflyfishes with strong reliance on corals appear to be constrained to settle in habitats that provide access to essential prey resources, precluding their use of distinct juvenile habitats. More generalist butterflyfishes, however, appear to utilize distinct juvenile habitats and exhibit marked differences in the distribution of juveniles versus adults.     

High potential for formation and persistence of chimeras following aggregated larval settlement in the broadcast spawning coral, Acropora millepora

In sessile modular marine invertebrates, chimeras can originate from fusions of closely settling larvae or of colonies that come into contact through growth or movement. While it has been shown that juveniles of brooding corals fuse under experimental conditions, chimera formation in broadcast spawning corals, the most abundant group of reef corals, has not been examined. This study explores the capacity of the broadcast spawning coral Acropora millepora to form chimeras under experimental conditions and to persist as chimeras in the field. Under experimental conditions, 1.5-fold more larvae settled in aggregations than solitarily, and analyses of nine microsatellite loci revealed that 50 per cent of juveniles tested harboured different genotypes within the same colony. Significantly, some chimeric colonies persisted for 23 months post-settlement, when the study ended. Genotypes within persisting chimeric colonies all showed a high level of relatedness, whereas rejecting colonies displayed variable levels of relatedness. The nearly threefold greater sizes of chimeras compared with solitary juveniles, from settlement through to at least three months, suggest that chimerism is likely to be an important strategy for maximizing survival of vulnerable early life-history stages of corals, although longer-term studies are required to more fully explore the potential benefits of chimerism.     

Major cellular and physiological impacts of ocean acidification on a reef building coral

As atmospheric levels of CO(2) increase, reef-building corals are under greater stress from both increased sea surface temperatures and declining sea water pH. To date, most studies have focused on either coral bleaching due to warming oceans or declining calcification due to decreasing oceanic carbonate ion concentrations. Here, through the use of physiology measurements and cDNA microarrays, we show that changes in pH and ocean chemistry consistent with two scenarios put forward by the Intergovernmental Panel on Climate Change (IPCC) drive major changes in gene expression, respiration, photosynthesis and symbiosis of the coral, Acropora millepora, before affects on biomineralisation are apparent at the phenotype level. Under high CO(2) conditions corals at the phenotype level lost over half their Symbiodinium populations, and had a decrease in both photosynthesis and respiration. Changes in gene expression were consistent with metabolic suppression, an increase in oxidative stress, apoptosis and symbiont loss. Other expression patterns demonstrate upregulation of membrane transporters, as well as the regulation of genes involved in membrane cytoskeletal interactions and cytoskeletal remodeling. These widespread changes in gene expression emphasize the need to expand future studies of ocean acidification to include a wider spectrum of cellular processes, many of which may occur before impacts on calcification.     

Responses of coral‐associated bacterial communities to heat stress differ with Symbiodinium type on the same coral host

This study compared the effect of heat stress on coral‐associated bacterial communities among juveniles of the coral, Acropora tenuis, hosting different Symbiodinium types. In comparison to a control temperature treatment (28 °C), we documented dramatic changes in bacterial associates on juvenile corals harbouring ITS 1 type D Symbiodinium when placed in a high (32 °C) temperature treatment. In particular, there was a marked increase in the number of retrieved Vibrio affiliated sequences, which coincided with a 44% decline in the photochemical efficiency of the D‐juveniles. Interestingly, these Vibrio sequences affiliated most closely with the coral pathogen, Vibrio coralliilyticus, which has been implicated in some coral disease outbreaks. In contrast, A. tenuis hosting ITS 1 type C1 Symbiodinium did not exhibit major bacterial shifts in the elevated temperature treatment, indicating a more stable bacterial community during thermal stress; concomitantly a decline (10%) in photochemical efficiency was minimal for this group. D juveniles that had been exposed to moderately elevated sea temperatures (30 °C) in the field before being placed in the control temperature treatment displayed a decrease in the number of Vibrio affiliated sequences and bacterial profiles shifted to become more similar to profiles of corals harbouring type C1 Symbiodinium. In combination, these results demonstrate that thermal stress can result in shifts in coral‐associated bacterial communities, which may lead to deteriorating coral health. The lower resilience of A. tenuis to thermal stress when harbouring Symbiodinium D highlights the importance of inter‐kingdom interactions among the coral host, dinoflagellate endosymbiont and bacterial associates for coral health and resilience.