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The limestone skeleton of Scleractinian corals is a complex and intricate environment consisting of an array of ecological microniches, which harbour a vast microbial community. In addition, recent studies have demonstrated that endolithic microbes play a variety of important ecological roles. Here, we use a combination of metabarcoding of the small subunit rRNA genes, microscopy and spectrophotometry to characterize the endolithic community of the coral Isopora palifera, one of the most common reef builders of the Great Barrier Reef. While a previous study suggested that the Isopora skeleton was dominated by anoxygenic phototrophs, our data show an abundance of chlorophyll a, highlighting the presence of oxygenic photosynthetic endolithic microbes. Proteobacteria, Bacteriodetes, Actinobacteria and Spirochaetes were consistently found, and the bacterial community was similar in shallow and deeper skeletal micro-samples. The micro-eukaryotic community was dominated by endolithic green algae, and the protist Labyrynthula, found at previously unreported high relative abundance.

Growth anomalies (GAs), a tumour-like disease affecting scleractinian corals, have been reported across the major reef systems of the Indo-Pacific and wider Atlantic regions, predominantly affecting Acropora and Porites species. In 2018, GAs were observed for the first time on Isopora palifera, an important observation from the isolated Cocos (Keeling) Islands in the East Indian Ocean, as the species is a key reef building coral at the atoll. In this study, the local distribution and abundance of GAs was quantified to determine if this occurrence could be classified as an outbreak, and the effects of this disease on I. palifera on reproductive potential and growth was described using histological and geochemical analysis. Growth anomalies were documented at 75% of sites and affected approximately one third of the I. palifera colonies examined. This disease compromises the biological and reproductive functioning of the host, as evidenced by a significant reduction in the density of oocytes, mesenteries, polyps, and zooxanthellae in infected tissues in comparison to healthy tissue. Furthermore, geochemical analysis indicates changes to key trace elements may be the result of bioerosion processes by infecting bacteria and the reprecipitation of calcite. The results of this study indicate the division of energy to the rapid skeletal development that characterises the disease, may have occurred at the detriment of the future reproductive potential of the population.

Background Endolithic microbes in coral skeletons are known to be a nutrient source for the coral host. In addition to aerobic endolithic algae and Cyanobacteria , which are usually described in the various corals and form a green layer beneath coral tissues, the anaerobic photoautotrophic green sulfur bacteria (GSB) Prosthecochloris is dominant in the skeleton of Isopora palifera . However, due to inherent challenges in studying anaerobic microbes in coral skeleton, the reason for its niche preference and function are largely unknown. Results This study characterized a diverse and dynamic community of endolithic microbes shaped by the availability of light and oxygen. In addition, anaerobic bacteria isolated from the coral skeleton were cultured for the first time to experimentally clarify the role of these GSB. This characterization includes GSB’s abundance, genetic and genomic profiles, organelle structure, and specific metabolic functions and activity. Our results explain the advantages endolithic GSB receive from living in coral skeletons, the potential metabolic role of a clade of coral-associated Prosthecochloris (CAP) in the skeleton, and the nitrogen fixation ability of CAP. Conclusion We suggest that the endolithic microbial community in coral skeletons is diverse and dynamic and that light and oxygen are two crucial factors for shaping it. This study is the first to demonstrate the ability of nitrogen uptake by specific coral-associated endolithic bacteria and shed light on the role of endolithic bacteria in coral skeletons.

Coral skeletons constitute sources of nutrients and energy for holobiont. Although bacteria predominate in endolithic microbiomes of corals, their ecological functions have long been masked by those of symbiotic microalgae. In the skeleton of Isopora palifera, previous studies showed the absence of microalgae and a green layer dominated by green sulfur bacteria. This system, which excludes a contribution from microalgae, provides a perfect model for studying the role of endolithic bacteria in corals. Using this model, we examined the metabolite profile and translocation of organic matter between coral tissue and skeleton. Chromatography-time-of-flight-mass spectrometry and ultra-high-performance liquid chromatography tandem mass spectrometry revealed distinct metabolic profiles in tissue and different skeletal layers. A stable isotope incubation experiment further demonstrated 13C translocation between tissue and the green layer, but no translocation of 15N. These findings suggest communication between the two compartments that is generally carbon-based, possibly in the form of carbohydrates and bioactive compounds, such as corticosterone and domoic acid. Nevertheless, some nitrogenous compounds appear to have an endolithic source, indicating a possible contribution of the skeleton to coral animal. Notably, antibiotic treatment greatly increased 15N translocation in the tissue but not in the green layer. This highlights an important role of bacteria in nitrogen cycling in the holobiont and in establishing the nitrogen-limiting green layer. Altogether, this study provides the first data about coral skeletal metabolomes. Based on these findings, we propose a model of interactions between coral animal and skeletal bacterial communities, offering a new perspective on the ecological role of endolithic bacteria in corals.

The dynamics and prevalence of mutualistic interactions, which are responsible for the maintenance and structuring of all ecological communities, are vulnerable to changes in abiotic and biotic environmental conditions. Mutualistic outcomes can quickly shift from cooperation to conflict, but it unclear how resilient and stable mutualistic outcomes are to more variable conditions. Tidally controlled coral atoll lagoons that experience extreme diurnal environmental shifts thus provide a model from which to test plasticity in mutualistic behavior of dedicated (formerly obligate) cleaner fish, which acquire all their food resources through client interactions. Here, we investigated cleaning patterns of a model cleaner fish species, the bluestreak wrasse (Labroides dimidiatus), in an isolated tidal lagoon on the Great Barrier Reef. Under tidally restricted conditions, uniquely both adults and juveniles were part‐time facultative cleaners, pecking on Isopora palifera coral. The mutualism was not completely abandoned, with adults also wandering across the reef in search of clients, rather than waiting at fixed site cleaning stations, a behavior not yet observed at any other reef. Contrary to well‐established patterns for this cleaner, juveniles appeared to exploit the system, by biting (“cheating”) their clients more frequently than adults. We show for the first time, that within this variable tidal environment, where mutualistic cleaning might not represent a stable food source, the prevalence and dynamics of this mutualism may be breaking down (through increased cheating and partial abandonment). Environmental variability could thus reduce the pervasiveness of mutualisms within our ecosystems, ultimately reducing the stability of the system. In a tidal lagoon in the Great Barrier Reef, we uniquely show that both adult and juvenile bluestreak cleaner wrasse (Labroides dimidiatus) are part‐time facultative cleaners also pecking on the coral Isopora palifera for food acquisition. We also show that, contrary to well‐established patterns for this cleaner species, juveniles bite (“cheat”) their clients more than adults, exploiting mutualistic cleaning. Overall, in this tidal environment, we document a partial breakdown in the prevalence and dynamics of this iconic mutualistic cleaning interaction.

Endolithic microbes in coral reefs may act as a nutrient source for their coral hosts. Increasing atmospheric CO 2 concentrations are causing ocean acidification (OA), which may affect marine organisms and ecosystems, especially calcifying organisms such as reef-building corals. However, knowledge of how OA affects marine microbes remains limited, and little research has been done on how coral endolithic communities respond to shifting environmental baselines. In this study, the endolithic communities of two common shallow water coral species, Isopora palifera and Porites lobata , were examined to investigate the microbial community dynamics under OA treatments. The colonies were placed in an environment with a partial pressure of carbon dioxide ( p CO 2 ) of 1,000 or 400 ppm (control) for 2 months. Several I. palifera colonies bleached and died at 1,000 ppm p CO 2 , but the P. lobata colonies remained unaffected. Inversely, the endolithic community in P. lobata skeletons showed significant changes after OA treatment, whereas no significant dynamics were observed among the I. palifera endoliths. Our findings suggest that the skeletal structures of different coral species may play a key role in corals host and endoliths under future high-OA scenarios.

The four fossil terraces of the Glorieuses Islands are described, and new dates are provided to resolve their stratigraphy, depositional setting, and tectonic behavior. Most outcrops consist of a single sedimentary unit that represents the remains of an extensive reef flat dominated by Isopora palifera corals. At Lys Island, this unit is locally overlain by dipping layered beds composed of Halimeda segments, tentatively interpreted as storm overwash. Reliable U/Th dates obtained from corals sampled from the fossil outcrops mostly fall between 127 and 123 kyr, suggesting that these reefs formed exclusively during the first MIS-5e sea-level highstand, when sea level reached +3 m. The mean elevation of these terraces being +4.5 m, an uplift of 0.012 ± 0.002 mm year −1 is inferred. This relative tectonic stability contrasts with the subsidence reported from Mayotte Island, suggesting a different geologic setting for the nearby Comoros and Glorieuses archipelagoes.

The rise in atmospheric carbon dioxide (CO2) concentration due to emissions associated with economic development is altering ocean chemistry, a process known as ocean acidification. The resultant decrease in oceanic pH will affect marine organisms, in particular those which build their skeletons through calcification such as scleractinian corals. The aim of this research was to analyse the likely impact of changing CO2 concentrations and thus seawater pH on the growth rate of two common corals, Isopora palifera and Acropora hyacinthus. This research was conducted at the Marine, Coastal and Small Island Research Centre, Universitas Hasanuddin, Indonesia. Samples of Isopora palifera and Acropora hyacinthus were collected along an inshore-offshore cross-shelf gradient from 3 sites: Pulau Karanrang (inner zone), Pulau Badi (intermediate zone), and Pulau Kapoposang (outer zone). A fully randomised research design was used with three replicates for each of three CO2 treatments: 390 ppm (control), 550 ppm (2030 prediction), 1000 ppm (2050 prediction). The samples were weighed weekly for 1 month (digital balance, accuracy 0.1 mg). ANOVA analysis with post hoc Tukey Test showed a significant (p < 0.05) between treatment difference in growth rate for both Isopora palifera and Acropora hyacinthus (P<0,05). The corals from all three zones exhibited positive growth at 390 ppm CO2, and negative growth at CO2 concentrations of 550 ppm and 1000 ppm.

Lanyu and Lutao Islands to the southeast of Taiwan are located in the northern extension of the Luzon Arc. Crustal deformation of these islands provides a key to understand the collision of the Luzon Arc against Taiwan. To clarify the style and the rate of vertical movement during the Holocene, uplifted coral reefs fringing these two islands were investigated. Living corals were also investigated for comparison with fossil corals. It was found that Isopora palifera lives dominantly in the upper slope of the present-day fringing coral reefs in Lanyu Island at an average depth of 101 ± 46 cm (one standard deviation) below mean sea level. Using I. palifera as an accurate indicator of paleo-sea levels, Holocene relative sea-level changes were reconstructed. Lanyu Island has been uplifted continuously at a rate of 2.0 mm yr −1 , at least during the late Holocene from 2,269 cal. yr BP to the present. Lutao Island has been uplifted at an average rate of 1.2 mm yr −1 , since at least 5,749 cal. yr BP, although it is unclear whether the uplift was continuous. The present observations, combined with the GPS displacement field and deep crustal structure, suggest that the continuous uplift is related to aseismic slip on the Longitudinal Valley Fault.

Endolithic microbial symbionts in the coral skeleton may play a pivotal role in maintaining coral health. However, compared to aerobic microorganisms, research on the roles of endolithic anaerobic microorganisms and microbe-microbe interactions in the coral skeleton are still in their infancy. In our previous study, we showed that a group of coral-associated Prosthecochloris (CAP), a genus of anaerobic green sulfur bacteria, was dominant in the skeleton of the coral Isopora palifera. Though CAP is diverse, the 16S rRNA phylogeny presents it as a distinct clade separate from other free-living Prosthecochloris. In this study, we build on previous research and further characterize the genomic and metabolic traits of CAP by recovering two new near-complete CAP genomes-Candidatus Prosthecochloris isoporaea and Candidatus Prosthecochloris sp. N1-from coral Isopora palifera endolithic cultures. Genomic analysis revealed that these two CAP genomes have high genomic similarities compared with other Prosthecochloris and harbor several CAP-unique genes. Interestingly, different CAP species harbor various pigment synthesis and sulfur metabolism genes, indicating that individual CAPs can adapt to a diversity of coral microenvironments. A novel near-complete SRB genome-Candidatus Halodesulfovibrio lyudaonia-was also recovered from the same culture. The fact that CAP and various sulfate-reducing bacteria (SRB) co-exist in coral endolithic cultures and coral skeleton highlights the importance of SRB in the coral endolithic community. Based on functional genomic analysis of Ca. P. sp. N1 and Ca. H. lyudaonia, we also propose a syntrophic relationship between the SRB and CAP in the coral skeleton.