Coral Acropora Research Articles

Gene expression microarray analysis during metamorphosis and early calcification in the scleractinian coral Acropora millepora

ABSTRACT In the face of global warming and ocean acidification, understanding the cellular mechanisms underlying coral metamorphosis and early calcification is essential, as both processes are likely to be affected by a changing environment. In this study, we used cDNA microarray expression analysis to compare transcription profiles between four distinct life stages in the ‘complexa’ coral Acropora millepora: 1) aposymbiotic non-calcifying planula, 2) aposymbiotic calcifying flat polyp, 3) aposymbiotic calcifying primary polyp and 4) symbiotic adult tip. Highly up-regulated genes in planulae were molecules involved in calcium signalling, lipid metabolism and development. Transcripts up-regulated in post-settlement juvenile stages regulate tissue morphogenesis, cell division and responses to oxidative stress. Transcripts with the highest expression in adult polyps are involved in responses to abiotic stimuli and asexual reproduction. Transcripts up-regulated in calcifying stages included carbonic anhydrases and organic matrix components. Additionally, our results suggest an overlap between intracellular secondary messengers following settlement and metamorphosis. A subset of fluorescent proteins were up-regulated at the planula stage but down-regulated after settlement, supporting the idea that these molecules might have a role in quenching reactive oxygen species. Altogether, our results suggest that Acropora developmental stages are transcriptionally distinct units in which transcription profiles reflect responses to different physiological and ecological conditions.

Climate adaptive loci revealed by seascape genomics correlate with phenotypic variation in heat tolerance of the coral Acropora millepora

One of the main challenges in coral reef conservation and restoration is the identification of coral populations resilient under global warming. Seascape genomics is a powerful tool to uncover genetic markers potentially involved in heat tolerance among large populations without prior information on phenotypes. Here, we aimed to provide first insights on the role of candidate heat associated loci identified using seascape genomics in driving the phenotypic response of Acropora millepora from New Caledonia to thermal stress. We subjected 7 colonies to a long-term ex-situ heat stress assay (4 °C above the maximum monthly mean) and investigated their physiological response along with their Symbiodiniaceae communities and genotypes. Despite sharing similar thermal histories and associated symbionts, these conspecific individuals differed greatly in their tolerance to heat stress. More importantly, the clustering of individuals based on their genotype at heat-associated loci matched the phenotypic variation in heat tolerance. Colonies that sustained on average lower mortality, higher Symbiodiniaceae/chlorophyll concentrations and photosynthetic efficiency under prolonged heat stress were also the closest based on their genotypes, although the low sample size prevented testing loci predictive accuracy. Together these preliminary results support the relevance of coupling seascape genomics and long-term heat stress experiments in the future, to evaluate the effect size of candidate heat associated loci and pave the way for genomic predictive models of corals heat tolerance.

Day–night expression patterns of opsin genes in the coral Acropora digitifera under natural and LED light conditions

Day–night expression patterns of opsin genes in the coral Acropora digitifera under natural and LED light conditions

Deciphering mechanisms of UV filter (benzophenone-3)- and high temperature-induced adverse effects in the coral Acropora tenuis, using ecotoxicogenomics

Coral reefs are at risk of bleaching due to various environmental and anthropogenic stressors such as global warming and chemical pollutants. However, there is little understanding of stressor-specific mechanisms that cause coral bleaching. Therefore, conducting accurate ecotoxicological risk assessments and deciphering modes of action of potentially deleterious ultraviolet (UV) filters (sunscreen compounds) are crucial issues. In this study, we evaluated the toxicity and bleaching effect of benzophenone-3 (BP-3), which is widely used in sunscreen products, on the reef-building coral Acropora tenuis. Furthermore, to understand differences in UV filter- and temperature-induced adverse effects, a comparative ecotoxicogenomic approach using RNA-seq was integrated into a toxicity test to clarify differences in gene expression changes induced by BP-3 and heat stress (31 °C). The lethal concentration 50 % (LC50) was calculated as 3.9 mg/L, indicating that the aquatic environmental risk on corals posed by BP-3 was low based on the risk assessment in this study. Differentially expressed genes related to oxidative stress and extracellular matrix organization were involved in coral responses to both BP-3 and heat stress, but their patterns differed. Whereas immune and heat-shock responses were activated in response to heat stress, activation of a drug metabolism pathway and several signal transduction pathways were identified in BP-3 treatment groups. Our study enhances understanding of stress responses in corals induced by UV filters and thermal stress. Using potential gene markers identified in this study for eco-epidemiological surveys of stressed corals, we urgently need to develop effective countermeasures.

Identification of putative coral pathogens in endangered Caribbean staghorn coral using machine learning.

Coral diseases contribute to the rapid decline in coral reefs worldwide, and yet coral bacterial pathogens have proved difficult to identify because 16S rRNA gene surveys typically identify tens to hundreds of disease-associate bacteria as putative pathogens. An example is white band disease (WBD), which has killed up to 95% of the now-endangered Caribbean Acropora corals since 1979, yet the pathogen is still unknown. The 16S rRNA gene surveys have identified hundreds of WBD-associated bacterial amplicon sequencing variants (ASVs) from at least nine bacterial families with little consensus across studies. We conducted a multi-year, multi-site 16S rRNA gene sequencing comparison of 269 healthy and 143 WBD-infected Acropora cervicornis and used machine learning modelling to accurately predict disease outcomes and identify the top ASVs contributing to disease. Our ensemble ML models accurately predicted disease with greater than 97% accuracy and identified 19 disease-associated ASVs and five healthy-associated ASVs that were consistently differentially abundant across sampling periods. Using a tank-based transmission experiment, we tested whether the 19 disease-associated ASVs met the assumption of a pathogen and identified two pathogenic candidate ASVs-ASV25 Cysteiniphilum litorale and ASV8 Vibrio sp. to target for future isolation, cultivation, and confirmation of Henle-Koch's postulate via transmission assays.

Diversity of fatty acids in different coral species collected in the coastal sea of Nha Trang, Khanh Hoa

The total of 15 coral samples belonging to soft coral species Sinularia flexibilis, hard coral Acropora sp., and the hydrocoral Millepora platypylla, were collected in the coastal sea of Nha Trang, Khanh Hoa, Vietnam. In these samples, 39 fatty acids were identified in which Sinularia flexibilis sample identified 26 fatty acids, Acropora sp. identified 27 fatty acids, and Millepora platyphylla has the most diverse fatty acid composition with 35 fatty acids. In the coral samples of S. flexibilis, the difference between the ratio of total saturated fatty acids and the polyunsaturated fatty acids was much smaller than that of the other two species. The n-3/n-6 ratio is the highest among Millepora species, up to 4.45; in S. flexibilis and Acropora, this ratio can be lower than 1. Fatty acids 16:0 and 18:0 are the two main fatty acids in total; the content varies between samples of different species but is quite similar amongst samples of the same species. Fatty acids characterized by symbiotic microalgae 16:2n-7, 18:3n-6, 18:4n-3 Fatty acids 18:3n-6 were absent in S. flexibilis samples, minor content in M. platyphylla samples, and relatively significant in Acropora sp. (from 7.07% to 9.59% total fatty acids). Two fatty acids 16:2n-7 and 18:4n-3 were present in all 3 species, the highest in the sample S. flexibilis. The tetracosapolyenoic fatty acids 24:5n-6 and 24:6n-3 are soft coral marker fatty acids, present in only 5 samples of S. flexibilis with 24:5n-6 content ranging from 2.56% to 5.58% total fatty acids, 24:6n-3 is much lower (0.24% to 0.76%). The two PUFAs with the highest concentration were 20:4n-6 and 22:6n-3. 20:4n-6 was present in the total fatty acids of S. flexibilis with a quite high content (9.76% to 17.12% of the total axb), in contrast, the proportion was very low in five Millepora samples and five Acropora samples. 22:6n-3 was significantly high in the five Millepora samples (12.63% to 25.29% total fatty acids) and minor in the samples of the other two species.

DNA barcodes are ineffective for species identification of Acropora corals from the aquarium trade.

Species identification of stony corals (Scleractinia), which are regulated under the Convention on International Trade in Endangered Species of Wild Fauna and Flora, is critical for effective control of harvest quotas, enforcement of trade regulations and species conservation in general. DNA barcoding has the potential to enhance species identification success, depending on the specific taxon concerned and genetic markers used. For Acropora, DNA barcoding, based on the mitochondrial putative control region (mtCR) and the nuclear PaxC intron (PaxC), has been commonly used for species identification and delimitation, but the reliability and robustness of these loci remain contentious. Therefore, we sought to verify the applicability of this approach. In this study, we obtained 127 Acropora colonies from the aquarium trade to test the effectiveness of barcoding mtCR and PaxC for species identification. We were able to recover sequences for both loci in over half of the samples (n = 68), while gene amplification and sequencing of mtCR (n = 125) outperformed PaxC (n = 70). Amongst the 68 samples with both loci recovered, just a single sample could be unambiguously identified to species. Preliminary identities, based on only one gene, were assigned for 40 and 65 samples with mtCR and PaxC, respectively. Further analyses of 110 complete mitochondrial genomes obtained from GenBank showed that, despite the full length of the sequences, only eight species were delimited, of which only three species were correspondingly monophyletic. Therefore, we conclude that the commonly used DNA barcoding markers for Acropora are ineffective for accurate species assignments due to limited variability in both markers and even across the entire mitochondrial genome. Therefore, we propose that barcoding markers should generally not be the only means for identifying corals.

Variability of the surface boundary layer of reef-building coral species

The coral-seawater interface is an important, highly dynamic microenvironment for reef-building corals. Also known as the concentration boundary layer (CBL), it is a thin layer of seawater bordering the coral surface that dictates the biochemical exchange between the coral colony and bulk seawater. The CBL is thus a key feature that modulates coral metabolism. However, CBL variation among small-polyped coral species remains largely unknown. Therefore, we recorded over 100 profiles of dissolved O2 concentration using microsensors to characterize CBL traits (thickness, surface O2 concentration, and flux) of three small-polyped branching coral species, Acropora cytherea, Pocillopora verrucosa, and Porites cylindrica. Measurements were conducted during light and darkness combined with low or moderate water flow (2 and 6 cm s−1). We found that CBL traits differed among species. CBL thickness was lowest in A. cytherea, while P. verrucosa showed the largest depletion of surface O2 in dark and highest dark flux. In addition, we found that O2 concentration gradients in the CBL occurred with three main profile shapes: diffusive, S-shaped, and complex. While diffusive profiles were the most common profile type, S-shaped and complex profiles were more frequent in P. verrucosa and P. cylindrica, respectively, and prevailed under low flow. Furthermore, profile types differed in CBL thickness and flux. Finally, low flow thickened CBLs, enhanced changes in surface O2 concentration, and reduced flux, compared to moderate flow. Overall, our findings reveal CBL variability among small-polyped branching corals and help understand CBL dynamics in response to changes in light and water flow conditions.

Bringing Back Reef Fish: Sustainable Impacts of Community-Based Restoration of Elkhorn Coral (Acropora palmata) in Vega Baja, Puerto Rico (2008–2023)

Bringing Back Reef Fish: Sustainable Impacts of Community-Based Restoration of Elkhorn Coral (Acropora palmata) in Vega Baja, Puerto Rico (2008–2023)

Patterns of methylation and transcriptional plasticity during thermal acclimation in a reef-building coral.

Phenotypic plasticity can buffer organisms against short-term environmental fluctuations. For example, previous exposure to increased temperatures can increase thermal tolerance in many species. Prior studies have found that acclimation to higher temperature can influence the magnitude of transcriptional response to subsequent acute thermal stress (hereafter, "transcriptional response modulation"). However, mechanisms mediating this gene expression response and, ultimately, phenotypic plasticity remain largely unknown. Epigenetic modifications are good candidates for modulating transcriptional response, as they broadly correlate with gene expression. Here, we investigate changes in DNA methylation as a possible mechanism controlling shifts in gene expression plasticity and thermal acclimation in the reef-building coral Acropora nana. We find that gene expression response to acute stress is altered in corals acclimated to different temperatures, with many genes exhibiting a dampened response to heat stress in corals pre-conditioned to higher temperatures. At the same time, we observe shifts in methylation during both acclimation (11 days) and acute heat stress (24 h). We observed that the acute heat stress results in shifts in gene-level methylation and elicits an acute transcriptional response in distinct gene sets. Further, acclimation-induced shifts in gene expression plasticity and differential methylation also largely occur in separate sets of genes. Counter to our initial hypothesis no overall correlation between the magnitude of differential methylation and the change in gene expression plasticity. We do find a small but statistically significant overlap in genes exhibiting both dampened expression response and shifts in methylation (14 genes), which could be candidates for further inquiry. Overall, our results suggest transcriptional response modulation occurs independently from methylation changes induced by thermal acclimation.

Benthic communities influence coral seeding success at fine spatial scales

The deployment of engineered substrates seeded with newly settled corals is a technique being developed to increase the numbers of juvenile corals on reefs with the goal of improving reef resilience in response to climate warming. Using a hierarchical sampling design, we explored the spatial scales at which seeded coral (spat) survival and growth varied in situ and investigated the environmental drivers of seeded spat success in the southern inshore Great Barrier Reef. After 10 months, variation in spat survival and size was greatest at the smallest spatial scale (1–2 m) (27 and 11% of variation, respectively), indicating the scale at which the main drivers of post‐settlement survival and growth are occurring. Crustose coralline algae (CCA) cover on seeding units prior to deployment was a significant driver of short‐ and long‐term spat survival (22% of variation). Survival of Acropora millepora and A. muricata spat did not differ according to benthic community variation. Increasing cover of branching Acropora corals was correlated with decreased survival and the size of Montipora aequituberculata spat, although CCA cover on plugs remained the most influential factor determining survival. Interspecific variation in spat survival and size and higher survival and size in the side‐facing orientation of the seeding units suggest natural variation in response to the seeding method, warranting further experiments to refine species selection and deployment methods prior to upscaling. High within‐site variation in seeded spat survival and size highlights the need for future studies of ecological factors driving post‐settlement mortality at fine spatial scales.

Effects of flows on transparent exopolymer particles released from branching Acropora coral colonies

Transparent exopolymer particles (TEP), a major component of coral mucus, are responsible for particle aggregation. These particles contribute substantially to the carbon cycle in coral reefs, and serve as an energy source for bacteria and other microorganisms. Water flows and induced turbulent mixing control material exchange between the coral canopy and the surrounding water, which is critical for coral health. However, how these factors affect TEP release by coral colonies has yet to be evaluated. Using a recirculating flume, we assessed TEP release by branching Acropora coral colonies and associated bacterial growth in the water column under different unidirectional flows. Changes in TEP and bacterial concentrations after 24-h incubation were quantified for flow speeds of 0, 5, 10, and 30 cm/s. Particle image velocimetry (PIV) measurements provided an estimate of turbulent mixing efficiency above the coral canopy. TEP and bacterial concentrations in the water column increased after 24 h of incubation. The increase in TEP and bacterial concentrations were 6.2–9.3 times and 3.4–5.1 times higher in the absence of flows, respectively, than mean values under water flows. Although mixing efficiency increased linearly with mean flow speeds, TEP release and bacterial growth differed only marginally at flows ranging from 5–30 cm/s. Detailed flow measurements combined with evaluation of TEP release suggest that the complex geometry of corals facilitates efficient material exchange at a range of flow speeds, and highlight the importance of considering these factors when estimating coral reef biogeochemistry.

Intraspecific variation in response to elevated pCO2 and temperature in the branching reef coral Acropora digitifera from different habitats

Intraspecific variation in response to elevated pCO2 and temperature in the branching reef coral Acropora digitifera from different habitats

Does high parasite load contribute to limitation of the poleward range of Acropora corals?

The role of species interactions in setting species range limits is rarely empirically explored. Here, we quantify host and parasite densities in subtropical eastern Australia (26.65°–30.20°S) to examine whether parasitism might contribute to range limitation of Acropora corals at their cold-range boundary. 79% of Acropora corals had endolithic barnacles (family Pyrgomatidae), with higher parasite load in larger corals and up to 141 barnacles per coral. Parasite load increased poleward and closer to the mainland and was greater in cooler and high nutrient environments. Parasite burden was higher at sites with fewer Acropora corals, broadly consistent with the hypothesis that parasites can fragment host populations where host densities are low, and the parasite is a better disperser than the host. Whilst the mechanism is unclear, our findings suggest that at the high densities recorded here, coral-barnacles could influence range dynamics of Acropora corals at their poleward range limit.

Connectivity modelling identifies sources and sinks of coral recruitment within reef clusters

Connectivity aids the recovery of populations following disturbances, such as coral bleaching and tropical cyclones. Coral larval connectivity is a function of physical connectivity and larval behaviour. In this study, we used OceanParcels, a particle tracking simulator, with 2D and 3D velocity outputs from a high resolution hydrodynamic-biogeochemical marine model (RECOM) to simulate the dispersal and settlement of larvae from broadcast spawning Acropora corals in the Moore Reef cluster, northern Great Barrier Reef, following the annual spawning events in 2015, 2016 and 2017. 3D velocity simulations showed 19.40–68.80% more links and sinks than those of 2D simulations. Although the patterns of connectivity among sites vary over days and years, coral larvae consistently dispersed from east to west in the cluster domain, with some sites consistently acting as sources or sinks for local larval recruitment. Results can inform coral reef intervention plans for climate change, such as the design of marine protected areas and the deployment of proposed interventions within reef clusters. For example, the wider benefits of interventions (e.g., deployment of heat adapted corals) may be optimised when deployed at locations that are a source of larvae to others within comparable habitats across the reef cluster.

Macroalgal presence decreases coral calcification rates more than ocean acidification

Global coral reef degradation has precipitated phase shifts toward macroalgal-dominated communities. Despite the negative repercussions for reefscapes, higher abundances of primary producers have the potential to positively impact the physicochemical environment and mitigate negative impacts of ocean acidification (OA). In this study, we investigated the influence of macroalgal (cf. Sargassum vulgare) density on coral (Acropora millepora and A. hemprichii) calcification rates under current and future OA conditions. Corals were resistant to OA up to ~ 1100 µatm, with no changes in calcification rates. However, the presence of (low and high density) algae reduced calcification rates by ~ 41.8%, suggesting either a chemical defense response due to algal metabolites or potential physical impacts from shading or abrasion. Documented beneficial buffering effects of macroalgae in OA may also elicit negative impacts on coral calcification, suggesting further work is needed to elucidate how species interactions influence responses to projected climate change.

In situ lesion recovery of Scleractinian branching coral wild colonies from asexual coral propagation

As coral reefs worldwide continue to degrade due to natural and anthropogenic threats, coral restoration efforts have been rapidly growing in recent decades to maintain the ecological function of coral reefs. In Malaysia, asexual propagation by fragmenting branches from healthy Acropora wild colonies is becoming the norm, but other coral genera are rarely considered in restoration efforts despite the need to enhance diversity and reef resilience. Additionally, restoration efforts in Malaysia mainly focus on the recovery of coral fragments in nurseries while overlooking the wild coral colonies they were sourced from. Lesion recovery from physical damage should be investigated to maximise restoration success and to ensure the wild coral populations do not degrade due to fragmentation from coral propagation efforts. To address this, we investigated the recuperation capabilities of two branching coral species, Acropora muricata and Echinopora horrida, in a shallow reef (<8 m) of Pulau Rawa, Johor, Malaysia. Coral colonies were induced with physical damage, and lesion recovery was measured via lesion site closure, colour score and relative growth of the broken colonies (n=30) over 129 days. The lesion site of A. muricata closed significantly more at 99.94±0.04SE%, compared to E. horrida with 86.97±3.53SE%. When compared to E. horrida, A. muricata had achieved full colour recovery by day 27 and more than double the value of relative growth (9.7 %). The differences in lesion recovery capabilities between A. muricata and E. horrida are hypothesised to be attributed to their different life adaptive strategies where A. muricata is an r adaptive strategist and E. horrida is a K adaptive strategist. The findings imply that future coral restoration efforts should investigate the recovery capabilities of the wild coral colonies before starting coral propagation efforts to prevent partial mortality of wild colonies and maintain species diversity and ecological functions of the reef.

Long-term aquarium records delineate the synchronized spawning strategy of Acropora corals.

Aligning spawning timing with seasonal environmental changes is critical for both terrestrial and aquatic organisms. However, mechanisms to regulate reproductive activity in response to environmental factors are not well understood, partly owing to the technical difficulty in maintaining detailed long-term observational data of the reproductive activities in the same population across years. In this study, we present an application of the aquarium system to examine the long-term spawning properties of corals. Spawning records over a 15-year period at the Okinawa Churaumi Aquarium revealed that the spawning timing of Acropora corals in aquarium tanks aligned well with that of wild corals from a neighbouring reef. Using the aquarium population as a model, we investigated the relationship between key environmental factors and the timing of the first and peak spawning dates of Acropora corals during a 15-year period. The results suggest that the spawning window of each spawning season is largely influenced by the water temperature and that the timing of peak spawning can be fine-tuned in response to environmental fluctuations. This behavioural feature can prevent synchronous spawning events during unfavourable environmental conditions and increase long-term reproductive reliability.

Conservation of Protein Kinase A Substrates in the Cnidarian Coral Spermatozoa Among Animals and Their Molecular Evolution.

The coral Acropora spp., known for its reef-building abilities, is a simultaneous hermaphroditic broadcast spawning species. Acropora spp. release gametes into seawater, activating sperm motility. This activation is mediated by adenylyl cyclase (AC) and protein kinase A (PKA). Notably, membrane-permeable cAMP (8-bromo-cAMP) promotes sperm motility activation of Acropora florida. While the signal transduction for PKA-dependent motility activation is highly conserved among animals, the downstream signaling of PKA remains unclear. In this study, we used mass spectrometry (MS) analyses to identify sperm proteins in the coral Acropora digitifera, as well as the serine/threonine residues of potential PKA substrates, and then, we investigated the conservation of these proteins from corals to vertebrates. We identified 148 sperm proteins of A. digitifera with typical PKA recognition motifs, namely RRXT and RRXS. We subsequently used ORTHOSCOPE to screen for orthologs encoding these 148 proteins from corals to vertebrates. Among the isolated orthologs, we identified positive selection in 48 protein-encoding genes from 18 Acropora spp. Subsequently, we compared the conservation rates of the PKA phosphorylation motif residues between the orthologs under positive and purifying selections. Notably, the serine residues of the orthologs under positive selection were more conserved. Therefore, adaptive evolution might have occurred in the orthologs of PKA substrate candidates from corals to vertebrates, accompanied by phosphorylation residue conservation. Collectively, our findings suggest that while PKA signal transduction, including substrates in sperm, may have been conserved, the substrates may have evolved to adapt to diverse fertilization conditions, such as synchronous broadcast spawning.

Corals survive severe bleaching event in refuges related to taxa, colony size, and water depth

Marine heatwaves are increasing in frequency and duration, threatening tropical reef ecosystems through intensified coral bleaching events. We examined a strikingly variable spatial pattern of bleaching in Moorea, French Polynesia following a heatwave that lasted from November 2018 to July 2019. In July 2019, four months after the onset of bleaching, we surveyed > 5000 individual colonies of the two dominant coral genera, Pocillopora and Acropora, at 10 m and 17 m water depths, at six forereef sites around the island where temperature was measured. We found severe bleaching increased with colony size for both coral genera, but Acropora bleached more severely than Pocillopora overall. Acropora bleached more at 10 m than 17 m, likely due to higher light availability at 10 m compared to 17 m, or greater daily temperature fluctuation at depth. Bleaching in Pocillopora corals did not differ with depth but instead varied with the interaction of colony size and Accumulated Heat Stress (AHS), in that larger colonies (> 30 cm) were more sensitive to AHS than mid-size (10–29 cm) or small colonies (5–9 cm). Our findings provide insight into complex interactions among coral taxa, colony size, and water depth that produce high spatial variation in bleaching and related coral mortality.